tantan-13/0000755000000000000000000000000012037256344011270 5ustar rootroottantan-13/README.txt0000644000000000000000000001437212037256344012775 0ustar rootroottantan ====== Introduction ------------ tantan is a tool for masking simple regions (low complexity and short-period tandem repeats) in biological sequences. The aim of tantan is to prevent false predictions when searching for homologous regions between two sequences. Simple repeats often align strongly to each other, causing false homology predictions. Setup ----- You need to have a C++ compiler. On Linux, you might need to install a package called "g++". On Mac, you might need to install command-line developer tools. On Windows, you might need to install Cygwin. Using the command line, go into the tantan directory. To compile it, type:: make Optionally, copy tantan to a standard "bin" directory (using "sudo" to request administrator permissions):: sudo make install Or copy it to your personal bin directory:: make install prefix=~ You might need to log out and back in for your computer to recognize the new program. Normal usage ------------ * Suppose you have some nucleotide sequences (DNA or RNA) in a FASTA-format file called "ntseqs.fa". You can identify simple repeats like this:: tantan ntseqs.fa > masked.fa This will create a new FASTA file called "masked.fa" that replaces all masked regions with lowercase letters. (tantan also works on FASTQ-format, though it does not use the quality data.) * To mask proteins effectively, tantan needs to use different algorithm parameters than for nucleotides. You have to tell it when you have proteins, using the "-p" option:: tantan -p aaseqs.fa > masked.fa If you omit "-p" and the sequences look proteinaceous, tantan will print a warning message. Advanced usage -------------- * By default, tantan indicates repetitive regions with lowercase letters. You can make it replace repetitive letters with (say) "N" by using the "-x" option:: tantan -x N ntseqs.fa > masked.fa * By default, tantan does not preserve lowercase letters in the input sequences. You can tell it to preserve them by using the "-c" option. So the output will have the union of the lowercase in the input and the lowercase assigned by tantan:: tantan -c ntseqs.fa > masked.fa * tantan's masking rate is usually OK, but you can alter it by changing the "-r" parameter from its default value of 0.005. Higher values increase the amount of masking, and lower values decrease it. This increases the masking rate:: tantan -r 0.02 ntseqs.fa > masked.fa * Finally, to mask extremely AT-rich DNA, you should change tantan's scoring matrix. The "test" directory contains a matrix "atMask.mat" that works well for DNA with ~80% A+T, such as Plasmodium and Dictyostelium genomes. We recommend masking such DNA like this:: tantan -m atMask.mat -r 0.01 atrich.fa > masked.fa The preceding examples cover all of tantan's options that you should ever need. Recommendations for homology search ----------------------------------- 1) Mask *both* (sets of) sequences. 2) If for some reason you wish to mask only one (set of) sequence(s), increase "-r" to 0.02 (0.05 for AT-rich DNA). 3) For DNA-versus-protein alignment, increase "-r" for the proteins to 0.02. If for some reason you mask only one (set of) sequence(s), make sure it's the proteins. 4) Some alignment tools exclude lowercase from their initial seeding phase, but treat lowercase identically to uppercase during their subsequent extension phase. Unfortunately, this does not reliably prevent false homology predictions. It is OK to re-align without masking after homology has been decided: FASTA and LAST can do this. For more information, please read the tantan publication (see below). FAQ --- Why does tantan sometimes mask isolated bases? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This happens when a region is borderline repetitive, and a single base creeps just over the threshold. Don't worry about it, it's not a problem (at least for tantan's aim of preventing false homology). Does tantan mask functional sequence? ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Of course. Proteins and protein-coding exons can contain simple repeats. Repeats can be functional. If we want to avoid false homology we have to mask them. Remember that tantan merely lowercases repeats, so it's easy to lift the masking after determining homology. Options ------- -p interpret the sequences as proteins -x letter to use for masking, instead of lowercase -c preserve uppercase/lowercase in non-masked regions -m file for letter pair scores (scoring matrix) -r probability of a repeat starting per position -e probability of a repeat ending per position -w maximum tandem repeat period to consider -d probability decay per period (period-(i+1) / period-i) -a gap existence cost -b gap extension cost -s minimum repeat probability for masking -f output type: 0=masked sequence, 1=repeat probabilities, 2=repeat counts, 3=BED -h, --help show help message, then exit --version show version information, then exit Advanced issues --------------- When tantan masks tandem repeats, it tends to leave the first (left-most) repeat unit unmasked. This sometimes allows us to find homologs we would otherwise miss:: TGCAAGCTA TTAGGCTTAGGTCAGTGC ttaagcttaggtcagtgc AACATA ||| ||| | |||||||||||||||||| ||| |||||||||||||| ||| || TGCTAGCAA TTAGGCTTAGGTCAGTGC ttaggcttaggtcagtgc AACGTA However, there is a danger of non-equivalent repeat units being unmasked. This happens especially if we mask DNA on one strand but align it on the other strand:: TGCAAGCTA TTAGGCTTAGGTCAGTGC ttaagcttaggtcagtgc AACATA |||||||||||||||||| TGCTAGCAA ttaggcttaggtcagtgc TTAGGCTTAGGTCAGTGC AACGTA (My thanks to Junko Tsuji and Paul Horton for finding these issues.) Miscellaneous ------------- tantan is distributed under the GNU General Public License, either version 3 of the License, or (at your option) any later version. For details, see COPYING.txt. If you use tantan in your research, please cite: "A new repeat-masking method enables specific detection of homologous sequences", MC Frith, Nucleic Acids Research 2011 39(4):e23. tantan's website is: http://www.cbrc.jp/tantan/ If you have any questions, comments, or problems concerning tantan, please email: tantan (ATmark) cbrc (dot) jp. tantan-13/COPYING.txt0000644000000000000000000010451312037256344013145 0ustar rootroot GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The GNU General Public License is a free, copyleft license for software and other kinds of works. The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things. To protect your rights, we need to prevent others from denying you these rights or asking you to surrender the rights. Therefore, you have certain responsibilities if you distribute copies of the software, or if you modify it: responsibilities to respect the freedom of others. For example, if you distribute copies of such a program, whether gratis or for a fee, you must pass on to the recipients the same freedoms that you received. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License giving you legal permission to copy, distribute and/or modify it. For the developers' and authors' protection, the GPL clearly explains that there is no warranty for this free software. For both users' and authors' sake, the GPL requires that modified versions be marked as changed, so that their problems will not be attributed erroneously to authors of previous versions. Some devices are designed to deny users access to install or run modified versions of the software inside them, although the manufacturer can do so. This is fundamentally incompatible with the aim of protecting users' freedom to change the software. The systematic pattern of such abuse occurs in the area of products for individuals to use, which is precisely where it is most unacceptable. Therefore, we have designed this version of the GPL to prohibit the practice for those products. If such problems arise substantially in other domains, we stand ready to extend this provision to those domains in future versions of the GPL, as needed to protect the freedom of users. Finally, every program is threatened constantly by software patents. States should not allow patents to restrict development and use of software on general-purpose computers, but in those that do, we wish to avoid the special danger that patents applied to a free program could make it effectively proprietary. To prevent this, the GPL assures that patents cannot be used to render the program non-free. The precise terms and conditions for copying, distribution and modification follow. TERMS AND CONDITIONS 0. Definitions. "This License" refers to version 3 of the GNU General Public License. "Copyright" also means copyright-like laws that apply to other kinds of works, such as semiconductor masks. "The Program" refers to any copyrightable work licensed under this License. Each licensee is addressed as "you". "Licensees" and "recipients" may be individuals or organizations. To "modify" a work means to copy from or adapt all or part of the work in a fashion requiring copyright permission, other than the making of an exact copy. The resulting work is called a "modified version" of the earlier work or a work "based on" the earlier work. A "covered work" means either the unmodified Program or a work based on the Program. To "propagate" a work means to do anything with it that, without permission, would make you directly or secondarily liable for infringement under applicable copyright law, except executing it on a computer or modifying a private copy. Propagation includes copying, distribution (with or without modification), making available to the public, and in some countries other activities as well. To "convey" a work means any kind of propagation that enables other parties to make or receive copies. Mere interaction with a user through a computer network, with no transfer of a copy, is not conveying. An interactive user interface displays "Appropriate Legal Notices" to the extent that it includes a convenient and prominently visible feature that (1) displays an appropriate copyright notice, and (2) tells the user that there is no warranty for the work (except to the extent that warranties are provided), that licensees may convey the work under this License, and how to view a copy of this License. If the interface presents a list of user commands or options, such as a menu, a prominent item in the list meets this criterion. 1. Source Code. The "source code" for a work means the preferred form of the work for making modifications to it. "Object code" means any non-source form of a work. A "Standard Interface" means an interface that either is an official standard defined by a recognized standards body, or, in the case of interfaces specified for a particular programming language, one that is widely used among developers working in that language. The "System Libraries" of an executable work include anything, other than the work as a whole, that (a) is included in the normal form of packaging a Major Component, but which is not part of that Major Component, and (b) serves only to enable use of the work with that Major Component, or to implement a Standard Interface for which an implementation is available to the public in source code form. A "Major Component", in this context, means a major essential component (kernel, window system, and so on) of the specific operating system (if any) on which the executable work runs, or a compiler used to produce the work, or an object code interpreter used to run it. The "Corresponding Source" for a work in object code form means all the source code needed to generate, install, and (for an executable work) run the object code and to modify the work, including scripts to control those activities. However, it does not include the work's System Libraries, or general-purpose tools or generally available free programs which are used unmodified in performing those activities but which are not part of the work. For example, Corresponding Source includes interface definition files associated with source files for the work, and the source code for shared libraries and dynamically linked subprograms that the work is specifically designed to require, such as by intimate data communication or control flow between those subprograms and other parts of the work. The Corresponding Source need not include anything that users can regenerate automatically from other parts of the Corresponding Source. The Corresponding Source for a work in source code form is that same work. 2. Basic Permissions. All rights granted under this License are granted for the term of copyright on the Program, and are irrevocable provided the stated conditions are met. This License explicitly affirms your unlimited permission to run the unmodified Program. The output from running a covered work is covered by this License only if the output, given its content, constitutes a covered work. This License acknowledges your rights of fair use or other equivalent, as provided by copyright law. You may make, run and propagate covered works that you do not convey, without conditions so long as your license otherwise remains in force. You may convey covered works to others for the sole purpose of having them make modifications exclusively for you, or provide you with facilities for running those works, provided that you comply with the terms of this License in conveying all material for which you do not control copyright. Those thus making or running the covered works for you must do so exclusively on your behalf, under your direction and control, on terms that prohibit them from making any copies of your copyrighted material outside their relationship with you. Conveying under any other circumstances is permitted solely under the conditions stated below. Sublicensing is not allowed; section 10 makes it unnecessary. 3. Protecting Users' Legal Rights From Anti-Circumvention Law. No covered work shall be deemed part of an effective technological measure under any applicable law fulfilling obligations under article 11 of the WIPO copyright treaty adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention of such measures. When you convey a covered work, you waive any legal power to forbid circumvention of technological measures to the extent such circumvention is effected by exercising rights under this License with respect to the covered work, and you disclaim any intention to limit operation or modification of the work as a means of enforcing, against the work's users, your or third parties' legal rights to forbid circumvention of technological measures. 4. Conveying Verbatim Copies. You may convey verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice; keep intact all notices stating that this License and any non-permissive terms added in accord with section 7 apply to the code; keep intact all notices of the absence of any warranty; and give all recipients a copy of this License along with the Program. You may charge any price or no price for each copy that you convey, and you may offer support or warranty protection for a fee. 5. Conveying Modified Source Versions. You may convey a work based on the Program, or the modifications to produce it from the Program, in the form of source code under the terms of section 4, provided that you also meet all of these conditions: a) The work must carry prominent notices stating that you modified it, and giving a relevant date. b) The work must carry prominent notices stating that it is released under this License and any conditions added under section 7. This requirement modifies the requirement in section 4 to "keep intact all notices". c) You must license the entire work, as a whole, under this License to anyone who comes into possession of a copy. This License will therefore apply, along with any applicable section 7 additional terms, to the whole of the work, and all its parts, regardless of how they are packaged. This License gives no permission to license the work in any other way, but it does not invalidate such permission if you have separately received it. d) If the work has interactive user interfaces, each must display Appropriate Legal Notices; however, if the Program has interactive interfaces that do not display Appropriate Legal Notices, your work need not make them do so. A compilation of a covered work with other separate and independent works, which are not by their nature extensions of the covered work, and which are not combined with it such as to form a larger program, in or on a volume of a storage or distribution medium, is called an "aggregate" if the compilation and its resulting copyright are not used to limit the access or legal rights of the compilation's users beyond what the individual works permit. Inclusion of a covered work in an aggregate does not cause this License to apply to the other parts of the aggregate. 6. Conveying Non-Source Forms. You may convey a covered work in object code form under the terms of sections 4 and 5, provided that you also convey the machine-readable Corresponding Source under the terms of this License, in one of these ways: a) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by the Corresponding Source fixed on a durable physical medium customarily used for software interchange. b) Convey the object code in, or embodied in, a physical product (including a physical distribution medium), accompanied by a written offer, valid for at least three years and valid for as long as you offer spare parts or customer support for that product model, to give anyone who possesses the object code either (1) a copy of the Corresponding Source for all the software in the product that is covered by this License, on a durable physical medium customarily used for software interchange, for a price no more than your reasonable cost of physically performing this conveying of source, or (2) access to copy the Corresponding Source from a network server at no charge. c) Convey individual copies of the object code with a copy of the written offer to provide the Corresponding Source. This alternative is allowed only occasionally and noncommercially, and only if you received the object code with such an offer, in accord with subsection 6b. d) Convey the object code by offering access from a designated place (gratis or for a charge), and offer equivalent access to the Corresponding Source in the same way through the same place at no further charge. You need not require recipients to copy the Corresponding Source along with the object code. If the place to copy the object code is a network server, the Corresponding Source may be on a different server (operated by you or a third party) that supports equivalent copying facilities, provided you maintain clear directions next to the object code saying where to find the Corresponding Source. Regardless of what server hosts the Corresponding Source, you remain obligated to ensure that it is available for as long as needed to satisfy these requirements. e) Convey the object code using peer-to-peer transmission, provided you inform other peers where the object code and Corresponding Source of the work are being offered to the general public at no charge under subsection 6d. A separable portion of the object code, whose source code is excluded from the Corresponding Source as a System Library, need not be included in conveying the object code work. A "User Product" is either (1) a "consumer product", which means any tangible personal property which is normally used for personal, family, or household purposes, or (2) anything designed or sold for incorporation into a dwelling. In determining whether a product is a consumer product, doubtful cases shall be resolved in favor of coverage. For a particular product received by a particular user, "normally used" refers to a typical or common use of that class of product, regardless of the status of the particular user or of the way in which the particular user actually uses, or expects or is expected to use, the product. A product is a consumer product regardless of whether the product has substantial commercial, industrial or non-consumer uses, unless such uses represent the only significant mode of use of the product. "Installation Information" for a User Product means any methods, procedures, authorization keys, or other information required to install and execute modified versions of a covered work in that User Product from a modified version of its Corresponding Source. The information must suffice to ensure that the continued functioning of the modified object code is in no case prevented or interfered with solely because modification has been made. If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term (regardless of how the transaction is characterized), the Corresponding Source conveyed under this section must be accompanied by the Installation Information. But this requirement does not apply if neither you nor any third party retains the ability to install modified object code on the User Product (for example, the work has been installed in ROM). The requirement to provide Installation Information does not include a requirement to continue to provide support service, warranty, or updates for a work that has been modified or installed by the recipient, or for the User Product in which it has been modified or installed. Access to a network may be denied when the modification itself materially and adversely affects the operation of the network or violates the rules and protocols for communication across the network. Corresponding Source conveyed, and Installation Information provided, in accord with this section must be in a format that is publicly documented (and with an implementation available to the public in source code form), and must require no special password or key for unpacking, reading or copying. 7. Additional Terms. "Additional permissions" are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions. When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission. Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms: a) Disclaiming warranty or limiting liability differently from the terms of sections 15 and 16 of this License; or b) Requiring preservation of specified reasonable legal notices or author attributions in that material or in the Appropriate Legal Notices displayed by works containing it; or c) Prohibiting misrepresentation of the origin of that material, or requiring that modified versions of such material be marked in reasonable ways as different from the original version; or d) Limiting the use for publicity purposes of names of licensors or authors of the material; or e) Declining to grant rights under trademark law for use of some trade names, trademarks, or service marks; or f) Requiring indemnification of licensors and authors of that material by anyone who conveys the material (or modified versions of it) with contractual assumptions of liability to the recipient, for any liability that these contractual assumptions directly impose on those licensors and authors. All other non-permissive additional terms are considered "further restrictions" within the meaning of section 10. If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying. If you add terms to a covered work in accord with this section, you must place, in the relevant source files, a statement of the additional terms that apply to those files, or a notice indicating where to find the applicable terms. Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way. 8. Termination. You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11). However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation. Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice. Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10. 9. Acceptance Not Required for Having Copies. You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so. 10. Automatic Licensing of Downstream Recipients. Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License. An "entity transaction" is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party's predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts. You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it. 11. Patents. A "contributor" is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor's "contributor version". A contributor's "essential patent claims" are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, "control" includes the right to grant patent sublicenses in a manner consistent with the requirements of this License. Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor's essential patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version. In the following three paragraphs, a "patent license" is any express agreement or commitment, however denominated, not to enforce a patent (such as an express permission to practice a patent or covenant not to sue for patent infringement). To "grant" such a patent license to a party means to make such an agreement or commitment not to enforce a patent against the party. If you convey a covered work, knowingly relying on a patent license, and the Corresponding Source of the work is not available for anyone to copy, free of charge and under the terms of this License, through a publicly available network server or other readily accessible means, then you must either (1) cause the Corresponding Source to be so available, or (2) arrange to deprive yourself of the benefit of the patent license for this particular work, or (3) arrange, in a manner consistent with the requirements of this License, to extend the patent license to downstream recipients. "Knowingly relying" means you have actual knowledge that, but for the patent license, your conveying the covered work in a country, or your recipient's use of the covered work in a country, would infringe one or more identifiable patents in that country that you have reason to believe are valid. If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring conveyance of, a covered work, and grant a patent license to some of the parties receiving the covered work authorizing them to use, propagate, modify or convey a specific copy of the covered work, then the patent license you grant is automatically extended to all recipients of the covered work and works based on it. A patent license is "discriminatory" if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007. Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law. 12. No Surrender of Others' Freedom. If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program. 13. Use with the GNU Affero General Public License. Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such. 14. Revised Versions of this License. The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation. If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program. Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version. 15. Disclaimer of Warranty. THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 16. Limitation of Liability. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. 17. Interpretation of Sections 15 and 16. If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see . The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read . tantan-13/README.html0000644000000000000000000003610412037256344013117 0ustar rootroot tantan

tantan

Introduction

tantan is a tool for masking simple regions (low complexity and short-period tandem repeats) in biological sequences.

The aim of tantan is to prevent false predictions when searching for homologous regions between two sequences. Simple repeats often align strongly to each other, causing false homology predictions.

Setup

You need to have a C++ compiler. On Linux, you might need to install a package called "g++". On Mac, you might need to install command-line developer tools. On Windows, you might need to install Cygwin.

Using the command line, go into the tantan directory. To compile it, type:

make

Optionally, copy tantan to a standard "bin" directory (using "sudo" to request administrator permissions):

sudo make install

Or copy it to your personal bin directory:

make install prefix=~

You might need to log out and back in for your computer to recognize the new program.

Normal usage

  • Suppose you have some nucleotide sequences (DNA or RNA) in a FASTA-format file called "ntseqs.fa". You can identify simple repeats like this:

    tantan ntseqs.fa > masked.fa

    This will create a new FASTA file called "masked.fa" that replaces all masked regions with lowercase letters. (tantan also works on FASTQ-format, though it does not use the quality data.)

  • To mask proteins effectively, tantan needs to use different algorithm parameters than for nucleotides. You have to tell it when you have proteins, using the "-p" option:

    tantan -p aaseqs.fa > masked.fa

    If you omit "-p" and the sequences look proteinaceous, tantan will print a warning message.

Advanced usage

  • By default, tantan indicates repetitive regions with lowercase letters. You can make it replace repetitive letters with (say) "N" by using the "-x" option:

    tantan -x N ntseqs.fa > masked.fa

  • By default, tantan does not preserve lowercase letters in the input sequences. You can tell it to preserve them by using the "-c" option. So the output will have the union of the lowercase in the input and the lowercase assigned by tantan:

    tantan -c ntseqs.fa > masked.fa

  • tantan's masking rate is usually OK, but you can alter it by changing the "-r" parameter from its default value of 0.005. Higher values increase the amount of masking, and lower values decrease it. This increases the masking rate:

    tantan -r 0.02 ntseqs.fa > masked.fa

  • Finally, to mask extremely AT-rich DNA, you should change tantan's scoring matrix. The "test" directory contains a matrix "atMask.mat" that works well for DNA with ~80% A+T, such as Plasmodium and Dictyostelium genomes. We recommend masking such DNA like this:

    tantan -m atMask.mat -r 0.01 atrich.fa > masked.fa

The preceding examples cover all of tantan's options that you should ever need.

FAQ

Why does tantan sometimes mask isolated bases?

This happens when a region is borderline repetitive, and a single base creeps just over the threshold. Don't worry about it, it's not a problem (at least for tantan's aim of preventing false homology).

Does tantan mask functional sequence?

Of course. Proteins and protein-coding exons can contain simple repeats. Repeats can be functional. If we want to avoid false homology we have to mask them. Remember that tantan merely lowercases repeats, so it's easy to lift the masking after determining homology.

Options

-p interpret the sequences as proteins
-x letter to use for masking, instead of lowercase
-c preserve uppercase/lowercase in non-masked regions
-m file for letter pair scores (scoring matrix)
-r probability of a repeat starting per position
-e probability of a repeat ending per position
-w maximum tandem repeat period to consider
-d probability decay per period (period-(i+1) / period-i)
-a gap existence cost
-b gap extension cost
-s minimum repeat probability for masking
-f output type: 0=masked sequence, 1=repeat probabilities, 2=repeat counts, 3=BED
-h, --help show help message, then exit
--version show version information, then exit

Advanced issues

When tantan masks tandem repeats, it tends to leave the first (left-most) repeat unit unmasked. This sometimes allows us to find homologs we would otherwise miss:

TGCAAGCTA TTAGGCTTAGGTCAGTGC ttaagcttaggtcagtgc AACATA
||| ||| | |||||||||||||||||| ||| |||||||||||||| ||| ||
TGCTAGCAA TTAGGCTTAGGTCAGTGC ttaggcttaggtcagtgc AACGTA

However, there is a danger of non-equivalent repeat units being unmasked. This happens especially if we mask DNA on one strand but align it on the other strand:

                   TGCAAGCTA TTAGGCTTAGGTCAGTGC ttaagcttaggtcagtgc AACATA
                             ||||||||||||||||||
TGCTAGCAA ttaggcttaggtcagtgc TTAGGCTTAGGTCAGTGC AACGTA

(My thanks to Junko Tsuji and Paul Horton for finding these issues.)

Miscellaneous

tantan is distributed under the GNU General Public License, either version 3 of the License, or (at your option) any later version. For details, see COPYING.txt.

If you use tantan in your research, please cite: "A new repeat-masking method enables specific detection of homologous sequences", MC Frith, Nucleic Acids Research 2011 39(4):e23.

tantan's website is: http://www.cbrc.jp/tantan/

If you have any questions, comments, or problems concerning tantan, please email: tantan (ATmark) cbrc (dot) jp.

