src/LICENSE

+Copyright (C) 2001 UC Regents
+
+LICENSE files in subdirectories override the text of this LICENSE file.
+
+Permission is hereby granted, free of charge, to any person or non-commercial
+entity obtaining a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including without
+limitation the rights to use, copy, modify, merge, publish, distribute,
+sublicense, and/or sell copies of the Software, and to permit persons to whom
+the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
+IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+Commercial users should contact kent@soe.ucsc.edu for access to other modules
+including jkOwnLib and blat.
+
+Commercial users interested in the UCSC Genome Browser in particular please see
+    http://genome.ucsc.edu/license/.
+
+The code in /src/htslib is distributed with two licenses as noted in the LICENSE
+file in that directory.

src/blat/hCrea.geno

+>hCreaGeno
+CATGCCACATCCCCGGGGCGGGAGGGGGCTACATCCCCGGCTTTAGACGCGCGAGTCTCAGGTCCCGCTA
+ATTACCTGGCGGGTGCTGCCCACCCCTGCCCTCGCGCACCTAGCGCGTGGCAGCGGGAAGGCGGGGCCTG
+GGGGAGCCCCACCCCTGGAGACTGCGGCTGGGGCCTCCCTCTCCTCCGCCCGCCCGCCTGCCACTAGCTC
+ATTGCGCCTCTCCTGCAGTCTGATTGGGCACCGGCTCCCATTCCGGCTCCAGCCTCCAATCCGACCCCCA
+TTTCGGCTGCAGCCTCGGACCTAGCTCCGGCCCTCGGTCTATCCGGTTGCATCCTCCCTCCCTGTTCCGG
+ATCTTATCTTGCGCCAGCGCCTACTCCAGGATCCCGTAGCCAGACCTCAAGCCATGGCTGGTCCCTTCTC
+CCGTCTGCTGTCCGCCCGCCCGGGACTCAGGCTCCTGGCTTTGGCCGGAGCGGGGTCTCTAGCCGCTGGG
+TTTCTGCTCCGACCGGAACCTGTACGAGCTGCCAGTGAACGACGGAGGCTGTATCCCCCGAGGTAACAGT
+GCCTGAGGCGCGGGAGGAGGCGGGGGCAGGAGGTGATGGGAACGAAGGTGCGGGTAGAAGTGAGAATCCG
+GGCAACAGAGAAGGGCTATAATCACGAAGGCCCTGGAGCTGGAGGGCTGTGCAGTCTGCAGACCTCAGTG
+GGGTGGGGGTGGGGGCCAAAACCATAAAGCAAGAACATTCCTGGGGACCTGCCAAGACCAGCTCTGGCCC
+TACGAGTTCTAGCTGCACTGGCTGCCCAAATCCCTAATTGTAAAGCCAGGAACTATCCTTTTCGCTCCCC