tantan-13/Makefile0000644000000000000000000000101512037256344012725 0ustar rootrootCXXFLAGS = -O3 all: @cd src && ${MAKE} CXXFLAGS="${CXXFLAGS}" prefix = /usr/local exec_prefix = ${prefix} bindir = ${exec_prefix}/bin install: all mkdir -p ${bindir} cp src/tantan ${bindir} clean: @cd src && ${MAKE} clean README.html: README.txt rst2html README.txt > README.html log: hg log --style changelog > ChangeLog.txt distdir = tantan-`hg id -n` dist: README.html log @cd src && ${MAKE} version.hh rsync -rC --exclude tantan src test Makefile *.txt README.html ${distdir} zip -qrm ${distdir} ${distdir} tantan-13/ChangeLog.txt0000644000000000000000000000446612037256344013672 0ustar rootroot2012-10-16 Martin C. Frith * README.txt: Expanded the documentation: installation & FAQ [946a951b1a06] [tip] * src/CA_code/nrutil.c: Just fixed a compiler warning [fa79ce69a581] 2012-08-08 Martin C. Frith * Makefile: Avoid getting extra, unwanted files in the zip archive [d1d55af0e693] * test/tantan_test.sh: Made the test script less likely to use an unexpected version of tantan [894f9fc63c3e] * Makefile, README.txt: Added "make install", and HTML-ization of the README [674f2f7da185] * src/Makefile: Made the Makefile check the version number [ea0be7d72912] * README.txt: Converted the README to reStructuredText [25b631ab86b4] * src/Makefile: Generalized the Makefile [9c324ee14279] 2011-07-07 Martin C. Frith * README.txt: Just changed the documentation a bit [2d6dfe34fe33] 2011-03-22 Martin C. Frith * README.txt, src/mcf_tantan_options.cc, src/mcf_tantan_options.hh, src/tantan_app.cc: Added BED output option. Clarified the README (thanks: Joe Ryan). [db4af8e37a20] 2011-01-07 Martin C. Frith * README.txt, src/mcf_fasta_sequence.cc, src/mcf_fasta_sequence.hh, test/panda.fastq, test/tantan_test.out, test/tantan_test.sh: Made tantan work on fastq format, and improved the README [e7d454a5982d] 2010-11-16 Martin C. Frith * README.txt, src/Makefile, src/mcf_alphabet.cc, src/mcf_alphabet.hh, src/mcf_tantan_options.cc: Fixed compile error with g++ 4.0.1 [97a2b94e5835] 2010-10-13 Martin C. Frith * src/tantan_app.cc: Boost the version number to 1 [c5a20b01a563] * COPYING.txt, README.txt, src/CA_code/lambda_calculator.c, src/CA_code/lambda_calculator.h, src/CA_code/lubksb.c, src/CA_code/ludcmp.c, src/CA_code/nrutil.c, src/CA_code/nrutil.h, src/Makefile, src/mcf_alphabet.cc, src/mcf_alphabet.hh, src/mcf_fasta_sequence.cc, src/mcf_fasta_sequence.hh, src/mcf_score_matrix.cc, src/mcf_score_matrix.hh, src/mcf_score_matrix_probs.cc, src/mcf_score_matrix_probs.hh, src/mcf_tantan_options.cc, src/mcf_tantan_options.hh, src/mcf_util.cc, src/mcf_util.hh, src/tantan.cc, src/tantan.hh, src/tantan_app.cc, test/atMask.mat, test/hg19_chrM.fa, test/tantan_test.out, test/tantan_test.sh, test/titin_human.fa: First commit [4f9b0ba31588] tantan-13/test/0000755000000000000000000000000012037256344012247 5ustar rootroottantan-13/test/panda.fastq0000644000000000000000000005003212037256344014372 0ustar rootroot@SRR019778.1 I331_2_FC3076HAAXX:1:1:1416:1963 length=45 GTTCAATGGGGGAAAGGAGAGTCCTTCAACAAATGGTGCGGAGAA +SRR019778.1 I331_2_FC3076HAAXX:1:1:1416:1963 length=45 IIIIIIIIIIIIIIIIIIIIIIIIIIIB2IHH(-0+ @SRR019778.3 I331_2_FC3076HAAXX:1:1:1611:1333 length=45 GTTTTCCCATTTGTCCTTAATCCACCTAAAAAAGATTTGCATGGG +SRR019778.3 I331_2_FC3076HAAXX:1:1:1611:1333 length=45 IIIIIIIIIIIIIEIIIIG:IDIGECI454,10+0A?8/4+40%( @SRR019778.4 I331_2_FC3076HAAXX:1:1:1277:1927 length=45 GTTGTGTGTGTATTGTGTGTTGTGTGTGGTGTGTGTGTTTTTTTT +SRR019778.4 I331_2_FC3076HAAXX:1:1:1277:1927 length=45 IIIIIIIIIIIIII6IIIIIIDIII4I%4I*I0IAI+II8/3I+I @SRR019778.5 I331_2_FC3076HAAXX:1:1:1494:1984 length=45 GGATGTTTATTTTCCTGAACCAGGGTTTGGCATTGAAGAGACAGA +SRR019778.5 I331_2_FC3076HAAXX:1:1:1494:1984 length=45 IIIIIIIIIIIIIIIIIIIII/III@III@<-I6I'3I67-++>) @SRR019778.6 I331_2_FC3076HAAXX:1:1:682:1158 length=45 GTTTGTTTCCTAGAGTTAAGAGTCTCTCATGGTTTGTCTCCCTCT +SRR019778.6 I331_2_FC3076HAAXX:1:1:682:1158 length=45 IIIIIIIIIIIII:IIII=IEIIHI@IC2I9;I@@//?4DA5080,&, @SRR019778.13 I331_2_FC3076HAAXX:1:1:1245:2003 length=45 GTTTCCATAACCAGAAATATACAGCGGATTAGAGAAGTGATTTTT +SRR019778.13 I331_2_FC3076HAAXX:1:1:1245:2003 length=45 IIIIIIIIIIIIIIG>1I4I5I9IIII*II.I+G)-B7G&:B@C@ @SRR019778.14 I331_2_FC3076HAAXX:1:1:1226:1990 length=45 GGGAGGATCTAGCCTTAGAACCAAGAAACAAAATGTGAGGGGAAA +SRR019778.14 I331_2_FC3076HAAXX:1:1:1226:1990 length=45 IIIIIIIIIIIIIIII6IIIIIAII>.III-3/II3I1IIII.-- @SRR019778.15 I331_2_FC3076HAAXX:1:1:1879:1017 length=45 GTGATGTGCCATTGACCTATTTGTTTATCTTTATACCAATACTTC +SRR019778.15 I331_2_FC3076HAAXX:1:1:1879:1017 length=45 IIIIIIIIIIIIII2III/IIDGFII/I7IG:5CC;/0&=)+;4+ @SRR019778.16 I331_2_FC3076HAAXX:1:1:1478:1340 length=45 GTATTTTACAGAAGTTTCTCTGGGTCTCAGATTCCTACCTGACCC +SRR019778.16 I331_2_FC3076HAAXX:1:1:1478:1340 length=45 IIIIIIIIIIIIIIDIIIIII>;C;DI@D*3IE<2B/20;&'/-/ @SRR019778.17 I331_2_FC3076HAAXX:1:1:1489:1981 length=45 GGGAAAGATAGAGAGCCTTGTCTTCAAAATGGCTTATCCAGTAAG +SRR019778.17 I331_2_FC3076HAAXX:1:1:1489:1981 length=45 IIIIIIIIIIIIIIIIIIIIIIIII?+<5IIIIIB*66<%=3'(5 @SRR019778.18 I331_2_FC3076HAAXX:1:1:1710:940 length=45 GAGAATCCACAAGAAGTTGCTGTTAGGGATTTGTTCTTATTTTAA +SRR019778.18 I331_2_FC3076HAAXX:1:1:1710:940 length=45 IIIIIIIIIIIII0CIIIIIII@I(-?6-@?C.37,A:%D;:&** @SRR019778.19 I331_2_FC3076HAAXX:1:1:1339:973 length=45 GAAAAGGCATAAATATTTCATTCAATTGCAAGCTTAATATAAGTC +SRR019778.19 I331_2_FC3076HAAXX:1:1:1339:973 length=45 IIIIIIIIIIIIIIFIIIIHIIII:II;II63=IIC.GFI76(.. @SRR019778.20 I331_2_FC3076HAAXX:1:1:1408:1952 length=45 GAGTTTTCCATTTAAGAACTTGAGTGTCATCGCCTTAGGAAAGAC +SRR019778.20 I331_2_FC3076HAAXX:1:1:1408:1952 length=45 IIIIIIIIIIIII@FIFGIIII8I?+HIIDI=E>I>8?1)1&*// @SRR019778.21 I331_2_FC3076HAAXX:1:1:1468:1371 length=45 GAAGAGAAAGGAGATACCATCATTTGTCATTAACAGGATTACCTT +SRR019778.21 I331_2_FC3076HAAXX:1:1:1468:1371 length=45 IIIIIIIIIIIIIIIIIIIIIFIIII=I3I:13=A<@,/03I2<+:- @SRR019778.26 I331_2_FC3076HAAXX:1:1:1225:1945 length=45 GTAATGATTGAATAAATCTTATTAACTTCTTAATCTTTTAATTTT +SRR019778.26 I331_2_FC3076HAAXX:1:1:1225:1945 length=45 IIIIIIIIIIIIIIIIIIIIIIIB4HIIIII:3IIIIII5)IIGI @SRR019778.27 I331_2_FC3076HAAXX:1:1:1506:1294 length=45 GCTTCAAGAAGAAGGGCATGACTCACCCCCCAGGAACAGAAGCTG +SRR019778.27 I331_2_FC3076HAAXX:1:1:1506:1294 length=45 IIIIIIIIIIIIIIIIIIIIIIII@IIICDB15B+39.9*.B4:5 @SRR019778.28 I331_2_FC3076HAAXX:1:1:1318:1418 length=45 GATTTTATTCTTATTGTTTTGATGGTGACCTTTAATATTTTCTTA +SRR019778.28 I331_2_FC3076HAAXX:1:1:1318:1418 length=45 IIIIIIIIIIIIIIIIIIIIADI,BFIA..IIIC2$7IFEC1&;) @SRR019778.29 I331_2_FC3076HAAXX:1:1:1332:1930 length=45 GAGAATAAGTCAATACCAAGGTGAATTGAATAATGGCCAAGAATT +SRR019778.29 I331_2_FC3076HAAXX:1:1:1332:1930 length=45 IIIIIIIIIIIIIIIIGIHIIII58IIII5I@9AI8I0=,B,-3> @SRR019778.30 I331_2_FC3076HAAXX:1:1:1099:1168 length=45 GTTTATTCTCTATCATTTAGAGTCTCAGCTGTTTGGGTTTCTAGA +SRR019778.30 I331_2_FC3076HAAXX:1:1:1099:1168 length=45 IIIIIIIIIIIIII;IIII8I+BFII+C.2+8I.,&%3$$3/$)$ @SRR019778.31 I331_2_FC3076HAAXX:1:1:1529:1292 length=45 GGATAGCCCCAAGTGTTACAAATTGTAAGTAAATATTTGTAGGGA +SRR019778.31 I331_2_FC3076HAAXX:1:1:1529:1292 length=45 IIIIIIIIIIIIIIIII>I<<8IIIID2I=/7.;2EH@22/6+&* @SRR019778.32 I331_2_FC3076HAAXX:1:1:1256:1996 length=45 GTTGGGGATTAGAAAGTAGATGTAAGGAGTAGTAAAGGGAATACA +SRR019778.32 I331_2_FC3076HAAXX:1:1:1256:1996 length=45 IIIIIIIIIIIIIHIIIIIIIIHI6II5I;I3 @SRR019778.39 I331_2_FC3076HAAXX:1:1:1136:1244 length=45 GTTATATGTGAGTAATGAACCATTGAACACTACACCAAAAATTAA +SRR019778.39 I331_2_FC3076HAAXX:1:1:1136:1244 length=45 IIIIIIIIIIIIIIIIIIIIDIIIII:8B8IH3;72<8031D92- @SRR019778.40 I331_2_FC3076HAAXX:1:1:1819:927 length=45 GGGTTTGGAGTTTAAAGAGAGAATAAGTCATGTGCCAATATATGA +SRR019778.40 I331_2_FC3076HAAXX:1:1:1819:927 length=45 IIIIIIIIIIIIIIG;IFIIII6II?IEBE?8@A<79,D5<4F1) @SRR019778.41 I331_2_FC3076HAAXX:1:1:1250:1938 length=45 GTTTGTGTCCCTCTAAAGTTCATATACTGAAGCCCTAACCCCCAG +SRR019778.41 I331_2_FC3076HAAXX:1:1:1250:1938 length=45 IIIIIIIIIIIIIIII2IIIIIIIIIIII=:=IIEI3/I7I7G+0 @SRR019778.42 I331_2_FC3076HAAXX:1:1:1648:1646 length=45 GGTTGTGTGTGTGTGTGTGTGTGTGTGTGTTTGTTTTTTTTTTTA +SRR019778.42 I331_2_FC3076HAAXX:1:1:1648:1646 length=45 IIIIIIIIIIIIIIIIIIII7I@I.IDIB,.@%I0*-E(G%(/.% @SRR019778.43 I331_2_FC3076HAAXX:1:1:690:962 length=45 GTGAGATGATGTTCGTTGATATTTCCCTGTATTTTTTGTTTTTTC +SRR019778.43 I331_2_FC3076HAAXX:1:1:690:962 length=45 IIIIIIIIIIIIIIIIII>I?III??,I'$)II%:&B&'8(9$=$ @SRR019778.44 I331_2_FC3076HAAXX:1:1:1399:1957 length=45 GTTGATATTTCCCTGGACTGTGTGGGGTCTCAGAGACCACTATGG +SRR019778.44 I331_2_FC3076HAAXX:1:1:1399:1957 length=45 IIIIIIIIIIIIIIII=IIIIIIIIIIIIIG4>,I/9;*3D*:<+ @SRR019778.45 I331_2_FC3076HAAXX:1:1:1797:1797 length=45 GTGTGTATTGTGTGTGGGTGTGTGTGTTGTGTGTGTTTTGGGTGG +SRR019778.45 I331_2_FC3076HAAXX:1:1:1797:1797 length=45 IIIIIIIIIIIIII@IIIIIIIAII?II?I0(+D)II$:&5%'&% @SRR019778.46 I331_2_FC3076HAAXX:1:1:721:921 length=45 GATGTCATAGAAGTTGTTGCCTATGTTCTCCTCTAGAATTTTGAT +SRR019778.46 I331_2_FC3076HAAXX:1:1:721:921 length=45 IIIIIIIIIIIIIIIIIIH?CI6I7II0I11F5I+&+(ICIH&&= @SRR019778.47 I331_2_FC3076HAAXX:1:1:1584:1300 length=45 GGTAGTGAGTATCAGCCCTGTGCAGGTTTCTGCAGATGGCCATGT +SRR019778.47 I331_2_FC3076HAAXX:1:1:1584:1300 length=45 IIIII-IIIIIIIHIIIII4;GCIEI-II320-&-#)%,.,$-%$ @SRR019778.48 I331_2_FC3076HAAXX:1:1:1397:1963 length=45 GAAAACTTACTTACAAATTCATTCTATGAGGCCAGCATTACCCTG +SRR019778.48 I331_2_FC3076HAAXX:1:1:1397:1963 length=45 IIIIIIIIIIIIIIII:IIIIIIII4II4FIIH0F@*CI47><:1 @SRR019778.49 I331_2_FC3076HAAXX:1:1:1550:1296 length=45 GGTAGATGTGACTCTTGATCTCAGGGTCATGAGTTCAAGCCCCAT +SRR019778.49 I331_2_FC3076HAAXX:1:1:1550:1296 length=45 IIIIIIIIIIIIIIIIICIIBI6D%I9B5C;0I+;37-4)0**)3 @SRR019778.50 I331_2_FC3076HAAXX:1:1:913:1939 length=45 GTGTGTTGTGTGTTGAGTGTTTTGTGTGTGTGTTGTGTTTTTTGT +SRR019778.50 I331_2_FC3076HAAXX:1:1:913:1939 length=45 IIIIIIIIIIIIIII2IIIIIII@IIG2I.I,II&9&4%II,:%, @SRR019778.51 I331_2_FC3076HAAXX:1:1:1734:1009 length=45 GAAACAATGGTTTTCAAGACACTGGACATCAGCCTACAATGGACA +SRR019778.51 I331_2_FC3076HAAXX:1:1:1734:1009 length=45 IIIIIIIIIIIIIIIIIIEIBIIID.>2I?186C?)/&-8,1)1+ @SRR019778.52 I331_2_FC3076HAAXX:1:1:1355:100 length=45 GTACACAAATCTACGTGATATTTCGAAAGGTAAACAGATAATGCT +SRR019778.52 I331_2_FC3076HAAXX:1:1:1355:100 length=45 IIIIIIIIIIIII7I7,IIC&FD>1->9'+00 @SRR019778.56 I331_2_FC3076HAAXX:1:1:1759:1586 length=45 GGTACTCTAATAGCGTTTTATGGTAAGAGATGGTAGCTGTACTTG +SRR019778.56 I331_2_FC3076HAAXX:1:1:1759:1586 length=45 IIIIIIIIIF0I1III++;6.':594*7)4* @SRR019778.58 I331_2_FC3076HAAXX:1:1:1371:1534 length=45 GTGATGGGAAAGGAAAGAGCCAATCCTGTAGGGCCTGGTAGATCA +SRR019778.58 I331_2_FC3076HAAXX:1:1:1371:1534 length=45 I7IIIIIIIIIIIIIIIIIIII>III@*86IIIF??I7+)6-9+0 @SRR019778.59 I331_2_FC3076HAAXX:1:1:1780:1771 length=45 GTAAAATGGAGTAAATAGAGTAGAATAACATAAAAATTACAATGT +SRR019778.59 I331_2_FC3076HAAXX:1:1:1780:1771 length=45 IIIIIIIIIIIII;IIIE.-/0827:4./3- @SRR019778.60 I331_2_FC3076HAAXX:1:1:1539:1636 length=45 GTGTTGCTCTTTCTGAGGTGGTAATTGTGGTTTCCTTGGGCCTTT +SRR019778.60 I331_2_FC3076HAAXX:1:1:1539:1636 length=45 IIIIIIIIIIIIIIIIIICII:7III9I9IFII1(4I%%+&*1&. @SRR019778.61 I331_2_FC3076HAAXX:1:1:1360:1444 length=45 GTTGGGTTGATTTTCATTGGTGCTAATGTAATGGGGTATTGATCC +SRR019778.61 I331_2_FC3076HAAXX:1:1:1360:1444 length=45 IIIIIIIIIIIIIIIIIIIBI/GI>1II%).I),,+9'IB)+B+) @SRR019778.62 I331_2_FC3076HAAXX:1:1:1763:997 length=45 GAGATGAGTCAGCAGAGGTAAAAGCTAGAAGGATGTTAGGATGAT +SRR019778.62 I331_2_FC3076HAAXX:1:1:1763:997 length=45 IIIIIIIIIIIII?I@IID=II@A?E?I1;D=:C@6>-<0+A2.= @SRR019778.63 I331_2_FC3076HAAXX:1:1:996:1270 length=45 GTCAGGGACTTAATATCTTTCCCTTAAAATATGTGTGTTATTTTC +SRR019778.63 I331_2_FC3076HAAXX:1:1:996:1270 length=45 IIIIIIIIIIIIIIIIIIIIIEIII<:9)<(:I%: @SRR019778.66 I331_2_FC3076HAAXX:1:1:1314:76 length=45 GTGCTTAGCAGATAGGAGGGGCTCATTAACATGTTGAACAAATGT +SRR019778.66 I331_2_FC3076HAAXX:1:1:1314:76 length=45 IIIIIIIIIIIII7II7IIII?II4II/14+I*I@/.:/.6*F>>+ @SRR019778.68 I331_2_FC3076HAAXX:1:1:1459:1955 length=45 GTGTTCCCATACTTTAACTTGTGTGTGTTGTGGGGGGAAGCATAT +SRR019778.68 I331_2_FC3076HAAXX:1:1:1459:1955 length=45 IIIIIIIIDIIIIII>FIIIIIIIIIIII6I>47>I+*(/#$I$@ @SRR019778.69 I331_2_FC3076HAAXX:1:1:1381:1967 length=45 GCCCTAAGAACCAAGAAACAAAGTGTGAGGGGAAAGCCCTTGAAT +SRR019778.69 I331_2_FC3076HAAXX:1:1:1381:1967 length=45 IIIIIIIIIIIII:IE)CIC?1F4I+I8IIII.,/I959-:B&'9 @SRR019778.70 I331_2_FC3076HAAXX:1:1:1224:2001 length=45 GATACGTCAAATTTATGGAAGTGTTTTATAAGTGCATTTAAGTTT +SRR019778.70 I331_2_FC3076HAAXX:1:1:1224:2001 length=45 IIIIIIIIIIIIIIIIII8EI=IIIII8I4.9E9+$II&%+(:?& @SRR019778.71 I331_2_FC3076HAAXX:1:1:1771:1569 length=45 GTTTTTATAATGACTTCCTTAGGCTGTACCCCCAATTTACTATAT +SRR019778.71 I331_2_FC3076HAAXX:1:1:1771:1569 length=45 IIIIIIIIIIIIIIIIIIII*(IAB(4?'D'F @SRR019778.72 I331_2_FC3076HAAXX:1:1:1745:1606 length=45 GATTTGCAGTCAAGGACAGGTCCACACAGTCAGGACCACAGTGTT +SRR019778.72 I331_2_FC3076HAAXX:1:1:1745:1606 length=45 IIIIIIIIIIIIEIIII-I2; @SRR019778.73 I331_2_FC3076HAAXX:1:1:1279:1959 length=45 GGAGGAAGACCACAGAGCTGAAGCACCGTCCTCATCACATCAGGT +SRR019778.73 I331_2_FC3076HAAXX:1:1:1279:1959 length=45 IIIIIIIIIIIIIIIIIIIIHFII86II6IICI1CI4I4*5*4B( @SRR019778.74 I331_2_FC3076HAAXX:1:1:1769:1745 length=45 GAAGTGATGTAGATGCCTATATGAATACAGGCACATATGGTTTCC +SRR019778.74 I331_2_FC3076HAAXX:1:1:1769:1745 length=45 IIIIDIIIIIIIIIIIII7IIIIG>I0E2II=+7/:+7DA04*'7 @SRR019778.75 I331_2_FC3076HAAXX:1:1:721:1248 length=45 GACAAGTTTAGGAAGCCTGTTATTTTACTACATGAAACATTCATA +SRR019778.75 I331_2_FC3076HAAXX:1:1:721:1248 length=45 IIEIIIIIIIIIIIIIIII>IIIIII>III9AI+75>76?84-2I @SRR019778.76 I331_2_FC3076HAAXX:1:1:1306:616 length=45 GTTAAGATAAATCACAGAGCACCAACCTCAAGCGATGGCAGCTGC +SRR019778.76 I331_2_FC3076HAAXX:1:1:1306:616 length=45 IIIIIIIIIIIIIIIIIIIIIIIIAIC=B6:57:274.2,+(+%& @SRR019778.77 I331_2_FC3076HAAXX:1:1:1474:1625 length=45 GTAAAGGACTTTCAGGACCTAATTTAAATGATCACTCAGGCTGAG +SRR019778.77 I331_2_FC3076HAAXX:1:1:1474:1625 length=45 IIIIIIIIIIIIIIIIIIII>9III@7GII3IIFIIA34'1FA)7 @SRR019778.78 I331_2_FC3076HAAXX:1:1:1866:942 length=45 GACAGATACTGCCTTACTATGCCTTACTATGTGCACATATACACA +SRR019778.78 I331_2_FC3076HAAXX:1:1:1866:942 length=45 IIIIIIIIIIIIIIIIII5IIIIII1II.I+:,C33,?/;,,)/) @SRR019778.79 I331_2_FC3076HAAXX:1:1:1803:1776 length=45 GTAATATATAAACAGCATAGATAATATCAGATAAAAGGACTTTCT +SRR019778.79 I331_2_FC3076HAAXX:1:1:1803:1776 length=45 IIIIIIIIIIIII:II8IDI;I9:I/=E;I>AA0132/29>=/15 @SRR019778.80 I331_2_FC3076HAAXX:1:1:716:927 length=45 GCAAGGTAGGGACACGGGGACTCAGACAGATGAACAGATTAGACT +SRR019778.80 I331_2_FC3076HAAXX:1:1:716:927 length=45 IIIIIIIIIIIIIIIIIIIACIGBI=?2I6DA8;3+;/5:/./+1 @SRR019778.81 I331_2_FC3076HAAXX:1:1:1294:71 length=45 GTAAACATGGAACACAACAAAAAAACTTCAAAAAGGCAAAACTAG +SRR019778.81 I331_2_FC3076HAAXX:1:1:1294:71 length=45 IIIIIIIIIIIIIDIIII93I@AE.HE7I632-,63?72/1476, @SRR019778.82 I331_2_FC3076HAAXX:1:1:1486:1393 length=45 GATTTAAACAATTACATCAAAATGCATTGATTCAATTGTTTTTTA +SRR019778.82 I331_2_FC3076HAAXX:1:1:1486:1393 length=45 IIIIIIIIIIIIIIIIIIIBIIIID9:I@;4@8*B0I4A77 @SRR019778.83 I331_2_FC3076HAAXX:1:1:1880:1764 length=45 GTAAAAATAACTACATTAACTGTGACAAGGGATACCCAAGAAGAT +SRR019778.83 I331_2_FC3076HAAXX:1:1:1880:1764 length=45 IIIIIIIIIIIIIIIIIIIIIIAI:I8:IHI.52IG4'/4-+2)0 @SRR019778.84 I331_2_FC3076HAAXX:1:1:1410:1972 length=45 GCATGTGGATATCCAGTTTTCCCATTTCTTGAAAAGTGTGTCCTT +SRR019778.84 I331_2_FC3076HAAXX:1:1:1410:1972 length=45 IIIIIIIIIIIIII/IIIIIIII7IIIIII;3.)1=<<8-D86G> @SRR019778.85 I331_2_FC3076HAAXX:1:1:1681:1342 length=45 GTAGAAATGACCTTAGCCCACTATACTAGAAACTTCGGGTTTGTG +SRR019778.85 I331_2_FC3076HAAXX:1:1:1681:1342 length=45 IIIIIIIIIIIIIIIIIIFDII3IFIII)712145+.5,1&3+ @SRR019778.87 I331_2_FC3076HAAXX:1:1:1395:1991 length=45 GTGCTATCTCATCATGGTTTTGATCTGTATTTCCCTGATAATGAG +SRR019778.87 I331_2_FC3076HAAXX:1:1:1395:1991 length=45 IIIIIIIIIIIII?IIIIIIII2IIIIF7IIIGCEI;+D&-B+** @SRR019778.88 I331_2_FC3076HAAXX:1:1:1332:1959 length=45 GATAGTAACTCCTGTCTTCCTACGGGGTTAAAAAAAGCCTTCTGC +SRR019778.88 I331_2_FC3076HAAXX:1:1:1332:1959 length=45 IIIIIIIIIIIIIIIIIIII3IIIIII=ID-2/+824<;4?A872 @SRR019778.89 I331_2_FC3076HAAXX:1:1:1304:77 length=45 GAAGAGAGAAGTCTGGGGGATCAGAGGCCACCAAAAGCAAAACAA +SRR019778.89 I331_2_FC3076HAAXX:1:1:1304:77 length=45 IIIIIIIIIIIIIIICIDI?D97957@;+839,))+5-2*')**) @SRR019778.90 I331_2_FC3076HAAXX:1:1:1478:1372 length=45 GTTAAAGGTGAAGAAGGAAGAGAAGTTCCTTCCATTTGGCAGATT +SRR019778.90 I331_2_FC3076HAAXX:1:1:1478:1372 length=45 IIIIIIIIIIIIIIIIIIIIII2AI3II>IB@50A:3<*5+@):2 @SRR019778.91 I331_2_FC3076HAAXX:1:1:1518:630 length=45 GTAGTGGTGAAAGTATTTATTTTTCCCTATATCTTTGTTAATTGC +SRR019778.91 I331_2_FC3076HAAXX:1:1:1518:630 length=45 IIIIIIIIIIIIICIIII@IIIIIIDFI?I1I9IHC$:B.+BI%) @SRR019778.92 I331_2_FC3076HAAXX:1:1:1486:1973 length=45 GAAACAGACAAAAGCCTTAGTAACCTGGGGCTCAGCAAAAGGCCA +SRR019778.92 I331_2_FC3076HAAXX:1:1:1486:1973 length=45 IIIIIIIIIIIIIIIIIIIIIH?IIIIIIIIII3IH-//(I??I3 @SRR019778.93 I331_2_FC3076HAAXX:1:1:1296:1435 length=45 GAGTTTTGAACTCAGGCTGTTCTGGCCTCAAAATTCATGCTCATT +SRR019778.93 I331_2_FC3076HAAXX:1:1:1296:1435 length=45 IIIIIIIIIIIIIIIIIIIII4@&;74C1)01/9I)'9&-7+(29 @SRR019778.94 I331_2_FC3076HAAXX:1:1:1502:1287 length=45 GCACAGATGAGCCAAGAAGGGTTCCAGTTCCCCTGCTTCATTATG +SRR019778.94 I331_2_FC3076HAAXX:1:1:1502:1287 length=45 IIIIIIIIIIIIII;'*B63'20,%6- @SRR019778.96 I331_2_FC3076HAAXX:1:1:1878:956 length=45 GATAATATACTATGGCTCTGCAAGATAGTACTTGGGGGAAACAAA +SRR019778.96 I331_2_FC3076HAAXX:1:1:1878:956 length=45 IIIIIIIIIIIIIIIIII(/:*--01+1.2.-$/+0&6#,2&(&4 @SRR019778.97 I331_2_FC3076HAAXX:1:1:608:1209 length=45 GAAATTTTCCTTCAATAAAGGGAGATTCTAATCTACATATTTTAA +SRR019778.97 I331_2_FC3076HAAXX:1:1:608:1209 length=45 IIIIIIIIIIIIIIIIHH4I=A' "$@" | tr -cd a-z | wc -c } { tantan hg19_chrM.fa echo tantan -p -xx titin_human.fa echo tantan -p -f2 titin_human.fa echo tantan -c hg19_chrM.fa | countLowercaseLetters echo tantan -w50 -e.005 -d1 hg19_chrM.fa | countLowercaseLetters echo tantan -m atMask.mat -r.01 hg19_chrM.fa | countLowercaseLetters echo tantan -p -a11 -b2 titin_human.fa | countLowercaseLetters echo tantan panda.fastq } | diff tantan_test.out - tantan-13/test/titin_human.fa0000644000000000000000000010436412037256344015106 0ustar rootroot>sp|Q8WZ42|TITIN_HUMAN MTTQAPTFTQPLQSVVVLEGSTATFEAHISGFPVPEVSWFRDGQVISTST LPGVQISFSDGRAKLTIPAVTKANSGRYSLKATNGSGQATSTAELLVKAE TAPPNFVQRLQSMTVRQGSQVRLQVRVTGIPTPVVKFYRDGAEIQSSLDF QISQEGDLYSLLIAEAYPEDSGTYSVNATNSVGRATSTAELLVQGEEEVP AKKTKTIVSTAQISESRQTRIEKKIEAHFDARSIATVEMVIDGAAGQQLP HKTPHRIPPKPKSRSPTPPSIAAKAQLARQQSPSPIRHSPSPVRHVRAPT PSPVRSVSPAARISTSPIRSVRSPLLMRKTQASTVATGPEVPPPWKQEGY VASSSEAEMRETTLTTSTQIRTEERWEGRYGVQEQVTISGAAGAAASVSA SASYAAEAVATGAKEVKQDADKSAAVATVVAAVDMARVREPVISAVEQTA QRTTTTAVHIQPAQEQVRKEAEKTAVTKVVVAADKAKEQELKSRTKEVIT TKQEQMHVTHEQIRKETEKTFVPKVVISAAKAKEQETRISEEITKKQKQV TQEAIRQETEITAASMVVVATAKSTKLETVPGAQEETTTQQDQMHLSYEK IMKETRKTVVPKVIVATPKVKEQDLVSRGREGITTKREQVQITQEKMRKE AEKTALSTIAVATAKAKEQETILRTRETMATRQEQIQVTHGKVDVGKKAE AVATVVAAVDQARVREPREPGHLEESYAQQTTLEYGYKERISAAKVAEPP QRPASEPHVVPKAVKPRVIQAPSETHIKTTDQKGMHISSQIKKTTDLTTE RLVHVDKRPRTASPHFTVSKISVPKTEHGYEASIAGSAIATLQKELSATS SAQKITKSVKAPTVKPSETRVRAEPTPLPQFPFADTPDTYKSEAGVEVKK EVGVSITGTTVREERFEVLHGREAKVTETARVPAPVEIPVTPPTLVSGLK NVTVIEGESVTLECHISGYPSPTVTWYREDYQIESSIDFQITFQSGIARL MIREAFAEDSGRFTCSAVNEAGTVSTSCYLAVQVSEEFEKETTAVTEKFT TEEKRFVESRDVVMTDTSLTEEQAGPGEPAAPYFITKPVVQKLVEGGSVV FGCQVGGNPKPHVYWKKSGVPLTTGYRYKVSYNKQTGECKLVISMTFADD AGEYTIVVRNKHGETSASASLLEEADYELLMKSQQEMLYQTQVTAFVQEP KVGETAPGFVYSEYEKEYEKEQALIRKKMAKDTVVVRTYVEDQEFHISSF EERLIKEIEYRIIKTTLEELLEEDGEEKMAVDISESEAVESGFDLRIKNY RILEGMGVTFHCKMSGYPLPKIAWYKDGKRIKHGERYQMDFLQDGRASLR IPVVLPEDEGIYTAFASNIKGNAICSGKLYVEPAAPLGAPTYIPTLEPVS RIRSLSPRSVSRSPIRMSPARMSPARMSPARMSPARMSPGRRLEETDESQ LERLYKPVFVLKPVSFKCLEGQTARFDLKVVGRPMPETFWFHDGQQIVND YTHKVVIKEDGTQSLIIVPATPSDSGEWTVVAQNRAGRSSISVILTVEAV EHQVKPMFVEKLKNVNIKEGSQLEMKVRATGNPNPDIVWLKNSDIIVPHK YPKIRIEGTKGEAALKIDSTVSQDSAWYTATAINKAGRDTTRCKVNVEVE FAEPEPERKLIIPRGTYRAKEIAAPELEPLHLRYGQEQWEEGDLYDKEKQ QKPFFKKKLTSLRLKRFGPAHFECRLTPIGDPTMVVEWLHDGKPLEAANR LRMINEFGYCSLDYGVAYSRDSGIITCRATNKYGTDHTSATLIVKDEKSL VEESQLPEGRKGLQRIEELERMAHEGALTGVTTDQKEKQKPDIVLYPEPV RVLEGETARFRCRVTGYPQPKVNWYLNGQLIRKSKRFRVRYDGIHYLDIV DCKSYDTGEVKVTAENPEGVIEHKVKLEIQQREDFRSVLRRAPEPRPEFH VHEPGKLQFEVQKVDRPVDTTETKEVVKLKRAERITHEKVPEESEELRSK FKRRTEEGYYEAITAVELKSRKKDESYEELLRKTKDELLHWTKELTEEEK KALAEEGKITIPTFKPDKIELSPSMEAPKIFERIQSQTVGQGSDAHFRVR VVGKPDPECEWYKNGVKIERSDRIYWYWPEDNVCELVIRDVTAEDSASIM VKAINIAGETSSHAFLLVQAKQLITFTQELQDVVAKEKDTMATFECETSE PFVKVKWYKDGMEVHEGDKYRMHSDRKVHFLSILTIDTSDAEDYSCVLVE DENVKTTAKLIVEGAVVEFVKELQDIEVPESYSGELECIVSPENIEGKWY HNDVELKSNGKYTITSRRGRQNLTVKDVTKEDQGEYSFVIDGKKTTCKLK MKPRPIAILQGLSDQKVCEGDIVQLEVKVSLESVEGVWMKDGQEVQPSDR VHIVIDKQSHMLLIEDMTKEDAGNYSFTIPALGLSTSGRVSVYSVDVITP LKDVNVIEGTKAVLECKVSVPDVTSVKWYLNDEQIKPDDRVQAIVKGTKQ RLVINRTHASDEGPYKLIVGRVETNCNLSVEKIKIIRGLRDLTCTETQNV VFEVELSHSGIDVLWNFKDKEIKPSSKYKIEAHGKIYKLTVLNMMKDDEG KYTFYAGENITSGKLTVAGGAISKPLTDQTVAESQEAVFECEVANPDSKG EWLRDGKHLPLTNNIRSESDGHKRRLIIAATKLDDIGEYTYKVATSKTSA KLKVEAVKIKKTLKNLTVTETQDAVFTVELTHPNVKGVQWIKNGVVLESN EKYAISVKGTIYSLRIKNCAIVDESVYGFRLGRLGASARLHVETVKIIKK PKDVTALENATVAFEVSVSHDTVPVKWFHKNVEIKPSDKHRLVSERKVHK LMLQNISPSDAGEYTAVVGQLECKAKLFVETLHITKTMKNIEVPETKTAS FECEVSHFNVPSMWLKNGVEIEMSEKFKIVVQGKLHQLIIMNTSTEDSAE YTFVCGNDQVSATLTVTPIMITSMLKDINAEEKDTITFEVTVNYEGISYK WLKNGVEIKSTDKCQMRTKKLTHSLNIRNVHFGDAADYTFVAGKATSTAT LYVEARHIEFRKHIKDIKVLEKKRAMFECEVSEPDITVQWMKDDQELQIT DRIKIQKEKYVHRLLIPSTRMSDAGKYTVVAGGNVSTAKLFVEGRDVRIR SIKKEVQVIEKQRAVVEFEVNEDDVDAHWYKDGIEINFQVQERHKYVVER RIHRMFISETRQSDAGEYTFVAGRNRSSVTLYVNAPEPPQVLQELQPVTV QSGKPARFCAVISGRPQPKISWYKEEQLLSTGFKCKFLHDGQEYTLLLIE AFPEDAAVYTCEAKNDYGVATTSASLSVEVPEVVSPDQEMPVYPPAIITP LQDTVTSEGQPARFQCRVSGTDLKVSWYSKDKKIKPSRFFRMTQFEDTYQ LEIAEAYPEDEGTYTFVASNAVGQVSSTANLSLEAPESILHERIEQEIEM EMKEFSSSFLSAEEEGLHSAELQLSKINETLELLSESPVYSTKFDSEKEG TGPIFIKEVSNADISMGDVATLSVTVIGIPKPKIQWFFNGVLLTPSADYK FVFDGDDHSLIILFTKLEDEGEYTCMASNDYGKTICSAYLKINSKGEGHK DTETESAVAKSLEKLGGPCPPHFLKELKPIRCAQGLPAIFEYTVVGEPAP TVTWFKENKQLCTSVYYTIIHNPNGSGTFIVNDPQREDSGLYICKAENML GESTCAAELLVLLEDTDMTDTPCKAKSTPEAPEDFPQTPLKGPAVEALDS EQEIATFVKDTILKAALITEENQQLSYEHIAKANELSSQLPLGAQELQSI LEQDKLTPESTREFLCINGSIHFQPLKEPSPNLQLQIVQSQKTFSKEGIL MPEEPETQAVLSDTEKIFPSAMSIEQINSLTVEPLKTLLAEPEGNYPQSS IEPPMHSYLTSVAEEVLSPKEKTVSDTNREQRVTLQKQEAQSALILSQSL AEGHVESLQSPDVMISQVNYEPLVPSEHSCTEGGKILIESANPLENAGQD SAVRIEEGKSLRFPLALEEKQVLLKEEHSDNVVMPPDQIIESKREPVAIK KVQEVQGRDLLSKESLLSGIPEEQRLNLKIQICRALQAAVASEQPGLFSE WLRNIEKVEVEAVNITQEPRHIMCMYLVTSAKSVTEEVTIIIEDVDPQMA NLKMELRDALCAIIYEEIDILTAEGPRIQQGAKTSLQEEMDSFSGSQKVE PITEPEVESKYLISTEEVSYFNVQSRVKYLDATPVTKGVASAVVSDEKQD ESLKPSEEKEESSSESGTEEVATVKIQEAEGGLIKEDGPMIHTPLVDTVS EEGDIVHLTTSITNAKEVNWYFENKLVPSDEKFKCLQDQNTYTLVIDKVN TEDHQGEYVCEALNDSGKTATSAKLTVVKRAAPVIKRKIEPLEVALGHLA KFTCEIQSAPNVRFQWFKAGREIYESDKCSIRSSKYISSLEILRTQVVDC GEYTCKASNEYGSVSCTATLTVTEAYPPTFLSRPKSLTTFVGKAAKFICT VTGTPVIETIWQKDGAALSPSPNWKISDAENKHILELSNLTIQDRGVYSC KASNKFGADICQAELIIIDKPHFIKELEPVQSAINKKVHLECQVDEDRKV TVTWSKDGQKLPPGKDYKICFEDKIATLEIPLAKLKDSGTYVCTASNEAG SSSCSATVTVREPPSFVKKVDPSYLMLPGESARLHCKLKGSPVIQVTWFK NNKELSESNTVRMYFVNSEAILDITDVKVEDSGSYSCEAVNDVGSDSCST EIVIKEPPSFIKTLEPADIVRGTNALLQCEVSGTGPFEISWFKDKKQIRS SKKYRLFSQKSLVCLEIFSFNSADVGEYECVVANEVGKCGCMATHLLKEP PTFVKKVDDLIALGGQTVTLQAAVRGSEPISVTWMKGQEVIREDGKIKMS FSNGVAVLIIPDVQISFGGKYTCLAENEAGSQTSVGELIVKEPAKIIERA ELIQVTAGDPATLEYTVAGTPELKPKWYKDGRPLVASKKYRISFKNNVAQ LKFYSAELHDSGQYTFEISNEVGSSSCETTFTVLDRDIAPFFTKPLRNVD SVVNGTCRLDCKIAGSLPMRVSWFKDGKEIAASDRYRIAFVEGTASLEII RVDMNDAGNFTCRATNSVGSKDSSGALIVQEPPSFVTKPGSKDVLPGSAV CLKSTFQGSTPLTIRWFKGNKELVSGGSCYITKEALESSLELYLVKTSDS GTYTCKVSNVAGGVECSANLFVKEPATFVEKLEPSQLLKKGDATQLACKV TGTPPIKITWFANDREIKESSKHRMSFVESTAVLRLTDVGIEDSGEYMCE AQNEAGSDHCSSIVIVKESPYFTKEFKPIEVLKEYDVMLLAEVAGTPPFE ITWFKDNTILRSGRKYKTFIQDHLVSLQILKFVAADAGEYQCRVTNEVGS SICSARVTLREPPSFIKKIESTSSLRGGTAAFQATLKGSLPITVTWLKDS DEITEDDNIRMTFENNVASLYLSGIEVKHDGKYVCQAKNDAGIQRCSALL SVKEPATITEEAVSIDVTQGDPATLQVKFSGTKEITAKWFKDGQELTLGS KYKISVTDTVSILKIISTEKKDSGEYTFEVQNDVGRSSCKARINVLDLII PPSFTKKLKKMDSIKGSFIDLECIVAGSHPISIQWFKDDQEISASEKYKF SFHDNTAFLEISQLEGTDSGTYTCSATNKAGHNQCSGHLTVKEPPYFVEK PQSQDVNPNTRVQLKALVGGTAPMTIKWFKDNKELHSGAARSVWKDDTST SLELFAAKATDSGTYICQLSNDVGTATSKATLFVKEPPQFIKKPSPVLVL RNGQSTTFECQITGTPKIRVSWYLDGNEITAIQKHGISFIDGLATFQISG ARVENSGTYVCEARNDAGTASCSIELKVKEPPTFIRELKPVEVVKYSDVE LECEVTGTPPFEVTWLKNNREIRSSKKYTLTDRVSVFNLHITKCDPSDTG EYQCIVSNEGGSCSCSTRVALKEPPSFIKKIENTTTVLKSSATFQSTVAG SPPISITWLKDDQILDEDDNVYISFVDSVATLQIRSVDNGHSGRYTCQAK NESGVERCYAFLLVQEPAQIVEKAKSVDVTEKDPMTLECVVAGTPELKVK WLKDGKQIVPSRYFSMSFENNVASFRIQSVMKQDSGQYTFKVENDFGSSS CDAYLRVLDQNIPPSFTKKLTKMDKVLGSSIHMECKVSGSLPISAQWFKD GKEISTSAKYRLVCHERSVSLEVNNLELEDTANYTCKVSNVAGDDACSGI LTVKEPPSFLVKPGRQQAIPDSTVEFKAILKGTPPFKIKWFKDDVELVSG PKCFIGLEGSTSFLNLYSVDASKTGQYTCHVTNDVGSDSCTTMLLVTEPP KFVKKLEASKIVKAGDSSRLECKIAGSPEIRVVWFRNEHELPASDKYRMT FIDSVAVIQMNNLSTEDSGDFICEAQNPAGSTSCSTKVIVKEPPVFSSFP PIVETLKNAEVSLECELSGTPPFEVVWYKDKRQLRSSKKYKIASKNFHTS IHILNVDTSDIGEYHCKAQNEVGSDTCVCTVKLKEPPRFVSKLNSLTVVA GEPAELQASIEGAQPIFVQWLKEKEEVIRESENIRITFVENVATLQFAKA EPANAGKYICQIKNDGGMEENMATLMVLEPAVIVEKAGPMTVTVGETCTL ECKVAGTPELSVEWYKDGKLLTSSQKHKFSFYNKISSLRILSVERQDAGT YTFQVQNNVGKSSCTAVVDVSDRAVPPSFTRRLKNTGGVLGASCILECKV AGSSPISVAWFHEKTKIVSGAKYQTTFSDNVCTLQLNSLDSSDMGNYTCV AANVAGSDECRAVLTVQEPPSFVKEPEPLEVLPGKNVTFTSVIRGTPPFK VNWFRGARELVKGDRCNIYFEDTVAELELFNIDISQSGEYTCVVSNNAGQ ASCTTRLFVKEPAAFLKRLSDHSVEPGKSIILESTYTGTLPISVTWKKDG FNITTSEKCNIVTTEKTCILEILNSTKRDAGQYSCEIENEAGRDVCGALV STLEPPYFVTELEPLEAAVGDSVSLQCQVAGTPEITVSWYKGDTKLRPTP EYRTYFTNNVATLVFNKVNINDSGEYTCKAENSIGTASSKTVFRIQERQL PPSFARQLKDIEQTVGLPVTLTCRLNGSAPIQVCWYRDGVLLRDDENLQT SFVDNVATLKILQTDLSHSGQYSCSASNPLGTASSSARLTAREPKKSPFF DIKPVSIDVIAGESADFECHVTGAQPMRITWSKDNKEIRPGGNYTITCVG NTPHLRILKVGKGDSGQYTCQATNDVGKDMCSAQLSVKEPPKFVKKLEAS KVAKQGESIQLECKISGSPEIKVSWFRNDSELHESWKYNMSFINSVALLT INEASAEDSGDYICEAHNGVGDASCSTALTVKAPPVFTQKPSPVGALKGS DVILQCEISGTPPFEVVWVKDRKQVRNSKKFKITSKHFDTSLHILNLEAS DVGEYHCKATNEVGSDTCSCSVKFKEPPRFVKKLSDTSTLIGDAVELRAI VEGFQPISVVWLKDRGEVIRESENTRISFIDNIATLQLGSPEASNSGKYI CQIKNDAGMRECSAVLTVLEPARIIEKPEPMTVTTGNPFALECVVTGTPE LSAKWFKDGRELSADSKHHITFINKVASLKIPCAEMSDKGLYSFEVKNSV GKSNCTVSVHVSDRIVPPSFIRKLKDVNAILGASVVLECRVSGSAPISVG WFQDGNEIVSGPKCQSSFSENVCTLNLSLLEPSDTGIYTCVAANVAGSDE CSAVLTVQEPPSFEQTPDSVEVLPGMSLTFTSVIRGTPPFKVKWFKGSRE LVPGESCNISLEDFVTELELFEVQPLESGDYSCLVTNDAGSASCTTHLFV KEPATFVKRLADFSVETGSPIVLEATYTGTPPISVSWIKDEYLISQSERC SITMTEKSTILEILESTIEDYAQYSCLIENEAGQDICEALVSVLEPPYFI EPLEHVEAVIGEPATLQCKVDGTPEIRISWYKEHTKLRSAPAYKMQFKNN VASLVINKVDHSDVGEYSCKADNSVGAVASSAVLVIKERKLPPFFARKLK DVHETLGFPVAFECRINGSEPLQVSWYKDGVLLKDDANLQTSFVHNVATL QILQTDQSHIGQYNCSASNPLGTASSSAKLILSEHEVPPFFDLKPVSVDL ALGESGTFKCHVTGTAPIKITWAKDNREIRPGGNYKMTLVENTATLTVLK VGKGDAGQYTCYASNIAGKDSCSAHLGVQEPPRFIKKLEPSRIVKQDEFT RYECKIGGSPEIKVLWYKDETEIQESSKFRMSFVDSVAVLEMHNLSVEDS GDYTCEAHNAAGSASSSTSLKVKEPPIFRKKPHPIETLKGADVHLECELQ GTPPFHVSWYKDKRELRSGKKYKIMSENFLTSIHILNVDAADIGEYQCKA TNDVGSDTCVGSIALKAPPRFVKKLSDISTVVGKEVQLQTTIEGAEPISV VWFKDKGEIVRESDNIWISYSENIATLQFSRVEPANAGKYTCQIKNDAGM QECFATLSVLEPATIVEKPESIKVTTGDTCTLECTVAGTPELSTKWFKDG KELTSDNKYKISFFNKVSGLKIINVAPSDSGVYSFEVQNPVGKDSCTASL QVSDRTVPPSFTRKLKETNGLSGSSVVMECKVYGSPPISVSWFHEGNEIS SGRKYQTTLTDNTCALTVNMLEESDSGDYTCIATNMAGSDECSAPLTVRE PPSFVQKPDPMDVLTGTNVTFTSIVKGTPPFSVSWFKGSSELVPGDRCNV SLEDSVAELELFDVDTSQSGEYTCIVSNEAGKASCTTHLYIKAPAKFVKR LNDYSIEKGKPLILEGTFTGTPPISVTWKKNGINVTPSQRCNITTTEKSA ILEIPSSTVEDAGQYNCYIENASGKDSCSAQILILEPPYFVKQLEPVKVS VGDSASLQCQLAGTPEIGVSWYKGDTKLRPTTTYKMHFRNNVATLVFNQV DINDSGEYICKAENSVGEVSASTFLTVQEQKLPPSFSRQLRDVQETVGLP VVFDCAISGSEPISVSWYKDGKPLKDSPNVQTSFLDNTATLNIFKTDRSL AGQYSCTATNPIGSASSSARLILTEGKNPPFFDIRLAPVDAVVGESADFE CHVTGTQPIKVSWAKDSREIRSGGKYQISYLENSAHLTVLKVDKGDSGQY TCYAVNEVGKDSCTAQLNIKERLIPPSFTKRLSETVEETEGNSFKLEGRV AGSQPITVAWYKNNIEIQPTSNCEITFKNNTLVLQVRKAGMNDAGLYTCK VSNDAGSALCTSSIVIKEPKKPPVFDQHLTPVTVSEGEYVQLSCHVQGSE PIRIQWLKAGREIKPSDRCSFSFASGTAVLELRDVAKADSGDYVCKASNV AGSDTTKSKVTIKDKPAVAPATKKAAVDGRLFFVSEPQSIRVVEKTTATF IAKVGGDPIPNVKWTKGKWRQLNQGGRVFIHQKGDEAKLEIRDTTKTDSG LYRCVAFNEHGEIESNVNLQVDERKKQEKIEGDLRAMLKKTPILKKGAGE EEEIDIMELLKNVDPKEYEKYARMYGITDFRGLLQAFELLKQSQEEETHR LEIEEIERSERDEKEFEELVSFIQQRLSQTEPVTLIKDIENQTVLKDNDA VFEIDIKINYPEIKLSWYKGTEKLEPSDKFEISIDGDRHTLRVKNCQLKD QGNYRLVCGPHIASAKLTVIEPAWERHLQDVTLKEGQTCTMTCQFSVPNV KSEWFRNGRILKPQGRHKTEVEHKVHKLTIADVRAEDQGQYTCKYEDLET SAELRIEAEPIQFTKRIQNIVVSEHQSATFECEVSFDDAIVTWYKGPTEL TESQKYNFRNDGRCHYMTIHNVTPDDEGVYSVIARLEPRGEARSTAELYL TTKEIKLELKPPDIPDSRVPIPTMPIRAVPPEEIPPVVAPPIPLLLPTPE EKKPPPKRIEVTKKAVKKDAKKVVAKPKEMTPREEIVKKPPPPTTLIPAK APEIIDVSSKAEEVKIMTITRKKEVQKEKEAVYEKKQAVHKEKRVFIESF EEPYDELEVEPYTEPFEQPYYEEPDEDYEEIKVEAKKEVHEEWEEDFEEG QEYYEREEGYDEGEEEWEEAYQEREVIQVQKEVYEESHERKVPAKVPEKK APPPPKVIKKPVIEKIEKTSRRMEEEKVQVTKVPEVSKKIVPQKPSRTPV QEEVIEVKVPAVHTKKMVISEEKMFFASHTEEEVSVTVPEVQKEIVTEEK IHVAVSKRVEPPPKVPELPEKPAPEEVAPVPIPKKVEPPAPKVPEVPKKP VPEEKKPVPVPKKEPAAPPKVPEVPKKPVPEEKIPVPVAKKKEAPPAKVP EVQKRVVTEEKITIVTQREESPPPAVPEIPKKKVPEERKPVPRKEEEVPP PPKVPALPKKPVPEEKVAVPVPVAKKAPPPRAEVSKKTVVEEKRFVAEEK LSFAVPQRVEVTRHEVSAEEEWSYSEEEEGVSISVYREEEREEEEEAEVT EYEVMEEPEEYVVEEKLHIISKRVEAEPAEVTERQEKKIVLKPKIPAKIE EPPPAKVPEAPKKIVPEKKVPAPVPKKEKVPPPKVPEEPKKPVPEKKVPP KVIKMEEPLPAKVTERHMQITQEEKVLVAVTKKEAPPKARVPEEPKRAVP EEKVLKLKPKREEEPPAKVTEFRKRVVKEEKVSIEAPKREPQPIKEVTIM EEKERAYTLEEEAVSVQREEEYEEYEEYDYKEFEEYEPTEEYDQYEEYEE REYERYEEHEEYITEPEKPIPVKPVPEEPVPTKPKAPPAKVLKKAVPEEK VPVPIPKKLKPPPPKVPEEPKKVFEEKIRISITKREKEQVTEPAAKVPMK PKRVVAEEKVPVPRKEVAPPVRVPEVPKELEPEEVAFEEEVVTHVEEYLV EEEEEYIHEEEEFITEEEVVPVIPVKVPEVPRKPVPEEKKPVPVPKKKEA PPAKVPEVPKKPEEKVPVLIPKKEKPPPAKVPEVPKKPVPEEKVPVPVPK KVEAPPAKVPEVPKKPVPEKKVPVPAPKKVEAPPAKVPEVPKKLIPEEKK PTPVPKKVEAPPPKVPKKREPVPVPVALPQEEEVLFEEEIVPEEEVLPEE EEVLPEEEEVLPEEEEVLPEEEEIPPEEEEVPPEEEYVPEEEEFVPEEEV LPEVKPKVPVPAPVPEIKKKVTEKKVVIPKKEEAPPAKVPEVPKKVEEKR IILPKEEEVLPVEVTEEPEEEPISEEEIPEEPPSIEEVEEVAPPRVPEVI KKAVPEAPTPVPKKVEAPPAKVSKKIPEEKVPVPVQKKEAPPAKVPEVPK KVPEKKVLVPKKEAVPPAKGRTVLEEKVSVAFRQEVVVKERLELEVVEAE VEEIPEEEEFHEVEEYFEEGEFHEVEEFIKLEQHRVEEEHRVEKVHRVIE VFEAEEVEVFEKPKAPPKGPEISEKIIPPKKPPTKVVPRKEPPAKVPEVP KKIVVEEKVRVPEEPRVPPTKVPDVLPPKEVVPEKKVPVPPAKKPEAPPP KVPEAPKEVVPEKKVPVPPPKKPEVPPTKVPEVPKAAVPEKKVPEAIPPK PESPPPEVPEAPKEVVPEKKVPAAPPKKPEVTPVKVPEAPKEVVPEKKVP VPPPKKPEVPPTKVPEVPKVAVPEKKVPEAIPPKPESPPPEVFEEPEEVA LEEPPAEVVEEPEPAAPPQVTVPPKKPVPEKKAPAVVAKKPELPPVKVPE VPKEVVPEKKVPLVVPKKPEAPPAKVPEVPKEVVPEKKVAVPKKPEVPPA KVPEVPKKPVLEEKPAVPVPERAESPPPEVYEEPEEIAPEEEIAPEEEKP VPVAEEEEPEVPPPAVPEEPKKIIPEKKVPVIKKPEAPPPKEPEPEKVIE KPKLKPRPPPPPPAPPKEDVKEKIFQLKAIPKKKVPEKPQVPEKVELTPL KVPGGEKKVRKLLPERKPEPKEEVVLKSVLRKRPEEEEPKVEPKKLEKVK KPAVPEPPPPKPVEEVEVPTVTKRERKIPEPTKVPEIKPAIPLPAPEPKP KPEAEVKTIKPPPVEPEPTPIAAPVTVPVVGKKAEAKAPKEEAAKPKGPI KGVPKKTPSPIEAERRKLRPGSGGEKPPDEAPFTYQLKAVPLKFVKEIKD IILTESEFVGSSAIFECLVSPSTAITTWMKDGSNIRESPKHRFIADGKDR KLHIIDVQLSDAGEYTCVLRLGNKEKTSTAKLVVEELPVRFVKTLEEEVT VVKGQPLYLSCELNKERDVVWRKDGKIVVEKPGRIVPGVIGLMRALTIND ADDTDAGTYTVTVENANNLECSSCVKVVEVIRDWLVKPIRDQHVKPKGTA IFACDIAKDTPNIKWFKGYDEIPAEPNDKTEILRDGNHLYLKIKNAMPED IAEYAVEIEGKRYPAKLTLGEREVELLKPIEDVTIYEKESASFDAEISEA DIPGQWKLKGELLRPSPTCEIKAEGGKRFLTLRKVKLDQAGEVLYQALNA ITTAILTVKEIELDFAVPLKDVTVPERRQARFECVLTREANVIWSKGPDI IKSSDKFDIIADGKKHILVINDSQFDDEGVYTAEVEGKKTSARLFVTGIR LKFMSPLEDQTVKEGETATFVCELSHEKMHVVWFKNDAKLHTSRTVLISS EGKTHKLEMKEVTLDDISQIKAQVKELSSTAQLKVLEADPYFTVKLHDKT AVEKDEITLKCEVSKDVPVKWFKDGEEIVPSPKYSIKADGLRRILKIKKA DLKDKGEYVCDCGTDKTKANVTVEARLIKVEKPLYGVEVFVGETAHFEIE LSEPDVHGQWKLKGQPLTASPDCEIIEDGKKHILILHNCQLGMTGEVSFQ AANAKSAANLKVKELPLIFITPLSDVKVFEKDEAKFECEVSREPKTFRWL KGTQEITGDDRFELIKDGTKHSMVIKSAAFEDEAKYMFEAEDKHTSGKLI IEGIRLKFLTPLKDVTAKEKESAVFTVELSHDNIRVKWFKNDQRLHTTRS VSMQDEGKTHSITFKDLSIDDTSQIRVEAMGMSSEAKLTVLEGDPYFTGK LQDYTGVEKDEVILQCEISKADAPVKWFKDGKEIKPSKNAVIKADGKKRM LILKKALKSDIGQYTCDCGTDKTSGKLDIEDREIKLVRPLHSVEVMETET ARFETEISEDDIHANWKLKGEALLQTPDCEIKEEGKIHSLVLHNCRLDQT GGVDFQAANVKSSAHLRVKPRVIGLLRPLKDVTVTAGETATFDCELSYED IPVEWYLKGKKLEPSDKVVPRSEGKVHTLTLRDVKLEDAGEVQLTAKDFK THANLFVKEPPVEFTKPLEDQTVEEGATAVLECEVSRENAKVKWFKNGTE ILKSKKYEIVADGRVRKLVIHDCTPEDIKTYTCDAKDFKTSCNLNVVPPH VEFLRPLTDLQVREKEMARFECELSRENAKVKWFKDGAEIKKGKKYDIIS KGAVRILVINKCLLDDEAEYSCEVRTARTSGMLTVLEEEAVFTKNLANIE VSETDTIKLVCEVSKPGAEVIWYKGDEEIIETGRYEILTEGRKRILVIQN AHLEDAGNYNCRLPSSRTDGKVKVHELAAEFISKPQNLEILEGEKAEFVC SISKESFPVQWKRDDKTLESGDKYDVIADGKKRVLVVKDATLQDMGTYVV MVGAARAAAHLTVIEKLRIVVPLKDTRVKEQQEVVFNCEVNTEGAKAKWF RNEEAIFDSSKYIILQKDLVYTLRIRDAHLDDQANYNVSLTNHRGENVKS AANLIVEEEDLRIVEPLKDIETMEKKSVTFWCKVNRLNVTLKWTKNGEEV PFDNRVSYRVDKYKHMLTIKDCGFPDEGEYIVTAGQDKSVAELLIIEAPT EFVEHLEDQTVTEFDDAVFSCQLSREKANVKWYRNGREIKEGKKYKFEKD GSIHRLIIKDCRLDDECEYACGVEDRKSRARLFVEEIPVEIIRPPQDILE APGADVVFLAELNKDKVEVQWLRNNMVVVQGDKHQMMSEGKIHRLQICDI KPRDQGEYRFIAKDKEARAKLELAAAPKIKTADQDLVVDVGKPLTMVVPY DAYPKAEAEWFKENEPLSTKTIDTTAEQTSFRILEAKKGDKGRYKIVLQN KHGKAEGFINLKVIDVPGPVRNLEVTETFDGEVSLAWEEPLTDGGSKIIG YVVERRDIKRKTWVLATDRAESCEFTVTGLQKGGVEYLFRVSARNRVGTG EPVETDNPVEARSKYDVPGPPLNVTITDVNRFGVSLTWEPPEYDGGAEIT NYVIELRDKTSIRWDTAMTVRAEDLSATVTDVVEGQEYSFRVRAQNRIGV GKPSAATPFVKVADPIERPSPPVNLTSSDQTQSSVQLKWEPPLKDGGSPI LGYIIERCEEGKDNWIRCNMKLVPELTYKVTGLEKGNKYLYRVSAENKAG VSDPSEILGPLTADDAFVEPTMDLSAFKDGLEVIVPNPITILVPSTGYPR PTATWCFGDKVLETGDRVKMKTLSAYAELVISPSERSDKGIYTLKLENRV KTISGEIDVNVIARPSAPKELKFGDITKDSVHLTWEPPDDDGGSPLTGYV VEKREVSRKTWTKVMDFVTDLEFTVPDLVQGKEYLFKVCARNKCGPGEPA YVDEPVNMSTPATVPDPPENVKWRDRTANSIFLTWDPPKNDGGSRIKGYI VERCPRGSDKWVACGEPVAETKMEVTGLEEGKWYAYRVKALNRQGASKPS RPTEEIQAVDTQEAPEIFLDVKLLAGLTVKAGTKIELPATVTGKPEPKIT WTKADMILKQDKRITIENVPKKSTVTIVDSKRSDTGTYIIEAVNVCGRAT AVVEVNVLDKPGPPAAFDITDVTNESCLLTWNPPRDDGGSKITNYVVERR ATDSEVWHKLSSTVKDTNFKATKLIPNKEYIFRVAAENMYGVGEPVQASP ITAKYQFDPPGPPTRLEPSDITKDAVTLTWCEPDDDGGSPITGYWVERLD PDTDKWVRCNKMPVKDTTYRVKGLTNKKKYRFRVLAENLAGPGKPSKSTE PILIKDPIDPPWPPGKPTVKDVGKTSVRLNWTKPEHDGGAKIESYVIEML KTGTDEWVRVAEGVPTTQHLLPGLMEGQEYSFRVRAVNKAGESEPSEPSD PVLCREKLYPPSPPRWLEVINITKNTADLKWTVPEKDGGSPITNYIVEKR DVRRKGWQTVDTTVKDTKCTVTPLTEGSLYVFRVAAENAIGQSDYTEIED SVLAKDTFTTPGPPYALAVVDVTKRHVDLKWEPPKNDGGRPIQRYVIEKK ERLGTRWVKAGKTAGPDCNFRVTDVIEGTEVQFQVRAENEAGVGHPSEPT EILSIEDPTSPPSPPLDLHVTDAGRKHIAIAWKPPEKNGGSPIIGYHVEM CPVGTEKWMRVNSRPIKDLKFKVEEGVVPDKEYVLRVRAVNAIGVSEPSE ISENVVAKDPDCKPTIDLETHDIIVIEGEKLSIPVPFRAVPVPTVSWHKD GKEVKASDRLTMKNDHISAHLEVPKSVRADAGIYTITLENKLGSATASIN VKVIGLPGPCKDIKASDITKSSCKLTWEPPEFDGGTPILHYVLERREAGR RTYIPVMSGENKLSWTVKDLIPNGEYFFRVKAVNKVGGGEYIELKNPVIA QDPKQPPDPPVDVEVHNPTAEAMTITWKPPLYDGGSKIMGYIIEKIAKGE ERWKRCNEHLVPILTYTAKGLEEGKEYQFRVRAENAAGISEPSRATPPTK AVDPIDAPKVILRTSLEVKRGDEIALDASISGSPYPTITWIKDENVIVPE EIKKRAAPLVRRRKGEVQEEEPFVLPLTQRLSIDNSKKGESQLRVRDSLR PDHGLYMIKVENDHGIAKAPCTVSVLDTPGPPINFVFEDIRKTSVLCKWE PPLDDGGSEIINYTLEKKDKTKPDSEWIVVTSTLRHCKYSVTKLIEGKEY LFRVRAENRFGPGPPCVSKPLVAKDPFGPPDAPDKPIVEDVTSNSMLVKW NEPKDNGSPILGYWLEKREVNSTHWSRVNKSLLNALKANVDGLLEGLTYV FRVCAENAAGPGKFSPPSDPKTAHDPISPPGPPIPRVTDTSSTTIELEWE PPAFNGGGEIVGYFVDKQLVGTNEWSRCTEKMIKVRQYTVKEIREGADYK LRVSAVNAAGEGPPGETQPVTVAEPQEPPAVELDVSVKGGIQIMAGKTLR IPAVVTGRPVPTKVWTKEEGELDKDRVVIDNVGTKSELIIKDALRKDHGR YVITATNSCGSKFAAARVEVFDVPGPVLDLKPVVTNRKMCLLNWSDPEDD GGSEITGFIIERKDAKMHTWRQPIETERSKCDITGLLEGQEYKFRVIAKN KFGCGPPVEIGPILAVDPLGPPTSPERLTYTERTKSTITLDWKEPRSNGG SPIQGYIIEKRRHDKPDFERVNKRLCPTTSFLVENLDEHQMYEFRVKAVN EIGESEPSLPLNVVIQDDEVPPTIKLRLSVRGDTIKVKAGEPVHIPADVT GLPMPKIEWSKNETVIEKPTDALQITKEEVSRSEAKTELSIPKAVREDKG TYTVTASNRLGSVFRNVHVEVYDRPSPPRNLAVTDIKAESCYLTWDAPLD NGGSEITHYVIDKRDASRKKAEWEEVTNTAVEKRYGIWKLIPNGQYEFRV RAVNKYGISDECKSDKVVIQDPYRLPGPPGKPKVLARTKGSMLVSWTPPL DNGGSPITGYWLEKREEGSPYWSRVSRAPITKVGLKGVEFNVPRLLEGVK YQFRAMAINAAGIGPPSEPSDPEVAGDPIFPPGPPSCPEVKDKTKSSISL GWKPPAKDGGSPIKGYIVEMQEEGTTDWKRVNEPDKLITTCECVVPNLKE LRKYRFRVKAVNEAGESEPSDTTGEIPATDIQEEPEVFIDIGAQDCLVCK AGSQIRIPAVIKGRPTPKSSWEFDGKAKKAMKDGVHDIPEDAQLETAENS SVIIIPECKRSHTGKYSITAKNKAGQKTANCRVKVMDVPGPPKDLKVSDI TRGSCRLSWKMPDDDGGDRIKGYVIEKRTIDGKAWTKVNPDCGSTTFVVP DLLSEQQYFFRVRAENRFGIGPPVETIQRTTARDPIYPPDPPIKLKIGLI TKNTVHLSWKPPKNDGGSPVTHYIVECLAWDPTGTKKEAWRQCNKRDVEE LQFTVEDLVEGGEYEFRVKAVNAAGVSKPSATVGPCDCQRPDMPPSIDLK EFMEVEEGTNVNIVAKIKGVPFPTLTWFKAPPKKPDNKEPVLYDTHVNKL VVDDTCTLVIPQSRRSDTGLYTITAVNNLGTASKEMRLNVLGRPGPPVGP IKFESVSADQMTLSWFPPKDDGGSKITNYVIEKREANRKTWVHVSSEPKE CTYTIPKLLEGHEYVFRIMAQNKYGIGEPLDSEPETARNLFSVPGAPDKP TVSSVTRNSMTVNWEEPEYDGGSPVTGYWLEMKDTTSKRWKRVNRDPIKA MTLGVSYKVTGLIEGSDYQFRVYAINAAGVGPASLPSDPATARDPIAPPG PPFPKVTDWTKSSADLEWSPPLKDGGSKVTGYIVEYKEEGKEEWEKGKDK EVRGTKLVVTGLKEGAFYKFRVSAVNIAGIGEPGEVTDVIEMKDRLVSPD LQLDASVRDRIVVHAGGVIRIIAYVSGKPPPTVTWNMNERTLPQEATIET TAISSSMVIKNCQRSHQGVYSLLAKNEAGERKKTIIVDVLDVPGPVGTPF LAHNLTNESCKLTWFSPEDDGGSPITNYVIEKRESDRRAWTPVTYTVTRQ NATVQGLIQGKAYFFRIAAENSIGMGPFVETSEALVIREPITVPERPEDL EVKEVTKNTVTLTWNPPKYDGGSEIINYVLESRLIGTEKFHKVTNDNLLS RKYTVKGLKEGDTYEYRVSAVNIVGQGKPSFCTKPITCKDELAPPTLHLD FRDKLTIRVGEAFALTGRYSGKPKPKVSWFKDEADVLEDDRTHIKTTPAT LALEKIKAKRSDSGKYCVVVENSTGSRKGFCQVNVVDRPGPPVGPVSFDE VTKDYMVISWKPPLDDGGSKITNYIIEKKEVGKDVWMPVTSASAKTTCKV SKLLEGKDYIFRIHAENLYGISDPLVSDSMKAKDRFRVPDAPDQPIVTEV TKDSALVTWNKPHDGGKPITNYILEKRETMSKRWARVTKDPIHPYTKFRV PDLLEGCQYEFRVSAENEIGIGDPSPPSKPVFAKDPIAKPSPPVNPEAID TTCNSVDLTWQPPRHDGGSKILGYIVEYQKVGDEEWRRANHTPESCPETK YKVTGLRDGQTYKFRVLAVNAAGESDPAHVPEPVLVKDRLEPPELILDAN MAREQHIKVGDTLRLSAIIKGVPFPKVTWKKEDRDAPTKARIDVTPVGSK LEIRNAAHEDGGIYSLTVENPAGSKTVSVKVLVLDKPGPPRDLEVSEIRK DSCYLTWKEPLDDGGSVITNYVVERRDVASAQWSPLSATSKKKSHFAKHL NEGNQYLFRVAAENQYGRGPFVETPKPIKALDPLHPPGPPKDLHHVDVDK TEVSLVWNKPDRDGGSPITGYLVEYQEEGTQDWIKFKTVTNLECVVTGLQ QGKTYRFRVKAENIVGLGLPDTTIPIECQEKLVPPSVELDVKLIEGLVVK AGTTVRFPAIIRGVPVPTAKWTTDGSEIKTDEHYTVETDNFSSVLTIKNC LRRDTGEYQITVSNAAGSKTVAVHLTVLDVPGPPTGPINILDVTPEHMTI SWQPPKDDGGSPVINYIVEKQDTRKDTWGVVSSGSSKTKLKIPHLQKGCE YVFRVRAENKIGVGPPLDSTPTVAKHKFSPPSPPGKPVVTDITENAATVS WTLPKSDGGSPITGYYMERREVTGKWVRVNKTPIADLKFRVTGLYEGNTY EFRVFAENLAGLSKPSPSSDPIKACRPIKPPGPPINPKLKDKSRETADLV WTKPLSDGGSPILGYVVECQKPGTAQWNRINKDELIRQCAFRVPGLIEGN EYRFRIKAANIVGEGEPRELAESVIAKDILHPPEVELDVTCRDVITVRVG QTIRILARVKGRPEPDITWTKEGKVLVREKRVDLIQDLPRVELQIKEAVR ADHGKYIISAKNSSGHAQGSAIVNVLDRPGPCQNLKVTNVTKENCTISWE NPLDNGGSEITNFIVEYRKPNQKGWSIVASDVTKRLIKANLLANNEYYFR VCAENKVGVGPTIETKTPILAINPIDRPGEPENLHIADKGKTFVYLKWRR PDYDGGSPNLSYHVERRLKGSDDWERVHKGSIKETHYMVDRCVENQIYEF RVQTKNEGGESDWVKTEEVVVKEDLQKPVLDLKLSGVLTVKAGDTIRLEA GVRGKPFPEVAWTKDKDATDLTRSPRVKIDTRADSSKFSLTKAKRSDGGK YVVTATNTAGSFVAYATVNVLDKPGPVRNLKIVDVSSDRCTVCWDPPEDD GGCEIQNYILEKCETKRMVWSTYSATVLTPGTTVTRLIEGNEYIFRVRAE NKIGTGPPTESKPVIAKTKYDKPGRPDPPEVTKVSKEEMTVVWNPPEYDG GKSITGYFLEKKEKHSTRWVPVNKSAIPERRMKVQNLLPDHEYQFRVKAE NEIGIGEPSLPSRPVVAKDPIEPPGPPTNFRVVDTTKHSITLGWGKPVYD GGAPIIGYVVEMRPKIADASPDEGWKRCNAAAQLVRKEFTVTSLDENQEY EFRVCAQNQVGIGRPAELKEAIKPKEILEPPEIDLDASMRKLVIVRAGCP IRLFAIVRGRPAPKVTWRKVGIDNVVRKGQVDLVDTMAFLVIPNSTRDDS GKYSLTLVNPAGEKAVFVNVRVLDTPGPVSDLKVSDVTKTSCHVSWAPPE NDGGSQVTHYIVEKREADRKTWSTVTPEVKKTSFHVTNLVPGNEYYFRVT AVNEYGPGVPTDVPKPVLASDPLSEPDPPRKLEVTEMTKNSATLAWLPPL RDGGAKIDGYITSYREEEQPADRWTEYSVVKDLSLVVTGLKEGKKYKFRV AARNAVGVSLPREAEGVYEAKEQLLPPKILMPEQITIKAGKKLRIEAHVY GKPHPTCKWKKGEDEVVTSSHLAVHKADSSSILIIKDVTRKDSGYYSLTA ENSSGTDTQKIKVVVMDAPGPPQPPFDISDIDADACSLSWHIPLEDGGSN ITNYIVEKCDVSRGDWVTALASVTKTSCRVGKLIPGQEYIFRVRAENRFG ISEPLTSPKMVAQFPFGVPSEPKNARVTKVNKDCIFVAWDRPDSDGGSPI IGYLIERKERNSLLWVKANDTLVRSTEYPCAGLVEGLEYSFRIYALNKAG SSPPSKPTEYVTARMPVDPPGKPEVIDVTKSTVSLIWARPKHDGGSKIIG YFVEACKLPGDKWVRCNTAPHQIPQEEYTATGLEEKAQYQFRAIARTAVN ISPPSEPSDPVTILAENVPPRIDLSVAMKSLLTVKAGTNVCLDATVFGKP MPTVSWKKDGTLLKPAEGIKMAMQRNLCTLELFSVNRKDSGDYTITAENS SGSKSATIKLKVLDKPGPPASVKINKMYSDRAMLSWEPPLEDGGSEITNY IVDKRETSRPNWAQVSATVPITSCSVEKLIEGHEYQFRICAENKYGVGDP VFTEPAIAKNPYDPPGRCDPPVISNITKDHMTVSWKPPADDGGSPITGYL LEKRETQAVNWTKVNRKPIIERTLKATGLQEGTEYEFRVTAINKAGPGKP SDASKAAYARDPQYPPAPPAFPKVYDTTRSSVSLSWGKPAYDGGSPIIGY LVEVKRADSDNWVRCNLPQNLQKTRFEVTGLMEDTQYQFRVYAVNKIGYS DPSDVPDKHYPKDILIPPEGELDADLRKTLILRAGVTMRLYVPVKGRPPP KITWSKPNVNLRDRIGLDIKSTDFDTFLRCENVNKYDAGKYILTLENSCG KKEYTIVVKVLDTPGPPVNVTVKEISKDSAYVTWEPPIIDGGSPIINYVV QKRDAERKSWSTVTTECSKTSFRVANLEEGKSYFFRVFAENEYGIGDPGE TRDAVKASQTPGPVVDLKVRSVSKSSCSIGWKKPHSDGGSRIIGYVVDFL TEENKWQRVMKSLSLQYSAKDLTEGKEYTFRVSAENENGEGTPSEITVVA RDDVVAPDLDLKGLPDLCYLAKENSNFRLKIPIKGKPAPSVSWKKGEDPL ATDTRVSVESSAVNTTLIVYDCQKSDAGKYTITLKNVAGTKEGTISIKVV GKPGIPTGPIKFDEVTAEAMTLKWAPPKDDGGSEITNYILEKRDSVNNKW VTCASAVQKTTFRVTRLHEGMEYTFRVSAENKYGVGEGLKSEPIVARHPF DVPDAPPPPNIVDVRHDSVSLTWTDPKKTGGSPITGYHLEFKERNSLLWK RANKTPIRMRDFKVTGLTEGLEYEFRVMAINLAGVGKPSLPSEPVVALDP IDPPGKPEVINITRNSVTLIWTEPKYDGGHKLTGYIVEKRDLPSKSWMKA NHVNVPECAFTVTDLVEGGKYEFRIRAKNTAGAISAPSESTETIICKDEY EAPTIVLDPTIKDGLTIKAGDTIVLNAISILGKPLPKSSWSKAGKDIRPS DITQITSTPTSSMLTIKYATRKDAGEYTITATNPFGTKVEHVKVTVLDVP GPPGPVEISNVSAEKATLTWTPPLEDGGSPIKSYILEKRETSRLLWTVVS EDIQSCRHVATKLIQGNEYIFRVSAVNHYGKGEPVQSEPVKMVDRFGPPG PPEKPEVSNVTKNTATVSWKRPVDDGGSEITGYHVERREKKSLRWVRAIK TPVSDLRCKVTGLQEGSTYEFRVSAENRAGIGPPSEASDSVLMKDAAYPP GPPSNPHVTDTTKKSASLAWGKPHYDGGLEITGYVVEHQKVGDEAWIKDT TGTALRITQFVVPDLQTKEKYNFRISAINDAGVGEPAVIPDVEIVEREMA PDFELDAELRRTLVVRAGLSIRIFVPIKGRPAPEVTWTKDNINLKNRANI ENTESFTLLIIPECNRYDTGKFVMTIENPAGKKSGFVNVRVLDTPGPVLN LRPTDITKDSVTLHWDLPLIDGGSRITNYIVEKREATRKSYSTATTKCHK CTYKVTGLSEGCEYFFRVMAENEYGIGEPTETTEPVKASEAPSPPDSLNI MDITKSTVSLAWPKPKHDGGSKITGYVIEAQRKGSDQWTHITTVKGLECV VRNLTEGEEYTFQVMAVNSAGRSAPRESRPVIVKEQTMLPELDLRGIYQK LVIAKAGDNIKVEIPVLGRPKPTVTWKKGDQILKQTQRVNFETTATSTIL NINECVRSDSGPYPLTARNIVGEVGDVITIQVHDIPGPPTGPIKFDEVSS DFVTFSWDPPENDGGVPISNYVVEMRQTDSTTWVELATTVIRTTYKATRL TTGLEYQFRVKAQNRYGVGPGITSACIVANYPFKVPGPPGTPQVTAVTKD SMTISWHEPLSDGGSPILGYHVERKERNGILWQTVSKALVPGNIFKSSGL TDGIAYEFRVIAENMAGKSKPSKPSEPMLALDPIDPPGKPVPLNITRHTV TLKWAKPEYTGGFKITSYIVEKRDLPNGRWLKANFSNILENEFTVSGLTE DAAYEFRVIAKNAAGAISPPSEPSDAITCRDDVEAPKIKVDVKFKDTVIL KAGEAFRLEADVSGRPPPTMEWSKDGKELEGTAKLEIKIADFSTNLVNKD STRRDSGAYTLTATNPGGFAKHIFNVKVLDRPGPPEGPLAVTEVTSEKCV LSWFPPLDDGGAKIDHYIVQKRETSRLAWTNVASEVQVTKLKVTKLLKGN EYIFRVMAVNKYGVGEPLESEPVLAVNPYGPPDPPKNPEVTTITKDSMVV CWGHPDSDGGSEIINYIVERRDKAGQRWIKCNKKTLTDLRYKVSGLTEGH EYEFRIMAENAAGISAPSPTSPFYKACDTVFKPGPPGNPRVLDTSRSSIS IAWNKPIYDGGSEITGYMVEIALPEEDEWQIVTPPAGLKATSYTITGLTE NQEYKIRIYAMNSEGLGEPALVPGTPKAEDRMLPPEIELDADLRKVVTIR ACCTLRLFVPIKGRPAPEVKWARDHGESLDKASIESTSSYTLLIVGNVNR FDSGKYILTVENSSGSKSAFVNVRVLDTPGPPQDLKVKEVTKTSVTLTWD PPLLDGGSKIKNYIVEKRESTRKAYSTVATNCHKTSWKVDQLQEGCSYYF RVLAENEYGIGLPAETAESVKASERPLPPGKITLMDVTRNSVSLSWEKPE HDGGSRILGYIVEMQTKGSDKWATCATVKVTEATITGLIQGEEYSFRVSA QNEKGISDPRQLSVPVIAKDLVIPPAFKLLFNTFTVLAGEDLKVDVPFIG RPTPAVTWHKDNVPLKQTTRVNAESTENNSLLTIKDACREDVGHYVVKLT NSAGEAIETLNVIVLDKPGPPTGPVKMDEVTADSITLSWGPPKYDGGSSI NNYIVEKRDTSTTTWQIVSATVARTTIKACRLKTGCEYQFRIAAENRYGK STYLNSEPTVAQYPFKVPGPPGTPVVTLSSRDSMEVQWNEPISDGGSRVI GYHLERKERNSILWVKLNKTPIPQTKFKTTGLEEGVEYEFRVSAENIVGI GKPSKVSECYVARDPCDPPGRPEAIIVTRNSVTLQWKKPTYDGGSKITGY IVEKKELPEGRWMKASFTNIIDTHFEVTGLVEDHRYEFRVIARNAAGVFS EPSESTGAITARDEVDPPRISMDPKYKDTIVVHAGESFKVDADIYGKPIP TIQWIKGDQELSNTARLEIKSTDFATSLSVKDAVRVDSGNYILKAKNVAG ERSVTVNVKVLDRPGPPEGPVVISGVTAEKCTLAWKPPLQDGGSDIINYI VERRETSRLVWTVVDANVQTLSCKVTKLLEGNEYTFRIMAVNKYGVGEPL ESEPVVAKNPFVVPDAPKAPEVTTVTKDSMIVVWERPASDGGSEILGYVL EKRDKEGIRWTRCHKRLIGELRLRVTGLIENHDYEFRVSAENAAGLSEPS PPSAYQKACDPIYKPGPPNNPKVIDITRSSVFLSWSKPIYDGGCEIQGYI VEKCDVSVGEWTMCTPPTGINKTNIEVEKLLEKHEYNFRICAINKAGVGE HADVPGPIIVEEKLEAPDIDLDLELRKIINIRAGGSLRLFVPIKGRPTPE VKWGKVDGEIRDAAIIDVTSSFTSLVLDNVNRYDSGKYTLTLENSSGTKS AFVTVRVLDTPSPPVNLKVTEITKDSVSITWEPPLLDGGSKIKNYIVEKR EATRKSYAAVVTNCHKNSWKIDQLQEGCSYYFRVTAENEYGIGLPAQTAD PIKVAEVPQPPGKITVDDVTRNSVSLSWTKPEHDGGSKIIQYIVEMQAKH SEKWSECARVKSLQAVITNLTQGEEYLFRVVAVNEKGRSDPRSLAVPIVA KDLVIEPDVKPAFSSYSVQVGQDLKIEVPISGRPKPTITWTKDGLPLKQT TRINVTDSLDLTTLSIKETHKDDGGQYGITVANVVGQKTASIEIVTLDKP DPPKGPVKFDDVSAESITLSWNPPLYTGGCQITNYIVQKRDTTTTVWDVV SATVARTTLKVTKLKTGTEYQFRIFAENRYGQSFALESDPIVAQYPYKEP GPPGTPFATAISKDSMVIQWHEPVNNGGSPVIGYHLERKERNSILWTKVN KTIIHDTQFKAQNLEEGIEYEFRVYAENIVGVGKASKNSECYVARDPCDP PGTPEPIMVKRNEITLQWTKPVYDGGSMITGYIVEKRDLPDGRWMKASFT NVIETQFTVSGLTEDQRYEFRVIAKNAAGAISKPSDSTGPITAKDEVELP RISMDPKFRDTIVVNAGETFRLEADVHGKPLPTIEWLRGDKEIEESARCE IKNTDFKALLIVKDAIRIDGGQYILRASNVAGSKSFPVNVKVLDRPGPPE GPVQVTGVTSEKCSLTWSPPLQDGGSDISHYVVEKRETSRLAWTVVASEV VTNSLKVTKLLEGNEYVFRIMAVNKYGVGEPLESAPVLMKNPFVLPGPPK SLEVTNIAKDSMTVCWNRPDSDGGSEIIGYIVEKRDRSGIRWIKCNKRRI TDLRLRVTGLTEDHEYEFRVSAENAAGVGEPSPATVYYKACDPVFKPGPP TNAHIVDTTKNSITLAWGKPIYDGGSEILGYVVEICKADEEEWQIVTPQT GLRVTRFEISKLTEHQEYKIRVCALNKVGLGEATSVPGTVKPEDKLEAPE LDLDSELRKGIVVRAGGSARIHIPFKGRPTPEITWSREEGEFTDKVQIEK GVNYTQLSIDNCDRNDAGKYILKLENSSGSKSAFVTVKVLDTPGPPQNLA VKEVRKDSAFLVWEPPIIDGGAKVKNYVIDKRESTRKAYANVSSKCSKTS FKVENLTEGAIYYFRVMAENEFGVGVPVETVDAVKAAEPPSPPGKVTLTD VSQTSASLMWEKPEHDGGSRVLGYVVEMQPKGTEKWSIVAESKVCNAVVT GLSSGQEYQFRVKAYNEKGKSDPRVLGVPVIAKDLTIQPSLKLPFNTYSI QAGEDLKIEIPVIGRPRPNISWVKDGEPLKQTTRVNVEETATSTVLHIKE GNKDDFGKYTVTATNSAGTATENLSVIVLEKPGPPVGPVRFDEVSADFVV ISWEPPAYTGGCQISNYIVEKRDTTTTTWHMVSATVARTTIKITKLKTGT EYQFRIFAENRYGKSAPLDSKAVIVQYPFKEPGPPGTPFVTSISKDQMLV QWHEPVNDGGTKIIGYHLEQKEKNSILWVKLNKTPIQDTKFKTTGLDEGL EYEFKVSAENIVGIGKPSKVSECFVARDPCDPPGRPEAIVITRNNVTLKW KKPAYDGGSKITGYIVEKKDLPDGRWMKASFTNVLETEFTVSGLVEDQRY EFRVIARNAAGNFSEPSDSSGAITARDEIDAPNASLDPKYKDVIVVHAGE TFVLEADIRGKPIPDVVWSKDGKELEETAARMEIKSTIQKTTLVVKDCIR TDGGQYILKLSNVGGTKSIPITVKVLDRPGPPEGPLKVTGVTAEKCYLAW NPPLQDGGANISHYIIEKRETSRLSWTQVSTEVQALNYKVTKLLPGNEYI FRVMAVNKYGIGEPLESGPVTACNPYKPPGPPSTPEVSAITKDSMVVTWA RPVDDGGTEIEGYILEKRDKEGVRWTKCNKKTLTDLRLRVTGLTEGHSYE FRVAAENAAGVGEPSEPSVFYRACDALYPPGPPSNPKVTDTSRSSVSLAW SKPIYDGGAPVKGYVVEVKEAAADEWTTCTPPTGLQGKQFTVTKLKENTE YNFRICAINSEGVGEPATLPGSVVAQERIEPPEIELDADLRKVVVLRASA TLRLFVTIKGRPEPEVKWEKAEGILTDRAQIEVTSSFTMLVIDNVTRFDS GRYNLTLENNSGSKTAFVNVRVLDSPSAPVNLTIREVKKDSVTLSWEPPL IDGGAKITNYIVEKRETTRKAYATITNNCTKTTFRIENLQEGCSYYFRVL ASNEYGIGLPAETTEPVKVSEPPLPPGRVTLVDVTRNTATIKWEKPESDG GSKITGYVVEMQTKGSEKWSTCTQVKTLEATISGLTAGEEYVFRVAAVNE KGRSDPRQLGVPVIARDIEIKPSVELPFHTFNVKAREQLKIDVPFKGRPQ ATVNWRKDGQTLKETTRVNVSSSKTVTSLSIKEASKEDVGTYELCVSNSA GSITVPITIIVLDRPGPPGPIRIDEVSCDSITISWNPPEYDGGCQISNYI VEKKETTSTTWHIVSQAVARTSIKIVRLTTGSEYQFRVCAENRYGKSSYS ESSAVVAEYPFSPPGPPGTPKVVHATKSTMLVTWQVPVNDGGSRVIGYHL EYKERSSILWSKANKILIADTQMKVSGLDEGLMYEYRVYAENIAGIGKCS KSCEPVPARDPCDPPGQPEVTNITRKSVSLKWSKPHYDGGAKITGYIVER RELPDGRWLKCNYTNIQETYFEVTELTEDQRYEFRVFARNAADSVSEPSE STGPIIVKDDVEPPRVMMDVKFRDVIVVKAGEVLKINADIAGRPLPVISW AKDGIEIEERARTEIISTDNHTLLTVKDCIRRDTGQYVLTLKNVAGTRSV AVNCKVLDKPGPPAGPLEINGLTAEKCSLSWGRPQEDGGADIDYYIVEKR ETSHLAWTICEGELQMTSCKVTKLLKGNEYIFRVTGVNKYGVGEPLESVA IKALDPFTVPSPPTSLEITSVTKESMTLCWSRPESDGGSEISGYIIERRE KNSLRWVRVNKKPVYDLRVKSTGLREGCEYEYRVYAENAAGLSLPSETSP LIRAEDPVFLPSPPSKPKIVDSGKTTITIAWVKPLFDGGAPITGYTVEYK KSDDTDWKTSIQSLRGTEYTISGLTTGAEYVFRVKSVNKVGASDPSDSSD PQIAKEREEEPLFDIDSEMRKTLIVKAGASFTMTVPFRGRPVPNVLWSKP DTDLRTRAYVDTTDSRTSLTIENANRNDSGKYTLTIQNVLSAASLTLVVK VLDTPGPPTNITVQDVTKESAVLSWDVPENDGGAPVKNYHIEKREASKKA WVSVTNNCNRLSYKVTNLQEGAIYYFRVSGENEFGVGIPAETKEGVKITE KPSPPEKLGVTSISKDSVSLTWLKPEHDGGSRIVHYVVEALEKGQKNWVK CAVAKSTHHVVSGLRENSEYFFRVFAENQAGLSDPRELLLPVLIKEQLEP PEIDMKNFPSHTVYVRAGSNLKVDIPISGKPLPKVTLSRDGVPLKATMRF NTEITAENLTINLKESVTADAGRYEITAANSSGTTKAFINIVVLDRPGPP TGPVVISDITEESVTLKWEPPKYDGGSQVTNYILLKRETSTAVWTEVSAT VARTMMKVMKLTTGEEYQFRIKAENRFGISDHIDSACVTVKLPYTTPGPP STPWVTNVTRESITVGWHEPVSNGGSAVVGYHLEMKDRNSILWQKANKLV IRTTHFKVTTISAGLIYEFRVYAENAAGVGKPSHPSEPVLAIDACEPPRN VRITDISKNSVSLSWQQPAFDGGSKITGYIVERRDLPDGRWTKASFTNVT ETQFIISGLTQNSQYEFRVFARNAVGSISNPSEVVGPITCIDSYGGPVID LPLEYTEVVKYRAGTSVKLRAGISGKPAPTIEWYKDDKELQTNALVCVEN TTDLASILIKDADRLNSGCYELKLRNAMGSASATIRVQILDKPGPPGGPI EFKTVTAEKITLLWRPPADDGGAKITHYIVEKRETSRVVWSMVSEHLEEC IITTTKIIKGNEYIFRVRAVNKYGIGEPLESDSVVAKNAFVTPGPPGIPE VTKITKNSMTVVWSRPIADGGSDISGYFLEKRDKKSLGWFKVLKETIRDT RQKVTGLTENSDYQYRVCAVNAAGQGPFSEPSEFYKAADPIDPPGPPAKI RIADSTKSSITLGWSKPVYDGGSAVTGYVVEIRQGEEEEWTTVSTKGEVR TTEYVVSNLKPGVNYYFRVSAVNCAGQGEPIEMNEPVQAKDILEAPEIDL DVALRTSVIAKAGEDVQVLIPFKGRPPPTVTWRKDEKNLGSDARYSIENT DSSSLLTIPQVTRNDTGKYILTIENGVGEPKSSTVSVKVLDTPAACQKLQ VKHVSRGTVTLLWDPPLIDGGSPIINYVIEKRDATKRTWSVVSHKCSSTS FKLIDLSEKTPFFFRVLAENEIGIGEPCETTEPVKAAEVPAPIRDLSMKD STKTSVILSWTKPDFDGGSVITEYVVERKGKGEQTWSHAGISKTCEIEVS QLKEQSVLEFRVFAKNEKGLSDPVTIGPITVKELIITPEVDLSDIPGAQV TVRIGHNVHLELPYKGKPKPSISWLKDGLPLKESEFVRFSKTENKITLSI KNAKKEHGGKYTVILDNAVCRIAVPITVITLGPPSKPKGPIRFDEIKADS VILSWDVPEDNGGGEITCYSIEKRETSQTNWKMVCSSVARTTFKVPNLVK DAEYQFRVRAENRYGVSQPLVSSIIVAKHQFRIPGPPGKPVIYNVTSDGM SLTWDAPVYDGGSEVTGFHVEKKERNSILWQKVNTSPISGREYRATGLVE GLDYQFRVYAENSAGLSSPSDPSKFTLAVSPVDPPGTPDYIDVTRETITL KWNPPLRDGGSKIVGYSIEKRQGNERWVRCNFTDVSECQYTVTGLSPGDR YEFRIIARNAVGTISPPSQSSGIIMTRDENVPPIVEFGPEYFDGLIIKSG ESLRIKALVQGRPVPRVTWFKDGVEIEKRMNMEITDVLGSTSLFVRDATR DHRGVYTVEAKNASGSAKAEIKVKVQDTPGKVVGPIRFTNITGEKMTLWW DAPLNDGCAPITHYIIEKRETSRLAWALIEDKCEAQSYTAIKLINGNEYQ FRVSAVNKFGVGRPLDSDPVVAQIQYTVPDAPGIPEPSNITGNSITLTWA RPESDGGSEIQQYILERREKKSTRWVKVISKRPISETRFKVTGLTEGNEY EFHVMAENAAGVGPASGISRLIKCREPVNPPGPPTVVKVTDTSKTTVSLE WSKPVFDGGMEIIGYIIEMCKADLGDWHKVNAEACVKTRYTVTDLQAGEE YKFRVSAINGAGKGDSCEVTGTIKAVDRLTAPELDIDANFKQTHVVRAGA SIRLFIAYQGRPTPTAVWSKPDSNLSLRADIHTTDSFSTLTVENCNRNDA GKYTLTVENNSGSKSITFTVKVLDTPGPPGPITFKDVTRGSATLMWDAPL LDGGARIHHYVVEKREASRRSWQVISEKCTRQIFKVNDLAEGVPYYFRVS AVNEYGVGEPYEMPEPIVATEQPAPPRRLDVVDTSKSSAVLAWLKPDHDG GSRITGYLLEMRQKGSDFWVEAGHTKQLTFTVERLVEKTEYEFRVKAKND AGYSEPREAFSSVIIKEPQIEPTADLTGITNQLITCKAGSPFTIDVPISG RPAPKVTWKLEEMRLKETDRVSITTTKDRTTLTVKDSMRGDSGRYFLTLE NTAGVKTFSVTVVVIGRPGPVTGPIEVSSVSAESCVLSWGEPKDGGGTEI TNYIVEKRESGTTAWQLVNSSVKRTQIKVTHLTKYMEYSFRVSSENRFGV SKPLESAPIIAEHPFVPPSAPTRPEVYHVSANAMSIRWEEPYHDGGSKII GYWVEKKERNTILWVKENKVPCLECNYKVTGLVEGLEYQFRTYALNAAGV SKASEASRPIMAQNPVDAPGRPEVTDVTRSTVSLIWSAPAYDGGSKVVGY IIERKPVSEVGDGRWLKCNYTIVSDNFFTVTALSEGDTYEFRVLAKNAAG VISKGSESTGPVTCRDEYAPPKAELDARLHGDLVTIRAGSDLVLDAAVGG KPEPKIIWTKGDKELDLCEKVSLQYTGKRATAVIKFCDRSDSGKYTLTVK NASGTKAVSVMVKVLDSPGPCGKLTVSRVTQEKCTLAWSLPQEDGGAEIT HYIVERRETSRLNWVIVEGECPTLSYVVTRLIKNNEYIFRVRAVNKYGPG VPVESEPIVARNSFTIPSPPGIPEEVGTGKEHIIIQWTKPESDGGNEISN YLVDKREKKSLRWTRVNKDYVVYDTRLKVTSLMEGCDYQFRVTAVNAAGN SEPSEASNFISCREPSYTPGPPSAPRVVDTTKHSISLAWTKPMYDGGTDI VGYVLEMQEKDTDQWYRVHTNATIRNTEFTVPDLKMGQKYSFRVAAVNVK GMSEYSESIAEIEPVERIEIPDLELADDLKKTVTIRAGASLRLMVSVSGR PPPVITWSKQGIDLASRAIIDTTESYSLLIVDKVNRYDAGKYTIEAENQS GKKSATVLVKVYDTPGPCPSVKVKEVSRDSVTITWEIPTIDGGAPVNNYI VEKREAAMRAFKTVTTKCSKTLYRISGLVEGTMYYFRVLPENIYGIGEPC ETSDAVLVSEVPLVPAKLEVVDVTKSTVTLAWEKPLYDGGSRLTGYVLEA CKAGTERWMKVVTLKPTVLEHTVTSLNEGEQYLFRIRAQNEKGVSEPRET VTAVTVQDLRVLPTIDLSTMPQKTIHVPAGRPVELVIPIAGRPPPAASWF FAGSKLRESERVTVETHTKVAKLTIRETTIRDTGEYTLELKNVTGTTSET IKVIILDKPGPPTGPIKIDEIDATSITISWEPPELDGGAPLSGYVVEQRD AHRPGWLPVSESVTRSTFKFTRLTEGNEYVFRVAATNRFGIGSYLQSEVI ECRSSIRIPGPPETLQIFDVSRDGMTLTWYPPEDDGGSQVTGYIVERKEV RADRWVRVNKVPVTMTRYRSTGLTEGLEYEHRVTAINARGSGKPSRPSKP IVAMDPIAPPGKPQNPRVTDTTRTSVSLAWSVPEDEGGSKVTGYLIEMQK VDQHEWTKCNTTPTKIREYTLTHLPQGAEYRFRVLACNAGGPGEPAEVPG TVKVTEMLEYPDYELDERYQEGIFVRQGGVIRLTIPIKGKPFPICKWTKE GQDISKRAMIATSETHTELVIKEADRGDSGTYDLVLENKCGKKAVYIKVR VIGSPNSPEGPLEYDDIQVRSVRVSWRPPADDGGADILGYILERREVPKA AWYTIDSRVRGTSLVVKGLKENVEYHFRVSAENQFGISKPLKSEEPVTPK TPLNPPEPPSNPPEVLDVTKSSVSLSWSRPKDDGGSRVTGYYIERKETST DKWVRHNKTQITTTMYTVTGLVPDAEYQFRIIAQNDVGLSETSPASEPVV CKDPFDKPSQPGELEILSISKDSVTLQWEKPECDGGKEILGYWVEYRQSG DSAWKKSNKERIKDKQFTIGGLLEATEYEFRVFAENETGLSRPRRTAMSI KTKLTSGEAPGIRKEMKDVTTKLGEAAQLSCQIVGRPLPDIKWYRFGKEL IQSRKYKMSSDGRTHTLTVMTEEQEDEGVYTCIATNEVGEVETSSKLLLQ ATPQFHPGYPLKEKYYGAVGSTLRLHVMYIGRPVPAMTWFHGQKLLQNSE NITIENTEHYTHLVMKNVQRKTHAGKYKVQLSNVFGTVDAILDVEIQDKP DKPTGPIVIEALLKNSAVISWKPPADDGGSWITNYVVEKCEAKEGAEWQL VSSAISVTTCRIVNLTENAGYYFRVSAQNTFGISDPLEVSSVVIIKSPFE KPGAPGKPTITAVTKDSCVVAWKPPASDGGAKIRNYYLEKREKKQNKWIS VTTEEIRETVFSVKNLIEGLEYEFRVKCENLGGESEWSEISEPITPKSDV PIQAPHFKEELRNLNVRYQSNATLVCKVTGHPKPIVKWYRQGKEIIADGL KYRIQEFKGGYHQLIIASVTDDDATVYQVRATNQGGSVSGTASLEVEVPA KIHLPKTLEGMGAVHALRGEVVSIKIPFSGKPDPVITWQKGQDLIDNNGH YQVIVTRSFTSLVFPNGVERKDAGFYVVCAKNRFGIDQKTVELDVADVPD PPRGVKVSDVSRDSVNLTWTEPASDGGSKITNYIVEKCATTAERWLRVGQ ARETRYTVINLFGKTSYQFRVIAENKFGLSKPSEPSEPTITKEDKTRAMN YDEEVDETREVSMTKASHSSTKELYEKYMIAEDLGRGEFGIVHRCVETSS KKTYMAKFVKVKGTDQVLVKKEISILNIARHRNILHLHESFESMEELVMI FEFISGLDIFERINTSAFELNEREIVSYVHQVCEALQFLHSHNIGHFDIR PENIIYQTRRSSTIKIIEFGQARQLKPGDNFRLLFTAPEYYAPEVHQHDV VSTATDMWSLGTLVYVLLSGINPFLAETNQQIIENIMNAEYTFDEEAFKE ISIEAMDFVDRLLVKERKSRMTASEALQHPWLKQKIERVSTKVIRTLKHR RYYHTLIKKDLNMVVSAARISCGGAIRSQKGVSVAKVKVASIEIGPVSGQ IMHAVGEEGGHVKYVCKIENYDQSTQVTWYFGVRQLENSEKYEITYEDGV AILYVKDITKLDDGTYRCKVVNDYGEDSSYAELFVKGVREVYDYYCRRTM KKIKRRTDTMRLLERPPEFTLPLYNKTAYVGENVRFGVTITVHPEPHVTW YKSGQKIKPGDNDKKYTFESDKGLYQLTINSVTTDDDAEYTVVARNKYGE DSCKAKLTVTLHPPPTDSTLRPMFKRLLANAECQEGQSVCFEIRVSGIPP PTLKWEKDGQPLSLGPNIEIIHEGLDYYALHIRDTLPEDTGYYRVTATNT AGSTSCQAHLQVERLRYKKQEFKSKEEHERHVQKQIDKTLRMAEILSGTE SVPLTQVAKEALREAAVLYKPAVSTKTVKGEFRLEIEEKKEERKLRMPYD VPEPRKYKQTTIEEDQRIKQFVPMSDMKWYKKIRDQYEMPGKLDRVVQKR PKRIRLSRWEQFYVMPLPRITDQYRPKWRIPKLSQDDLEIVRPARRRTPS PDYDFYYRPRRRSLGDISDEELLLPIDDYLAMKRTEEERLRLEEELELGF SASPPSRSPPHFELSSLRYSSPQAHVKVEETRKDFRYSTYHIPTKAEAST SYAELRERHAQAAYRQPKQRQRIMAEREDEELLRPVTTTQHLSEYKSELD FMSKEEKSRKKSRRQREVTEITEIEEEYEISKHAQRESSSSASRLLRRRR SLSPTYIELMRPVSELIRSRPQPAEEYEDDTERRSPTPERTRPRSPSPVS SERSLSRFERSARFDIFSRYESMKAALKTQKTSERKYEVLSQQPFTLDHA PRITLRMRSHRVPCGQNTRFILNVQSKPTAEVKWYHNGVELQESSKIHYT NTSGVLTLEILDCHTDDSGTYRAVCTNYKGEASDYATLDVTGGDYTTYAS QRRDEEVPRSVFPELTRTEAYAVSSFKKTSEMEASSSVREVKSQMTETRE SLSSYEHSASAEMKSAALEEKSLEEKSTTRKIKTTLAARILTKPRSMTVY EGESARFSCDTDGEPVPTVTWLRKGQVLSTSARHQVTTTKYKSTFEISSV QASDEGNYSVVVENSEGKQEAEFTLTIQKARVTEKAVTSPPRVKSPEPRV KSPEAVKSPKRVKSPEPSHPKAVSPTETKPTPTEKVQHLPVSAPPKITQF LKAEASKEIAKLTCVVESSVLRAKEVTWYKDGKKLKENGHFQFHYSADGT YELKINNLTESDQGEYVCEISGEGGTSKTNLQFMGQAFKSIHEKVSKISE TKKSDQKTTESTVTRKTEPKAPEPISSKPVIVTGLQDTTVSSDSVAKFAV KATGEPRPTAIWTKDGKAITQGGKYKLSEDKGGFFLEIHKTDTSDSGLYT CTVKNSAGSVSSSCKLTIKAIKDTEAQKVSTQKTSEITPQKKAVVQEEIS QKALRSEEIKMSEAKSQEKLALKEEASKVLISEEVKKSAATSLEKSIVHE EITKTSQASEEVRTHAEIKAFSTQMSINEGQRLVLKANIAGATDVKWVLN GVELTNSEEYRYGVSGSDQTLTIKQASHRDEGILTCISKTKEGIVKCQYD LTLSKELSDAPAFISQPRSQNINEGQNVLFTCEISGEPSPEIEWFKNNLP ISISSNVSISRSRNVYSLEIRNASVSDSGKYTIKAKNFRGQCSATASLMV LPLVEEPSREVVLRTSGDTSLQGSFSSQSVQMSASKQEASFSSFSSSSAS SMTEMKFASMSAQSMSSMQESFVEMSSSSFMGISNMTQLESSTSKMLKAG IRGIPPKIEALPSDISIDEGKVLTVACAFTGEPTPEVTWSCGGRKIHSQE QGRFHIENTDDLTTLIIMDVQKQDGGLYTLSLGNEFGSDSATVNIHIRSI tantan-13/test/tantan_test.out0000644000000000000000000021736612037256344015343 0ustar rootroot>chrM GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT TTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTG GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATT CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACCTACTA AAGTGTGTTAATtaattaaTGCTTGTAGGACATAATAATAACAATTGAAT GTCTGCACAGCCGCTTTCCACACAGACATCATAACAaaaaatttccacca aacccccccctccccccGCTTCTGGCCACAGCACTTAAACACATCTCTGC CAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAAT TTTATCTTTAGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACA TTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCC GCCCATCCTACCCAGCACacacacaCCGCTGCTAACCCCATACCCCGAAC CAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAA ATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGC AAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAG GGACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCC ACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGT TTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTT TAGATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAA CTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAAC ACACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGC CCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGA GCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGC TCAGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGT AAGCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGG TGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTT ATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTGAGAGTAGAGT GCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATA GAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAaagtgcacTTGGACG AACCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTT CAACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCAC CTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGG CGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTT CTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAA GACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCC GTCTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCT ACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTT TAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGA GTAAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGA AAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACT GAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAA TGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCA GATCAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAG GAAAGGTTAAAAAAAGTAAAAGGAACTCGGCAAACCTTACCCCGCCTGTT TACCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCC CAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAAAGGTAGCA TAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGT TCAGCTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGG CGGGCATGACACAGCAAGACGAGAAGACCCTATGGAGCTTTAATTTATTA ATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCA TTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAacctccgagca gtaCATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGAT CCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATC CTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT CAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGA TTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTT CTATCTACTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCC TACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTAT TATACCCACACCCACCCAAGAACAGGGTTTGTTAAGATGGCAGAGCCCGG TAATCGCATAAAACTTAaaactTTACAGTCAGAGGTTCAATTCCTCTTCT TAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAA TCGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATA CAACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACC CTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCA CATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATC GCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCT CAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACT CAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGC GCACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCAT CATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCC TTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTG GCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTT CGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAAT ACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATT ATtataataAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGA CGCACTCTCCCCTGAACTCTACACAACATATTTTGTCACCAAGACCCTAC TTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCCCCGATTCCGC TACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCT AGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTC CCCCTCAAACCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGT AAATAATAGGAGCTTAAACCCCCTTATTTCTAGGACTATGAGAATCGAAC CCATCCCTGAGAATCCAAAATTCTCCGTGCCACCTATCACACCCCATCCT AAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTG GTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTAC TCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATT TTTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTC TAACCAAAAAAATAAACCCTCGTTCCACAGAAGCTGCCATCAAGTATTTC CTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATCCTCTTCAA CAATATACTCTCCGGACAATGAACCATAACCAATACTACCAatcaatact catcattaataatcataatGGCTATAGCAATAAAACTAGGAATAGCCCCC TTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGG CCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACC AAATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTA TCCATCATAGCAGGCAGTTGAGGTGGATTAAACCAAACCCAGCTACGCAA AATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAATAGCAGTTC TACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATC CTAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGAC CCTACTACTATCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAA TTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTT TTGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCAT CATCCCCACcatcatagccaccatcaCCCTCCTTAACCTCTACTTCTACC TACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAAC GTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCC CACACTCATCGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATAC TAATAATCTTATAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAG CCCTCAGTAAGTTGCAATACTTAATTTCTGCAACAGCTAAGGACTGCAAA ACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAA GCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGC TAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAA AAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCA ATTCAATATGAAAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTG TCTTTAGATTTACAGTCCAATGCTTCACTCAGCCATTTTACCTCACCCCC ACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTG GAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCT CTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGG TAACGACCACATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAA TCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTA GTTCCCCTAAtaaTCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAA CATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTGCTCGCATCTG CTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTA GCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTC CTTACACCTAGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCA CAACAATTATCAATATAAAACCCCCTGCCATAACCCAATACCAAACGCCC CTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCT CCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGACCGCAACCTCA AcaccaccttcttcgaccccgccggaggaggagACCCCATTCTATACCAA CACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACC AGGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAG AACCATTTGGATACATAGGTATGGTCTGAGCTATGATATCAATTGGCTTC CTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGAATAGACGT AGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCA CCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATG AAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCAC CGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCG TACTACACGACACGTACTACGTTGTAGCTCACTTCCACTATGTCCTATCA ATAGGAGCTGTATTTGCCATCATAGGAGGCTTCATTCACTGATTTCCCCT ATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCCATTTCACTA TCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGC CTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCAC ATGAAACATCCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAA TattaataattttcatgatTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTC CTAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCC CCCACCCTACCACACATTCGAAGAACCCGTATACATAAAATCTAGACAAA AAAGGAAGGAATCGAACCCCCCAAAGCTGGTTTCAAGCCAACCCCATGGC CTCCATGACTTTTTCAAAAAGGTATTAGAAAAACCATTTCATAACTTTGT CAAAGTTAAATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGC GCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCA CCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTC CTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACAT CTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCA TCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGAC GAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTA CTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACA TACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTT GACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTAC ATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAA CAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGA CCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAG TTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAG GGCCCGTATTTACCCTATAGCACCCCCTCTaccccctctaGAGCCCACTG TAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAAC ACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCA TAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATA TTAAACACAAACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAA AAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTC ATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTC TATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGA CTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGAT AGCCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCT TAATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCA TTTACACCAAccacccaactatctATAAACCTAGCCATGGCCATCCCCTT ATGAGCGGGCGCAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCC TAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTA GTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGT ACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTG GAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATC ATCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTT AATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACA ACACATAATGACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCC CATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTA GCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACT AACCAACACACTAACCATATACCAATGGTGGCGCGATGTAACACGAGAAA GCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATAC GGGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTT CTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAACTAGGAGGGC ACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTC CTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCA CCATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTA TTACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTAC TTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTT TGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCC TCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACAT CACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGT TTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTA GTATAAATAGTACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAA AAAAGAGTAATAAACTTCGCCTTAATTTTAATAATCAACACCCTCCTAGC CTTACtactaataattattaCATTTTGACTACCACAACTCAACGGCTACA TAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCC CGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATT ATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAA CAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTaatcatcatC CTAGCCCTAAGTCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAGC CGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGACTCATTAAATT ATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTA GCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCAT ATCCTCCCTACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAG CTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAATATTGTGCCT ATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCT ACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTACATAACCTAA ACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCAC TGACATGACTTTCCAAAAAGCACATAATTTGAATCAACACAACCACCCAC AGCCTAATTATTAGcatcatccccctactattttTTAACCAAATCAACAA CAACCTATTTAGCTGTTCCCCAACCTTTTCCTCCGACCCCCTAACAACCC CCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATCATGGCAAGC CAACGCCACTTATCCAGCGAACCACTATCACGAAAAAAACTCTACCTCTC TATACTAAtctccctacaaatctccttaATTATAACATTCACAGCCACAG AACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTG GCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCAC ATACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCAC TAATTTACACTCACAACACCCTAGGCTCACTAAACATTCTACTACTCACT CTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTTAATATGACT AGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACT TATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTA CTTGCCGCAGTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCAC ACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTAC TATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACA GACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACATAGCCCTCGT AGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCA TTCTCATAATCGCCCACGGACTCACATCCTCATTACTATTCTGCCTAGCA AACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGG ACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCC TCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCT GTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGG ACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAA CACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTC ACACGagaaaacACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCT ATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTT TAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTACGACCCCTT ATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAA CAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTA GGCCccaaaaatttTGGTGCAACTCCAAATAAAAGTAATAACCATGCACA CTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACC ACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATC CATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCA TGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACC CAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAAT ATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCAC TGTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTA CTCATTTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATT CCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCA TCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCA GTCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATG ATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAA ACGCTAATCCAAGCCTCACCCCACTACTAGGCCTcctcctagcagcagca gGCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGA AGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAG CAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCA CTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGC AGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCT CCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAA CCACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCAT ACTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAG ATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACC TCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGG TTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAA ACGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCC TATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCC CACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTA AACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAAC ATTTCCCCCGCATCCCCCTtccaaacaacaatccccCTCTACCTAAAACT CACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCA ACTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTAT TTCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCC CTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACC TAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATC TCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTT CCTCTCTTTcttcttcccactcatcctaaccctactcctaaTCACATAAC CTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGT TCAACCAGTAACCACTACTAATCAACGCCCATAATCATACAAAGCCCCCG CACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATT ATTCAGCTTCCTACACTATTAAAGTTTACCACAaccaccaccccATCATA CTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAA CACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCA ATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATA AATtaaaaaaactattaaacCCATATAACCTCCCCCAAAATTCAGAATAA TAACACACCCGACCACACCGCTAACAATCAGTACTAAACCCCCATAAATA GGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACT CAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGA CCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATG ACCCCAATACGCAAAATTAACCCCCTAATAAAATTAATTAACCACTCATT CATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCT CACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTA GCCATACACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCA CATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCA ATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGC CTATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTAT CCTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGT GAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCC GCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTA CTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATct tacccttcaTTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCAC GAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAAT CACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTct tccttctctccttaatGACATTAACACTATTCTCACCAGACCTCCTAGGC GACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACAT CAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCC CTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTA GCAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCG CCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTC TAACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGA CAAGTAGCATCCGTACTATACTTCACAACAATCCTaatcctaatacCAAC TATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTA TAAACTAATACACCAGTCTTGTAAACCGGAGACGAAAACCTTTTTCCAAG GACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAA GATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGG TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC ATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCA CCTGTAGTACATAAAAACCCAACCCACATCAaaccccccccccccATGCT TACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAAC TCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTT AACAGTACATAGTACATAAAGTCAtttaccgtacatagcacatTACAGTC AAATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTG ACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCT CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC ATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCC CTTAAATAAGACATCACGATG >sp|Q8WZ42|TITIN_HUMAN MTTQAPTFTQPLQSVVVLEGSTATFEAHISGFPVPEVSWFRDGQVISTST LPGVQISFSDGRAKLTIPAVTKANSGRYSLKATNGSGQATSTAELLVKAE TAPPNFVQRLQSMTVRQGSQVRLQVRVTGIPTPVVKFYRDGAEIQSSLDF QISQEGDLYSLLIAEAYPEDSGTYSVNATNSVGRATSTAELLVQGEEEVP AKKTKTIVSTAQISESRQTRIEKKIEAHFDARSIATVEMVIDGAAGQQLP HKTPHRIPPKPKSRSxxxPSIAAKAQLARQQSPSPIxxxxxxxxxxxxxx PSPVRSVSPAAxxxxxxxxxxxxxxLMRKTQASTVATGPEVPPPWKQEGY VASSSEAEMRETTLTTSTQIRTEERWEGRYGVQExxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxDMARVREPVISAVEQTA QRTTTTAVHIQxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxISEEITxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxVPGAQEETTTQQxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxPREPGHLEESYAQQTTLEYGYKERISAAKVAEPP QRPASEPHVVPKAVKPRVIQAPSETHIKTTDQKGMHISSQIKKTTDLTTE RLVHVDKRPRTASPHFTVSKISVPKTEHGYEASIAGSAIATLQKELSATS SAQKITKSVKAPTVKPSETRVRAEPTPLPQFPFADTPDTYKSEAGVEVKK EVGVSITGTTVREERFEVLHGREAKVTETARVPAPVEIPVTPPTLVSGLK NVTVIEGESVTLECHISGYPSPTVTWYREDYQIESSIDFQITFQSGIARL MIREAFAEDSGRFTCSAVNEAGTVSTSCYLAVQVSEEFEKETTAVTEKFT TEEKRFVESRDVVMTDTSLTEEQAGPGEPAAPYFITKPVVQKLVEGGSVV FGCQVGGNPKPHVYWKKSGVPLTTGYRYKVSYNKQTGECKLVISMTFADD AGEYTIVVRNKHGETSASASLLEEADYELLMKSQQEMLYQTQVTAFVQEP KVGETAPGFVYSEYEKxxxxxQALIRKKMAKDTVVVRTYVEDQEFHISSF EERxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxSGFDLRIKNY RILEGMGVTFHCKMSGYPLPKIAWYKDGKRIKHGERYQMDFLQDGRASLR IPVVLPEDEGIYTAFASNIKGNAICSGKLYVEPAAPLGAPTYIPTLEPVS RIRSLSPxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxLEETDESQ LERLYKPVFVLKPVSFKCLEGQTARFDLKVVGRPMPETFWFHDGQQIVND YTHKVVIKEDGTQSLIIVPATPSDSGEWTVVAQNRAGRSSISVILTVEAV EHQVKPMFVEKLKNVNIKEGSQLEMKVRATGNPNPDIVWLKNSDIIVPHK YPKIRIEGTKGEAALKIDSTVSQDSAWYTATAINKAGRDTTRCKVNVEVE FAEPEPERKLIIPRGTYRAKEIAAPELEPLHLRYGQEQWEEGDLYDKEKQ QKPFFKKKLTSLRLKRFGPAHFECRLTPIGDPTMVVEWLHDGKPLEAANR LRMINEFGYCSLDYGVAYSRDSGIITCRATNKYGTDHTSATLIVKDEKSL VEESQLPEGRKGLQRIEELERMAHEGALTGVTTDQKEKQKPDIVLYPEPV RVLEGETARFRCRVTGYPQPKVNWYLNGQLIRKSKRFRVRYDGIHYLDIV DCKSYDTGEVKVTAENPEGVIEHKVKLEIQQREDFRSVLRRAPEPRPEFH VHEPGKLQFEVQKVDRPVDTTETKEVVKLKRAERITHEKVPEESEELRSK FKRRTEEGYYEAITAVELKSRKKDESYEELLRKTxxxxxxxxxxxxxxxx xxxxxxxxITIPTFKPDKIELSPSMEAPKIFERIQSQTVGQGSDAHFRVR VVGKPDPECEWYKNGVKIERSDRIYWYWPEDNVCELVIRDVTAEDSASIM VKAINIAGETSSHAFLLVQAKQLITFTQELQDVVAKEKDTMATFECETSE PFVKVKWYKDGMEVHEGDKYRMHSDRKVHFLSILTIDTSDAEDYSCVLVE DENVKTTAKLIVEGAVVEFVKELQDIEVPESYSGELECIVSPENIEGKWY HNDVELKSNGKYTITSRRGRQNLTVKDVTKEDQGEYSFVIDGKKTTCKLK MKPRPIAILQGLSDQKVCEGDIVQLEVKVSLESVEGVWMKDGQEVQPSDR VHIVIDKQSHMLLIEDMTKEDAGNYSFTIPALGLSTSGRVSVYSVDVITP LKDVNVIEGTKAVLECKVSVPDVTSVKWYLNDEQIKPDDRVQAIVKGTKQ RLVINRTHASDEGPYKLIVGRVETNCNLSVEKIKIIRGLRDLTCTETQNV VFEVELSHSGIDVLWNFKDKEIKPSSKYKIEAHGKIYKLTVLNMMKDDEG KYTFYAGENITSGKLTVAGGAISKPLTDQTVAESQEAVFECEVANPDSKG EWLRDGKHLPLTNNIRSESDGHKRRLIIAATKLDDIGEYTYKVATSKTSA KLKVEAVKIKKTLKNLTVTETQDAVFTVELTHPNVKGVQWIKNGVVLESN EKYAISVKGTIYSLRIKNCAIVDESVYGFRLGRLGASARLHVETVKIIKK PKDVTALENATVAFEVSVSHDTVPVKWFHKNVEIKPSDKHRLVSERKVHK LMLQNISPSDAGEYTAVVGQLECKAKLFVETLHITKTMKNIEVPETKTAS FECEVSHFNVPSMWLKNGVEIEMSEKFKIVVQGKLHQLIIMNTSTEDSAE YTFVCGNDQVSATLTVTPIMITSMLKDINAEEKDTITFEVTVNYEGISYK WLKNGVEIKSTDKCQMRTKKLTHSLNIRNVHFGDAADYTFVAGKATSTAT LYVEARHIEFRKHIKDIKVLEKKRAMFECEVSEPDITVQWMKDDQELQIT DRIKIQKEKYVHRLLIPSTRMSDAGKYTVVAGGNVSTAKLFVEGRDVRIR SIKKEVQVIEKQRAVVEFEVNEDDVDAHWYKDGIEINFQVQERHKYVVER RIHRMFISETRQSDAGEYTFVAGRNRSSVTLYVNAPEPPQVLQELQPVTV QSGKPARFCAVISGRPQPKISWYKEEQLLSTGFKCKFLHDGQEYTLLLIE AFPEDAAVYTCEAKNDYGVATTSASLSVEVPEVVSPDQEMPVYPPAIITP LQDTVTSEGQPARFQCRVSGTDLKVSWYSKDKKIKPSRFFRMTQFEDTYQ LEIAEAYPEDEGTYTFVASNAVGQVSSTANLSLEAPESILHERIEQEIEM EMKEFSSSFLSAEEEGLHSAELQLSKINETLELLSESPVYSTKFDSEKEG TGPIFIKEVSNADISMGDVATLSVTVIGIPKPKIQWFFNGVLLTPSADYK FVFDGDDHSLIILFTKLEDEGEYTCMASNDYGKTICSAYLKINSKGEGHK DTETESAVAKSLEKLGGPCPPHFLKELKPIRCAQGLPAIFEYTVVGEPAP TVTWFKENKQLCTSVYYTIIHNPNGSGTFIVNDPQREDSGLYICKAENML GESTCAAELLVLLEDTDMTDTPCKAKSTPEAPEDFPQTPLKGPAVEALDS EQEIATFVKDTILKAALITEENQQLSYEHIAKANELSSQLPLGAQELQSI LEQDKLTPESTREFLCINGSIHFQPLKEPSPNLQLQIVQSQKTFSKEGIL MPEEPETQAVLSDTEKIFPSAMSIEQINSLTVEPLKTLLAEPEGNYPQSS IEPPMHSYLTSVAEEVLSPKEKTVSDTNREQRVTLQKQEAQSALILSQSL AEGHVESLQSPDVMISQVNYEPLVPSEHSCTEGGKILIESANPLENAGQD SAVRIEEGKSLRFPLALEEKQVLLKEEHSDNVVMPPDQIIESKREPVAIK KVQEVQGRDLLSKESLLSGIPEEQRLNLKIQICRALQAAVASEQPGLFSE WLRNIEKVEVEAVNITQEPRHIMCMYLVTSAKSVTEEVTIIIEDVDPQMx xxxxxxxxALxAIIYEEIDILTAEGPRIQQGAKTSLQEEMDSFSGSQKVE PITEPEVESKYLISTEEVSYFNVQSRVKYLDATPVTKGVASAxxxxxxxx xxxxxxxxxxxxxxxxxxxxVATVKIQEAEGGLIKEDGPMIHTPLVDTVS EEGDIVHLTTSITNAKEVNWYFENKLVPSDEKFKCLQDQNTYTLVIDKVN TEDHQGEYVCEALNDSGKTATSAKLTVVKRAAPVIKRKIEPLEVALGHLA KFTCEIQSAPNVRFQWFKAGREIYESDKCSIRSSKYISSLEILRTQVVDC GEYTCKASNEYGSVSCTATLTVTEAYPPTFLSRPKSLTTFVGKAAKFICT VTGTPVIETIWQKDGAALSPSPNWKISDAENKHILELSNLTIQDRGVYSC KASNKFGADICQAELIIIDKPHFIKELEPVQSAINKKVHLECQVDEDRKV TVTWSKDGQKLPPGKDYKICFEDKIATLEIPLAKLKDSGTYVCTASNEAG SSSCSATVTVREPPSFVKKVDPSYLMLPGESARLHCKLKGSPVIQVTWFK NNKELSESNTVRMYFVNSEAILDITDVKVEDSGSYSCEAVNDVGSDSCST EIVIKEPPSFIKTLEPADIVRGTNALLQCEVSGTGPFEISWFKDKKQIRS SKKYRLFSQKSLVCLEIFSFNSADVGEYECVVANEVGKCGCMATHLLKEP PTFVKKVDDLIALGGQTVTLQAAVRGSEPISVTWMKGQEVIREDGKIKMS FSNGVAVLIIPDVQISFGGKYTCLAENEAGSQTSVGELIVKEPAKIIERA ELIQVTAGDPATLEYTVAGTPELKPKWYKDGRPLVASKKYRISFKNNVAQ LKFYSAELHDSGQYTFEISNEVGSSSCETTFTVLDRDIAPFFTKPLRNVD SVVNGTCRLDCKIAGSLPMRVSWFKDGKEIAASDRYRIAFVEGTASLEII RVDMNDAGNFTCRATNSVGSKDSSGALIVQEPPSFVTKPGSKDVLPGSAV CLKSTFQGSTPLTIRWFKGNKELVSGGSCYITKEALESSLELYLVKTSDS GTYTCKVSNVAGGVECSANLFVKEPATFVEKLEPSQLLKKGDATQLACKV TGTPPIKITWFANDREIKESSKHRMSFVESTAVLRLTDVGIEDSGEYMCE AQNEAGSDHCSSIVIVKESPYFTKEFKPIEVLKEYDVMLLAEVAGTPPFE ITWFKDNTILRSGRKYKTFIQDHLVSLQILKFVAADAGEYQCRVTNEVGS SICSARVTLREPPSFIKKIESTSSLRGGTAAFQATLKGSLPITVTWLKDS DEITEDDNIRMTFENNVASLYLSGIEVKHDGKYVCQAKNDAGIQRCSALL SVKEPATITEEAVSIDVTQGDPATLQVKFSGTKEITAKWFKDGQELTLGS KYKISVTDTVSILKIISTEKKDSGEYTFEVQNDVGRSSCKARINVLDLII PPSFTKKLKKMDSIKGSFIDLECIVAGSHPISIQWFKDDQEISASEKYKF SFHDNTAFLEISQLEGTDSGTYTCSATNKAGHNQCSGHLTVKEPPYFVEK PQSQDVNPNTRVQLKALVGGTAPMTIKWFKDNKELHSGAARSVWKDDTST SLELFAAKATDSGTYICQLSNDVGTATSKATLFVKEPPQFIKKPSPVLVL RNGQSTTFECQITGTPKIRVSWYLDGNEITAIQKHGISFIDGLATFQISG ARVENSGTYVCEARNDAGTASCSIELKVKEPPTFIRELKPVEVVKYSDVE LECEVTGTPPFEVTWLKNNREIRSSKKYTLTDRVSVFNLHITKCDPSDTG EYQCIVSNEGGSCSCSTRVALKEPPSFIKKIENTTTVLKSSATFQSTVAG SPPISITWLKDDQILDEDDNVYISFVDSVATLQIRSVDNGHSGRYTCQAK NESGVERCYAFLLVQEPAQIVEKAKSVDVTEKDPMTLECVVAGTPELKVK WLKDGKQIVPSRYFSMSFENNVASFRIQSVMKQDSGQYTFKVENDFGSSS CDAYLRVLDQNIPPSFTKKLTKMDKVLGSSIHMECKVSGSLPISAQWFKD GKEISTSAKYRLVCHERSVSLEVNNLELEDTANYTCKVSNVAGDDACSGI LTVKEPPSFLVKPGRQQAIPDSTVEFKAILKGTPPFKIKWFKDDVELVSG PKCFIGLEGSTSFLNLYSVDASKTGQYTCHVTNDVGSDSCTTMLLVTEPP KFVKKLEASKIVKAGDSSRLECKIAGSPEIRVVWFRNEHELPASDKYRMT FIDSVAVIQMNNLSTEDSGDFICEAQNPAGSTSCSTKVIVKEPPVFSSFP PIVETLKNAEVSLECELSGTPPFEVVWYKDKRQLRSSKKYKIASKNFHTS IHILNVDTSDIGEYHCKAQNEVGSDTCVCTVKLKEPPRFVSKLNSLTVVA GEPAELQASIEGAQPIFVQWLKEKEEVIRESENIRITFVENVATLQFAKA EPANAGKYICQIKNDGGMEENMATLMVLEPAVIVEKAGPMTVTVGETCTL ECKVAGTPELSVEWYKDGKLLTSSQKHKFSFYNKISSLRILSVERQDAGT YTFQVQNNVGKSSCTAVVDVSDRAVPPSFTRRLKNTGGVLGASCILECKV AGSSPISVAWFHEKTKIVSGAKYQTTFSDNVCTLQLNSLDSSDMGNYTCV AANVAGSDECRAVLTVQEPPSFVKEPEPLEVLPGKNVTFTSVIRGTPPFK VNWFRGARELVKGDRCNIYFEDTVAELELFNIDISQSGEYTCVVSNNAGQ ASCTTRLFVKEPAAFLKRLSDHSVEPGKSIILESTYTGTLPISVTWKKDG FNITTSEKCNIxxxxxTCILEILNSTKRDAGQYSCEIENEAGRDVCGALV STLEPPYFVTELEPLEAAVGDSVSLQCQVAGTPEITVSWYKGDTKLRPTP EYRTYFTNNVATLVFNKVNINDSGEYTCKAENSIGTASSKTVFRIQERQL PPSFARQLKDIEQTVGLPVTLTCRLNGSAPIQVCWYRDGVLLRDDENLQT SFVDNVATLKILQTDLSHSGQYSCSASNPLGTASSSARLTAREPKKSPFF DIKPVSIDVIAGESADFECHVTGAQPMRITWSKDNKEIRPGGNYTITCVG NTPHLRILKVGKGDSGQYTCQATNDVGKDMCSAQLSVKEPPKFVKKLEAS KVAKQGESIQLECKISGSPEIKVSWFRNDSELHESWKYNMSFINSVALLT INEASAEDSGDYICEAHNGVGDASCSTALTVKAPPVFTQKPSPVGALKGS DVILQCEISGTPPFEVVWVKDRKQVRNSKKFKITSKHFDTSLHILNLEAS DVGEYHCKATNEVGSDTCSCSVKFKEPPRFVKKLSDTSTLIGDAVELRAI VEGFQPISVVWLKDRGEVIRESENTRISFIDNIATLQLGSPEASNSGKYI CQIKNDAGMRECSAVLTVLEPARIIEKPEPMTVTTGNPFALECVVTGTPE LSAKWFKDGRELSADSKHHITFINKVASLKIPCAEMSDKGLYSFEVKNSV GKSNCTVSVHVSDRIVPPSFIRKLKDVNAILGASVVLECRVSGSAPISVG WFQDGNEIVSGPKCQSSFSENVCTLNLSLLEPSDTGIYTCVAANVAGSDE CSAVLTVQEPPSFEQTPDSVEVLPGMSLTFTSVIRGTPPFKVKWFKGSRE LVPGESCNISLEDFVTELELFEVQPLESGDYSCLVTNDAGSASCTTHLFV KEPATFVKRLADFSVETGSPIVLEATYTGTPPISVSWIKDEYLISQSERC SITMTEKSTILEILESTIEDYAQYSCLIENEAGQDICEALVSVLEPPYFI EPLEHVEAVIGEPATLQCKVDGTPEIRISWYKEHTKLRSAPAYKMQFKNN VASLVINKVDHSDVGEYSCKADNSVGAVASSAVLVIKERKLPPFFARKLK DVHETLGFPVAFECRINGSEPLQVSWYKDGVLLKDDANLQTSFVHNVATL QILQTDQSHIGQYNCSASNPLGTASSSAKLILSEHEVPPFFDLKPVSVDL ALGESGTFKCHVTGTAPIKITWAKDNREIRPGGNYKMTLVENTATLTVLK VGKGDAGQYTCYASNIAGKDSCSAHLGVQEPPRFIKKLEPSRIVKQDEFT RYECKIGGSPEIKVLWYKDETEIQESSKFRMSFVDSVAVLEMHNLSVEDS GDYTCEAHNAAGSASSSTSLKVKEPPIFRKKPHPIETLKGADVHLECELQ GTPPFHVSWYKDKRELRSGKKYKIMSENFLTSIHILNVDAADIGEYQCKA TNDVGSDTCVGSIALKAPPRFVKKLSDISTVVGKEVQLQTTIEGAEPISV VWFKDKGEIVRESDNIWISYSENIATLQFSRVEPANAGKYTCQIKNDAGM QECFATLSVLEPATIVEKPESIKVTTGDTCTLECTVAGTPELSTKWFKDG KELTSDNKYKISFFNKVSGLKIINVAPSDSGVYSFEVQNPVGKDSCTASL QVSDRTVPPSFTRKLKETNGLSGSSVVMECKVYGSPPISVSWFHEGNEIS SGRKYQTTLTDNTCALTVNMLEESDSGDYTCIATNMAGSDECSAPLTVRE PPSFVQKPDPMDVLTGTNVTFTSIVKGTPPFSVSWFKGSSELVPGDRCNV SLEDSVAELELFDVDTSQSGEYTCIVSNEAGKASCTTHLYIKAPAKFVKR LNDYSIEKGKPLILEGTFTGTPPISVTWKKNGINVTPSQRCNITTTEKSA ILEIPSSTVEDAGQYNCYIENASGKDSCSAQILILEPPYFVKQLEPVKVS VGDSASLQCQLAGTPEIGVSWYKGDTKLRPTTTYKMHFRNNVATLVFNQV DINDSGEYICKAENSVGEVSASTFLTVQEQKLPPSFSRQLRDVQETVGLP VVFDCAISGSEPISVSWYKDGKPLKDSPNVQTSFLDNTATLNIFKTDRSL AGQYSCTATNPIGSASSSARLILTEGKNPPFFDIRLAPVDAVVGESADFE CHVTGTQPIKVSWAKDSREIRSGGKYQISYLENSAHLTVLKVDKGDSGQY TCYAVNEVGKDSCTAQLNIKERLIPPSFTKRLSETVEETEGNSFKLEGRV AGSQPITVAWYKNNIEIQPTSNCEITFKNNTLVLQVRKAGMNDAGLYTCK VSNDAGSALCTSSIVIKEPKKPPVFDQHLTPVTVSEGEYVQLSCHVQGSE PIRIQWLKAGREIKPSDRCSFSFASGTAVLELRDVAKADSGDYVCKASNV AGSDTTKSKVTIKDKPAVAPATKKAAVDGRLFFVSEPQSIRVVEKTTATF IAKVGGDPIPNVKWTKGKWRQLNQGGRVFIHQKGDEAKLEIRDTTKTDSG LYRCVAFNEHGEIESNVNLQVDERKKQEKIEGDLRAMLKKTPILKKGAGE EEEIDIMELLKNVDPKEYEKYARMYGITDFRGLLQAFELLKQSQEEETHR LEIxxxxxxxxxxxxxxxxxSFIQQRLSQTEPVTLIKDIENQTVLKDNDA VFEIDIKINYPEIKLSWYKGTEKLEPSDKFEISIDGDRHTLRVKNCQLKD QGNYRLVCGPHIASAKLTVIEPAWERHLQDVTLKEGQTCTMTCQFSVPNV KSEWFRNGRILKPQGRHKTEVEHKVHKLTIADVRAEDQGQYTCKYEDLET SAELRIEAEPIQFTKRIQNIVVSEHQSATFECEVSFDDAIVTWYKGPTEL TESQKYNFRNDGRCHYMTIHNVTPDDEGVYSVIARLEPRGEARSTAELYL TTKEIKLELKPPDIPDSxxxxxxxxxxxxxxxxxxxxxxxxxPLLLPTxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxPAK APEIIDVSSKAEEVKIMTITRKKEVQKxxxxxxxxxxxxxxxxxxFIESx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxPVIEKIEKTSRRMEEEKVQVTKVPEVSKKIVPQKPxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xSFAVPQRVEVTRHEVSAxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx EYEVMEEPxxxxxxxxxxxxxxxxxxxxxxxxxxxEKKIVLKPKIPAKxx xxxxxxxxxxxxxxxxxxKVPAPVPxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx EEKERAYTLEEEAVSVQRExxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxITEPEKPIxxxxxxxxxxxxxxxxxxxxxLKxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxSITKREKEQVxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxEVAxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxKxxxxxxxxxxxxxxxxxxxxxxxxxxxxVxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxKREPVPVPVALPQEEEVLxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxKVVIPxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxExxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxEKVxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxRTVLEEKVSVAFRQEVVVKERLELEVVEAE VEEIPxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxEKPKAPPKGPEISEKIIPPKKPPxxxxxxxxxxxxxxxVP xKxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxAxxxxxxxxxx xxxxxxxxxxxxxxxxxxxPERAESPPPEVYxxxxxxxxxxxxxxxxxxP VPVxxxxxxxxxxxxxxxxxxxxxxxxxxPVIxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxVELTPL KVPGGEKKVRKLLPERKPEPKEEVVLxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxGKKAEAKAPKEEAAKPKGPI KGVPKKTPSPIEAERRKLRPGSGGEKPPDEAPFTYQLKAVPLKFVKEIKD IILTESEFVGSSAIFECLVSPSTAITTWMKDGSNIRESPKHRFIADGKDR KLHIIDVQLSDAGEYTCVLRLGNKEKTSTAKLVVEELPVRFVKTLEEEVT VVKGQPLYLSCELNKERDVVWRKDGKIVVEKPGRIVPGVIGLMRALTIND ADDTDAGTYTVTVENANNLECSSCVKVVEVIRDWLVKPIRDQHVKPKGTA IFACDIAKDTPNIKWFKGYDEIPAEPNDKTEILRDGNHLYLKIKNAMPED IAEYAVEIEGKRYPAKLTLGEREVELLKPIEDVTIYEKESASFDAEISEA DIPGQWKLKGELLRPSPTCEIKAEGGKRFLTLRKVKLDQAGEVLYQALNA ITTAILTVKEIELDFAVPLKDVTVPERRQARFECVLTREANVIWSKGPDI IKSSDKFDIIADGKKHILVINDSQFDDEGVYTAEVEGKKTSARLFVTGIR LKFMSPLEDQTVKEGETATFVCELSHEKMHVVWFKNDAKLHTSRTVLISS EGKTHKLEMKEVTLDDISQIKAQVKELSSTAQLKVLEADPYFTVKLHDKT AVEKDEITLKCEVSKDVPVKWFKDGEEIVPSPKYSIKADGLRRILKIKKA DLKDKGEYVCDCGTDKTKANVTVEARLIKVEKPLYGVEVFVGETAHFEIE LSEPDVHGQWKLKGQPLTASPDCEIIEDGKKHILILHNCQLGMTGEVSFQ AANAKSAANLKVKELPLIFITPLSDVKVFEKDEAKFECEVSREPKTFRWL KGTQEITGDDRFELIKDGTKHSMVIKSAAFEDEAKYMFEAEDKHTSGKLI IEGIRLKFLTPLKDVTAKEKESAVFTVELSHDNIRVKWFKNDQRLHTTRS VSMQDEGKTHSITFKDLSIDDTSQIRVEAMGMSSEAKLTVLEGDPYFTGK LQDYTGVEKDEVILQCEISKADAPVKWFKDGKEIKPSKNAVIKADGKKRM LILKKALKSDIGQYTCDCGTDKTSGKLDIEDREIKLVRPLHSVEVMETET ARFETEISEDDIHANWKLKGEALLQTPDCEIKEEGKIHSLVLHNCRLDQT GGVDFQAANVKSSAHLRVKPRVIGLLRPLKDVTVTAGETATFDCELSYED IPVEWYLKGKKLEPSDKVVPRSEGKVHTLTLRDVKLEDAGEVQLTAKDFK THANLFVKEPPVEFTKPLEDQTVEEGATAVLECEVSRENAKVKWFKNGTE ILKSKKYEIVADGRVRKLVIHDCTPEDIKTYTCDAKDFKTSCNLNVVPPH VEFLRPLTDLQVREKEMARFECELSRENAKVKWFKDGAEIKKGKKYDIIS KGAVRILVINKCLLDDEAEYSCEVRTARTSGMLTVLEEEAVFTKNLANIE VSETDTIKLVCEVSKPGAEVIWYKGxxxxxxxxxxxxxxxxxxxxxVIQN AHLEDAGNYNCRLPSSRTDGKVKVHELAAEFISKPQNLEILEGEKAEFVC SISKESFPVQWKRDDKTLESGDKYDVIADGKKRVLVVKDATLQDMGTYVV MVGAARAAAHLTVIEKLRIVVPLKDTRVKEQQEVVFNCEVNTEGAKAKWF RNEEAIFDSSKYIILQKDLVYTLRIRDAHLDDQANYNVSLTNHRGENVKS AANLIVEEEDLRIVEPLKDIETMEKKSVTFWCKVNRLNVTLKWTKNGEEV PFDNRVSYRVDKYKHMLTIKDCGFPDEGEYIVTAGQDKSVAELLIIEAPT EFVEHLEDQTVTEFDDAVFSCQLSREKANVKWYRNGREIKEGKKYKFEKD GSIHRLIIKDCRLDDECEYACGVEDRKSRARLFVEEIPVEIIRPPQDILE APGADVVFLAELNKDKVEVQWLRNNMVVVQGDKHQMMSEGKIHRLQICDI KPRDQGEYRFIAKDKEARAKLELAAAPKIKTADQDLVVDVGKPLTMVVPY DAYPKAEAEWFKENEPLSTKTIDTTAEQTSFRILEAKKGDKGRYKIVLQN KHGKAEGFINLKVIDVPGPVRNLEVTETFDGEVSLAWEEPLTDGGSKIIG YVVERRDIKRKTWVLATDRAESCEFTVTGLQKGGVEYLFRVSARNRVGTG EPVETDNxxEARSKYDVPGPPLNVTITDVNRFGVSLTWEPPEYDGGAEIT NYVIELRDKTSIRWDTAMTVRAEDLSATVTDVVEGQEYSFRVRAQNRIGV GKPSAATPFVKVADPIERPSPPVNLTSSDQTQSSVQLKWEPPLKDGGSPI LGYIIERCEEGKDNWIRCNMKLVPELTYKVTGLEKGNKYLYRVSAENKAG VSDPSEILGPLTADDAFVEPTMDLSAFKDGLEVIVPNPITILVPSTGYPR PTATWCFGDKVLETGDRVKMKTLSAYAELVISPSERSDKGIYTLKLENRV KTISGEIDVNVIARPSAPKELKFGDITKDSVHLTWEPPDDDGGSPLTGYV VEKREVSRKTWTKVMDFVTDLEFTVPDLVQGKEYLFKVCARNKCGPGEPA YVDEPVNMSTPATVPDPPENVKWRDRTANSIFLTWDPPKNDGGSRIKGYI VERCPRGSDKWVACGEPVAETKMEVTGLEEGKWYAYRVKALNRQGASKPS RPTEEIQAVDTQEAPEIFLDVKLLAGLTVKAGTKIELPATVTGKPEPKIT WTKADMILKQDKRITIENVPKKSTVTIVDSKRSDTGTYIIEAVNVCGRAT AVVEVNVLDKPGPPAAFDITDVTNESCLLTWNPPRDDGGSKITNYVVERR ATDSEVWHKLSSTVKDTNFKATKLIPNKEYIFRVAAENMYGVGEPVQASP ITAKYQFDPPGPPTRLEPSDITKDAVTLTWCEPDDDGGSPITGYWVERLD PDTDKWVRCNKMPVKDTTYRVKGLTNKKKYRFRVLAENLAGPGKPSKSTE PILIKDPIDPPWPPGKPTVKDVGKTSVRLNWTKPEHDGGAKIESYVIEML KTGTDEWVRVAEGVPTTQHLLPGLMEGQEYSFRVRAVNKAGExxxxxxxx xVLCREKLYPPSPPRWLEVINITKNTADLKWTVPEKDGGSPITNYIVEKR DVRRKGWQTVDTTVKDTKCTVTPLTEGSLYVFRVAAENAIGQSDYTEIED SVLAKDTFTTPGPPYALAVVDVTKRHVDLKWEPPKNDGGRPIQRYVIEKK ERLGTRWVKAGKTAGPDCNFRVTDVIEGTEVQFQVRAENEAGVGHPSEPx xxxxxxxxxxxxxxxLDLHVTDAGRKHIAIAWKPPEKNGGSPIIGYHVEM CPVGTEKWMRVNSRPIKDLKFKVEEGVVPDKEYVLRVRAVNAIGVSEPSE ISENVVAKDPDCKPTIDLETHDIIVIEGEKLSIPVPFRAVPVPTVSWHKD GKEVKASDRLTMKNDHISAHLEVPKSVRADAGIYTITLENKLGSATASIN VKVIGLPGPCKDIKASDITKSSCKLTWEPPEFDGGTPILHYVLERREAGR RTYIPVMSGENKLSWTVKDLIPNGEYFFRVKAVNKVGGGEYIELKNPVIA QDPKQPPDPPVDVEVHNPTAEAMTITWKPPLYDGGSKIMGYIIEKIAKGE ERWKRCNEHLVPILTYTAKGLEEGKEYQFRVRAENAAGISEPSRATPPTK AVDPIDAPKVILRTSLEVKRGDEIALDASISGSPYPTITWIKDENVIVPE EIKKRAAPLVRRRKGEVQEEEPFVLPLTQRLSIDNSKKGESQLRVRDSLR PDHGLYMIKVENDHGIAKAPCTVSVLDTPGPPINFVFEDIRKTSVLCKWE