+TCCATCTCCTTCCCTCATTTCCTCAATTCCTCTCCTTAGGCTTTTCCCCTCCTCCATCCGTAGTGTTGTG
+TCATGGGAGGAAAGAACTGAGCAGATCTGAAGAAACTGAGCTGGCCAGCCAGAGGCAACTAGAACTATTA
+GGAAAGCATAGACTCTGAAAGTCCCTAAAGAGATTACCAAGGTTTACCCTCTTTCTAATTCCCCTCCTCC
+CGCGGAGCAAAGCCAGACATGGCCAACTGGACAGCTCCCAGGTAACTGCACTAGGTCTAGGCGTCTGTGA
+CCCTCCCTCCATGGTTACTGGGTACCCCCTCCCCAGCGCTGAGTACCCAGACCTCCGAAAGCACAACAAC
+TGCATGGCCAGTCACCTGACCCCAGCAGTCTATGCACGGCTCTGCGACAAGACCACACCCACTGGTTGGA
+CGCTAGATCAGTGTATCCAGACTGGCGTGGACAACCCTGGCCACCCCTTCATCAAGACTGTGGGCATGGT
+GGCTGGAGATGAGGAGACCTATGAGGTAGGGGGTCCCCAGAGTCTCCCTGATGATCCAATTCATCTTCCC
+AGTAATCCCAGCTCCTTTCCCTTAAAGACCTCTCACTTTCCCCCAAGACTCTGAGCCCCCCATACTTAAG
+TTTTCTGAACCAGTGAAATCAATGCACAATTGAAGTCTGGGGAGGGATTCCCTCTCCTTAACCATCTCTC
+CCTCTTAACTCCCCTTAGGTATTTGCTGACCTGTTTGACCCTGTGATCCAAGAGCGACACAATGGATATG
+ACCCCCGGACAATGAAGCACACCACGGATCTAGATGCCAGTAAAGTGAGTTCAAATATCCCACTTCTGAT
+TTGCATTGCCTGTGTACAACACTCTGTATCTCCAACCCCTTCACCTTATTTCCTGACTCATGGTCATTAT
+ACTGCTGAGCTTTTAATCTTAATGTAAGGAAAGAATCATATCTTAAGGGGCAGCATATATGGAGATGGAA
+GGATAGATAAGAATGACCATGACCCAAGGTGGGTGGTTTGGGGACGGGTCTGCAATGCCCCCTTCAATTC
+CAGTGCTTTCCCAAAGGGCCTCTTCTTCCAATGCATGCAGGAAGAATGCACACAGAGTCCTCTAATGCCT
+AAGGAAGGTCTCTCCTTTCCCAGGGGCCCTCAGTTCCCACCGTGTTTCTGTGACTTACATTCATTTCCCT
+TATCTCCCAGATCCGTTCTGGCTACTTTGATGAGAGGTATGTATTGTCCTCTAGAGTCAGAACTGGCCGA
+AGCATCCGAGGACTCAGTCTGCCTCCAGCTTGCACTCGAGCAGAGCGACGAGAGGTGGAACGTGTTGTGG
+TGGATGCACTGAGTGGCCTGAAGGGTGACCTGGCTGGACGTTACTATAGGCTCAGTGAGATGACAGAGGC
+TGAACAGCAGCAGCTTATTGATGTGAGGGCCTTAAGAGGGTGCTGGTTGGTGGGAGCAGATGGGGAAGGC
+TGGGCCAGATGAGACATGGGCTCTGAAAGGCCCAGGGGCCACCATGAAGATTCTTAACCCAAGTCCCGTT
+ACTCTTCCCAGGACCACTTTCTGTTTGATAAGCCTGTGTCCCCGTTGCTGACTGCAGCAGGAATGGCTCG
+AGACTGGCCAGATGCTCGTGGAATTTGGTATGAAGCTGCTCATTACCTCTTTTGTCTTCATGCCCTCATA
+AATGCTTTTTTTCCCTCTATCTCTCCCAATTCTTGCCTTGCCTCTTGATCACTGTCCCTCTCCGGCCCTC