PPLDDGGSEIINYTLEKKDKTKPDSEWIVVTSTLRHCKYSVTKLIEGKEY LFRVRAENRFGPGPPCVSKPLVAKDPFGPPDAPDKPIVEDVTSNSMLVKW NEPKDNGSPILGYWLEKREVNSTHWSRVNKSLLNALKANVDGLLEGLTYV FRVCAENAAGPGKFSPPSDPKTAHDPISxxxxxxxxVTDTSSTTIELEWE PPAFNGGGEIVGYFVDKQLVGTNEWSRCTEKMIKVRQYTVKEIREGADYK LRVSAVNAAGEGPPGETQPVTVAEPQEPPAVELDVSVKGGIQIMAGKTLR IPAVVTGRPVPTKVWTKEEGELDKDRVVIDNVGTKSELIIKDALRKDHGR YVITATNSCGSKFAAARVEVFDVPGPVLDLKPVVTNRKMCLLNWSDPEDD GGSEITGFIIERKDAKMHTWRQPIETERSKCDITGLLEGQEYKFRVIAKN KFGCGPPVEIGPILAVDPLGPPTSPERLTYTERTKSTITLDWKEPRSNGG SPIQGYIIEKRRHDKPDFERVNKRLCPTTSFLVENLDEHQMYEFRVKAVN EIGESEPSLPLNVVIQDDEVPPTIKLRLSVRGDTIKVKAGEPVHIPADVT GLPMPKIEWSKNETVIEKPTDALQITKEEVSRSEAKTELSIPKAVREDKG TYTVTASNRLGSVFRNVHVEVYDRPSPPRNLAVTDIKAESCYLTWDAPLD NGGSEITHYVIDKRDASRKKAEWEEVTNTAVEKRYGIWKLIPNGQYEFRV RAVNKYGISDECKSDKVVIQDPYRLPGPPGKPKVLARTKGSMLVSWTPPL DNGGSPITGYWLEKREEGSPYWSRVSRAPITKVGLKGVEFNVPRLLEGVK YQFRAMAINAAGIGPPSEPSDPEVAGDPxxxxxxxxxxxxxDKTKSSISL GWKPPAKDGGSPIKGYIVEMQEEGTTDWKRVNEPDKLITTCECVVPNLKE LRKYRFRVKAVNEAGESEPSDTTGEIPATDIQEEPEVFIDIGAQDCLVCK AGSQIRIPAVIKGRPTPKSSWEFDGKAKKAMKDGVHDIPEDAQLETAENS SVIIIPECKRSHTGKYSITAKNKAGQKTANCRVKVMDVPGPPKDLKVSDI TRGSCRLSWKMPDDDGGDRIKGYVIEKRTIDGKAWTKVNPDCGSTTFVVP DLLSEQQYFFRVRAENRFGIGPPVETIQRTTARDPIYPPDPPIKLKIGLI TKNTVHLSWKPPKNDGGSPVTHYIVECLAWDPTGTKKEAWRQCNKRDVEE LQFTVEDLVEGGEYEFRVKAVNAAGVSKPSATVGPCDCQRPDMPPSIDLK EFMEVEEGTNVNIVAKIKGVPFPTLTWFKAPPKKPDNKEPVLYDTHVNKL VVDDTCTLVIPQSRRSDTGLYTITAVNNLGTASKEMRLNVLGRPGPPVGP IKFESVSADQMTLSWFPPKDDGGSKITNYVIEKREANRKTWVHVSSEPKE CTYTIPKLLEGHEYVFRIMAQNKYGIGEPLDSEPETARNLFSVPGAPDKP TVSSVTRNSMTVNWEEPEYDGGSPVTGYWLEMKDTTSKRWKRVNRDPIKA MTLGVSYKVTGLIEGSDYQFRVYAINAAGVGPASLPSDPATARDPIAPPG PPFPKVTDWTKSSADLEWSPPLKDGGSKVTGYIVEYKEEGKEEWEKxKDK EVRGTKLVVTGLKEGAFYKFRVSAVNIAGIGEPGEVTDVIEMKDRLVSPD LQLDASVRDRIVVHAGGVIRIIAYVSGKPPPTVTWNMNERTLPQEATIET TAISSSMVIKNCQRSHQGVYSLLAKNEAGERKKTIIVDVLDVPGPVGTPF LAHNLTNESCKLTWFSPEDDGGSPITNYVIEKRESDRRAWTPVTYTVTRQ NATVQGLIQGKAYFFRIAAENSIGMGPFVETSEALVIREPITVPERPEDL EVKEVTKNTVTLTWNPPKYDGGSEIINYVLESRLIGTEKFHKVTNDNLLS RKYTVKGLKEGDTYEYRVSAVNIVGQGKPSFCTKPITCKDELAPPTLHLD FRDKLTIRVGEAFALTGRYSGKPKPKVSWFKDEADVLEDDRTHIKTTPAT LALEKIKAKRSDSGKYCVVVENSTGSRKGFCQVNVVDRPGPPVGPVSFDE VTKDYMVISWKPPLDDGGSKITNYIIEKKEVGKDVWMPVTSASAKTTCKV SKLLEGKDYIFRIHAENLYGISDPLVSDSMKAKDRFRVPDAPDQPIVTEV TKDSALVTWNKPHDGGKPITNYILEKRETMSKRWARVTKDPIHPYTKFRV PDLLEGCQYEFRVSAENEIGIGDPSPPSKPVFAKDPIAxxxxxxxPEAID TTCNSVDLTWQPPRHDGGSKILGYIVEYQKVGDEEWRRANHTPESCPETK YKVTGLRDGQTYKFRVLAVNAAGESDPAHVPEPVLVKDRLEPPELILDAN MAREQHIKVGDTLRLSAIIKGVPFPKVTWKKEDRDAPTKARIDVTPVGSK LEIRNAAHEDGGIYSLTVENPAGSKTVSVKVLVLDKPGPPRDLEVSEIRK DSCYLTWKEPLDDGGSVITNYVVERRDVASAQWSPLSATSKKKSHFAKHL NEGNQYLFRVAAENQYGRGPFVETPKPIKALDPLHPPGPPKDLHHVDVDK TEVSLVWNKPDRDGGSPITGYLVEYQEEGTQDWIKFKTVTNLECVVTGLQ QGKTYRFRVKAENIVGLGLPDTTIPIECQEKLVPPSVELDVKLIEGLVVK AGTTVRFPAIIRGVPVPTAKWTTDGSEIKTDEHYTVETDNFSSVLTIKNC LRRDTGEYQITVSNAAGSKTVAVHxxxLDVPGPPTGPINILDVTPEHMTI SWQPPKDDGGSPVINYIVEKQDTRKDTWGVVSSGSSKTKLKIPHLQKGCE YVFRVRAENKIGVGPPLDSTPTVAKHKFSPPSPPGKPVVTDITENAATVS WTLPKSDGGSPITGYYMERREVTGKWVRVNKTPIADLKFRVTGLYEGNTY EFRVFAENLAGLSKPSPSSDPIKACRPIKPPGPPINPKLKDKSRETADLV WTKPLSDGGSPILGYVVECQKPGTAQWNRINKDELIRQCAFRVPGLIEGN EYRFRIKAANIVGEGEPRELAESVIAKDILHPPEVELDVTCRDVITVRVG QTIRILARVKGRPEPDITWTKEGKVLVREKRVDLIQDLPRVELQIKEAVR ADHGKYIISAKNSSGHAQGSAIVNVLDRPGPCQNLKVTNVTKENCTISWE NPLDNGGSEITNFIVEYRKPNQKGWSIVASDVTKRLIKANLLANNEYYFR VCAENKVGVGPTIETKTPILAINPIDRPGEPENLHIADKGKTFVYLKWRR PDYDGGSPNLSYHVERRLKGSDDWERVHKGSIKETHYMVDRCVENQIYEF RVQTKNEGGESDWVKTEEVVVKEDLQKPVLDLKLSGVLTVKAGDTIRLEA GVRGKPFPEVAWTKDKDATDLTRSPRVKIDTRADSSKFSLTKAKRSDGGK YVVTATNTAGSFVAYATVNVLDKPGPVRNLKIVDVSSDRCTVCWDPPEDD GGCEIQNYILEKCETKRMVWSTYSATVLTPGTTVTRLIEGNEYIFRVRAE NKIGTGPPTESKPVIAKTKYDKPGRPDPPEVTKVSKEEMTVVWNPPEYDG GKSITGYFLEKKEKHSTRWVPVNKSAIPERRMKVQNLLPDHEYQFRVKAE NEIGIGEPSLPSRPVVAKDPIEPPGPPTNFRVVDTTKHSITLGWGKPVYD GGAPIIGYVVEMRPKIADASPDEGWKRCNAAAQLVRKEFTVTSLDENQEY EFRVCAQNQVGIGRPAELKEAIKPKEILEPPEIDLDASMRKLVIVRAGCP IRLFAIVRGRPAPKVTWRKVGIDNVVRKGQVDLVDTMAFLVIPNSTRDDS GKYSLTLVNPAGEKAVFVNVRVLDTPGPVSDLKVSDVTKTSCHVSWAPPE NDGGSQVTHYIVEKREADRKTWSTVTPEVKKTSFHVTNLVPGNEYYFRVT AVNEYGPGVPTDVPKPVLASDPLSEPDPPRKLEVTEMTKNSATLAWLPPL RDGGAKIDGYITSYREEEQPADRWTEYSVVKDLSLVVTGLKEGKKYKFRV AARNAVGVSLPREAEGVYEAKEQLLPPKILMPEQITIKAGKKLRIEAHVY GKPHPTCKWKKGEDEVVTSSHLAVHKADSSSILIIKDVTRKDSGYYSLTA ENSSGTDTQKIKVVVMDAPGPPQPPFDISDIDADACSLSWHIPLEDGGSN ITNYIVEKCDVSRGDWVTALASVTKTSCRVGKLIPGQEYIFRVRAENRFG ISEPLTSPKMVAQFPFGVPSEPKNARVTKVNKDCIFVAWDRPDSDGGSPI IGYLIERKERNSLLWVKANDTLVRSTEYPCAGLVEGLEYSFRIYALNKAG SSPPSKPTEYVTARMPVDPPGKPEVIDVTKSTVSLIWARPKHDGGSKIIG YFVEACKLPGDKWVRCNTAPHQIPQEEYTATGLEEKAQYQFRAIARTAVN ISPPSEPSDPVTILAENVPPRIDLSVAMKSLLTVKAGTNVCLDATVFGKP MPTVSWKKDGTLLKPAEGIKMAMQRNLCTLELFSVNRKDSGDYTITAENS SGSKSATIKLKVLDKPGPPASVKINKMYSDRAMLSWEPPLEDGGSEITNY IVDKRETSRPNWAQVSATVPITSCSVEKLIEGHEYQFRICAENKYGVGDP VFTEPAIAKNPYDPPGRCDPPVISNITKDHMTVSWKPPADDGGSPITGYL LEKRETQAVNWTKVNRKPIIERTLKATGLQEGTEYEFRVTAINKAGPGKx xxxxxxxxxxxxxxxxxxxxxxKVYDTTRSSVSLSWGKPAYDGGSPIIGY LVEVKRADSDNWVRCNLPQNLQKTRFEVTGLMEDTQYQFRVYAVNKIGYS DPSDVPDKHYPKDILIPPEGELDADLRKTLILRAGVTMRLYVPVKGRPPP KITWSKPNVNLRDRIGLDIKSTDFDTFLRCENVNKYDAGKYILTLENSCG KKEYTIVVKVLDTPGPPVNVTVKEISKDSAYVTWEPPIIDGGSPIINYVV QKRDAERKSWSTVTTECSKTSFRVANLEEGKSYFFRVFAENEYGIGDPGE TRDAVKASQTPGPVVDLKVRSVSKSSCSIGWKKPHSDGGSRIIGYVVDFL TEENKWQRVMKSLSLQYSAKDLTEGKEYTFRVSAENENGEGTPSEITVVA RDDVVAPDLDLKGLPDLCYLAKENSNFRLKIPIKGKPAPSVSWKKGEDPL ATDTRVSVESSAVNTTLIVYDCQKSDAGKYTITLKNVAGTKEGTISIKVV GKPGIPTGPIKFDEVTAEAMTLKWAPPKDDGGSEITNYILEKRDSVNNKW VTCASAVQKTTFRVTRLHEGMEYTFRVSAENKYGVGEGLKSEPIVARHPF DVPDAPPPPNIVDVRHDSVSLTWTDPKKTGGSPITGYHLEFKERNSLLWK RANKTPIRMRDFKVTGLTEGLEYEFRVMAINLAGVGKPSLPSEPVVALDP IDPPGKPEVINITRNSVTLIWTEPKYDGGHKLTGYIVEKRDLPSKSWMKA NHVNVPECAFTVTDLVEGGKYEFRIRAKNTAGAISAPSESTETIICKDEY EAPTIVLDPTIKDGLxxxxxDTIVLNAISILGKPLPKSSWSKAGKDIRPS DITQITSTPTSSMLTIKYATRKDAGEYTITATNPFGTKVEHVKVTVLDVP GPPGPVEISNVSAEKATLTWTPPLEDGGSPIKSYILEKRETSRLLWTVVS EDIQSCRHVATKLIQGNEYIFRVSAVNHYGKGEPVQSEPVKMVDRFGPPx xxxxxxxxxxxxxxATVSWKRPVDDGGSEITGYHVERREKKSLRWVRAIK TPVSDLRCKVTGLQEGSTYEFRVSAENRAGIGPPSEASDSVLMKDAAYPP GPPSNPHVTDTTKKSASLAWGKPHYDGGLEITGYVVEHQKVGDEAWIKDT TGTALRITQFVVPDLQTKEKYNFRISAINDAGVGEPAVIPDVEIVEREMA PDFELDAELRRTLVVRAGLSIRIFVPIKGRPAPEVTWTKDNINLKNRANI ENTESFTLLIIPECNRYDTGKFVMTIENPAGKKSGFVNVRVLDTPGPVLN LRPTDITKDSVTLHWDLPLIDGGSRITNYIVEKREATRKSYSTATTKCHK CTYKVTGLSEGCEYFFRVMAENEYGIGEPTETTEPVKASEAPSPPDSLNI MDITKSTVSLAWPKPKHDGGSKITGYVIEAQRKGSDQWTHITTVKGLECV VRNLTEGEEYTFQVMAVNSAGRSAPRESRPVIVKEQTMLPELDLRGIYQK LVIAKAGDNIKVEIPVLGRPKPTVTWKKGDQILKQTQRVNFETTATSTIL NINECVRSDSGPYPLTARNIVGEVGDVITIQVHDIPGPPTGPIKFDEVSS DFVTFSWDPPENDGGVPISNYVVEMRQTDSTTWVELATTVIRTTYKATRL TTGLEYQFRVKAQNRYGVGPGITSACIVANYPFKVPGPPGTPQVTAVTKD SMTISWHEPLSDGGSPILGYHVERKERNGILWQTVSKALVPGNIFKSSGL TDGIAYEFRVIAENMAGKSKxxxxxxxxxxxxxxxxxxxxVPLNITRHTV TLKWAKPEYTGGFKITSYIVEKRDLPNGRWLKANFSNILENEFTVSGLTE DAAYEFRVIAKNAAGAISPPSEPSDAITCRDDVEAPKIKVDVKFKDTVIL KAGEAFRLEADVSGRPPPTMEWSKDGKELEGTAKLEIKIADFSTNLVNKD STRRDSGAYTLTATNPGGFAKHIFNVKVLDRPGPPEGPLAVTEVTSEKCV LSWFPPLDDGGAKIDHYIVQKRETSRLAWTNVASEVQVTKLKVTKLLKGN EYIFRVMAVNKYGVGEPLESEPxxxxxxxxxxxxxxxxxxxxITKDSMVV CWGHPDSDGGSEIINYIVERRDKAGQRWIKCNKKTLTDLRYKVSGLTEGH EYEFRIMAENAAGISAPSPTSPFYKACDTVFKPGPPGNPRVLDTSRSSIS IAWNKPIYDGGSEITGYMVEIALPEEDEWQIVTPPAGLKATSYTITGLTE NQEYKIRIYAMNSEGLGEPALVPGTPKAEDRMLPPEIELDADLRKVVTIR ACCTLRLFVPIKGRPAPEVKWARDHGESLDKASIESTSSYTLLIVGNVNR FDSGKYILTVENSSGSKSAFVNVRVLDTPGPPQDLKVKEVTKTSVTLTWD PPLLDGGSKIKNYIVEKRESTRKAYSTVATNCHKTSWKVDQLQEGCSYYF RVLAENEYGIGLPAETAESVKASERPLPPGKITLMDVTRNSVSLSWEKPE HDGGSRILGYIVEMQTKGSDKWATCATVKVTEATITGLIQGEEYSFRVSA QNEKGISDPRQLSVPVIAKDLVIPPAFKLLFNTFTVLAGEDLKVDVPFIG RPTPAVTWHKDNVPLKQTTRVNAESTENNSLLTIKDACREDVGHYVVKLT NSAGEAIETLNVIVLDKPGPPTGPVKMDEVTADSITLSWGPPKYDGGSSI NNYIVEKRDTSTTTWQIVSATVARTTIKACRLKTGCEYQFRIAAENRYGK STYLNSEPTVAQYPFKVPGPPGTPVVTLSSRDSMEVQWNEPISDGGSRVI GYHLERKERNSILWVKLNKTPIPQTKFKTTGLEEGVEYEFRVSAENIVGI GKPSKVSECYVARDPCDPPGRPEAIIVTRNSVTLQWKKPTYDGGSKITGY IVEKKELPEGRWMKASFTNIIDTHFEVTGLVEDHRYEFRVIARNAAGVFS EPSESTGAITARDEVDPPRISMDPKYKDTIVVHAGESFKVDADIYGKPIP TIQWIKGDQELSNTARLEIKSTDFATSLSVKDAVRVDSGNYILKAKNVAG ERSVTVNVKVLDRPGPPEGPVVISGVTAEKCTLAWKPPLQDGGSDIINYI VERRETSRLVWTVVDANVQTLSCKVTKLLEGNEYTFRIMAVNKYGVGEPL ESEPVVAKNPFVVPDAPKAPEVTTVTKDSMIVVWERPASDGGSEILGYVL EKRDKEGIRWTRCHKRLIGELRLRVTGLIENHDYEFRVSAENAAGLSEPS PPSAYQKACDPIYKPGPPNNPKVIDITRSSVFLSWSKPIYDGGCEIQGYI VEKCDVSVGEWTMCTPPTGINKTNIEVEKLLEKHEYNFRICAINKAGVGE HADVPGPIIVEEKLEAPDIDLDLELRKIINIRAGGSLRLFVPIKGRPTPE VKWGKVDGEIRDAAIIDVTSSFTSLVLDNVNRYDSGKYTLTLENSSGTKS AFVTVRVLDTPSPPVNLKVTEITKDSVSITWEPPLLDGGSKIKNYIVEKR EATRKSYAAVVTNCHKNSWKIDQLQEGCSYYFRVTAENEYGIGLPAQTAD PIKVAEVPQPPGKITVDDVTRNSVSLSWTKPEHDGGSKIIQYIVEMQAKH SEKWSECARVKSLQAVITNLTQGEEYLFRVVAVNEKGRSDPRSLAVPIVA KDLVIEPDVKPAFSSYSVQVGQDLKIEVPISGRPKPTITWTKDGLPLKQT TRINVTDSLDLTTLSIKETHKDDGGQYGITVANVVGQKTASIEIVTLDKP DPPKGPVKFDDVSAESITLSWNPPLYTGGCQITNYIVQKRDTTTTVWDVV SATVARTTLKVTKLKTGTEYQFRIFAENRYGQSFALESDPIVAQYPYKEP GPPGTPFATAISKDSMVIQWHEPVNNGGSPVIGYHLERKERNSILWTKVN KTIIHDTQFKAQNLEEGIEYEFRVYAENIVGVGKASKNSECYVARDPCDP PGTPEPIMVKRNEITLQWTKPVYDGGSMITGYIVEKRDLPDGRWMKASFT NVIETQFTVSGLTEDQRYEFRVIAKNAAGAISKPSDSTGPITAKDEVELP RISMDPKFRDTIVVNAGETFRLEADVHGKPLPTIEWLRGDKEIEESARCE IKNTDFKALLIVKDAIRIDGGQYILRASNVAGSKSFPVNVKVLDRPGPPE GPVQVTGVTSEKCSLTWSPPLQDGGSDISHYVVEKRETSRLAWTVVASEV VTNSLKVTKLLEGNEYVFRIMAVNKYGVGEPLESAPVLMKNPFVLPGPPK SLEVTNIAKDSMTVCWNRPDSDGGSEIIGYIVEKRDRSGIRWIKCNKRRI TDLRLRVTGLTEDHEYEFRVSAENAAGVGEPSPATVYYKACDPVFKPGPP TNAHIVDTTKNSITLAWGKPIYDGGSEILGYVVEICKADEEEWQIVTPQT GLRVTRFEISKLTEHQEYKIRVCALNKVGLGEATSVPGTVKPEDKLEAPE LDLDSELRKGIVVRAGGSARIHIPFKGRPTPEITWSREEGEFTDKVQIEK GVNYTQLSIDNCDRNDAGKYILKLENSSGSKSAFVTVKVLDTPGPPQNLA VKEVRKDSAFLVWEPPIIDGGAKVKNYVIDKRESTRKAYANVSSKCSKTS FKVENLTEGAIYYFRVMAENEFGVGVPVETVDAVKAAEPPSPPGKVTLTD VSQTSASLMWEKPEHDGGSRVLGYVVEMQPKGTEKWSIVAESKVCNAVVT GLSSGQEYQFRVKAYNEKGKSDPRVLGVPVIAKDLTIQPSLKLPFNTYSI QAGEDLKIEIPVIGRPRPNISWVKDGEPLKQTTRVNVEETATSTVLHIKE GNKDDFGKYTVTATNSAGTATENLSVIVLEKPGPPVGPVRFDEVSADFVV ISWEPPAYTGGCQISNYIVEKRDTTTTTWHMVSATVARTTIKITKLKTGT EYQFRIFAENRYGKSAPLDSKAVIVQYPFKEPGPPGTPFVTSISKDQMLV QWHEPVNDGGTKIIGYHLEQKEKNSILWVKLNKTPIQDTKFKTTGLDEGL EYEFKVSAENIVGIGKPSKVSECFVARDPCDPPGRPEAIVITRNNVTLKW KKPAYDGGSKITGYIVEKKDLPDGRWMKASFTNVLETEFTVSGLVEDQRY EFRVIARNAAGNFSEPSDSSGAITARDEIDAPNASLDPKYKDVIVVHAGE TFVLEADIRGKPIPDVVWSKDGKELEETAARMEIKSTIQKTTLVVKDCIR TDGGQYILKLSNVGGTKSIPITVKVLDRPGPPEGPLKVTGVTAEKCYLAW NPPLQDGGANISHYIIEKRETSRLSWTQVSTEVQALNYKVTKLLPGNEYI FRVMAVNKYGIGEPLESGPVTACNPYKPPGPPSTPEVSAITKDSMVVTWA RPVDDGGTEIEGYILEKRDKEGVRWTKCNKKTLTDLRLRVTGLTEGHSYE FRVAAENAAGVGEPSEPSVFYRACDALYPPGPPSNPKVTDTSRSSVSLAW SKPIYDGGAPVKGYVVEVKEAAADEWTTCTPPTGLQGKQFTVTKLKENTE YNFRICAINSEGVGEPATLPGSVVAQERIEPPEIELDADLRKVVVLRASA TLRLFVTIKGRPEPEVKWEKAEGILTDRAQIEVTSSFTMLVIDNVTRFDS GRYNLTLENNSGSKTAFVNVRVLDSPSAPVNLTIREVKKDSVTLSWEPPL IDGGAKITNYIVEKRETTRKAYATITNNCTKTTFRIENLQEGCSYYFRVL ASNEYGIGLPAETTEPVKVSEPPLPPGRVTLVDVTRNTATIKWEKPESDG GSKITGYVVEMQTKGSEKWSTCTQVKTLEATISGLTAGEEYVFRVAAVNE KGRSDPRQLGVPVIARDIEIKPSVELPFHTFNVKAREQLKIDVPFKGRPQ ATVNWRKDGQTLKETTRVNVSSSKTVTSLSIKEASKEDVGTYELCVSNSA GSITVPITIIVLDRPGPPGPIRIDEVSCDSITISWNPPEYDGGCQISNYI VEKKETTSTTWHIVSQAVARTSIKIVRLTTGSEYQFRVCAENRYGKSSYS ESSAVVAEYPFSxxxxxxxxxxVHATKSTMLVTWQVPVNDGGSRVIGYHL EYKERSSILWSKANKILIADTQMKVSGLDEGLMYEYRVYAENIAGIGKCS KSCEPVPARDPCDPPGQPEVTNITRKSVSLKWSKPHYDGGAKITGYIVER RELPDGRWLKCNYTNIQETYFEVTELTEDQRYEFRVFARNAADSVSEPSE STGPIIVKDDVEPPRVMMDVKFRDVIVVKAGEVLKINADIAGRPLPVISW AKDGIEIEERARTEIISTDNHTLLTVKDCIRRDTGQYVLTLKNVAGTRSV AVNCKVLDKPGPPAGPLEINGLTAEKCSLSWGRPQEDGGADIDYYIVEKR ETSHLAWTICEGELQMTSCKVTKLLKGNEYIFRVTGVNKYGVGEPLESVA IKALDPFTVPSPPTSLEITSVTKESMTLCWSRPESDGGSEISGYIIERRE KNSLRWVRVNKKPVYDLRVKSTGLREGCEYEYRVYAENAAGLSLPSETSP LIRAEDPVFLPSPPSKPKIVDSGKTTITIAWVKPLFDGGAPITGYTVEYK KSDDTDWKTSIQSLRGTEYTISGLTTGAEYVFRVKSVNKVGASDPSDSSD PQIAKEREEEPLFDIDSEMRKTLIVKAGASFTMTVPFRGRPVPNVLWSKP DTDLRTRAYVDTTDSRTSLTIENANRNDSGKYTLTIQNVLSAASLTLVVK VLDTPGPPTNITVQDVTKESAVLSWDVPENDGGAPVKNYHIEKREASKKA WVSVTNNCNRLSYKVTNLQEGAIYYFRVSGENEFGVGIPAETKEGVKITE KPSPPEKLGVTSISKDSVSLTWLKPEHDGGSRIVHYVVEALEKGQKNWVK CAVAKSTHHVVSGLRENSEYFFRVFAENQAGLSDPRELLLPVLIKEQLEP PEIDMKNFPSHTVYVRAGSNLKVDIPISGKPLPKVTLSRDGVPLKATMRF NTEITAENLTINLKESVTADAGRYEITAANSSGTTKAFINIVVLDRPGPP TGPVVISDITEESVTLKWEPPKYDGGSQVTNYILLKRETSTAVWTEVSAT VARTMMKVMKLTTGEEYQFRIKAENRFGISDHIDSACVTVKLPYTTPGPP STPWVTNVTRESITVGWHEPVSNGGSAVVGYHLEMKDRNSILWQKANKLV IRTTHFKVTTISAGLIYEFRVYAENAAGVGKPSHPSEPVLAIDACEPPRN VRITDISKNSVSLSWQQPAFDGGSKITGYIVERRDLPDGRWTKASFTNVT ETQFIISGLTQNSQYEFRVFARNAVGSISNPSEVVGPITCIDSYGGPVID LPLEYTEVVKYRAGTSVKLRAGISGKPAPTIEWYKDDKELQTNALVCVEN TTDLASILIKDADRLNSGCYELKLRNAMGSASATIRVQILDKPGPPGGPI EFKTVTAEKITLLWRPPADDGGAKITHYIVEKRETSRVVWSMVSEHLEEC IITTTKIIKGNEYIFRVRAVNKYGIGEPLESDSVVAKNAFVTPGPxxxxx xxxxxxNSMTVVWSRPIADGGSDISGYFLEKRDKKSLGWFKVLKETIRDT RQKVTGLTENSDYQYRVCAVNAAGQGPFSEPSEFYKAADPIDPPGPPAKI RIADSTKSSITLGWSKPVYDGGSAVTGYVVEIRQGEEEEWTTVSTKGEVR TTEYVVSNLKPGVNYYFRVSAVNCAGQGEPIEMNEPVQAKDILEAPEIDL DVALRTSVIAKAGEDVQVLIPFKGRPPPTVTWRKDEKNLGSDARYSIENT DSSSLLTIPQVTRNDTGKYILTIENGVGEPKSSTVSVKVLDTPAACQKLQ VKHVSRGTVTLLWDPPLIDGGSPIINYVIEKRDATKRTWSVVSHKCSSTS FKLIDLSEKTPFFFRVLAENEIGIGEPCETTEPVKAAEVPAPIRDLSMKD STKTSVILSWTKPDFDGGSVITEYVVERKGKGEQTWSHAGISKTCEIEVS QLKEQSVLEFRVFAKNEKGLSDPVTIGPITVKELIITPEVDLSDIPGAQV TVRIGHNVHLELPYKGKPKPSISWLKDGLPLKESEFVRFSKTENKITLSI KNAKKEHGGKYTVILDNAVCRIAVPITVITLGPPSKPKGPIRFDEIKADS VILSWDVPEDNGGGEITCYSIEKRETSQTNWKMVCSSVARTTFKVPNLVK DAEYQFRVRAENRYGVSQPLVSSIIVAKHQFRIPGPPGKPVIYNVTSDGM SLTWDAPVYDGGSEVTGFHVEKKERNSILWQKVNTSPISGREYRATGLVE GLDYQFRVYAENSAGLSSPSDPSKFTLAVSPVDPPGTPDYIDVTRETITL KWNPPLRDGGSKIVGYSIEKRQGNERWVRCNFTDVSECQYTVTGLSPGDR YEFRIIARNAVGTISPPSQSSGIIMTRDENVPPIVEFGPEYFDGLIIKSG ESLRIKALVQGRPVPRVTWFKDGVEIEKRMNMEITDVLGSTSLFVRDATR DHRGVYTVEAKNASGSAKAEIKVKVQDTPGKVVGPIRFTNITGEKMTLWW DAPLNDGCAPITHYIIEKRETSRLAWALIEDKCEAQSYTAIKLINGNEYQ FRVSAVNKFGVGRPLDSDPVVAQIQYTVPDAPGIPEPSNITGNSITLTWA RPESDGGSEIQQYILERREKKSTRWVKVISKRPISETRFKVTGLTEGNEY EFHVMAENAAGVGPASGISRLIKCREPVNPPGPPTVVKVTDTSKTTVSLE WSKPVFDGGMEIIGYIIEMCKADLGDWHKVNAEACVKTRYTVTDLQAGEE YKFRVSAINGAGKGDSCEVTGTIKAVDRLTAPELDIDANFKQTHVVRAGA SIRLFIAYQGRPTPTAVWSKPDSNLSLRADIHTTDSFSTLTVENCNRNDA GKYxxxxxxxxxxxxxxxxxxxxDTPGPPGPITFKDVTRGSATLMWDAPL LDGGARIHHYVVEKREASRRSWQVISEKCTRQIFKVNDLAEGVPYYFRVS AVNEYGVGEPYEMPEPIVATEQPAPPRRLDVVDTSKSSAVLAWLKPDHDG GSRITGYLLEMRQKGSDFWVEAGHTKQLTFTVERLVEKTEYEFRVKAKND AGYSEPREAFSSVIIKEPQIEPTADLTGITNQLITCKAGSPFTIDVPISG RPAPKVTWKLEEMRLKETDRVSITTTKDRTTLTVKDSMRGDSGRYFLTLE NTAGVKTFSVTVVVIGRPGPVTGPIEVSSVSAESCVLSWGEPKDGGGTEI TNYIVEKRESGTTAWQLVNSSVKRTQIKVTHLTKYMEYSFRVSSENRFGV SKPLESAPIIAEHPFVPPSAPTRPEVYHVSANAMSIRWEEPYHDGGSKII GYWVEKKERNTILWVKENKVPCLECNYKVTGLVEGLEYQFRTYALNAAGV SKASEASRPIMAQNPVDAPGRPEVTDVTRSTVSLIWSAPAYDGGSKVVGY IIERKPVSEVGDGRWLKCNYTIVSDNFFTVTALSEGDTYEFRVLAKNAAG VISKGSESTGPVTCRDEYAPPKAELDARLHGDLVTIRAGSDLVLDAAVGG KPEPKIIWTKGDKELDLCEKVSLQYTGKRATAVIKFCDRSDSGKYTLTVK NASGTKAVSVMVKVLDSPGPCGKLTVSRVTQEKCTLAWSLPQEDGGAEIT HYIVERRETSRLNWVIVEGECPTLSYVVTRLIKNNEYIFRVRAVNKYGPG VPVESEPIVARNSFTIPSPPGIPEEVGTGKEHIIIQWTKPESDGGNEISN YLVDKREKKSLRWTRVNKDYVVYDTRLKVTSLMEGCDYQFRVTAVNAAGN SEPSEASNFISCREPSYTPGPPSAPRVVDTTKHSISLAWTKPMYDGGTDI VGYVLEMQEKDTDQWYRVHTNATIRNTEFTVPDLKMGQKYSFRVAAVNVK GMSEYSESIAEIEPVERIEIPDLELADDLKKTVTIRAGASLRLMVSVSGR PPPVITWSKQGIDLASRAIIDTTESYSLLIVDKVNRYDAGKYTIEAENQS GKKSATVLVKVYDTPGPCPSVKVKEVSRDSVTITWEIPTIDGGAPVNNYI VEKREAAMRAFKTVTTKCSKTLYRISGLVEGTMYYFRVLPENIYGIGEPC ETSDAVLVSEVPLVPAKLEVVDVTKSTVTLAWEKPLYDGGSRLTGYVLEA CKAGTERWMKVVTLKPTVLEHTVTSLNEGEQYLFRIRAQNEKGVSEPRET VTAVTVQDLRVLPTIDLSTMPQKTIHVPAGRPVELVIPIAGRPPPAASWF FAGSKLRESERVTVETHTKVAKLTIRETTIRDTGEYTLELKNVTGTTSET IKVIILDKPGPPTGPIKIDEIDATSITISWEPPELDGGAPLSGYVVEQRD AHRPGWLPVSESVTRSTFKFTRLTEGNEYVFRVAATNRFGIGSYLQSEVI ECRSSIRIPGPPETLQIFDVSRDGMTLTWYPPEDDGGSQVTGYIVERKEV RADRWVRVNKVPVTMTRYRSTGLTEGLEYEHRVTAINARGSGKPxxxxxx xxxxxxxxxxxxxxxxxxxxxxRTSVSLAWSVPEDEGGSKVTGYLIEMQK VDQHEWTKCNTTPTKIREYTLTHLPQGAEYRFRVLACNAGGPGEPAEVPG TVKVTEMLEYPDYELDERYQEGIFVRQGGVIRLTIPIKGKPFPICKWTKE GQDISKRAMIATSETHTELVIKEADRGDSGTYDLVLENKCGKKAVYIKVR VIGSPNSPEGPLEYDDIQVRSVRVSWRPPADDGGADILGYILERREVPKA AWYTIDSRVRGTSLVVKGLKENVEYHFRVSAENQFGISKPLKSEEPVxxx xxxxxxxxxxxxxxxLDVTKSSVSLSWSRPKDDGGSRVTGYYIERKETST DKWVRHNKTQITTTMYTVTGLVPDAEYQFRIIAQNDVGLSETSPASEPVV CKDPFDKPSQPGELEILSISKDSVTLQWEKPECDGGKEILGYWVEYRQSG DSAWKKSNKERIKDKQFTIGGLLEATEYEFRVFAENETGLSRPRRTAMSI KTKLTSGEAPGIRKEMKDVTTKLGEAAQLSCQIVGRPLPDIKWYRFGKEL IQSRKYKMSSDGRTHTLTVMTEEQEDEGVYTCIATNEVGEVETSSKLLLQ ATPQFHPGYPLKEKYYGAVGSTLRLHVMYIGRPVPAMTWFHGQKLLQNSE NITIENTEHYTHLVMKNVQRKTHAGKYKVQLSNVFGTVDAILDVEIQDKP DKPTGPIVIEALLKNSAVISWKPPADDGGSWITNYVVEKCEAKEGAEWQL VSSAISVTTCRIVNLTENAGYYFRVSAQNTFGISDPLEVSSVVIIKSPFE KPGAPGKPTITAVTKDSCVVAWKPPASDGGAKIRNYYLEKREKKQNKWIS VTTEEIRETVFSVKNLIEGLEYEFRVKCENLGGESEWSEISEPITPKSDV PIQAPHFKEELRNLNVRYQSNATLVCKVTGHPKPIVKWYRQGKEIIADGL KYRIQEFKGGYHQLIIASVTDDDATVYQVRATNQGGSVSGTASLEVEVPA KIHLPKTLEGMGAVHALRGEVVSIKIPFSGKPDPVITWQKGQDLIDNNGH YQVIVTRSFTSLVFPNGVERKDAGFYVVCAKNRFGIDQKTVELDVADVPD PPRGVKVSDVSRDSVNLTWTEPASDGGSKITNYIVEKCATTAERWLRVGQ ARETRYTVINLFGKTSYQFRVIAENKFGLSKPSxxxxxTITKEDKTRAMN YDEEVDETREVSMTKASHSSTKELYEKYMIAEDLGRGEFGIVHRCVETSS KKTYMAKFVKVKGTDQVLVKKEISILNIARHRNILHLHESFESMEELVMI FEFISGLDIFERINTSAFELNEREIVSYVHQVCEALQFLHSHNIGHFDIR PENIIYQTRRSSTIKIIEFGQARQLKPGDNFRLLFTAPEYYAPEVHQHDV VSTATDMWSLGTLVYVLLSGINPFLAETNQQIIENIMNAEYTFDEEAFKE ISIEAMDFVDRLLVKERKSRMTASEALQHPWLKQKIERVSTKVIRTLKHR RYYHTLIKKDLNMVVSAARISCGGAIRSQKGVSVAKVKVASIEIGPVSGQ IMHAVGEEGGHVKYVCKIENYDQSTQVTWYFGVRQLENSEKYEITYEDGV AILYVKDITKLDDGTYRCKVVNDYGEDSSYAELFVKGVREVYDYYCRRTM KKIKRRTDTMRLLERPPEFTLPLYNKTAYVGENVRFGVTITVHPEPHVTW YKSGQKIKPGDNDKKYTFESDKGLYQLTINSVTTDDDAEYTVVARNKYGE DSCKAKLTVTLHPPPTDSTLRPMFKRLLANAECQEGQSVCFEIRVSGIPP PTLKWEKDGQPLSLGPNIEIIHEGLDYYALHIRDTLPEDTGYYRVTATNT AGSTSCQAHLQVERLRYKKQEFKSKEEHERHVQKQIDKTLRMAEILSGTE SVPLTQVAKEALREAAVLYKPAVSTKTVKGEFRLEIEEKKEERKLRMPYD VPEPRKYKQTTIEEDQRIKQFVPMSDMKWYKKIRDQYEMPGKLDRVVQKR PKRIRLSRWEQFYVMPLPRITDQYRPKWRIPKLSQDDLEIVRPARRRTPS PDYDFYYRPRRRSLGDISDEELLLPIDDYLAMKRTEEERLRLEEELELGF SASPPSRSPPHFELSSLRYSSPQAHVKVEETRKDFRYSTYHIPTKAEAST SYAELRERHAQAAYRQPKQRQRIMAEREDEELLRPVTTTQHLSEYKSELD FMSKExxxxxxxxxxxxxxxxxxxxxxxxxSKHAxxxxxxxxxxxxxxxx SLSPTYIELMRPVSELIRSRPQPAEEYEDDTERRSPTPExxxxxxxxxVS SERSLSRFERSARFDIFSRYESMKAALKTQKTSERKYEVLSQQPFTLDHA PRITLRMRSHRVPCGQNTRFILNVQSKPTAEVKWYHNGVELQESSKIHYT NTSGVLTLEILDCHTDDSGTYRAVCTNYKGEASDYATLDVTGGDYTTYAS QRRDEEVPRSVFPELTRTEAYAVSSFKKTSEMEASSxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxTLAARILTKPRSMTVY EGESARFSCDTDGEPVPTVTWLRKGQVLSTSARHQVTTTKYKSTFEISSV QASDEGNYSVVVENSEGKQEAEFTLTIQKARVTEKAVTSPPRVKSxxxxx xxxxxxxxxxxxxxxxxxHxKAVSxxxxxxxxxEKVQHLPVSAPPKITQF LKAEASKEIAKLTCVVESSVLRAKEVTWYKDGKKLKENGHFQFHYSADGT YELKINNLTESDQGEYVCEISGEGGTSKTNLQFMGQAFKSIHEKVSKISE xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxVTGLQDTTVSSDSVAKFAV KATGEPRPTAIWTKDGKAITQGGKYKLSEDKGGFFLEIHKTDTSDSGLYT CTVKNSAGSVSSSCKLTIKAIKDTEAQKVSTQKTSEITPQKKAVVQEEIS QxxxxxxxxxxxxxxxxxKLAxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxVRTHAEIKAFSTQMSINEGQRLVLKANIAGATDVKWVLN GVELTNSEEYRYGVSGSDQTLTIKQASHRDEGILTCISKTKEGIVKCQYD LTLSKELSDAPAFISQPRSQNINEGQNVLFTCEISGEPSPEIEWFKNNLP ISISSxxxxxxxxxVYSLEIRNASVSDSGKYTIKAKNFRGQCSATASLMV LPLVEEPSREVVLRTSGDTSLQGSFSSQSVQMSASKxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxLKAG IRGIPPKIEALPSDISIDEGKVLTVACAFTGEPTPEVTWSCGGRKIHSQE QGRFHIENTDDLTTLIIMDVQKQDGGLYTLSLGNEFGSDSATVNIHIRSI #period estimated number of tracts 1 11.5539 2 12.071 3 23.5112 4 8.6641 5 10.2403 6 10.2883 7 11.3853 8 11.585 9 4.50516 10 4.75721 11 8.23821 12 3.43443 13 4.34498 14 2.43048 15 6.08299 16 5.03573 17 3.15392 18 1.90906 19 2.38249 20 1.69083 21 1.64297 22 1.36296 23 1.42971 24 1.31135 25 3.43442 26 5.87207 27 2.84509 28 5.23273 29 0.737526 30 0.733329 31 1.04262 32 0.994512 33 0.406413 34 0.253399 35 0.214558 36 1.24664 37 0.817335 38 0.361951 39 0.299148 40 0.221853 41 0.147372 42 1.56514 43 0.211522 44 0.0943722 45 0.327042 46 2.10489 47 0.0983897 48 0.488297 49 0.0632472 50 0.0948114 # estimated total number of repetitive tracts: 182.92 # estimated number of background-to-background transitions: 30295.5 # total number of transitions (#letters + #sequences): 34351 # best-fit probability decay per period: 0.914731 # best-fit probability of a repeat starting per position: 0.00600163 # best-fit probability of a repeat ending per position: 0.0472345 817 234 934 3615 @SRR019778.1 I331_2_FC3076HAAXX:1:1:1416:1963 length=45 GTTCAATGGGGGAAAGGAGAGTCCTTCAACAAATGGTGCGGAGAA +SRR019778.1 I331_2_FC3076HAAXX:1:1:1416:1963 length=45 IIIIIIIIIIIIIIIIIIIIIIIIIIIB2IHH(-0+ @SRR019778.3 I331_2_FC3076HAAXX:1:1:1611:1333 length=45 GTTTTCCCATTTGTCCTTAATCCACCTAAAAAAGATTTGCATGGG +SRR019778.3 I331_2_FC3076HAAXX:1:1:1611:1333 length=45 IIIIIIIIIIIIIEIIIIG:IDIGECI454,10+0A?8/4+40%( @SRR019778.4 I331_2_FC3076HAAXX:1:1:1277:1927 length=45 GTTGtgtgtgtattgtgtgttgtgtgtggtgtgtgtgtttttttt +SRR019778.4 I331_2_FC3076HAAXX:1:1:1277:1927 length=45 IIIIIIIIIIIIII6IIIIIIDIII4I%4I*I0IAI+II8/3I+I @SRR019778.5 I331_2_FC3076HAAXX:1:1:1494:1984 length=45 GGATGTTTATTTTCCTGAACCAGGGTTTGGCATTGAAGAGACAGA +SRR019778.5 I331_2_FC3076HAAXX:1:1:1494:1984 length=45 IIIIIIIIIIIIIIIIIIIII/III@III@<-I6I'3I67-++>) @SRR019778.6 I331_2_FC3076HAAXX:1:1:682:1158 length=45 GTTTGTTTCCTAGAGTTAAGAGTCTCTCATGGTTTGTCTCCCTCT +SRR019778.6 I331_2_FC3076HAAXX:1:1:682:1158 length=45 IIIIIIIIIIIII:IIII=IEIIHI@IC2I9;I@@//?4DA5080,&, @SRR019778.13 I331_2_FC3076HAAXX:1:1:1245:2003 length=45 GTTTCCATAACCAGAAATATACAGCGGATTAGAGAAGTGATTTTT +SRR019778.13 I331_2_FC3076HAAXX:1:1:1245:2003 length=45 IIIIIIIIIIIIIIG>1I4I5I9IIII*II.I+G)-B7G&:B@C@ @SRR019778.14 I331_2_FC3076HAAXX:1:1:1226:1990 length=45 GGGAGGATCTAGCCTTAGAACCAAGAAACAAAATGTGAGGGGAAA +SRR019778.14 I331_2_FC3076HAAXX:1:1:1226:1990 length=45 IIIIIIIIIIIIIIII6IIIIIAII>.III-3/II3I1IIII.-- @SRR019778.15 I331_2_FC3076HAAXX:1:1:1879:1017 length=45 GTGATGTGCCATTGACCTATTTGTTTATCTTTATACCAATACTTC +SRR019778.15 I331_2_FC3076HAAXX:1:1:1879:1017 length=45 IIIIIIIIIIIIII2III/IIDGFII/I7IG:5CC;/0&=)+;4+ @SRR019778.16 I331_2_FC3076HAAXX:1:1:1478:1340 length=45 GTATTTTACAGAAGTTTCTCTGGGTCTCAGATTCCTACCTGACCC +SRR019778.16 I331_2_FC3076HAAXX:1:1:1478:1340 length=45 IIIIIIIIIIIIIIDIIIIII>;C;DI@D*3IE<2B/20;&'/-/ @SRR019778.17 I331_2_FC3076HAAXX:1:1:1489:1981 length=45 GGGAAAGATAGAGAGCCTTGTCTTCAAAATGGCTTATCCAGTAAG +SRR019778.17 I331_2_FC3076HAAXX:1:1:1489:1981 length=45 IIIIIIIIIIIIIIIIIIIIIIIII?+<5IIIIIB*66<%=3'(5 @SRR019778.18 I331_2_FC3076HAAXX:1:1:1710:940 length=45 GAGAATCCACAAGAAGTTGCTGTTAGGGATTTGTTCTTATTTTAA +SRR019778.18 I331_2_FC3076HAAXX:1:1:1710:940 length=45 IIIIIIIIIIIII0CIIIIIII@I(-?6-@?C.37,A:%D;:&** @SRR019778.19 I331_2_FC3076HAAXX:1:1:1339:973 length=45 GAAAAGGCATAAATATTTCATTCAATTGCAAGCTTAATATAAGTC +SRR019778.19 I331_2_FC3076HAAXX:1:1:1339:973 length=45 IIIIIIIIIIIIIIFIIIIHIIII:II;II63=IIC.GFI76(.. @SRR019778.20 I331_2_FC3076HAAXX:1:1:1408:1952 length=45 GAGTTTTCCATTTAAGAACTTGAGTGTCATCGCCTTAGGAAAGAC +SRR019778.20 I331_2_FC3076HAAXX:1:1:1408:1952 length=45 IIIIIIIIIIIII@FIFGIIII8I?+HIIDI=E>I>8?1)1&*// @SRR019778.21 I331_2_FC3076HAAXX:1:1:1468:1371 length=45 GAAGAGAAAGGAGATACCATCATTTGTCATTAACAGGATTACCTT +SRR019778.21 I331_2_FC3076HAAXX:1:1:1468:1371 length=45 IIIIIIIIIIIIIIIIIIIIIFIIII=I3I:13=A<@,/03I2<+:- @SRR019778.26 I331_2_FC3076HAAXX:1:1:1225:1945 length=45 GTAATGATTGAATAAATCTTATTAActtcttaatcttttaatTTT +SRR019778.26 I331_2_FC3076HAAXX:1:1:1225:1945 length=45 IIIIIIIIIIIIIIIIIIIIIIIB4HIIIII:3IIIIII5)IIGI @SRR019778.27 I331_2_FC3076HAAXX:1:1:1506:1294 length=45 GCTTCAAGAAGAAGGGCATGACTCACCCCCCAGGAACAGAAGCTG +SRR019778.27 I331_2_FC3076HAAXX:1:1:1506:1294 length=45 IIIIIIIIIIIIIIIIIIIIIIII@IIICDB15B+39.9*.B4:5 @SRR019778.28 I331_2_FC3076HAAXX:1:1:1318:1418 length=45 GATTTTATTCTTATTGTTTTGATGGTGACCTTTAATATTTTCTTA +SRR019778.28 I331_2_FC3076HAAXX:1:1:1318:1418 length=45 IIIIIIIIIIIIIIIIIIIIADI,BFIA..IIIC2$7IFEC1&;) @SRR019778.29 I331_2_FC3076HAAXX:1:1:1332:1930 length=45 GAGAATAAGTCAATACCAAGGTGAATTGAATAATGGCCAAGAATT +SRR019778.29 I331_2_FC3076HAAXX:1:1:1332:1930 length=45 IIIIIIIIIIIIIIIIGIHIIII58IIII5I@9AI8I0=,B,-3> @SRR019778.30 I331_2_FC3076HAAXX:1:1:1099:1168 length=45 GTTTATTCTCTATCATTTAGAGTCTCAGCTGTTTGGGTTTCTAGA +SRR019778.30 I331_2_FC3076HAAXX:1:1:1099:1168 length=45 IIIIIIIIIIIIII;IIII8I+BFII+C.2+8I.,&%3$$3/$)$ @SRR019778.31 I331_2_FC3076HAAXX:1:1:1529:1292 length=45 GGATAGCCCCAAGTGTTACAAATTGTAAGTAAATATTTGTAGGGA +SRR019778.31 I331_2_FC3076HAAXX:1:1:1529:1292 length=45 IIIIIIIIIIIIIIIII>I<<8IIIID2I=/7.;2EH@22/6+&* @SRR019778.32 I331_2_FC3076HAAXX:1:1:1256:1996 length=45 GTTGGGGATTAGAAAGTAGATGTAAGGAGTAGTAAAGGGAATACA +SRR019778.32 I331_2_FC3076HAAXX:1:1:1256:1996 length=45 IIIIIIIIIIIIIHIIIIIIIIHI6II5I;I3 @SRR019778.39 I331_2_FC3076HAAXX:1:1:1136:1244 length=45 GTTATATGTGAGTAATGAACCATTGAACACTACACCAAAAATTAA +SRR019778.39 I331_2_FC3076HAAXX:1:1:1136:1244 length=45 IIIIIIIIIIIIIIIIIIIIDIIIII:8B8IH3;72<8031D92- @SRR019778.40 I331_2_FC3076HAAXX:1:1:1819:927 length=45 GGGTTTGGAGTTTAAAGAGAGAATAAGTCATGTGCCAATATATGA +SRR019778.40 I331_2_FC3076HAAXX:1:1:1819:927 length=45 IIIIIIIIIIIIIIG;IFIIII6II?IEBE?8@A<79,D5<4F1) @SRR019778.41 I331_2_FC3076HAAXX:1:1:1250:1938 length=45 GTTTGTGTCCCTCTAAAGTTCATATACTGAAGCCCTAACCCCCAG +SRR019778.41 I331_2_FC3076HAAXX:1:1:1250:1938 length=45 IIIIIIIIIIIIIIII2IIIIIIIIIIII=:=IIEI3/I7I7G+0 @SRR019778.42 I331_2_FC3076HAAXX:1:1:1648:1646 length=45 GGTTGTgtgtgtgtgtgtgtgtgtgtgtgtttgtttttttttttA +SRR019778.42 I331_2_FC3076HAAXX:1:1:1648:1646 length=45 IIIIIIIIIIIIIIIIIIII7I@I.IDIB,.@%I0*-E(G%(/.% @SRR019778.43 I331_2_FC3076HAAXX:1:1:690:962 length=45 GTGAGATGATGTTCGTTGATATTTCCCTGTATTTTTTGTTTTTTC +SRR019778.43 I331_2_FC3076HAAXX:1:1:690:962 length=45 IIIIIIIIIIIIIIIIII>I?III??,I'$)II%:&B&'8(9$=$ @SRR019778.44 I331_2_FC3076HAAXX:1:1:1399:1957 length=45 GTTGATATTTCCCTGGACTGTGTGGGGTCTCAGAGACCACTATGG +SRR019778.44 I331_2_FC3076HAAXX:1:1:1399:1957 length=45 IIIIIIIIIIIIIIII=IIIIIIIIIIIIIG4>,I/9;*3D*:<+ @SRR019778.45 I331_2_FC3076HAAXX:1:1:1797:1797 length=45 GTgtgtattgtgtgtgggtgtgtgtgttgtgtgtgttttGGGTGG +SRR019778.45 I331_2_FC3076HAAXX:1:1:1797:1797 length=45 IIIIIIIIIIIIII@IIIIIIIAII?II?I0(+D)II$:&5%'&% @SRR019778.46 I331_2_FC3076HAAXX:1:1:721:921 length=45 GATGTCATAGAAGTTGTTGCCTATGTTCTCCTCTAGAATTTTGAT +SRR019778.46 I331_2_FC3076HAAXX:1:1:721:921 length=45 IIIIIIIIIIIIIIIIIIH?CI6I7II0I11F5I+&+(ICIH&&= @SRR019778.47 I331_2_FC3076HAAXX:1:1:1584:1300 length=45 GGTAGTGAGTATCAGCCCTGTGCAGGTTTCTGCAGATGGCCATGT +SRR019778.47 I331_2_FC3076HAAXX:1:1:1584:1300 length=45 IIIII-IIIIIIIHIIIII4;GCIEI-II320-&-#)%,.,$-%$ @SRR019778.48 I331_2_FC3076HAAXX:1:1:1397:1963 length=45 GAAAACTTACTTACAAATTCATTCTATGAGGCCAGCATTACCCTG +SRR019778.48 I331_2_FC3076HAAXX:1:1:1397:1963 length=45 IIIIIIIIIIIIIIII:IIIIIIII4II4FIIH0F@*CI47><:1 @SRR019778.49 I331_2_FC3076HAAXX:1:1:1550:1296 length=45 GGTAGATGTGACTCTTGATCTCAGGGTCATGAGTTCAAGCCCCAT +SRR019778.49 I331_2_FC3076HAAXX:1:1:1550:1296 length=45 IIIIIIIIIIIIIIIIICIIBI6D%I9B5C;0I+;37-4)0**)3 @SRR019778.50 I331_2_FC3076HAAXX:1:1:913:1939 length=45 GTGtgttgtgtgttgagtgttttgtgtgtgtgttgtgttttttGT +SRR019778.50 I331_2_FC3076HAAXX:1:1:913:1939 length=45 IIIIIIIIIIIIIII2IIIIIII@IIG2I.I,II&9&4%II,:%, @SRR019778.51 I331_2_FC3076HAAXX:1:1:1734:1009 length=45 GAAACAATGGTTTTCAAGACACTGGACATCAGCCTACAATGGACA +SRR019778.51 I331_2_FC3076HAAXX:1:1:1734:1009 length=45 IIIIIIIIIIIIIIIIIIEIBIIID.>2I?186C?)/&-8,1)1+ @SRR019778.52 I331_2_FC3076HAAXX:1:1:1355:100 length=45 GTACACAAATCTACGTGATATTTCGAAAGGTAAACAGATAATGCT +SRR019778.52 I331_2_FC3076HAAXX:1:1:1355:100 length=45 IIIIIIIIIIIII7I7,IIC&FD>1->9'+00 @SRR019778.56 I331_2_FC3076HAAXX:1:1:1759:1586 length=45 GGTACTCTAATAGCGTTTTATGGTAAGAGATGGTAGCTGTACTTG +SRR019778.56 I331_2_FC3076HAAXX:1:1:1759:1586 length=45 IIIIIIIIIF0I1III++;6.':594*7)4* @SRR019778.58 I331_2_FC3076HAAXX:1:1:1371:1534 length=45 GTGATGGGAAAGGAAAGAGCCAATCCTGTAGGGCCTGGTAGATCA +SRR019778.58 I331_2_FC3076HAAXX:1:1:1371:1534 length=45 I7IIIIIIIIIIIIIIIIIIII>III@*86IIIF??I7+)6-9+0 @SRR019778.59 I331_2_FC3076HAAXX:1:1:1780:1771 length=45 GTAAAATGGAGTAAATAGAGTAGAATAACATAAAAATTACAATGT +SRR019778.59 I331_2_FC3076HAAXX:1:1:1780:1771 length=45 IIIIIIIIIIIII;IIIE.-/0827:4./3- @SRR019778.60 I331_2_FC3076HAAXX:1:1:1539:1636 length=45 GTGTTGCTCTTTCTGAGGTGGTAATTGTGGTTTCCTTGGGCCTTT +SRR019778.60 I331_2_FC3076HAAXX:1:1:1539:1636 length=45 IIIIIIIIIIIIIIIIIICII:7III9I9IFII1(4I%%+&*1&. @SRR019778.61 I331_2_FC3076HAAXX:1:1:1360:1444 length=45 GTTGGGTTGATTTTCATTGGTGCTAATGTAATGGGGTATTGATCC +SRR019778.61 I331_2_FC3076HAAXX:1:1:1360:1444 length=45 IIIIIIIIIIIIIIIIIIIBI/GI>1II%).I),,+9'IB)+B+) @SRR019778.62 I331_2_FC3076HAAXX:1:1:1763:997 length=45 GAGATGAGTCAGCAGAGGTAAAAGCTAGAAGGATGTTAGGATGAT +SRR019778.62 I331_2_FC3076HAAXX:1:1:1763:997 length=45 IIIIIIIIIIIII?I@IID=II@A?E?I1;D=:C@6>-<0+A2.= @SRR019778.63 I331_2_FC3076HAAXX:1:1:996:1270 length=45 GTCAGGGACTTAATATCTTTCCCTTAAAATATGTGTGTTATTTTC +SRR019778.63 I331_2_FC3076HAAXX:1:1:996:1270 length=45 IIIIIIIIIIIIIIIIIIIIIEIII<:9)<(:I%: @SRR019778.66 I331_2_FC3076HAAXX:1:1:1314:76 length=45 GTGCTTAGCAGATAGGAGGGGCTCATTAACATGTTGAACAAATGT +SRR019778.66 I331_2_FC3076HAAXX:1:1:1314:76 length=45 IIIIIIIIIIIII7II7IIII?II4II/14+I*I@/.:/.6*F>>+ @SRR019778.68 I331_2_FC3076HAAXX:1:1:1459:1955 length=45 GTGTTCCCATACTTTAACTTGtgtgtgttgtggggggAAGCATAT +SRR019778.68 I331_2_FC3076HAAXX:1:1:1459:1955 length=45 IIIIIIIIDIIIIII>FIIIIIIIIIIII6I>47>I+*(/#$I$@ @SRR019778.69 I331_2_FC3076HAAXX:1:1:1381:1967 length=45 GCCCTAAGAACCAAGAAACAAAGTGTGAGGGGAAAGCCCTTGAAT +SRR019778.69 I331_2_FC3076HAAXX:1:1:1381:1967 length=45 IIIIIIIIIIIII:IE)CIC?1F4I+I8IIII.,/I959-:B&'9 @SRR019778.70 I331_2_FC3076HAAXX:1:1:1224:2001 length=45 GATACGTCAAATTTATGGAAGTGTTTTATAAGTGCATTTAAGTTT +SRR019778.70 I331_2_FC3076HAAXX:1:1:1224:2001 length=45 IIIIIIIIIIIIIIIIII8EI=IIIII8I4.9E9+$II&%+(:?& @SRR019778.71 I331_2_FC3076HAAXX:1:1:1771:1569 length=45 GTTTTTATAATGACTTCCTTAGGCTGTACCCCCAATTTACTATAT +SRR019778.71 I331_2_FC3076HAAXX:1:1:1771:1569 length=45 IIIIIIIIIIIIIIIIIIII*(IAB(4?'D'F @SRR019778.72 I331_2_FC3076HAAXX:1:1:1745:1606 length=45 GATTTGCAGTCAAGGACAGGTCCACACAGTCAGGACCACAGTGTT +SRR019778.72 I331_2_FC3076HAAXX:1:1:1745:1606 length=45 IIIIIIIIIIIIEIIII-I2; @SRR019778.73 I331_2_FC3076HAAXX:1:1:1279:1959 length=45 GGAGGAAGACCACAGAGCTGAAGCACCGTCCTCATCACATCAGGT +SRR019778.73 I331_2_FC3076HAAXX:1:1:1279:1959 length=45 IIIIIIIIIIIIIIIIIIIIHFII86II6IICI1CI4I4*5*4B( @SRR019778.74 I331_2_FC3076HAAXX:1:1:1769:1745 length=45 GAAGTGATGTAGATGCCTATATGAATACAGGCACATATGGTTTCC +SRR019778.74 I331_2_FC3076HAAXX:1:1:1769:1745 length=45 IIIIDIIIIIIIIIIIII7IIIIG>I0E2II=+7/:+7DA04*'7 @SRR019778.75 I331_2_FC3076HAAXX:1:1:721:1248 length=45 GACAAGTTTAGGAAGCCTGTTATTTTACTACATGAAACATTCATA +SRR019778.75 I331_2_FC3076HAAXX:1:1:721:1248 length=45 IIEIIIIIIIIIIIIIIII>IIIIII>III9AI+75>76?84-2I @SRR019778.76 I331_2_FC3076HAAXX:1:1:1306:616 length=45 GTTAAGATAAATCACAGAGCACCAACCTCAAGCGATGGCAGCTGC +SRR019778.76 I331_2_FC3076HAAXX:1:1:1306:616 length=45 IIIIIIIIIIIIIIIIIIIIIIIIAIC=B6:57:274.2,+(+%& @SRR019778.77 I331_2_FC3076HAAXX:1:1:1474:1625 length=45 GTAAAGGACTTTCAGGACCTAATTTAAATGATCACTCAGGCTGAG +SRR019778.77 I331_2_FC3076HAAXX:1:1:1474:1625 length=45 IIIIIIIIIIIIIIIIIIII>9III@7GII3IIFIIA34'1FA)7 @SRR019778.78 I331_2_FC3076HAAXX:1:1:1866:942 length=45 GACAGATACTGCCTTACTAtgccttactatgTGCACATATACACA +SRR019778.78 I331_2_FC3076HAAXX:1:1:1866:942 length=45 IIIIIIIIIIIIIIIIII5IIIIII1II.I+:,C33,?/;,,)/) @SRR019778.79 I331_2_FC3076HAAXX:1:1:1803:1776 length=45 GTAATATATAAACAGCATAGATAATATCAGATAAAAGGACTTTCT +SRR019778.79 I331_2_FC3076HAAXX:1:1:1803:1776 length=45 IIIIIIIIIIIII:II8IDI;I9:I/=E;I>AA0132/29>=/15 @SRR019778.80 I331_2_FC3076HAAXX:1:1:716:927 length=45 GCAAGGTAGGGACACGGGGACTCAGACAGATGAACAGATTAGACT +SRR019778.80 I331_2_FC3076HAAXX:1:1:716:927 length=45 IIIIIIIIIIIIIIIIIIIACIGBI=?2I6DA8;3+;/5:/./+1 @SRR019778.81 I331_2_FC3076HAAXX:1:1:1294:71 length=45 GTAAACATGGAACACAACAAAAAAACTTCAAAAAGGCAAAACTAG +SRR019778.81 I331_2_FC3076HAAXX:1:1:1294:71 length=45 IIIIIIIIIIIIIDIIII93I@AE.HE7I632-,63?72/1476, @SRR019778.82 I331_2_FC3076HAAXX:1:1:1486:1393 length=45 GATTTAAACAATTACATCAAAATGCATTGATTCAATTGTTTTTTA +SRR019778.82 I331_2_FC3076HAAXX:1:1:1486:1393 length=45 IIIIIIIIIIIIIIIIIIIBIIIID9:I@;4@8*B0I4A77 @SRR019778.83 I331_2_FC3076HAAXX:1:1:1880:1764 length=45 GTAAAAATAACTACATTAACTGTGACAAGGGATACCCAAGAAGAT +SRR019778.83 I331_2_FC3076HAAXX:1:1:1880:1764 length=45 IIIIIIIIIIIIIIIIIIIIIIAI:I8:IHI.52IG4'/4-+2)0 @SRR019778.84 I331_2_FC3076HAAXX:1:1:1410:1972 length=45 GCATGTGGATATCCAGTTTTCCCATTTCTTGAAAAGTGTGTCCTT +SRR019778.84 I331_2_FC3076HAAXX:1:1:1410:1972 length=45 IIIIIIIIIIIIII/IIIIIIII7IIIIII;3.)1=<<8-D86G> @SRR019778.85 I331_2_FC3076HAAXX:1:1:1681:1342 length=45 GTAGAAATGACCTTAGCCCACTATACTAGAAACTTCGGGTTTGTG +SRR019778.85 I331_2_FC3076HAAXX:1:1:1681:1342 length=45 IIIIIIIIIIIIIIIIIIFDII3IFIII)712145+.5,1&3+ @SRR019778.87 I331_2_FC3076HAAXX:1:1:1395:1991 length=45 GTGCTATCTCATCATGGTTTTGATCTGTATTTCCCTGATAATGAG +SRR019778.87 I331_2_FC3076HAAXX:1:1:1395:1991 length=45 IIIIIIIIIIIII?IIIIIIII2IIIIF7IIIGCEI;+D&-B+** @SRR019778.88 I331_2_FC3076HAAXX:1:1:1332:1959 length=45 GATAGTAACTCCTGTCTTCCTACGGGGTTAAAAAAAGCCTTCTGC +SRR019778.88 I331_2_FC3076HAAXX:1:1:1332:1959 length=45 IIIIIIIIIIIIIIIIIIII3IIIIII=ID-2/+824<;4?A872 @SRR019778.89 I331_2_FC3076HAAXX:1:1:1304:77 length=45 GAAGAGAGAAGTCTGGGGGATCAGAGGCCACCAAAAGCAAAACAA +SRR019778.89 I331_2_FC3076HAAXX:1:1:1304:77 length=45 IIIIIIIIIIIIIIICIDI?D97957@;+839,))+5-2*')**) @SRR019778.90 I331_2_FC3076HAAXX:1:1:1478:1372 length=45 GTTAAAGGTGAAGAAGGAAGAGAAGTTCCTTCCATTTGGCAGATT +SRR019778.90 I331_2_FC3076HAAXX:1:1:1478:1372 length=45 IIIIIIIIIIIIIIIIIIIIII2AI3II>IB@50A:3<*5+@):2 @SRR019778.91 I331_2_FC3076HAAXX:1:1:1518:630 length=45 GTAGTGGTGAAAGTATTTATTTTTCCCTATATCTTTGTTAATTGC +SRR019778.91 I331_2_FC3076HAAXX:1:1:1518:630 length=45 IIIIIIIIIIIIICIIII@IIIIIIDFI?I1I9IHC$:B.+BI%) @SRR019778.92 I331_2_FC3076HAAXX:1:1:1486:1973 length=45 GAAACAGACAAAAGCCTTAGTAACCTGGGGCTCAGCAAAAGGCCA +SRR019778.92 I331_2_FC3076HAAXX:1:1:1486:1973 length=45 IIIIIIIIIIIIIIIIIIIIIH?IIIIIIIIII3IH-//(I??I3 @SRR019778.93 I331_2_FC3076HAAXX:1:1:1296:1435 length=45 GAGTTTTGAACTCAGGCTGTTCTGGCCTCAAAATTCATGCTCATT +SRR019778.93 I331_2_FC3076HAAXX:1:1:1296:1435 length=45 IIIIIIIIIIIIIIIIIIIII4@&;74C1)01/9I)'9&-7+(29 @SRR019778.94 I331_2_FC3076HAAXX:1:1:1502:1287 length=45 GCACAGATGAGCCAAGAAGGGTTCCAGTTCCCCTGCTTCATTATG +SRR019778.94 I331_2_FC3076HAAXX:1:1:1502:1287 length=45 IIIIIIIIIIIIII;'*B63'20,%6- @SRR019778.96 I331_2_FC3076HAAXX:1:1:1878:956 length=45 GATAATATACTATGGCTCTGCAAGATAGTACTTGGGGGAAACAAA +SRR019778.96 I331_2_FC3076HAAXX:1:1:1878:956 length=45 IIIIIIIIIIIIIIIIII(/:*--01+1.2.-$/+0&6#,2&(&4 @SRR019778.97 I331_2_FC3076HAAXX:1:1:608:1209 length=45 GAAATTTTCCTTCAATAAAGGGAGATTCTAATCTACATATTTTAA +SRR019778.97 I331_2_FC3076HAAXX:1:1:608:1209 length=45 IIIIIIIIIIIIIIIIHH4I=AchrM GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT TTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTG GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATT CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACCTACTA AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT GTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGC CAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAAT TTTATCTTTAGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACA TTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCC GCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAAC CAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAA ATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGC AAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAG GGACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCC ACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGT TTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTT TAGATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAA CTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAAC ACACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGC CCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGA GCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGC TCAGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGT AAGCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGG TGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTT ATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTGAGAGTAGAGT GCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATA GAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACG AACCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTT CAACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCAC CTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGG CGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTT CTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAA GACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCC GTCTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCT ACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTT TAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGA GTAAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGA AAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACT GAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAA TGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCA GATCAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAG GAAAGGTTAAAAAAAGTAAAAGGAACTCGGCAAACCTTACCCCGCCTGTT TACCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCC CAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAaaggtagca taatcacttgttccttaaatagggacctgtatgaatggctccacgagggt tcagctgtctcttacttttaaccagtgaaattgacctgcccgtgaagagg cgggcatgacacagcaagacgagaagaccctatggagctttaatttaTTA ATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCA TTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCA GTACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGAT CCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATC CTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT CAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGA TTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTT CTATCTACTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCC TACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTAT TATACCCACACCCACCCAAGAACAGGGTTTgttaagatggcagagcccgg taatcgcataaaacttaaaactttacagtcagaggttcaattcctcttct taacaacaTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAA TCGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATA CAACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACC CTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCA CATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATC GCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCT CAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACT CAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGC GCACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCAT CATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCC TTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTG GCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTT CGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAAT ACGCCGCAGGCCCCTTCGCCCTATTCTTCATAGCCGAATACACAAACATT ATTATAATAAACACCCTCACCACTACAATCTTCCTAGGAACAACATATGA CGCACTCTCCCCTGAACTCTACACAACATATTTTGTCACCAAGACCCTAC TTCTAACCTCCCTGTTCTTATGAATTCGAACAGCATACCCCCGATTCCGC TACGACCAACTCATACACCTCCTATGAAAAAACTTCCTACCACTCACCCT AGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTC CCCCTCAAACCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGT AAATAATAGGAGCTTAAACCCCCTTATTTctaggactatgagaatcgaac ccatccctgagaatccaaaattctccgtgccacctatcacaccccatcct aAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTG GTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTAC TCTACCATCTTTGCAGGCACACTCATCACAGCGCTAAGCTCGCACTGATT TTTTACCTGAGTAGGCCTAGAAATAAACATGCTAGCTTTTATTCCAGTTC TAACCAAAAAAATAAACCCTCGTTCCACAGAAGCTGCCATCAAGTATTTC CTCACGCAAGCAACCGCATCCATAATCCTTCTAATAGCTATCCTCTTCAA CAATATACTCTCCGGACAATGAACCATAACCAATACTACCAATCAATACT CATCATTAATAATCATAATGGCTATAGCAATAAAACTAGGAATAGCCCCC TTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGG CCTGCTTCTTCTCACATGACAAAAACTAGCCCCCATCTCAATCATATACC AAATCTCTCCCTCACTAAACGTAAGCCTTCTCCTCACTCTCTCAATCTTA TCCATCATAGCAGGCAGTTGAGGTGGATTAAACCAAACCCAGCTACGCAA AATCTTAGCATACTCCTCAATTACCCACATAGGATGAATAATAGCAGTTC TACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTATATTATC CTAACTACTACCGCATTCCTACTACTCAACTTAAACTCCAGCACCACGAC CCTACTACTATCTCGCACCTGAAACAAGCTAACATGACTAACACCCTTAA TTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTT TTGCCCAAATGGGCCATTATCGAAGAATTCACAAAAAACAATAGCCTCAT CATCCCCACCATCATAGCCACCATCACCCTCCTTAACCTCTACTTCTACC TACGCCTAATCTACTCCACCTCAATCACACTACTCCCCATATCTAACAAC GTAAAAATAAAATGACAGTTTGAACATACAAAACCCACCCCATTCCTCCC CACACTCATCGCCCTTACCACGCTACTCCTACCTATCTCCCCTTTTATAC TAATAATCTTATAGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAG CCCTCAGTAAGTTGCAATACTTAATTTCTGCAACAGCTAAGGACTGCAAA ACCCCACTCTGCATCAACTGAACGCAAATCAGCCACTTTAATTAAGCTAA GCCCTTACTAGACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGC TAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGGAAA AAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCA ATTCAATATGAAAATCACCTCGGAGCTGGTAAAAAGAGGCCTAACCCCTG TCTTTAGATTTACAGTCCAATGCTTCACTCAGCCATTTTACCTCACCCCC ACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGACATTG GAACACTATACCTATTATTCGGCGCATGAGCTGGAGTCCTAGGCACAGCT CTAAGCCTCCTTATTCGAGCCGAGCTGGGCCAGCCAGGCAACCTTCTAGG TAACGACCACATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAA TCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTA GTTCCCCTAATAATCGGTGCCCCCGATATGGCGTTTCCCCGCATAAACAA CATAAGCTTCTGACTCTTACCTCCCTCTCTCCTACTCCTGCTCGCATCTG CTATAGTGGAGGCCGGAGCAGGAACAGGTTGAACAGTCTACCCTCCCTTA GCAGGGAACTACTCCCACCCTGGAGCCTCCGTAGACCTAACCATCTTCTC CTTACACCTAGCAGGTGTCTCCTCTATCTTAGGGGCCATCAATTTCATCA CAACAATTATCAATATAAAACCCCCTGCCATAACCCAATACCAAACGCCC CTCTTCGTCTGATCCGTCCTAATCACAGCAGTCCTACTTCTCCTATCTCT CCCAGTCCTAGCTGCTGGCATCACTATACTACTAACAGACCGCAACCTCA ACACCACCTTCTTCGACCCCGCCGGAGGAGGAGACCCCATTCTATACCAA CACCTATTCTGATTTTTCGGTCACCCTGAAGTTTATATTCTTATCCTACC AGGCTTCGGAATAATCTCCCATATTGTAACTTACTACTCCGGAAAAAAAG AACCATTTGGATACATAGGTATGGTCTGAGCTATGATATCAATTGGCTTC CTAGGGTTTATCGTGTGAGCACACCATATATTTACAGTAGGAATAGACGT AGACACACGAGCATATTTCACCTCCGCTACCATAATCATCGCTATCCCCA CCGGCGTCAAAGTATTTAGCTGACTCGCCACACTCCACGGAAGCAATATG AAATGATCTGCTGCAGTGCTCTGAGCCCTAGGATTCATCTTTCTTTTCAC CGTAGGTGGCCTGACTGGCATTGTATTAGCAAACTCATCACTAGACATCG TACTACACGACACGTACTACGTTGTAGCTCACTTCCACTATGTCCTATCA ATAGGAGCTGTATTTGCCATCATAGGAGGCTTCATTCACTGATTTCCCCT ATTCTCAGGCTACACCCTAGACCAAACCTACGCCAAAATCCATTTCACTA TCATATTCATCGGCGTAAATCTAACTTTCTTCCCACAACACTTTCTCGGC CTATCCGGAATGCCCCGACGTTACTCGGACTACCCCGATGCATACACCAC ATGAAACATCCTATCATCTGTAGGCTCATTCATTTCTCTAACAGCAGTAA TATTAATAATTTTCATGATTTGAGAAGCCTTCGCTTCGAAGCGAAAAGTC CTAATAGTAGAAGAACCCTCCATAAACCTGGAGTGACTATATGGATGCCC CCCACCCTACCACACATTCGAAGAACCCGTATACATAAAATCTAGACAaa aaaggaaggaatcgaaccccccaaagctggtttcaagccaaccccatggc ctccatgactttttcAAAAAGGTATTAGAAAAACCATTTCATAACTTTGT CAAAGTTAAATTATAGGCTAAATCCTATATATCTTAATGGCACATGCAGC GCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCA CCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTC CTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACAT CTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCA TCCTAGTCCTCATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGAC GAGGTCAACGATCCCTCCCTTACCATCAAATCAATTGGCCACCAATGGTA CTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACA TACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTT GACAATCGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTAC ATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAA CAGATGCAATTCCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGA CCGGGGGTATACTACGGTCAATGCTCTGAAATCTGTGGAGCAAACCACAG TTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAG GGCCCGTATTTACCCTATAGCACCCCCTCTACCCCCTCTAGAGCCCACTG TAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAAC ACCTCTTTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCA TAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATA TTAAACACAAACTACCACCTACCTCCCTCACCAAAGCCCATAAAAATAAA AAATTATAACAAACCCTGAGAACCAAAATGAACGAAAATCTGTTCGCTTC ATTCATTGCCCCCACAATCCTAGGCCTACCCGCCGCAGTACTGATCATTC TATTTCCCCCTCTATTGATCCCCACCTCCAAATATCTCATCAACAACCGA CTAATCACCACCCAACAATGACTAATCAAACTAACCTCAAAACAAATGAT AGCCATACACAACACTAAAGGACGAACCTGATCTCTTATACTAGTATCCT TAATCATTTTTATTGCCACAACTAACCTCCTCGGACTCCTGCCTCACTCA TTTACACCAACCACCCAACTATCTATAAACCTAGCCATGGCCATCCCCTT ATGAGCGGGCGCAGTGATTATAGGCTTTCGCTCTAAGATTAAAAATGCCC TAGCCCACTTCTTACCACAAGGCACACCTACACCCCTTATCCCCATACTA GTTATTATCGAAACCATCAGCCTACTCATTCAACCAATAGCCCTGGCCGT ACGCCTAACCGCTAACATTACTGCAGGCCACCTACTCATGCACCTAATTG GAAGCGCCACCCTAGCAATATCAACCATTAACCTTCCCTCTACACTTATC ATCTTCACAATTCTAATTCTACTGACTATCCTAGAAATCGCTGTCGCCTT AATCCAAGCCTACGTTTTCACACTTCTAGTAAGCCTCTACCTGCACGACA ACACATAATGACCCACCAATCACATGCCTATCATATAGTAAAACCCAGCC CATGACCCCTAACAGGGGCCCTCTCAGCCCTCCTAATGACCTCCGGCCTA GCCATGTGATTTCACTTCCACTCCATAACGCTCCTCATACTAGGCCTACT AACCAACACACTAACCATATACCAATGGTGGCGCGATGTAACACGAGAAA GCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATAC GGGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTT CTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAACTAGGAGGGC ACTGGCCCCCAACAGGCATCACCCCGCTAAATCCCCTAGAAGTCCCACTC CTAAACACATCCGTATTACTCGCATCAGGAGTATCAATCACCTGAGCTCA CCATAGTCTAATAGAAAACAACCGAAACCAAATAATTCAAGCACTGCTTA TTACAATTTTACTGGGTCTCTATTTTACCCTCCTACAAGCCTCAGAGTAC TTCGAGTCTCCCTTCACCATTTCCGACGGCATCTACGGCTCAACATTTTT TGTAGCCACAGGCTTCCACGGACTTCACGTCATTATTGGCTCAACTTTCC TCACTATCTGCTTCATCCGCCAACTAATATTTCACTTTACATCCAAACAT CACTTTGGCTTCGAAGCCGCCGCCTGATACTGGCATTTTGTAGATGTGGT TTGACTATTTCTGTATGTCTCCATCTATTGATGAGGGTCTTACTCTTTTA GTATAAATAGTACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAA AAAAGAGTAATAAACTTCGCCTTAATTTTAATAATCAACACCCTCCTAGC CTTACTACTAATAATTATTACATTTTGACTACCACAACTCAACGGCTACA TAGAAAAATCCACCCCTTACGAGTGCGGCTTCGACCCTATATCCCCCGCC CGCGTCCCTTTCTCCATAAAATTCTTCTTAGTAGCTATTACCTTCTTATT ATTTGATCTAGAAATTGCCCTCCTTTTACCCCTACCATGAGCCCTACAAA CAACTAACCTGCCACTAATAGTTATGTCATCCCTCTTATTAATCATCATC CTAGCCCTAAGTCTGGCCTATGAGTGACTACAAAAAGGATTAGACTGAGC CGAATTGGTATATAGTTTAAACAAAACGAATGATTTCGACTCATTAAATT ATGATAATCATATTTACCAAATGCCCCTCATTTACATAAATATTATACTA GCATTTACCATCTCACTTCTAGGAATACTAGTATATCGCTCACACCTCAT ATCCTCCCTACTATGCCTAGAAGGAATAATACTATCGCTGTTCATTATAG CTACTCTCATAACCCTCAACACCCACTCCCTCTTAGCCAATATTGTGCCT ATTGCCATACTAGTCTTTGCCGCCTGCGAAGCAGCGGTGGGCCTAGCCCT ACTAGTCTCAATCTCCAACACATATGGCCTAGACTACGTACATAACCTAA ACCTACTCCAATGCTAAAACTAATCGTCCCAACAATTATATTACTACCAC TGACATGACTTTCCAAAAAGCACATAATTTGAATCAACACAACCACCCAC AGCCTAATTATTAGCATCATCCCCCTACTATTTTTTAACCAAATCAACAA CAACCTATTTAGCTGTTCCCCAACCTTTTCCTCCGACCCCCTAACAACCC CCCTCCTAATACTAACTACCTGACTCCTACCCCTCACAATCATGGCAAGC CAACGCCACTTATCCAGCGAACCACTATCACGAAAAAAACTCTACCTCTC TATACTAATCTCCCTACAAATCTCCTTAATTATAACATTCACAGCCACAG AACTAATCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTG GCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACGCAGGCAC ATACTTCCTATTCTACACCCTAGTAGGCTCCCTTCCCCTACTCATCGCAC TAATTTACACTCACAACACCCTAGGCTCACTAAACATTCTACTACTCACT CTCACTGCCCAAGAACTATCAAACTCCTGAGCCAACAACTTAATATGACT AGCTTACACAATAGCTTTTATAGTAAAGATACCTCTTTACGGACTCCACT TATGACTCCCTAAAGCCCATGTCGAAGCCCCCATCGCTGGGTCAATAGTA CTTGCCGCAGTACTCTTAAAACTAGGCGGCTATGGTATAATACGCCTCAC ACTCATTCTCAACCCCCTGACAAAACACATAGCCTACCCCTTCCTTGTAC TATCCCTATGAGGCATAATTATAACAAGCTCCATCTGCCTACGACAAACA GACCTAAAATCGCTCATTGCATACTCTTCAATCAGCCACATAGCCCTCGT AGTAACAGCCATTCTCATCCAAACCCCCTGAAGCTTCACCGGCGCAGTCA TTCTCATAATCGCCCACGGACTCACATCCTCATTACTATTCTGCCTAGCA AACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGG ACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCC TCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCT GTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGG ACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAA CACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTC ACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCT ATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTT TAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTACGACCCCTT ATTTACCGAGAAAGCTCACAAGAACTGCTAACTCATGCCCCCATGTCTAA CAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTA GGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACA CTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACC ACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATC CATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCA TGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACC CAAACAACCCAGCTCTCCCTAAGCTTCAAACTAGACTACTTCTCCATAAT ATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCAC TGTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTA CTCATTTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATT CCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCA TCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCA GTCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATG ATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAA ACGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCA GGCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGA AGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAG CAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCA CTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGC AGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCT CCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAA CCACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCAT ACTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAG ATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACC TCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGG TTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAA ACGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCC TATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCC CACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTA AACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAAC ATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACT CACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCA ACTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTAT TTCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCC CTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACC TAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATC TCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTT CCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAAC CTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGT TCAACCAGTAACCACTACTAATCAACGCCCATAATCATACAAAGCCCCCG CACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATT ATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATA CTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAA CACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCA ATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATA AATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAA TAACACACCCGACCACACCGCTAACAATCAGTACTAAACCCCCATAAATA GGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACT CAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGA CCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATG ACCCCAATACGCAAAATTAACCCCCTAATAAAATTAATTAACCACTCATT CATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCT CACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTA GCCATACACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCA CATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCA ATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGC CTATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTAT CCTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGT GAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCC GCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTA CTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCT TACCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCAC GAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAAT CACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCT TCCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGC GACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACAT CAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCC CTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTA GCAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCG CCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTC TAACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGA CAAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAAC TATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTA TAAACTAATACACCAGTCTTGTAAACCGGAGACGAAAACCTTTTTCCAAG GACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAA GATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGG TACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTAC ATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCA CCTGTAGTACATAAAAACCCAACCCACATCAAACCCCCCCCCCCCATGCT TACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAAC TCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTT AACAGTACATAGTACATAAAGTCATTTACCGTACATAGCACATTACAGTC AAATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTG ACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCT CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC ATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCC CTTAAATAAGACATCACGATG tantan-13/src/0000755000000000000000000000000012037256344012057 5ustar rootroottantan-13/src/version.hh0000644000000000000000000000000512037256344014060 0ustar rootroot"13" tantan-13/src/mcf_score_matrix.hh0000644000000000000000000000372512037256344015733 0ustar rootroot// Copyright 2010 Martin C. Frith // This class reads and writes scoring matrices in NCBI BLAST format. // It can't be used directly: the idea is to copy it into a "fast" // matrix, and then use that. #ifndef MCF_SCORE_MATRIX_HH #define MCF_SCORE_MATRIX_HH #include #include #include namespace mcf { typedef unsigned char uchar; class ScoreMatrix { // These preserve (upper/lower)case of letters labeling rows & columns. friend std::istream &operator>>(std::istream &s, ScoreMatrix &m); friend std::ostream &operator<<(std::ostream &s, const ScoreMatrix &m); public: static const char* blosum62; // Initializes the matrix with simple match/mismatch scores. void initMatchMismatch(int matchScore, // usually > 0 int mismatchCost, // usually > 0 const std::string &letters); // case is preserved // Gets the minimum score in the matrix. int minScore() const; // Copies the ScoreMatrix into a "fast" matrix. // fastMatrixSize: the number of rows & columns in the fast matrix. // letterToIndex: mapping from letters, to indices in the fast // matrix. If any index is >= fastMatrixSize, an error is thrown. // defaultScore: for cells in the fast matrix that lack any // corresponding cell in the ScoreMatrix. // isCaseSensitive: if false, then each cell in the ScoreMatrix will // be copied to uppercase and lowercase locations in the fast // matrix. // It is possible that multiple ScoreMatrix cells might map to one // fast matrix cell: there is currently no check for this, and later // ones will overwrite earlier ones. void makeFastMatrix(int **fastMatrix, int fastMatrixSize, const uchar *letterToIndex, int defaultScore, bool isCaseSensitive) const; private: std::vector rowLetters; std::vector colLetters; std::vector< std::vector > scores; }; } #endif tantan-13/src/tantan.cc0000644000000000000000000003434012037256344013657 0ustar rootroot// Copyright 2010 Martin C. Frith #include "tantan.hh" #include // fill, max #include #include // pow, abs #include // cerr #include // accumulate #include #define BEG(v) ((v).empty() ? 0 : &(v).front()) #define END(v) ((v).empty() ? 