+AGGCACAACAATGAGAAGAGCTTCCTGATCTGGGTGAATGAGGAGGATCATACACGGGTGATCTCCATGG
+AGAAGGGTGGTAACATGAAGAGAGTGTTTGAAAGATTCTGCCGAGGCCTCAAAGAGGTTAGAGAAGACTA
+TGTAGGGGAGCTAGGTGGGAGGACATAAGGAAAACCAAAGAGTAGCATAAATAGATTATGTAATTTACCA
+ACCAACCCAGGACATGTCTTATAGTAAAAAGGACTATCTAGGACTCACTCCAGGACTAAAGGTGTAAACC
+AGCTGGGACCATACTGGGAAAACCAGGACATGTGGTCACACTAAGATTAGGAAAAGAAAGAGTGTCAGGA
+ATCTTAGGAAGTGAACAAGGCTTTTGACAGAGAGTGCAAAGAAGGAATAAATGAGATGGCACGTCAGTGC
+CTGGGATGTGTGCAGTGGGATGGTGAGGTGTGCAGATAAGGAAAACATTCGAGCTTAGATTGATGTTGGC
+GGGGAGAGGTTGCTGTGTTCATGACTCTAATATAACCACCCAGTTCTGAGACAAGGTAGGCCTTGACTCT
+GGATTCTATCATTCTTGTTAAAGTTTCGGGTCTAGGCTTTAAGTTGAGAGTTCGGAGAGAGACTGGGGAA
+GGTGGAGGATAGAATGGTTCGAGTTCTAGAATATGTGGCTCTAGATGAGAGGTTGAACTGAATCATCAAT
+CCTACATGGATTGGGTCTCCGTATTCAAGTCTACATTAGAAATCCCCATAAACTCAATTCAATTCTTACT
+GTATGTTCTCAAACATACAGTTCTATTTTAGGTTTGCAAAGAAAAAGAGCTCCTCTTTTAGATTCTGAGA
+AGTTTCTACTATTTTTGGCAAGTAATAGATAACATATTCTGACTATGAGTGGGtagggaagtacctttaa
+attatatgcctcagtttcctcatctgtaaaattgggataatgagattttctacattttaggttgttgtgg
+ggattaagtgaaatacaggtaaagtacttggtccacagtaagtgcttaataagtgttaaagtgttagctg
+caatattattCTGGATGGAAGAGTTTCCCCCCATGTTCAGCATGTAAGATATCCCCTATGGCATGGTTCC
+TTCTGAACTATAAAGAGGATCCCTTTACTCATGTTGGGTTGTGGTCTTTGTGACCATCATTCTGCTAGAT
+CCCTTGTCTCTTGAACTCTAATAGTCATCTTCATGACTACATGGTTAAGTGAAGCCAAACGCCTTCCCCC
+CGCCCCCTATTCCTATGAATCTGGCTTTTCTGCTCTGTTTTCATCTTTCTCTGCATTCACACAGGTGCTC
+CGTTCACAGCTAACAGAATGTTATCTTACCTCTTCCTGGCAAAGCTTACACCTTCATCTTCTGTCTGAAG
+GGACCCTTCTAAGCTCTAGGCTCATTAGCAAAGCAAAGATAATCGATGCATGCAGACCTCATTGAATAAT
+CAGTCATCTCTCAGTTCAGTTTACCACCTCTGTTCATTTCCCTAGATCATCCTTAATACACCACTCCTTC
+GAGTTTTCTTCTTCCACATAAGATATTTTTTCACAATCTCATTATTATGCACATCATAATTTTGCATCAT
+GCATGCATGAAAACAATAACAAACCTTTTTCATTTAAAAAAAGACCAATGTCATTCATTCACAGCCAAGT
+TTCTGTTCTAGACATATTTCTAGTGTTCTTGTGGGTCTAGCTAAGGGAGGGTCCAGGGTTAATGAAATAT
+CCCTGATTTTTCGTTAACAAAACCTTTGTGGACTCAGGTGGAGAGACTTATCCAAGAACGTGGCTGGGAG
+TTCATGTGGAATGAGCGTTTGGGATACATCTTGACCTGTCCATCTAACCTGGGCACTGGACTTCGGGCAG
+GAGTGCACATCAAACTGCCCCTGCTAAGCAAAGTAAAGGAGTTGTGGGGTTACAGAGGGGTGTGAGTAAG
+GAAGGGTGGGTTGTGGATGGGGAGGGAGTGGACCCTTTGGAAAGGAGCCAAACATGTTGTGGCTAAAGGG
+TCAGAGGACAggccaggcacagtggctcatgcctctaatcccaacacttgggaggccaaggcaggcagat
+tacttgagcccaggagttcaagaccagcctgggcaacctggtgaaaccccatctctacctacaaatacaa
+aagttagctgggtgtagtggaggctgaggtgagaggatcacttaagcctgggaagtcgaggcttcagtga
+gctgtgatcactccagcctgggtgacagagagagaccctgtctaaaaaaaattaaaaaagaaaaaagaaa
+aaaGGAAAAAAAAAGTTCAGGAGACAGAGCTCTGAGCAGGTTCAGGGCTCTTTCAGGTAGGACCTAGTCT
+CTGCCTCTATTGACCCTGCTCCCAATCCCTATCTCCTCTCTAGGATAGCCGCTTCCCAAAGATCCTGGAG
+AACCTAAGACTCCAAAAACGTGGTACTGGAGGAGTGGACACTGCTGCTACAGGCGGTGTCTTTGATATTT
+CTAATTTGGACCGACTAGGCAAATCAGAGGTGAGATCCTAAGGGATTAGGACAAGGAGAGGTATAGGTCT
+GCGAGGGCCGAAATATGGCAGTGAGTGAGCCTCCGGGATGTAACATAATCTGAAATGAAATTCAGGTTGA
+GTGGGAGGCAATTGGAAATGAGCAGGCAAGTCAGTCAGTGATAAAGAAAAACTCAGACTGTAGGAAGCAG
+ATCAAAGATTAGTGTCCCTTAGGTGGAGCTGGTGCAACTGGTCATCGATGGAGTAAACTATTTGATTGAT
+TGTGAACGGCGTCTGGAGAGAGGCCAGGATATCCGCATCCCCACACCTGTCATCCACACCAAGCATTAAC
+TCCCCATCGCCAGCTGATGACTCAAGATTCCCAGGAGTTTTGCTCATTCTAATGATGGCCCATTCTACTT
+GCTCTGGACCTGCCCCCGCATCCCCTGCCTCCATCCTAGTAAAGACTCCTTGCTATGCTGCAGCTGTCTG
+TGTTACTTCTAATGGTGGGGTGAGGAGGGAGCAGCCTTCAGGAAATGAAAAGAGGCAGTGGGATTATTTA
+TGATGGAAAGAGACTCCAGATATGGCAACCCAGGAACACTGATTCTCAGGTGGGTGGAAAGCATTAACAT
+TTTACCCATATTCCTCATCAGCTTCTGAAAATAATCAGGATGCACTTCTGTTTGCACTTTATTCATTATG
+ACTTAAGATTTCTCTCCCCACAATCTCCTTCTACTGTAGAGACAGGCTCATAGCAGGTGGCCAAGGAAGC
+TGATAGTCAATACCAGGGACCAGGAAGGTCGTGACCAGTCCTGGAGGCCCCAGGCTGTACTTCGACCTAT
+AATAGACAGGGAATGGGAGTAATATCACAACTCAGCTCTCCAGGAGCATTGATACTTGGAAATTAGCGCT
+CTGCCTGTAGACTCCTTCACTCCAGGGATCTCCCTGGGTGCACTCTAAGAGCCAGACAGCACCAAATTAG