0 : &(v).back() + 1) namespace tantan { void multiplyAll(std::vector &v, double factor) { for (std::vector::iterator i = v.begin(); i < v.end(); ++i) *i *= factor; } double firstRepeatOffsetProb(double probMult, int maxRepeatOffset) { if (probMult < 1 || probMult > 1) return (1 - probMult) / (1 - std::pow(probMult, maxRepeatOffset)); else return 1.0 / maxRepeatOffset; } void checkForwardAndBackwardTotals(double fTot, double bTot) { double x = std::abs(fTot); double y = std::abs(bTot); // ??? Is 1e6 suitable here ??? if (std::abs(fTot - bTot) > std::max(x, y) / 1e6) std::cerr << "tantan: warning: possible numeric inaccuracy\n" << "tantan: forward algorithm total: " << fTot << "\n" << "tantan: backward algorithm total: " << bTot << "\n"; } struct Tantan { enum { scaleStepSize = 16 }; const uchar *seqBeg; // start of the sequence const uchar *seqEnd; // end of the sequence const uchar *seqPtr; // current position in the sequence int maxRepeatOffset; const const_double_ptr *likelihoodRatioMatrix; double b2b; // transition probability from background to background double f2b; // transition probability from foreground to background double g2g; // transition probability from gap/indel to gap/indel //double f2g; // transition probability from foreground to gap/indel //double g2f; // transition probability from gap/indel to foreground double oneGapProb; // f2g * g2f double endGapProb; // f2g * 1 double f2f0; // foreground to foreground, if there are 0 indel transitions double f2f1; // foreground to foreground, if there is 1 indel transition double f2f2; // foreground to foreground, if there are 2 indel transitions double b2fDecay; double b2fGrowth; double b2fFirst; // background state to first foreground state double b2fLast; // background state to last foreground state double backgroundProb; std::vector foregroundProbs; std::vector insertionProbs; std::vector scaleFactors; Tantan(const uchar *seqBeg, const uchar *seqEnd, int maxRepeatOffset, const const_double_ptr *likelihoodRatioMatrix, double repeatProb, double repeatEndProb, double repeatOffsetProbDecay, double firstGapProb, double otherGapProb) { assert(maxRepeatOffset > 0); assert(repeatProb >= 0 && repeatProb < 1); // (if repeatProb==1, then any sequence is impossible) assert(repeatEndProb >= 0 && repeatEndProb <= 1); assert(repeatOffsetProbDecay > 0 && repeatOffsetProbDecay <= 1); assert(otherGapProb >= 0 && otherGapProb <= 1); assert(firstGapProb >= 0); assert(repeatEndProb + firstGapProb * 2 <= 1); this->seqBeg = seqBeg; this->seqEnd = seqEnd; this->seqPtr = seqBeg; this->maxRepeatOffset = maxRepeatOffset; this->likelihoodRatioMatrix = likelihoodRatioMatrix; b2b = 1 - repeatProb; f2b = repeatEndProb; g2g = otherGapProb; //f2g = firstGapProb; //g2f = 1 - otherGapProb; oneGapProb = firstGapProb * (1 - otherGapProb); endGapProb = firstGapProb * 1; f2f0 = 1 - repeatEndProb; f2f1 = 1 - repeatEndProb - firstGapProb; f2f2 = 1 - repeatEndProb - firstGapProb * 2; b2fDecay = repeatOffsetProbDecay; b2fGrowth = 1 / repeatOffsetProbDecay; b2fFirst = repeatProb * firstRepeatOffsetProb(b2fDecay, maxRepeatOffset); b2fLast = repeatProb * firstRepeatOffsetProb(b2fGrowth, maxRepeatOffset); foregroundProbs.resize(maxRepeatOffset); insertionProbs.resize(maxRepeatOffset - 1); scaleFactors.resize((seqEnd - seqBeg) / scaleStepSize); } void initializeForwardAlgorithm() { backgroundProb = 1.0; std::fill(foregroundProbs.begin(), foregroundProbs.end(), 0.0); std::fill(insertionProbs.begin(), insertionProbs.end(), 0.0); } double forwardTotal() { double fromForeground = std::accumulate(foregroundProbs.begin(), foregroundProbs.end(), 0.0); fromForeground *= f2b; double total = backgroundProb * b2b + fromForeground; assert(total > 0); return total; } void initializeBackwardAlgorithm() { backgroundProb = b2b; std::fill(foregroundProbs.begin(), foregroundProbs.end(), f2b); std::fill(insertionProbs.begin(), insertionProbs.end(), 0.0); } double backwardTotal() { assert(backgroundProb > 0); return backgroundProb; } void calcForwardTransitionProbsWithGaps() { double fromBackground = backgroundProb * b2fLast; double *foregroundPtr = &foregroundProbs.back(); double f = *foregroundPtr; double fromForeground = f; if (insertionProbs.empty()) { *foregroundPtr = fromBackground + f * f2f0; } else { double *insertionPtr = &insertionProbs.back(); double i = *insertionPtr; *foregroundPtr = fromBackground + f * f2f1 + i * endGapProb; double d = f; --foregroundPtr; fromBackground *= b2fGrowth; while (foregroundPtr > &foregroundProbs.front()) { f = *foregroundPtr; fromForeground += f; i = *(insertionPtr - 1); *foregroundPtr = fromBackground + f * f2f2 + (i + d) * oneGapProb; *insertionPtr = f + i * g2g; d = f + d * g2g; --foregroundPtr; --insertionPtr; fromBackground *= b2fGrowth; } f = *foregroundPtr; fromForeground += f; *foregroundPtr = fromBackground + f * f2f1 + d * endGapProb; *insertionPtr = f; } fromForeground *= f2b; backgroundProb = backgroundProb * b2b + fromForeground; } void calcBackwardTransitionProbsWithGaps() { double toBackground = f2b * backgroundProb; double *foregroundPtr = &foregroundProbs.front(); double f = *foregroundPtr; double toForeground = f; if (insertionProbs.empty()) { *foregroundPtr = toBackground + f2f0 * f; } else { double *insertionPtr = &insertionProbs.front(); double i = *insertionPtr; *foregroundPtr = toBackground + f2f1 * f + i; double d = endGapProb * f; ++foregroundPtr; toForeground *= b2fGrowth; while (foregroundPtr < &foregroundProbs.back()) { f = *foregroundPtr; toForeground += f; i = *(insertionPtr + 1); *foregroundPtr = toBackground + f2f2 * f + (i + d); double oneGapProb_f = oneGapProb * f; *insertionPtr = oneGapProb_f + g2g * i; d = oneGapProb_f + g2g * d; ++foregroundPtr; ++insertionPtr; toForeground *= b2fGrowth; } f = *foregroundPtr; toForeground += f; *foregroundPtr = toBackground + f2f1 * f + d; *insertionPtr = endGapProb * f; } toForeground *= b2fLast; backgroundProb = b2b * backgroundProb + toForeground; } void calcForwardTransitionProbs() { if (endGapProb > 0) return calcForwardTransitionProbsWithGaps(); double fromBackground = backgroundProb * b2fLast; double fromForeground = 0; double *foregroundPtr = END(foregroundProbs); double *foregroundBeg = BEG(foregroundProbs); while (foregroundPtr > foregroundBeg) { --foregroundPtr; double f = *foregroundPtr; fromForeground += f; *foregroundPtr = fromBackground + f * f2f0; fromBackground *= b2fGrowth; } fromForeground *= f2b; backgroundProb = backgroundProb * b2b + fromForeground; } void calcBackwardTransitionProbs() { if (endGapProb > 0) return calcBackwardTransitionProbsWithGaps(); double toBackground = f2b * backgroundProb; double toForeground = 0; double *foregroundPtr = BEG(foregroundProbs); double *foregroundEnd = END(foregroundProbs); while (foregroundPtr < foregroundEnd) { toForeground *= b2fGrowth; double f = *foregroundPtr; toForeground += f; *foregroundPtr = toBackground + f2f0 * f; ++foregroundPtr; } toForeground *= b2fLast; backgroundProb = b2b * backgroundProb + toForeground; } void addEndCounts(double forwardProb, double totalProb, double *transitionCounts) { double toEnd = forwardProb * b2b / totalProb; transitionCounts[0] += toEnd; } void addTransitionCounts(double forwardProb, double totalProb, double *transitionCounts) { double toBg = forwardProb * b2b / totalProb; double toFg = forwardProb * b2fFirst / totalProb; transitionCounts[0] += backgroundProb * toBg; for (double *i = BEG(foregroundProbs); i < END(foregroundProbs); ++i) { ++transitionCounts; *transitionCounts += *i * toFg; toFg *= b2fDecay; } } void calcEmissionProbs() { const double *lrRow = likelihoodRatioMatrix[*seqPtr]; bool isNearSeqBeg = (seqPtr - seqBeg < maxRepeatOffset); const uchar *seqStop = isNearSeqBeg ? seqBeg : seqPtr - maxRepeatOffset; double *foregroundPtr = BEG(foregroundProbs); const uchar *offsetPtr = seqPtr; while (offsetPtr > seqStop) { --offsetPtr; *foregroundPtr *= lrRow[*offsetPtr]; ++foregroundPtr; } while (foregroundPtr < END(foregroundProbs)) { *foregroundPtr *= 0; ++foregroundPtr; } } void rescale(double scale) { backgroundProb *= scale; multiplyAll(foregroundProbs, scale); multiplyAll(insertionProbs, scale); } void rescaleForward() { if ((seqPtr - seqBeg) % scaleStepSize == scaleStepSize - 1) { assert(backgroundProb > 0); double scale = 1 / backgroundProb; scaleFactors[(seqPtr - seqBeg) / scaleStepSize] = scale; rescale(scale); } } void rescaleBackward() { if ((seqPtr - seqBeg) % scaleStepSize == scaleStepSize - 1) { double scale = scaleFactors[(seqPtr - seqBeg) / scaleStepSize]; rescale(scale); } } void calcRepeatProbs(float *letterProbs) { initializeForwardAlgorithm(); while (seqPtr < seqEnd) { calcForwardTransitionProbs(); calcEmissionProbs(); rescaleForward(); *letterProbs = static_cast(backgroundProb); ++letterProbs; ++seqPtr; } double z = forwardTotal(); initializeBackwardAlgorithm(); while (seqPtr > seqBeg) { --seqPtr; --letterProbs; double nonRepeatProb = *letterProbs * backgroundProb / z; // Convert nonRepeatProb to a float, so that it is more likely // to be exactly 1 when it should be, e.g. for the 1st letter of // a sequence: *letterProbs = 1 - static_cast(nonRepeatProb); rescaleBackward(); calcEmissionProbs(); calcBackwardTransitionProbs(); } double z2 = backwardTotal(); checkForwardAndBackwardTotals(z, z2); } void countTransitions(double *transitionCounts) { std::vector p(seqEnd - seqBeg); float *letterProbs = BEG(p); initializeForwardAlgorithm(); while (seqPtr < seqEnd) { *letterProbs = static_cast(backgroundProb); calcForwardTransitionProbs(); calcEmissionProbs(); rescaleForward(); ++letterProbs; ++seqPtr; } double z = forwardTotal(); addEndCounts(backgroundProb, z, transitionCounts); initializeBackwardAlgorithm(); while (seqPtr > seqBeg) { --seqPtr; --letterProbs; rescaleBackward(); calcEmissionProbs(); addTransitionCounts(*letterProbs, z, transitionCounts); calcBackwardTransitionProbs(); } double z2 = backwardTotal(); checkForwardAndBackwardTotals(z, z2); } }; void maskSequences(uchar *seqBeg, uchar *seqEnd, int maxRepeatOffset, const const_double_ptr *likelihoodRatioMatrix, double repeatProb, double repeatEndProb, double repeatOffsetProbDecay, double firstGapProb, double otherGapProb, double minMaskProb, const uchar *maskTable) { std::vector p(seqEnd - seqBeg); float *probabilities = BEG(p); getProbabilities(seqBeg, seqEnd, maxRepeatOffset, likelihoodRatioMatrix, repeatProb, repeatEndProb, repeatOffsetProbDecay, firstGapProb, otherGapProb, probabilities); maskProbableLetters(seqBeg, seqEnd, probabilities, minMaskProb, maskTable); } void getProbabilities(const uchar *seqBeg, const uchar *seqEnd, int maxRepeatOffset, const const_double_ptr *likelihoodRatioMatrix, double repeatProb, double repeatEndProb, double repeatOffsetProbDecay, double firstGapProb, double otherGapProb, float *probabilities) { Tantan tantan(seqBeg, seqEnd, maxRepeatOffset, likelihoodRatioMatrix, repeatProb, repeatEndProb, repeatOffsetProbDecay, firstGapProb, otherGapProb); tantan.calcRepeatProbs(probabilities); } void maskProbableLetters(uchar *seqBeg, uchar *seqEnd, const float *probabilities, double minMaskProb, const uchar *maskTable) { while (seqBeg < seqEnd) { if (*probabilities >= minMaskProb) *seqBeg = maskTable[*seqBeg]; ++probabilities; ++seqBeg; } } void countTransitions(const uchar *seqBeg, const uchar *seqEnd, int maxRepeatOffset, const const_double_ptr *likelihoodRatioMatrix, double repeatProb, double repeatEndProb, double repeatOffsetProbDecay, double firstGapProb, double otherGapProb, double *transitionCounts) { Tantan tantan(seqBeg, seqEnd, maxRepeatOffset, likelihoodRatioMatrix, repeatProb, repeatEndProb, repeatOffsetProbDecay, firstGapProb, otherGapProb); tantan.countTransitions(transitionCounts); } } tantan-13/src/mcf_score_matrix_probs.cc0000644000000000000000000000211712037256344017120 0ustar rootroot// Copyright 2010 Martin C. Frith #include "mcf_score_matrix_probs.hh" namespace lambda { extern "C" { #include "CA_code/lambda_calculator.h" } } namespace mcf { void ScoreMatrixProbs::setBad() { lambda_ = -1; letterProbs1_.clear(); letterProbs2_.clear(); } void ScoreMatrixProbs::init(const const_int_ptr *scoreMatrix, unsigned alphabetSize) { // We need to pass the parameters as 1-based pointers, hence the +1s // and -1s. std::vector cells(alphabetSize * alphabetSize + 1); std::vector pointers(alphabetSize + 1); for (unsigned i = 0; i < alphabetSize; ++i) { pointers[i+1] = &cells[i * alphabetSize]; for (unsigned j = 0; j < alphabetSize; ++j) { cells[i * alphabetSize + j + 1] = scoreMatrix[i][j]; } } letterProbs1_.resize(alphabetSize); letterProbs2_.resize(alphabetSize); lambda_ = lambda::calculate_lambda(&pointers[0], alphabetSize, &letterProbs1_[0] - 1, &letterProbs2_[0] - 1); if (lambda_ < 0) setBad(); } } tantan-13/src/tantan.hh0000644000000000000000000001116412037256344013670 0ustar rootroot// Copyright 2010 Martin C. Frith // These are routines for masking simple regions (low-complexity and // short-period tandem repeats) in biological sequences. To // understand them in detail, see the published article (in // preparation). // Typically, you would just use the maskSequences routine. The other // routines are more specialized. The inputs to maskSequences are as // follows. // seqBeg: pointer to the start of the sequence. // seqEnd: pointer to one-past-the-end of the sequence. // maxRepeatOffset: the maximum tandem-repeat period-size to consider. // likelihoodRatioMatrix: a matrix of the form Qxy / (Px * Py), where // Qxy is the probability of seeing letters x and y in equivalent // positions of a tandem repeat, and Px and Py are the background // probabilities of the letters. This matrix is related to a scoring // matrix (e.g. blosum62) by: // likelihoodRatioMatrix[x][y] = exp(lambda * scoringMatrix[x][y]). // The uchars in the sequence will be used as indexes into the matrix // (e.g. likelihoodRatioMatrix[x][y]). So typically the uchars are // small integers (e.g. 0, 1, 2, 3). The matrix needs to have entries // for any uchars that can occur. // repeatProb: the probability of a repetitive segment starting per position. // repeatEndProb: the probability of a repetitive segment ending per position. // repeatOffsetProbDecay: the probability of a period-(i) repeat // divided by the probability of a period-(i-1) repeat. // firstGapProb: the probability of initiating an insertion or // deletion in a repetitive region. // otherGapProb: the probability of extending an insertion or deletion // by one more letter. // minMaskProb: mask letters whose posterior probability of being // repetitive is >= this. // maskTable: how to do the masking. Letter x will be changed to // maskTable[x]. So maskTable needs to have entries for any uchar // that can occur. // Typical usage: // tantan::maskSequences(seqBeg, seqEnd, 100, likelihoodRatioMatrix, // 0.005, 0.05, 0.9, 0, 0, 0.5, maskTable) #ifndef TANTAN_HH #define TANTAN_HH namespace tantan { typedef unsigned char uchar; typedef const double *const_double_ptr; void maskSequences(uchar *seqBeg, uchar *seqEnd, int maxRepeatOffset, const const_double_ptr *likelihoodRatioMatrix, double repeatProb, double repeatEndProb, double repeatOffsetProbDecay, double firstGapProb, double otherGapProb, double minMaskProb, const uchar *maskTable); // The following routine gets the posterior probability that each // letter is repetitive. It stores the results in "probabilities", // which must point to enough pre-allocated space to fit the results. void getProbabilities(const uchar *seqBeg, const uchar *seqEnd, int maxRepeatOffset, const const_double_ptr *likelihoodRatioMatrix, double repeatProb, double repeatEndProb, double repeatOffsetProbDecay, double firstGapProb, double otherGapProb, float *probabilities); // The following routine masks each letter whose corresponding entry // in "probabilities" is >= minMaskProb. void maskProbableLetters(uchar *seqBeg, uchar *seqEnd, const float *probabilities, double minMaskProb, const uchar *maskTable); // The following routine counts the expected number of transitions // from the background (non-repeat) state to other states. It adds // the results to "transitionCounts", which must point to // pre-initialized space for (maxRepeatOffset+1) items. The // background->background transition count is stored in // transitionCounts[0]. The background->(period-i repeat) transition // count is stored in transitionCounts[i]. // (In this routine, the HMM begin and end states are counted as // background states. Thus, begin->X is added to background->X, and // X->end is added to X->background.) void countTransitions(const uchar *seqBeg, const uchar *seqEnd, int maxRepeatOffset, const const_double_ptr *likelihoodRatioMatrix, double repeatProb, double repeatEndProb, double repeatOffsetProbDecay, double firstGapProb, double otherGapProb, double *transitionCounts); } #endif tantan-13/src/mcf_util.hh0000644000000000000000000000206312037256344014203 0ustar rootroot// Copyright 2010 Martin C. Frith #ifndef MCF_UTIL_HH #define MCF_UTIL_HH #include #include #include #include #include namespace mcf { // open an input file, but if the name is "-", just return cin std::istream &openIn(const std::string &fileName, std::ifstream &ifs); // open an output file, but if the name is "-", just return cout std::ostream &openOut(const std::string &fileName, std::ofstream &ofs); template std::string stringify(const T &x) { std::ostringstream oss; oss << x; assert(oss); return oss.str(); } template void unstringify(T& x, const std::string &s) { std::istringstream iss(s); if (!(iss >> x) || !(iss >> std::ws).eof()) throw std::runtime_error("can't interpret: " + s); } template void unfilify(T& x, const std::string &fileName) { std::ifstream ifs; std::istream &input = openIn(fileName, ifs); input >> x; if (!input) throw std::runtime_error("can't read file: " + fileName); // check for junk at end of file? } } #endif tantan-13/src/mcf_util.cc0000644000000000000000000000105712037256344014173 0ustar rootroot// Copyright 2010 Martin C. Frith #include "mcf_util.hh" #include namespace mcf { std::istream &openIn(const std::string &fileName, std::ifstream &ifs) { if (fileName == "-") return std::cin; ifs.open(fileName.c_str()); if (!ifs) throw std::runtime_error("can't open file: " + fileName); return ifs; } std::ostream &openOut(const std::string &fileName, std::ofstream &ofs) { if (fileName == "-") return std::cout; ofs.open(fileName.c_str()); if (!ofs) throw std::runtime_error("can't open file: " + fileName); return ofs; } } tantan-13/src/mcf_tantan_options.cc0000644000000000000000000001112212037256344016250 0ustar rootroot// Copyright 2010 Martin C. Frith #include "mcf_tantan_options.hh" #include "mcf_util.hh" #include #include // EXIT_SUCCESS #include #include namespace mcf { typedef std::runtime_error Error; static void badopt(char opt, const char *arg) { throw Error(std::string("bad option value: -") + opt + " " + arg); } static void writeAndQuit(const std::string &text) { std::cout << text; throw EXIT_SUCCESS; } static int myGetopt(int argc, char **argv, const char *optstring, const std::string &help, const std::string &version) { if (optind < argc) { std::string nextarg = argv[optind]; if (nextarg == "--help") writeAndQuit(help); if (nextarg == "--version") writeAndQuit(version); } return getopt(argc, argv, optstring); } std::istream &operator>>(std::istream &s, TantanOptions::OutputType &x) { int i = 0; s >> i; if (i < 0 || i > 3) s.setstate(std::ios::failbit); if (s) x = static_cast(i); return s; } TantanOptions::TantanOptions() : isProtein(false), maskSymbol(0), isPreserveLowercase(false), scoreMatrixFileName(0), repeatProb(0.005), repeatEndProb(0.05), maxCycleLength(-1), // depends on isProtein repeatOffsetProbDecay(0.9), gapExistenceCost(0), gapExtensionCost(-1), // means: no gaps minMaskProb(0.5), outputType(maskOut), indexOfFirstNonOptionArgument(-1) {} void TantanOptions::fromArgs(int argc, char **argv) { std::string help = "\ Usage: tantan [options] fasta-sequence-file(s)\n\ Find simple repeats in sequences\n\ \n\ Options (default settings):\n\ -p interpret the sequences as proteins\n\ -x letter to use for masking, instead of lowercase\n\ -c preserve uppercase/lowercase in non-masked regions\n\ -m file for letter pair scores (+1/-1, but -p selects BLOSUM62)\n\ -r probability of a repeat starting per position (" + stringify(repeatProb) + ")\n\ -e probability of a repeat ending per position (" + stringify(repeatEndProb) + ")\n\ -w maximum tandem repeat period to consider (100, but -p selects 50)\n\ -d probability decay per period (" + stringify(repeatOffsetProbDecay) + ")\n\ -a gap existence cost (" + stringify(gapExistenceCost) + ")\n\ -b gap extension cost (infinite: no gaps)\n\ -s minimum repeat probability for masking (" + stringify(minMaskProb) + ")\n\ -f output type: 0=masked sequence, 1=repeat probabilities,\n\ 2=repeat counts, 3=BED (" + stringify(outputType) + ")\n\ -h, --help show help message, then exit\n\ --version show version information, then exit\n\ \n\ Report bugs to: tantan@cbrc.jp\n\ Home page: http://www.cbrc.jp/tantan/\n\ "; std::string version = "tantan " #include "version.hh" "\n"; const char *optstring = "px:cm:r:e:w:d:a:b:s:f:h"; int i; while ((i = myGetopt(argc, argv, optstring, help, version)) != -1) { char c = static_cast(i); switch (c) { case 'p': isProtein = true; break; case 'x': unstringify(maskSymbol, optarg); break; case 'c': isPreserveLowercase = true; break; case 'm': scoreMatrixFileName = optarg; break; case 'r': unstringify(repeatProb, optarg); if (repeatProb < 0 || repeatProb >= 1) badopt(c, optarg); break; case 'e': unstringify(repeatEndProb, optarg); if (repeatEndProb < 0 || repeatEndProb > 1) badopt(c, optarg); break; case 'w': unstringify(maxCycleLength, optarg); if (maxCycleLength <= 0 ) badopt(c, optarg); break; case 'd': unstringify(repeatOffsetProbDecay, optarg); if (repeatOffsetProbDecay <= 0 || repeatOffsetProbDecay > 1) badopt(c, optarg); break; case 'a': unstringify(gapExistenceCost, optarg); break; case 'b': unstringify(gapExtensionCost, optarg); if (gapExtensionCost <= 0) badopt(c, optarg); break; case 's': unstringify(minMaskProb, optarg); // don't bother checking for stupid values? break; case 'f': unstringify(outputType, optarg); break; case 'h': writeAndQuit(help); case '?': throw Error("bad option"); } } if (gapExtensionCost > 0 && gapExistenceCost + gapExtensionCost <= 0) throw Error("gap existence + extension cost is too low"); if (maxCycleLength < 0) maxCycleLength = (isProtein ? 50 : 100); indexOfFirstNonOptionArgument = optind; } } tantan-13/src/mcf_alphabet.hh0000644000000000000000000000246212037256344015011 0ustar rootroot// Copyright 2010 Martin C. Frith // An "Alphabet" consists of two things: // 1) A mapping from ASCII letters to small integers. // 2) A distinction between "normal" and "abnormal" letters. The // letters that map to the first "size" integers are normal. For // example, for DNA, ACGT would be normal. #ifndef MCF_ALPHABET_HH #define MCF_ALPHABET_HH #include namespace mcf { typedef unsigned char uchar; struct Alphabet { static const char* dna; static const char* protein; static const unsigned capacity = 256; // Initializes the Alphabet with the given normal letters. void fromString(const std::string &normalLetters); // case is preserved // Makes lowercase letters map to the same numbers that uppercase // letters do. void makeCaseInsensitive(); // Maps letters to numbers in the given range. void encodeInPlace(uchar *beg, uchar *end) const; // Maps numbers back to letters in the given range. void decodeInPlace(uchar *beg, uchar *end) const; unsigned size; // number of "normal" letters in the alphabet uchar lettersToNumbers[capacity]; uchar numbersToLetters[capacity]; uchar numbersToUppercase[capacity]; uchar numbersToLowercase[capacity]; private: void addLetters(const std::string &letters, uchar &number); void initCaseConversions(); }; } #endif tantan-13/src/mcf_fasta_sequence.hh0000644000000000000000000000077312037256344016222 0ustar rootroot// Copyright 2010, 2011 Martin C. Frith #ifndef MCF_FASTA_SEQUENCE_HH #define MCF_FASTA_SEQUENCE_HH #include #include #include namespace mcf { typedef unsigned char uchar; struct FastaSequence { std::string title; std::vector sequence; // Used for fastq: std::string secondTitle; std::vector qualityCodes; }; std::istream &operator>>(std::istream &s, FastaSequence &f); std::ostream &operator<<(std::ostream &s, const FastaSequence &f); } #endif tantan-13/src/mcf_fasta_sequence.cc0000644000000000000000000000565012037256344016207 0ustar rootroot// Copyright 2010, 2011 Martin C. Frith #include "mcf_fasta_sequence.hh" #include // isspace //#include // for debugging #include #include // istreambuf_iterator, ostreambuf_iterator #include namespace mcf { static void readSequence(std::istream &s, std::vector &sequence, char delimiter) { if (!s) return; std::istreambuf_iterator inpos(s); std::istreambuf_iterator endpos; while (inpos != endpos) { char c = *inpos; if (c == delimiter) break; uchar u = static_cast(c); if (!std::isspace(u)) sequence.push_back(u); ++inpos; } } static void readQualityCodes(std::istream &s, std::vector &qualityCodes, std::vector::size_type howMany) { if (!s) return; std::istreambuf_iterator inpos(s); std::istreambuf_iterator endpos; while (inpos != endpos) { if (qualityCodes.size() == howMany) break; char c = *inpos; uchar u = static_cast(c); if (!std::isspace(u)) qualityCodes.push_back(u); ++inpos; } } std::istream &operator>>(std::istream &s, FastaSequence &f) { std::string title; std::vector sequence; std::string secondTitle; std::vector qualityCodes; char firstChar = '>'; s >> firstChar; if (firstChar != '>' && firstChar != '@') s.setstate(std::ios::failbit); getline(s, title); if (firstChar == '>') { readSequence(s, sequence, '>'); } else { readSequence(s, sequence, '+'); char secondChar; s >> secondChar; getline(s, secondTitle); readQualityCodes(s, qualityCodes, sequence.size()); // perhaps check whether we read enough quality codes } if (!s) return s; f.title.swap(title); f.sequence.swap(sequence); f.secondTitle.swap(secondTitle); f.qualityCodes.swap(qualityCodes); return s; } static void writeOneLine(std::ostream &s, const std::vector &v) { std::ostreambuf_iterator o(s); std::vector::const_iterator b = v.begin(); std::vector::const_iterator e = v.end(); while (b != e) { o = static_cast(*b); ++b; } o = '\n'; } static void writeMultiLines(std::ostream &s, const std::vector &v) { const int lettersPerLine = 50; // ? std::ostreambuf_iterator o(s); std::vector::const_iterator b = v.begin(); std::vector::const_iterator e = v.end(); std::vector::const_iterator i = b; while (i != e) { o = static_cast(*i); ++i; if (i - b == lettersPerLine || i == e) { o = '\n'; b = i; } } } std::ostream &operator<<(std::ostream &s, const FastaSequence &f) { if (f.qualityCodes.empty()) { s << '>' << f.title << '\n'; writeMultiLines(s, f.sequence); } else { s << '@' << f.title << '\n'; writeOneLine(s, f.sequence); s << '+' << f.secondTitle << '\n'; writeOneLine(s, f.qualityCodes); } return s; } } tantan-13/src/Makefile0000644000000000000000000000106112037256344013515 0ustar rootrootCXXFLAGS = -O3 -Wall -W -Wcast-qual -Wswitch-enum -Wundef \ -Wcast-align -Wold-style-cast # -Wconversion CFLAGS = -Wall COBJ = CA_code/lambda_calculator.o all: tantan tantan: *.cc *.hh version.hh Makefile $(COBJ) $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) -o $@ *.cc $(COBJ) $(COBJ): CA_code/*.c CA_code/*.h Makefile $(CC) $(CPPFLAGS) $(CFLAGS) -c -o $@ CA_code/lambda_calculator.c clean: rm -f tantan $(COBJ) VERSION = \"`hg id -n`\" version.hh: FORCE if test -e ../.hg; \ then echo $(VERSION) | cmp -s $@ - || echo $(VERSION) > $@ ; \ fi FORCE: tantan-13/src/mcf_alphabet.cc0000644000000000000000000000421212037256344014772 0ustar rootroot// Copyright 2010 Martin C. Frith #include "mcf_alphabet.hh" #include // fill_n #include #include namespace mcf { // consts have internal linkage, apparently. // If I make these into static const class members, g++ 4.0.1 complains. const uchar defaultNumber = 255; const uchar defaultLetter = '!'; const char* Alphabet::dna = "ACGT"; // U=selenocysteine, O=pyrrolysine, *=stop? const char* Alphabet::protein = "ACDEFGHIKLMNPQRSTVWY"; void Alphabet::fromString(const std::string &normalLetters) { std::fill_n(lettersToNumbers, capacity, defaultNumber); std::fill_n(numbersToLetters, capacity, defaultLetter); uchar number = 0; addLetters(normalLetters, number); size = number; addLetters("ABCDEFGHIJKLMNOPQRSTUVWXYZ", number); addLetters("abcdefghijklmnopqrstuvwxyz", number); addLetters("*", number); // sometimes appears in protein sequences initCaseConversions(); } void Alphabet::addLetters(const std::string &letters, uchar &number) { for (unsigned i = 0; i < letters.size(); ++i) { uchar letter = static_cast(letters[i]); if (lettersToNumbers[letter] == defaultNumber) { lettersToNumbers[letter] = number; numbersToLetters[number] = letter; ++number; } } } void Alphabet::initCaseConversions() { for (unsigned i = 0; i < capacity; ++i) { uchar letter = numbersToLetters[i]; numbersToUppercase[i] = lettersToNumbers[std::toupper(letter)]; numbersToLowercase[i] = lettersToNumbers[std::tolower(letter)]; } } void Alphabet::makeCaseInsensitive() { for (unsigned i = 0; i < capacity; ++i) { lettersToNumbers[i] = lettersToNumbers[std::toupper(i)]; } } void Alphabet::encodeInPlace(uchar *beg, uchar *end) const { while (beg != end) { uchar letter = *beg; uchar number = lettersToNumbers[letter]; if (number == defaultNumber) { throw std::runtime_error(std::string("bad symbol: ") + char(letter)); } *beg = number; ++beg; } } void Alphabet::decodeInPlace(uchar *beg, uchar *end) const { while (beg != end) { uchar number = *beg; uchar letter = numbersToLetters[number]; *beg = letter; ++beg; } } } tantan-13/src/mcf_tantan_options.hh0000644000000000000000000000111312037256344016261 0ustar rootroot// Copyright 2010 Martin C. Frith #ifndef MCF_TANTAN_OPTIONS_HH #define MCF_TANTAN_OPTIONS_HH namespace mcf { struct TantanOptions { TantanOptions(); void fromArgs(int argc, char** argv); bool isProtein; char maskSymbol; bool isPreserveLowercase; const char *scoreMatrixFileName; double repeatProb; double repeatEndProb; int maxCycleLength; double repeatOffsetProbDecay; int gapExistenceCost; int gapExtensionCost; double minMaskProb; enum OutputType { maskOut, probOut, countOut, bedOut } outputType; int indexOfFirstNonOptionArgument; }; } #endif tantan-13/src/tantan_app.cc0000644000000000000000000002313412037256344014516 0ustar rootroot// Copyright 2010 Martin C. Frith // Mask simple regions (low complexity & short-period tandem repeats) // in biological sequences. #include "mcf_alphabet.hh" #include "mcf_fasta_sequence.hh" #include "mcf_score_matrix.hh" #include "mcf_score_matrix_probs.hh" #include "mcf_tantan_options.hh" #include "mcf_util.hh" #include "tantan.hh" #include // copy, fill_n #include #include #include // strchr #include // EXIT_SUCCESS, EXIT_FAILURE #include // exception #include #include #include // bad_alloc #define BEG(v) ((v).empty() ? 0 : &(v).front()) #define END(v) ((v).empty() ? 