+GGGTTTGATTCTGGGTCAGGAGATGGAGGATCAAGCTGTGCAGCTGGGAACTCACCTTGCTGTTCTGGGC
+TCTCCTTTCCCTCATGTTGGGCCCATGCAACTGCTCGTCGCTGCTCAGGACTCAGAAAGGCCATTTGCTC
+AGGAGTGACAGCCACAGCCTGAGCACTGGTGAGACTAGATAGTTGGATGGGACTAAACACCACCTGAGGG
+CAGGGGTAGGAATCAGTGCATGCATGTAGTCCCCATTGGGCCCTGGCTCTCCTGTGGTCACCCCAGTCCA
+TTAATACTTACAGCAAATTTAGGAGGAGGGATGACAGAAATGGCAAGAGGAGTAACGCCCTGGATCTGTC
+CCCGCAGCAGTGCTGAAAGAGCCAGGTCTGGGATCCCAGCTGTTGAAGCAAGTGGCATCCAAACATTGTC
+TTAGACTGACCTTCCCTCTCTTCAAACCTATAGACCTTCTCTAACTACTCCCAAAGTGCCCTATCATAGA
+CCTTCCCCAATATGTCTCTAGCCCCTTATTTAAACACCCTCAGGCCCCCACCTTAAGAATTGCAGGGCAG
+TCTTCCATCCAGTCCACCCATGGTATAGAAACCAAACCAACTTGCACCAGCAGTGGCCCAGCTCCCCACC
+TGCTATGGTGCCAATTTCAGTGAAGATCTCAGGCCCCCAGTTACTGATTGGGCCAAACCCACCAGGCAGT
+ACAAGTAGGTGGGCCAGAACCTCCAGTTGTTCCTCAGAGCACTGCAGATGCAGGGTGCCGAGGAAGAGAG
+CTGCTTGGCTGTAGAACAGTGGGAAGGAAGGAAGAA

src/blat/hCrea.mrna

+>hCreaMrna
+CCGGCTCCCATTCCGGCTCCAGCCTCCAATCCGACCCCCATTTCGGCTGCAGCCTCGGACCTAGCTCCGG
+CCCTCGGTCTATCCGGTTGCATCCTCCCTCCCTGTTCCGGATCTTATCTTGCGCCAGCGCCTACTCCAGG
+ATCCCGTAGCCAGACCTCAAGCCATGGCTGGTCCCTTCTCCCGTCTGCTGTCCGCCCGCCCGGGACTCAG
+GCTCCTGGCTTTGGCCGGAGCGGGGTCTCTAGCCGCTGGGTTTCTGCTCCGACCGGAACCTGTACGAGCT
+GCCAGTGAACGACGGAGGCTGTATCCCCCGAGCGCTGAGTACCCAGACCTCCGAAAGCACAACAACTGCA
+TGGCCAGTCACCTGACCCCAGCAGTCTATGCACGGCTCTGCGACAAGACCACACCCACTGGTTGGACGCT
+AGATCAGTGTATCCAGACTGGCGTGGACAACCCTGGCCACCCCTTCATCAAGACTGTGGGCATGGTGGCT
+GGAGATGAGGAGACCTATGAGGTATTTGCTGACCTGTTTGACCCTGTGATCCAAGAGCGACACAATGGAT
+ATGACCCCCGGACAATGAAGCACACCACGGATCTAGATGCCAGTAAAATCCGTTCTGGCTACTTTGATGA
+GAGGTATGTATTGTCCTCTAGAGTCAGAACTGGCCGAAGCATCCGAGGACTCAGTCTGCCTCCAGCTTGC
+ACTCGAGCAGAGCGACGAGAGGTGGAACGTGTTGTGGTGGATGCACTGAGTGGCCTGAAGGGTGACCTGG
+CTGGACGTTACTATAGGCTCAGTGAGATGACAGAGGCTGAACAGCAGCAGCTTATTGATGACCACTTTCT
+GTTTGATAAGCCTGTGTCCCCGTTGCTGACTGCAGCAGGAATGGCTCGAGACTGGCCAGATGCTCGTGGA
+ATTTGGCACAACAATGAGAAGAGCTTCCTGATCTGGGTGAATGAGGAGGATCATACACGGGTGATCTCCA
+TGGAGAAGGGTGGTAACATGAAGAGAGTGTTTGAAAGATTCTGCCGAGGCCTCAAAGAGGTGGAGAGACT
+TATCCAAGAACGTGGCTGGGAGTTCATGTGGAATGAGCGTTTGGGATACATCTTGACCTGTCCATCTAAC
+CTGGGCACTGGACTTCGGGCAGGAGTGCACATCAAACTGCCCCTGCTAAGCAAAGATAGCCGCTTCCCAA
+AGATCCTGGAGAACCTAAGACTCCAAAAACGTGGTACTGGAGGAGTGGACACTGCTGCTACAGGCGGTGT
+CTTTGATATTTCTAATTTGGACCGACTAGGCAAATCAGAGGTGGAGCTGGTGCAACTGGTCATCGATGGA
+GTAAACTATTTGATTGATTGTGAACGGCGTCTGGAGAGAGGCCAGGATATCCGCATCCCCACACCTGTCA
+TCCACACCAAGCATTAACTCCCCATCGCCAGCTGATGACTCAAGATTCCCAGGAGTTTTGCTCATTCTAA
+TGATGGCCCATTCTACTTGCTCTGGACCTGCCCCCGCATCCCCTGCCTCCATCCTAGTAAAAAAAAAAAA

src/blat/hCrea.pep

+>hCreaPep
+MAGPFSRLLSARPGLRLLALAGAGSLAAGFLLRPEPVRAASERRRLYPPSAEYPDLRKHNNCMASHLTPA
+VYARLCDKTTPTGWTLDQCIQTGVDNPGHPFIKTVGMVAGDEETYEVFADLFDPVIQERHNGYDPRTMKH
+TTDLDASKIRSGYFDERYVLSSRVRTGRSIRGLSLPPACTRAERREVERVVVDALSGLKGDLAGRYYRLS
+EMTEAEQQQLIDDHFLFDKPVSPLLTAAGMARDWPDARGIWHNNEKSFLIWVNEEDHTRVISMEKGGNMK
+RVFERFCRGLKEVERLIQERGWEFMWNERLGYILTCPSNLGTGLRAGVHIKLPLLSKDSRFPKILENLRL
+QKRGTGGVDTAATGGVFDISNLDRLGKSEVELVQLVIDGVNYLIDCERRLERGQDIRIPTPVIHTKH

src/blat/mCrea.geno

+>mCreatGeno
+GAATTCATCAAGGGATAAATCCATTAATTAGAGTAGAGCCCTTTTGAGCTTTTTGCAATAGCTGGTAATT
+AACCAAACCCCAATACATGAGCCAGTAAAGAACATTTCTTATCGAAAAAGAATTGATGATACTGATGATA
+TGAAAGCTTATTTACGCATATGTTACTGTTGACCTTGAATCTTCATTTAGGAGTTTGAGTGCCCCCATTT
+GTTCTCTATAATTTTGGGAACCTAGGAATTGTCCTAGTTAGATGCCTCATCTTACTGAAACCTCTGCCCC
+AGGCTTCCTGAATTGATAGAGATAGATTCTAAGAGCAGAATCTACAAAGAATCAGTGATAGTTAGGGCTC
+AGACTCATTCCTCTTCTACCACTCCAACCCTGGGAGCGAGTAATTACCGCAGCTCCCAGCTGTAAACAGC
+CTCCAGCGACCCCACTGGCATACTGAGCCTCACAAAGAATTTAAAAAGTGCACAAATCGATGAGCCCTCT
+TGGAAGAGCTATTGTTTCCCATAGGAAGGCATTTNCCAAATTTGAATGACTTCTCTGTACCCTGGCTGCC
+TTTACTTCTTCTGTTAGCCTCTCTTCCCACACCCCACTCCTGAACACCTTCTCAGCCAAATAATAGCCCA