0 : &(v).back() + 1) typedef std::runtime_error Error; using namespace mcf; // move this function to a reusable file? bool isDubiousDna(const uchar *beg, const uchar *end) { int badLetters = 0; if (end - beg > 100) end = beg + 100; // just check the first 100 letters while (beg < end) { if (!std::strchr("AaCcGgTtNnUu", *beg)) { ++badLetters; if (badLetters > 10) return true; } ++beg; } return false; } namespace { TantanOptions options; Alphabet alphabet; enum { scoreMatrixSize = 64 }; int fastMatrix[scoreMatrixSize][scoreMatrixSize]; int *fastMatrixPointers[scoreMatrixSize]; double probMatrix[scoreMatrixSize][scoreMatrixSize]; double *probMatrixPointers[scoreMatrixSize]; double firstGapProb; double otherGapProb; uchar hardMaskTable[Alphabet::capacity]; const uchar *maskTable; std::vector transitionCounts; double transitionTotal; } void initAlphabet() { if (options.isProtein) alphabet.fromString(Alphabet::protein); else alphabet.fromString(Alphabet::dna); } void initScoresAndProbabilities() { std::copy(fastMatrix, fastMatrix + scoreMatrixSize, fastMatrixPointers); std::copy(probMatrix, probMatrix + scoreMatrixSize, probMatrixPointers); ScoreMatrix scoreMatrix; if (options.scoreMatrixFileName) unfilify(scoreMatrix, options.scoreMatrixFileName); else if (options.isProtein) unstringify(scoreMatrix, ScoreMatrix::blosum62); else scoreMatrix.initMatchMismatch(1, 1, "ACGTU"); // allow for RNA scoreMatrix.makeFastMatrix(fastMatrixPointers, scoreMatrixSize, alphabet.lettersToNumbers, scoreMatrix.minScore(), false); ScoreMatrixProbs smp(fastMatrixPointers, alphabet.size); if (smp.isBad()) throw Error("can't calculate probabilities for this score matrix"); for (int i = 0; i < scoreMatrixSize; ++i) for (int j = 0; j < scoreMatrixSize; ++j) probMatrix[i][j] = std::exp(smp.lambda() * fastMatrix[i][j]); if (options.gapExtensionCost > 0) { int firstGapCost = options.gapExistenceCost + options.gapExtensionCost; firstGapProb = std::exp(-smp.lambda() * firstGapCost); otherGapProb = std::exp(-smp.lambda() * options.gapExtensionCost); // the gap existence cost includes the gap ending cost: firstGapProb /= (1 - otherGapProb); // XXX check if firstGapProb is too high } //std::cerr << "lambda: " << smp.lambda() << "\n"; //std::cerr << "firstGapProb: " << firstGapProb << "\n"; //std::cerr << "otherGapProb: " << otherGapProb << "\n"; } void initMaskTable() { uchar maskSymbol = static_cast(options.maskSymbol); uchar maskNumber = alphabet.lettersToNumbers[maskSymbol]; std::fill_n(hardMaskTable, Alphabet::capacity, maskNumber); if (maskSymbol == 0) maskTable = alphabet.numbersToLowercase; else maskTable = hardMaskTable; } std::string firstWord(const std::string &s) { std::string word; std::istringstream iss(s); iss >> word; return word; // might be empty } void writeBedLine(const std::string &seqName, const float *origin, const float *beg, const float *end, std::ostream &out) { out << seqName << '\t' << (beg - origin) << '\t' << (end - origin) << '\n'; } void writeBed(const float *probBeg, const float *probEnd, const std::string &seqName, std::ostream &output) { if (seqName.empty()) throw Error("missing sequence name"); const float *maskBeg = 0; // pointer to start of masked tract for (const float *i = probBeg; i < probEnd; ++i) { if (*i >= options.minMaskProb) { // this position is masked if (maskBeg == 0) maskBeg = i; } else { // this position is not masked if (maskBeg) writeBedLine(seqName, probBeg, maskBeg, i, output); maskBeg = 0; } } if (maskBeg) writeBedLine(seqName, probBeg, maskBeg, probEnd, output); } void processOneSequence(FastaSequence &f, std::ostream &output) { uchar *beg = BEG(f.sequence); uchar *end = END(f.sequence); alphabet.encodeInPlace(beg, end); if (options.outputType == options.maskOut) { tantan::maskSequences(beg, end, options.maxCycleLength, probMatrixPointers, options.repeatProb, options.repeatEndProb, options.repeatOffsetProbDecay, firstGapProb, otherGapProb, options.minMaskProb, maskTable); alphabet.decodeInPlace(beg, end); output << f; } else if (options.outputType == options.countOut) { tantan::countTransitions(beg, end, options.maxCycleLength, probMatrixPointers, options.repeatProb, options.repeatEndProb, options.repeatOffsetProbDecay, firstGapProb, otherGapProb, BEG(transitionCounts)); double sequenceLength = static_cast(f.sequence.size()); transitionTotal += sequenceLength + 1; } else { std::vector probabilities(end - beg); float *probBeg = BEG(probabilities); float *probEnd = END(probabilities); tantan::getProbabilities(beg, end, options.maxCycleLength, probMatrixPointers, options.repeatProb, options.repeatEndProb, options.repeatOffsetProbDecay, firstGapProb, otherGapProb, probBeg); if (options.outputType == options.probOut) { output << '>' << f.title << '\n'; for (float *i = probBeg; i < probEnd; ++i) output << *i << '\n'; } else { writeBed(probBeg, probEnd, firstWord(f.title), output); } } } void processOneFile(std::istream &input, std::ostream &output) { bool isFirstSequence = true; // This code strives to minimize memory usage. The sequence-reading // operation does not overwrite the sequence until it finishes // reading successfully. So, we don't want to overwrite a large, // old sequence. Hence, we make a brand-new FastaSequence each time // through the loop. while (true) { FastaSequence f; if (!(input >> f)) break; if (isFirstSequence && !options.isProtein && isDubiousDna(BEG(f.sequence), END(f.sequence))) std::cerr << "tantan: that's some funny-lookin DNA\n"; processOneSequence(f, output); isFirstSequence = false; } } void writeCounts(std::ostream &output) { double bg2bg = transitionCounts[0]; output << "#period" << '\t' << "estimated number of tracts" << '\n'; double repeatCountSum = 0; double weightedSum = 0; for (int i = 1; i <= options.maxCycleLength; ++i) { assert(transitionCounts[i] >= 0); output << i << '\t' << transitionCounts[i] << '\n'; repeatCountSum += transitionCounts[i]; weightedSum += i * transitionCounts[i]; } output << "# estimated total number of repetitive tracts: " << repeatCountSum << '\n'; output << "# estimated number of background-to-background transitions: " << bg2bg << '\n'; output << "# total number of transitions (#letters + #sequences): " << transitionTotal << '\n'; double probDecay = 1 - repeatCountSum / weightedSum; output << "# best-fit probability decay per period: " << probDecay << '\n'; double repeatProb = repeatCountSum / (repeatCountSum + bg2bg); output << "# best-fit probability of a repeat starting per position: " << repeatProb << '\n'; if (firstGapProb > 0) return; // The remaining calculations are correct only if there are no gaps. // If repeatProb and repeatEndProb are fixed to be the same value, // and there are no gaps: // repeatProb = 2 * repeatCountSum / transitionTotal; double fg2fg = transitionTotal - bg2bg - 2 * repeatCountSum; double repeatEndProb = repeatCountSum / (repeatCountSum + fg2fg); output << "# best-fit probability of a repeat ending per position: " << repeatEndProb << '\n'; } int main(int argc, char **argv) try { options.fromArgs(argc, argv); initAlphabet(); initScoresAndProbabilities(); initMaskTable(); // do this after initMaskTable, so that the mask symbol can be lowercase: if (!options.isPreserveLowercase) alphabet.makeCaseInsensitive(); if (options.outputType == options.countOut) transitionCounts.resize(options.maxCycleLength + 1); std::ostream &output = std::cout; if (options.outputType == options.probOut) output.precision(3); if (options.indexOfFirstNonOptionArgument == argc) processOneFile(std::cin, output); for (int i = options.indexOfFirstNonOptionArgument; i < argc; ++i) { std::ifstream ifs; std::istream &input = openIn(argv[i], ifs); processOneFile(input, output); } if (options.outputType == options.countOut) writeCounts(output); return EXIT_SUCCESS; } catch( const std::bad_alloc& e ) { // bad_alloc::what() may be unfriendly std::cerr << "tantan: out of memory\n"; return EXIT_FAILURE; } catch (const std::exception &e) { std::cerr << "tantan: " << e.what() << '\n'; return EXIT_FAILURE; } catch (int i) { return i; } tantan-13/src/mcf_score_matrix.cc0000644000000000000000000001374512037256344015724 0ustar rootroot// Copyright 2010 Martin C. Frith #include "mcf_score_matrix.hh" #include // min, fill_n #include #include #include // setw #include #include #include namespace mcf { typedef std::runtime_error Error; // copied from NCBI BLAST: const char* ScoreMatrix::blosum62 = "\ A R N D C Q E G H I L K M F P S T W Y V B J Z X *\n\ A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 -1 -1 -4\n\ R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 -2 0 -1 -4\n\ N -2 0 6 1 -3 0 0 0 1 -3 -3 0 -2 -3 -2 1 0 -4 -2 -3 4 -3 0 -1 -4\n\ D -2 -2 1 6 -3 0 2 -1 -1 -3 -4 -1 -3 -3 -1 0 -1 -4 -3 -3 4 -3 1 -1 -4\n\ C 0 -3 -3 -3 9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -1 -3 -1 -4\n\ Q -1 1 0 0 -3 5 2 -2 0 -3 -2 1 0 -3 -1 0 -1 -2 -1 -2 0 -2 4 -1 -4\n\ E -1 0 0 2 -4 2 5 -2 0 -3 -3 1 -2 -3 -1 0 -1 -3 -2 -2 1 -3 4 -1 -4\n\ G 0 -2 0 -1 -3 -2 -2 6 -2 -4 -4 -2 -3 -3 -2 0 -2 -2 -3 -3 -1 -4 -2 -1 -4\n\ H -2 0 1 -1 -3 0 0 -2 8 -3 -3 -1 -2 -1 -2 -1 -2 -2 2 -3 0 -3 0 -1 -4\n\ I -1 -3 -3 -3 -1 -3 -3 -4 -3 4 2 -3 1 0 -3 -2 -1 -3 -1 3 -3 3 -3 -1 -4\n\ L -1 -2 -3 -4 -1 -2 -3 -4 -3 2 4 -2 2 0 -3 -2 -1 -2 -1 1 -4 3 -3 -1 -4\n\ K -1 2 0 -1 -3 1 1 -2 -1 -3 -2 5 -1 -3 -1 0 -1 -3 -2 -2 0 -3 1 -1 -4\n\ M -1 -1 -2 -3 -1 0 -2 -3 -2 1 2 -1 5 0 -2 -1 -1 -1 -1 1 -3 2 -1 -1 -4\n\ F -2 -3 -3 -3 -2 -3 -3 -3 -1 0 0 -3 0 6 -4 -2 -2 1 3 -1 -3 0 -3 -1 -4\n\ P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4 7 -1 -1 -4 -3 -2 -2 -3 -1 -1 -4\n\ S 1 -1 1 0 -1 0 0 0 -1 -2 -2 0 -1 -2 -1 4 1 -3 -2 -2 0 -2 0 -1 -4\n\ T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 1 5 -2 -2 0 -1 -1 -1 -1 -4\n\ W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1 1 -4 -3 -2 11 2 -3 -4 -2 -2 -1 -4\n\ Y -2 -2 -2 -3 -2 -1 -2 -3 2 -1 -1 -2 -1 3 -3 -2 -2 2 7 -1 -3 -1 -2 -1 -4\n\ V 0 -3 -3 -3 -1 -2 -2 -3 -3 3 1 -2 1 -1 -2 -2 0 -3 -1 4 -3 2 -2 -1 -4\n\ B -2 -1 4 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 -3 0 -1 -4\n\ J -1 -2 -3 -3 -1 -2 -3 -4 -3 3 3 -3 2 0 -3 -2 -1 -2 -1 2 -3 3 -3 -1 -4\n\ Z -1 0 0 1 -3 4 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -2 -2 -2 0 -3 4 -1 -4\n\ X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -4\n\ * -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1\n\ "; void ScoreMatrix::initMatchMismatch(int matchScore, int mismatchCost, const std::string &letters) { rowLetters.assign(letters.begin(), letters.end()); colLetters.assign(letters.begin(), letters.end()); unsigned size = letters.size(); assert(size == letters.size()); scores.resize(size); for (unsigned i = 0; i < size; ++i) { scores[i].assign(size, -mismatchCost); scores[i][i] = matchScore; } } int ScoreMatrix::minScore() const { int m = std::numeric_limits::max(); for (unsigned i = 0; i < scores.size(); ++i) for (unsigned j = 0; j < scores[i].size(); ++j) m = std::min(m, scores[i][j]); return m; } static uchar indexOrDie(uchar letter, const uchar *letterToIndex, int tooBig) { uchar x = letterToIndex[letter]; if (x >= tooBig) throw Error(std::string("bad letter in score matrix: ") + static_cast(letter)); return x; } void ScoreMatrix::makeFastMatrix(int **fastMatrix, int fastMatrixSize, const uchar *letterToIndex, int defaultScore, bool isCaseSensitive) const { for (int i = 0; i < fastMatrixSize; ++i) std::fill_n(fastMatrix[i], fastMatrixSize, defaultScore); for (unsigned i = 0; i < rowLetters.size(); ++i) { for (unsigned j = 0; j < colLetters.size(); ++j) { uchar x = static_cast(rowLetters[i]); uchar y = static_cast(colLetters[j]); if (isCaseSensitive) { uchar a = indexOrDie(x, letterToIndex, fastMatrixSize); uchar b = indexOrDie(y, letterToIndex, fastMatrixSize); fastMatrix[a][b] = scores[i][j]; } else { uchar a = indexOrDie(std::toupper(x), letterToIndex, fastMatrixSize); uchar b = indexOrDie(std::tolower(x), letterToIndex, fastMatrixSize); uchar c = indexOrDie(std::toupper(y), letterToIndex, fastMatrixSize); uchar d = indexOrDie(std::tolower(y), letterToIndex, fastMatrixSize); fastMatrix[a][c] = scores[i][j]; fastMatrix[a][d] = scores[i][j]; fastMatrix[b][c] = scores[i][j]; fastMatrix[b][d] = scores[i][j]; } } } } std::istream &operator>>(std::istream &s, ScoreMatrix &m) { std::vector tmpRowLetters; std::vector tmpColLetters; std::vector< std::vector > tmpScores; std::string line; while (std::getline(s, line)) { std::istringstream iss(line); char c; if (!(iss >> c)) continue; // skip blank lines if (c == '#') continue; // skip comment lines if (tmpColLetters.empty()) { do { tmpColLetters.push_back(c); } while (iss >> c); } else { tmpRowLetters.push_back(c); tmpScores.resize(tmpScores.size() + 1); int score; while (iss >> score) { tmpScores.back().push_back(score); } if (tmpScores.back().size() != tmpColLetters.size()) s.setstate(std::ios::failbit); } } if (s.eof() && !s.bad() && !tmpScores.empty()) { s.clear(); tmpRowLetters.swap(m.rowLetters); tmpColLetters.swap(m.colLetters); tmpScores.swap(m.scores); } return s; } std::ostream &operator<<(std::ostream &s, const ScoreMatrix &m) { s << ' '; for (unsigned j = 0; j < m.colLetters.size(); ++j) s << ' ' << std::setw(2) << m.colLetters[j]; s << '\n'; for (unsigned i = 0; i < m.rowLetters.size(); ++i) { s << m.rowLetters[i]; for (unsigned j = 0; j < m.colLetters.size(); ++j) { s << ' ' << std::setw(2) << m.scores[i][j]; } s << '\n'; } return s; } } tantan-13/src/CA_code/0000755000000000000000000000000012037256344013334 5ustar rootroottantan-13/src/CA_code/ludcmp.c0000644000000000000000000000212112037256344014760 0ustar rootroot// Public domain code from Yi-Kuo Yu & Stephen Altschul, NCBI #include #define TINY 1.0e-20; void ludcmp(a,n,indx,d) int n,*indx; double **a,*d; { int i,imax,j,k; double big,dum,sum,temp; double *vv,*dvector(); void nrerror(),free_dvector(); vv=dvector(1,n); *d=1.0; for (i=1;i<=n;i++) { big=0.0; for (j=1;j<=n;j++) if ((temp=fabs(a[i][j])) > big) big=temp; if (big == 0.0) nrerror("Singular matrix in routine LUDCMP"); vv[i]=1.0/big; } for (j=1;j<=n;j++) { for (i=1;i= big) { big=dum; imax=i; } } if (j != imax) { for (k=1;k<=n;k++) { dum=a[imax][k]; a[imax][k]=a[j][k]; a[j][k]=dum; } *d = -(*d); vv[imax]=vv[j]; } indx[j]=imax; if (a[j][j] == 0.0) a[j][j]=TINY; if (j != n) { dum=1.0/(a[j][j]); for (i=j+1;i<=n;i++) a[i][j] *= dum; } } free_dvector(vv,1,n); } #undef TINY tantan-13/src/CA_code/nrutil.c0000644000000000000000000001047712037256344015026 0ustar rootroot// Public domain code from Yi-Kuo Yu & Stephen Altschul, NCBI //#include #include #include void nrerror(error_text) char error_text[]; { void exit(); fprintf(stderr,"Numerical Recipes run-time error...\n"); fprintf(stderr,"%s\n",error_text); fprintf(stderr,"...now exiting to system...\n"); exit(1); } float *vector(nl,nh) int nl,nh; { float *v; v=(float *)malloc((unsigned) (nh-nl+1)*sizeof(float)); if (!v) nrerror("allocation failure in vector()"); return v-nl; } int *ivector(nl,nh) int nl,nh; { int *v; v=(int *)malloc((unsigned) (nh-nl+1)*sizeof(int)); if (!v) nrerror("allocation failure in ivector()"); return v-nl; } double *dvector(nl,nh) int nl,nh; { double *v; v=(double *)malloc((unsigned) (nh-nl+1)*sizeof(double)); if (!v) nrerror("allocation failure in dvector()"); return v-nl; } float **matrix(nrl,nrh,ncl,nch) int nrl,nrh,ncl,nch; { int i; float **m; m=(float **) malloc((unsigned) (nrh-nrl+1)*sizeof(float *)); if (!m) nrerror("allocation failure 1 in matrix()"); m -= nrl; for(i=nrl;i<=nrh;i++) { m[i]=(float *) malloc((unsigned) (nch-ncl+1)*sizeof(float)); if (!m[i]) nrerror("allocation failure 2 in matrix()"); m[i] -= ncl; } return m; } double **dmatrix(nrl,nrh,ncl,nch) int nrl,nrh,ncl,nch; { int i; double **m; m=(double **) malloc((unsigned) (nrh-nrl+1)*sizeof(double *)); if (!m) nrerror("allocation failure 1 in dmatrix()"); m -= nrl; for(i=nrl;i<=nrh;i++) { m[i]=(double *) malloc((unsigned) (nch-ncl+1)*sizeof(double)); if (!m[i]) nrerror("allocation failure 2 in dmatrix()"); m[i] -= ncl; } return m; } double ***darray3(n1l,n1h,n2l,n2h,n3l,n3h) int n1l,n1h,n2l,n2h,n3l,n3h; { int i; double ***m; m=(double ***) malloc((unsigned) (n1h-n1l+1)*sizeof(double **)); if (!m) nrerror("allocation failure 1 in darray3()"); m -= n1l; for(i=n1l;i<=n1h;i++) { m[i]=dmatrix(n2l,n2h,n3l,n3h); } return m; } double ****darray4(n1l,n1h,n2l,n2h,n3l,n3h,n4l,n4h) int n1l,n1h,n2l,n2h,n3l,n3h,n4l,n4h; { int i; double ****m; m=(double ****) malloc((unsigned) (n1h-n1l+1)*sizeof(double ***)); if (!m) nrerror("allocation failure 1 in darray4()"); m -= n1l; for(i=n1l;i<=n1h;i++) { m[i]=darray3(n2l,n2h,n3l,n3h,n4l,n4h); } return m; } int **imatrix(nrl,nrh,ncl,nch) int nrl,nrh,ncl,nch; { int i,**m; m=(int **)malloc((unsigned) (nrh-nrl+1)*sizeof(int *)); if (!m) nrerror("allocation failure 1 in imatrix()"); m -= nrl; for(i=nrl;i<=nrh;i++) { m[i]=(int *)malloc((unsigned) (nch-ncl+1)*sizeof(int)); if (!m[i]) nrerror("allocation failure 2 in imatrix()"); m[i] -= ncl; } return m; } float **submatrix(a,oldrl,oldrh,oldcl,oldch,newrl,newcl) float **a; int oldrl,oldrh,oldcl,oldch,newrl,newcl; { int i,j; float **m; m=(float **) malloc((unsigned) (oldrh-oldrl+1)*sizeof(float *)); if (!m) nrerror("allocation failure in submatrix()"); m -= newrl; for(i=oldrl,j=newrl;i<=oldrh;i++,j++) m[j]=a[i]+oldcl-newcl; return m; } void free_vector(v,nl,nh) float *v; int nl,nh; { free((char*) (v+nl)); } void free_ivector(v,nl,nh) int *v,nl,nh; { free((char*) (v+nl)); } void free_dvector(v,nl,nh) double *v; int nl,nh; { free((char*) (v+nl)); } void free_matrix(m,nrl,nrh,ncl,nch) float **m; int nrl,nrh,ncl,nch; { int i; for(i=nrh;i>=nrl;i--) free((char*) (m[i]+ncl)); free((char*) (m+nrl)); } void free_dmatrix(m,nrl,nrh,ncl,nch) double **m; int nrl,nrh,ncl,nch; { int i; for(i=nrh;i>=nrl;i--) free((char*) (m[i]+ncl)); free((char*) (m+nrl)); } void free_imatrix(m,nrl,nrh,ncl,nch) int **m; int nrl,nrh,ncl,nch; { int i; for(i=nrh;i>=nrl;i--) free((char*) (m[i]+ncl)); free((char*) (m+nrl)); } void free_darray3(m,n1l,n1h,n2l,n2h,n3l,n3h) double ***m; int n1l,n1h,n2l,n2h,n3l,n3h; { int i; for(i=n1h;i>=n1l;i--) free_dmatrix(m[i],n2l,n2h,n3l,n3h); free((char*) (m+n1l)); } void free_submatrix(b,nrl,nrh,ncl,nch) float **b; int nrl,nrh,ncl,nch; { free((char*) (b+nrl)); } float **convert_matrix(a,nrl,nrh,ncl,nch) float *a; int nrl,nrh,ncl,nch; { int i,j,nrow,ncol; float **m; nrow=nrh-nrl+1; ncol=nch-ncl+1; m = (float **) malloc((unsigned) (nrow)*sizeof(float*)); if (!m) nrerror("allocation failure in convert_matrix()"); m -= nrl; for(i=0,j=nrl;i<=nrow-1;i++,j++) m[j]=a+ncol*i-ncl; return m; } void free_convert_matrix(b,nrl,nrh,ncl,nch) float **b; int nrl,nrh,ncl,nch; { free((char*) (b+nrl)); } tantan-13/src/CA_code/lambda_calculator.h0000644000000000000000000000046112037256344017137 0ustar rootroot// Copyright 2008 Michiaki Hamada #ifndef __H_INCLUDE_LAMBDA_CALCULATOR_HH #define __H_INCLUDE_LAMBDA_CALCULATOR_HH // These pointers are 1-based! double calculate_lambda( const double** mat_b, int alpha_size, double* p, double* q ); #endif // __H_INCLUDE_LAMBDA_CALCULATOR_HH tantan-13/src/CA_code/lubksb.c0000644000000000000000000000063112037256344014762 0ustar rootroot// Public domain code from Yi-Kuo Yu & Stephen Altschul, NCBI void lubksb(a,n,indx,b) double **a,b[]; int n,*indx; { int i,ii=0,ip,j; double sum; for (i=1;i<=n;i++) { ip=indx[i]; sum=b[ip]; b[ip]=b[i]; if (ii) for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; else if (sum) ii=i; b[i]=sum; } for (i=n;i>=1;i--) { sum=b[i]; for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; b[i]=sum/a[i][i]; } } tantan-13/src/CA_code/nrutil.h0000644000000000000000000000063012037256344015021 0ustar rootroot// Public domain code from Yi-Kuo Yu & Stephen Altschul, NCBI float *vector(); float **matrix(); float **convert_matrix(); double *dvector(); double **dmatrix(); int *ivector(); int **imatrix(); float **submatrix(); void free_vector(); void free_dvector(); void free_ivector(); void free_matrix(); void free_dmatrix(); void free_imatrix(); void free_submatrix(); void free_convert_matrix(); void nrerror(); tantan-13/src/CA_code/lambda_calculator.c0000644000000000000000000003430112037256344017132 0ustar rootroot// Copyright 2008 Michiaki Hamada // Adapted from public domain code by Yi-Kuo Yu, NCBI /** * See lambda_calculator.h */ #include #include #include #include "nrutil.h" int Alphsize; #include "nrutil.c" #include "ludcmp.c" #include "lubksb.c" #include "lambda_calculator.h" #define Epsilon 1.0e-36 #define E_bound 1.0e-12 #define Infty 1000000.0 #define min(A,B) ((A) > (B) ? (B) : (A) ) #define max(A,B) ((A) > (B) ? (A) : (B) ) #define bool int #define true 1 #define false 0 double Lambda_UB; //lambda upper bound double r_max_m, c_max_m; //min of each row's (column's) max void makematrix( const double** mat_b, double **a, double lambda); typedef struct Lambda { double min; double max; int flag; // 1 means there is a range, -1 means no solution possible. } Lambda; typedef struct Sum { double value; int flag; // 1 means no negative bg_freq, -1 means there is negative bg_freq } Sum; Lambda Find_JP(const double** mat_b, double la_min, double la_max, double **JP, double *p_in, double *q_in); Sum Check_root(const double** mat_b, double **a, double lambda, double *p, double *q); double Check_det(const double** mat_b, double **a, double lambda); Sum Nail_lambda(const double** mat_b, int flag_sign, double lambda_min, double lambda_max, double *p, double *q, double *la_add); double Nail_det(const double** mat_b, int flag_sign, double lambda_min, double lambda_max); bool Check_range( const double** mat_b ); double *Locate_det_zero( const double** mat_b, int * ); //pointer to root list are returned with how many of them by int double calculate_lambda ( const double** mat_b, int alpha_size, double* p, double* q ) { double **JP/*, *q, *p*/; int k; double *root_location; int N_root; Lambda Lambda_local; Alphsize = alpha_size; if( ! Check_range( mat_b ) ) return -1.0; root_location = Locate_det_zero(mat_b, &N_root); if( root_location == NULL && N_root > 0 ) return -1.0; //q=dvector(1,Alphsize); //p=dvector(1,Alphsize); JP = dmatrix(1,Alphsize,1,Alphsize); if (N_root == 0){ Lambda_local = Find_JP(mat_b, 0, Lambda_UB, JP, p, q); if (1 == Lambda_local.flag) { // sensible solution found // Remember to find the right place to free the vectors //free_dvector(p, 1,Alphsize); //free_dvector(q, 1,Alphsize); free( root_location ); free_dmatrix( JP, 1, Alphsize, 1, Alphsize ); return (Lambda_local.min + Lambda_local.max) / 2.0; } else if (-1 == Lambda_local.flag) { //printf("matrix pass first screening but no sensible solution found. :-( \n"); } } else if (N_root > 0) { //printf("N_root = %d for this matirx \n", N_root); //for (i=0;i 0) { if (mat_b[i][j]> r_max) r_max = mat_b[i][j]; pos_flag_r = 1; } else if (mat_b[i][j] < 0) neg_flag_r = 1; if (mat_b[j][i] > 0) { if (mat_b[j][i] > c_max) c_max = mat_b[j][i]; pos_flag_c = 1; } else if (mat_b[j][i] < 0) neg_flag_c = 1; } if ((pos_flag_r == -1)||(neg_flag_r == -1)||(pos_flag_c == -1)||(neg_flag_c == -1)) { if ((pos_flag_r == -1)&&(neg_flag_r == -1)){ printf ("only zero score at row %d\n", i); L_r++; } else if ((pos_flag_c == -1)&& (neg_flag_c == -1)){ printf ("only zero score at column %d\n", i); L_c++; } else{ //printf("all positive or all negative at row or column %d\n", i); //printf("therefore invalid matrix. exit now. \n"); return false; //exit(1); } } if ((r_max < r_max_m)&&(r_max > 0)) r_max_m = r_max; if ((c_max < c_max_m)&&(c_max > 0)) c_max_m = c_max; } // Find the upper bound for lambda if (r_max_m > c_max_m) { Lambda_UB = 1.1*log(1.0*Alphsize-L_r)/r_max_m ; } else { Lambda_UB = 1.1*log(1.0*Alphsize-L_c)/c_max_m; } //printf("the upper bound for lambda is %lf\n", Lambda_UB); return true; } double Check_det(const double** mat_b, double **a, double lambda) { double d; int i, /*j,*/ *indx; indx = ivector(1,Alphsize); makematrix(mat_b, a,lambda); ludcmp(a,Alphsize,indx,&d); for(i=1;i<=Alphsize;i++) d *= a[i][i]; free_ivector(indx,1,Alphsize); return d; //returning the determinant } Sum Check_root(const double** mat_b, double **a, double lambda, double *p, double *q) { double **y, /* *col,*/ d; //double sum = 0.0; int i,j;//, *indx; Sum Sum_here; y=dmatrix(1,Alphsize,1,Alphsize); //indx = ivector(1,Alphsize); int indx[Alphsize+1]; //col = dvector(1,Alphsize); double col[Alphsize+1]; makematrix(mat_b, a,lambda); ludcmp(a,Alphsize,indx,&d); Sum_here.value = 0.0; for(i=1;i<=Alphsize;i++) q[i]=0.0; for(j=1;j<=Alphsize;j++){ for (i=1;i<=Alphsize;i++) col[i]=0.0; col[j]=1.0; lubksb(a,Alphsize,indx,col); p[j]=0.0; for (i=1;i<=Alphsize;i++) { y[i][j]=col[i]; Sum_here.value += y[i][j]; p[j]+=y[i][j]; q[i]+=y[i][j]; } } Sum_here.flag = 1; for (i=1;i 0.0 ) flag_sign = 1; if (fabs(s_here[0])/exp(l_here[0]*(r_max_m+c_max_m)/2.0) <= Epsilon) { root[zero_monitor++] = l_here[0]; flag_sign = 0; } for (i=1;iEpsilon)) { if (s_here[i-1]*s_here[i] < 0){ //printf("occurring at regular places\n"); lambda_root = Nail_det(mat_b, flag_sign, l_here[i-1], l_here[i]); root[zero_monitor++] = lambda_root; flag_sign = -flag_sign; // the flag switch sign after one sol found //printf("a (regular) root of det found at %12.10f, i= %d\n", lambda_root,i); } } else { if (s_here[i] < 0.0) flag_sign = -1; if (s_here[i] > 0.0 ) flag_sign = 1; if (fabs(s_here[i])/exp(l_here[i]*(r_max_m+c_max_m)/2.0) <= Epsilon) { root[zero_monitor++] = l_here[i]; } } } //printf("total number of solution found in range is %d\n", i_monitor); root_temp = (double *)malloc(zero_monitor*sizeof(double)); *N_root_add = zero_monitor; if (zero_monitor > 0) { if (zero_monitor >= N/4) { //printf("It is likely that uniform zero determinant is occurring.\n"); //printf("number of small det points = %d out of %d, exit now....\n",zero_monitor, N); free( root_temp ); return NULL; //exit(1); } for (i = 0; i < zero_monitor; i++){ root_temp[i] = root[i]; //printf("root_location[%d] = %lf\n",i,root_temp[i]); } } free_dmatrix( a, 1, Alphsize, 1, Alphsize ); return root_temp; } Lambda Find_JP(const double** mat_b, double la_min, double la_max, double **JP, double *p_in, double *q_in) { double **a, *q, *p; // a is the exponentiated matrix of socres, p and q are bg_freqs int i,j/*,k*/; int N; // number of points for first round double lambda/*, l_tmp, sum, sum_min, sum_max*/; double lambda_max, lambda_min, lambda_final, dlambda/*, dsum=0.5*/; //double *l_here, *s_here; //double error=0.000000000000001; //int validity_flag; // 1 means valid, -1 means not valid. int flag_sign; // 1 means small lambda sum > 1, -1 means otherwise int flag_done = -1; // 1 means find sensible solution, -1 means sensible not found int i_monitor = 0; // record number of solution found in the range, including nonsense ones int j_monitor; Lambda Lambda_local; //Sum *Sum_local; Sum Sum_local; lambda_min = la_min; lambda_max = la_max; q = q_in; p = p_in; a=dmatrix(1,Alphsize,1,Alphsize); //Sum_local = (Sum *)malloc(sizeof(Sum)); //Lambda_local = (Lambda *)malloc(sizeof(Lambda)); N = 2 + max(400, ((int) (lambda_max-lambda_min)/0.005)); //printf("N = %d in Find_JP\n", N); dlambda = (lambda_max-lambda_min)/(N*1.0); //l_here = (double *)malloc((N+1)*sizeof(double)); //s_here = (double *)malloc((N+1)*sizeof(double)); double l_here[N+1]; double s_here[N+1]; //printf("lambda_min enter = %12.10e, lambda_max = %12.10f\n", lambda_min, lambda_max); for (i=0; i< N-1 ; i++){ lambda = lambda_min + (i+1)*dlambda; makematrix(mat_b, a,lambda); Sum_local = Check_root(mat_b, a,lambda,p,q); l_here[i] = lambda; s_here[i] = Sum_local.value - 1.0; //printf("scan %d th time in Find_JP\n",i ); } //printf("finish first time scanining in Find_JP\n"); if (s_here[0] < 0.0) flag_sign = -1; else if (s_here[0] > 0.0 ) flag_sign = 1; else if (s_here[0] == 0.0) { //needs refined definition on flag_sign printf("enter the exact hit, rarely occurs other than when lambda = 0 \n"); j_monitor = 1; flag_sign = 0; while ((flag_sign == 0) &&(j_monitor < N)){ Sum_local = Check_root(mat_b, a,l_here[0]+ j_monitor*dlambda/N,p,q); if (Sum_local.value > 1.0) { flag_sign = 1; } else if (Sum_local.value <1.0){ flag_sign = -1; } j_monitor++; } } for (i=1;iE_bound){ if (flag_sign*(Sum_local.value-1.0)<0) lambda_max = lambda; else if (flag_sign*(Sum_local.value-1.0)> 0) lambda_min = lambda; // Added by MCF to avoid infinite loop: if (lambda == (lambda_min+lambda_max)/2.0){ Sum_local.flag = -1; break; } lambda = (lambda_min+lambda_max)/2.0; Sum_local = Check_root(mat_b, a, lambda, p, q); } free_dmatrix(a,1,Alphsize,1,Alphsize); *lam_add = lambda; return Sum_local; } double Nail_det(const double** mat_b, int flag_sign, double lambda_min, double lambda_max) { double **a; double lambda; double value; a = dmatrix(1,Alphsize,1,Alphsize); lambda = (lambda_min+lambda_max)/2.0; value = Check_det(mat_b, a, lambda); while ((fabs(value)>E_bound)&&(lambda > 0)){ if (flag_sign*(value)<0) lambda_max = lambda; else if (flag_sign*(value)> 0) lambda_min = lambda; lambda = (lambda_min+lambda_max)/2.0; value = Check_det(mat_b, a, lambda); } free_dmatrix(a,1,Alphsize,1,Alphsize); return lambda; } void makematrix(const double** mat_b, double **a, double lambda) { int i,j; for (i=1;i<=Alphsize;i++) for(j=1;j<=Alphsize;j++){ *(*(a+i)+j)=exp(lambda*mat_b[i][j]); } } tantan-13/src/mcf_score_matrix_probs.hh0000644000000000000000000000312512037256344017132 0ustar rootroot// Copyright 2010 Martin C. Frith // This class calculates the scale factor (lambda), and the letter // probabilities, that are implicit in a scoring matrix. The // calculation might fail for various reasons, putting it into a // "bad/undefined" state. // If the score matrix is symmetric, then the two sets of letter // probabilities should be identical. With this code, they might // differ minutely from exact identity. #ifndef MCF_SCORE_MATRIX_PROBS_HH #define MCF_SCORE_MATRIX_PROBS_HH #include namespace mcf { typedef const int *const_int_ptr; class ScoreMatrixProbs { public: ScoreMatrixProbs() { setBad(); } ScoreMatrixProbs(const const_int_ptr *scoreMatrix, unsigned alphabetSize) { init(scoreMatrix, alphabetSize); } void init(const const_int_ptr *scoreMatrix, unsigned alphabetSize); // Put us in the bad/undefined state. void setBad(); // Are we in the bad/undefined state? bool isBad() const { return (lambda_ < 0); } // The scale factor. In the bad/undefined state, it is negative. double lambda() const { return lambda_; } // The probabilities of letters corresponding to matrix rows (1st index). // In the bad/undefined state, it is an empty vector. const std::vector& letterProbs1() const { return letterProbs1_; } // The probabilities of letters corresponding to matrix columns (2nd index). // In the bad/undefined state, it is an empty vector. const std::vector& letterProbs2() const { return letterProbs2_; } private: double lambda_; std::vector letterProbs1_; std::vector letterProbs2_; }; } #endif