+ATTGCTCTCGAAGACTATCTCCTCCTTTTATCTGGGTAAATATCNCCATCCCAAGTAATTATATCACTTA
+CTCATACCTCNCCTTACCTGGATATGAACACCCACAGCACAGGTAACATTTTTTTTCCCTCTCCAAAAAT
+AAGGAAGTTCCACCAGTAGATCTCTATCTTGGAAAATGTGTTATGTTACCAAGAGAAGAGGCTTAAGTAA
+TGGAGCCAAAAGTGAAATGGATTCTTTCTAAGGATACNCACCAATGAGAAAGGTCAGAAAGGAGACATAT
+GGGGTGGGGACTTGAGGGAAATAATTAATGTATATAGTTGGGCCAGTGGGGATTATGAAGGGTAATTCTT
+TTTCCCAAGTACTTTCTTACAACTTCCAAATATCTTACTGTCTTCTGGAACATCAGGAAGCTGAAGGTAG
+ACATATTAANNNCAATATGTCTGCTTTTGCTTTGGCTGGCCCTCCGCACCCAAACCTCAGGTCTCTATCT
+CAGCTTCAGCTTTCATTCCCCTTCCCAATATGTCTGCTTTGCTTTGGCTGGCCCTCCGCACCCAAACCTC
+AGGTCTCTATCTCAGCTTCAGCTTTCATTCCCCTTCCTGCACTAATAAAAGTCAAGTTGCTCCTAGCCCA
+GCACGTAGCTGTGGAAACAAACCCTCTTGAGTCTGAGTATGCACTTCGCAAAAGAGAGAGCGGACCAGGA
+AGAAGACAGAGACTCCCTGATGACCTTATGCCCTTGGATACTACCAGCCTTCACACTCCAGTTTAAACTG
+CCTTAGCAAGCCAAGAGAGGAAGCACGAGTGGTTCGGGAGACCTGTGCCTGCCTGTTCCATTCCACACCC
+AGTCATCTCACCAGACCCTCCTCCTCTCTTTATATTCCCCCTCCAGTCCTAGGAACTGCCAGCTGCAGAG
+AAGAAGGAAGAGAAGGAAGAAGAAACTCACCATTCCCTGCCCAACCCCAGCCCCACACCCAGAGCAATCA
+ACAGGTAGGCTTTCAGACACTACTCAGGAAGAGTCCTTCGAACAGCAAACAGATTTAAGCCTGGAAAAGA
+AGAAGAGAAATAAAAGATCAAAGGTGAAGCAGGGGTTAGAGTAGAGGAAAAAAAGAAAAAAAAAGCAGGT
+CCCCAATGAGAGGCAGGAAATAGCCAAGCTGAAGACTTGGAGGCAGTGAGTTTGGGAGACAGGATTCTTA
+AGGGATCCTTTCTCGACCTTATTAGGAAAGCATAGGTGTAGCTGGAGTTCCCTGGTGCTTCCTGGTTCTT
+AGGGAAGGTGACTTGAGGCTGTGCTGTCTTTCCCCTGAGCTCGCTCAGTCTTCCTCCTCTATCTGTTTAT
+TCTGTGGTTTTCCTGCGGCTGACTCTCCTGGGGAAAATGGAGAGATGGCGTGCAGATCGAATTCAATTCA
+GAAAAGAGGCTGGGCAATGTCAACCTCCCCACCCCCACCCCCAAAACCCAGAAATAGACGGATTGGTTTC
+AGATTTAAACAGAGAGGGTATGAAAGAAGGGGGGTTTCAGGTTCGGGAATCCCCGTGGTGCTGTCCTCTA
+CTTAGTGCTGAAATCTGACACCCTCATCCTTGGTGGGCGTCTGTCTCCAGCCTCAGGGAGTAAATCTCCA
+GTCTTCTTAATTACCTGGCTAGTGCTACCCAACCCCACCCCCGCACACCTAGCGCGGTGGCAGGCGGGAA
+GGCGGAGCCTGAGTGAGCCCCACCCCTGGAGACTGCGGCTGGGGCCTCCCTCTGCTCTGGCTGGCTCCTT
+GCTTCGCTGCGCTTCTCCTGCAGCCTGGTAGGCACCGGCTGCCACTTCAGCTTCAGCCTTCATCGTGACC
+CCTATTTTGGCTCCAGTCTCCGACCCAGCTCCGTCCTCTCTCTACCCGGTTGCATCTTCCCTCCTAGTTC
+CTGACTTGCACCAGATCCTGCTCTGAATCTTTGTAGCCGCATCCCCAAGCCATGGCTGGTCCCTTCTCCC
+GTCTGCTGTCTGCCCGCCCTGGACTCAGGCTCCTGGCTTTGGCTGGAGCTGGGTCTCTCACCGCCGGGAT
+TCTGCTCCGCCCGGAATCTGTAGGAGCTGCCGCTGCTGAACGGAGGAGACTGTATCCCCCGAGGTATTAG
+AGCCTGAGATGCACGAGGTGGGGGCTGGGGGTGGTAGTGGTGGTGATGGGAACCGAACAGGTAGAGAGGA
+TAACCTGAGCAAAAGATAGGCCTCGAAGATGGATTTCCTGTACAGTTTGGAGATCCTAGCCCTGTAATGG
+AAGAACATGTCTAAGGACATGTCACCCGATGTCACTGCCTCCACACCAGCTTTACCTTTGCAAATTCTAG
+GTTCACCCACTGCCCAAATCCTTTTTGGATGACTAGAAGCTTTTTTTTTTTTTTTTTTTTTTTAATCTCG
+ACCTATTCTCCTTGTTCTCCCGAATTCTCCTGAGTCTCTCCCCTCCCCCATCTCTAATGTTATGCTCACT
+AGAGAAAAGCAACTCTGTAGACAAGGGGGAATTGAGGTGTTAGAACTATTAGGAAAGAAAAGACCCTGGA
+AATCCCTGAAGAGATTATCAAGATTTAGCCTACCTCTAATTCCCCCTCCTTCCAATAAGCAAAGCCAGAC
+ATGGCTCACTGGACAGCTCCCAGCTGACATCAGTAGGTCTAGGCTCCTGTGCCCTCCCTCCATGGTTACT
+GGGTACCCCCTTCCCAGCGCTGAGTACCCAGACCTCCGAAAGCACAACAACTGCATGGCCAGTCACCTGA
+CCCCAGCAGTCTATGCACGGCTCTGCGACAAGACCACACCCACTGGTTGGACACTAGATCAGTGCATCCA
+GACTGGAGTGGACAACCCTGGCCACCCCTTCATCAAGACTGTGGGCATGGTGGCTGGAGATGAGGAGACC
+TATGAGGTAGGGGGCCCCTCAGAAATCCCAGTTCCTTCCTCCTAAAGATCCCTCATGTCTGTTCCCTCAA
+GACTCTGGATTGTCTATACTCAAACGTTCTGATCCAGTGATATCAATCTACAACTCAAGTGTTTCTTCTT
+TATAATCGCCTCTTCCTCTTAACTCCTTTTCAGGTATTTGCTGAACTGTTTGACCCTGTGATCCAAGAGC
+GGCATAATGGATATGACCCCAGAACAATGAAGCACACCACTGACCTTGATGCCAGTAAAGTGAGCCAAAT
+GTGACACTTCCGATATGTGCAGCCTTGTGCACAATGTTCTGTATCTCCAATCATTACACCTTGTTTCCTG
+ACTCAGGGTTAGACTGCTGAGCTTTGTATATTGATAAGAGAAAGAATTGCATATCTTGAAGTATAGCAGA
+TAGGAGGACGTAGTGGATAAGAGTCTGGATAATGGAGTTGAGGAGAATCTGATCAAAGTACAAAATGGTG
+AAAGAATTTTTAAGAAGTGACTATGTCCTGGCTGGGTGTGGTGGCTCACACCTGTAATCTCAGCTCTCAG
+ACGGCTCAGAAGAGCACTCCTCCCTCCACCAAAAAAAAAAAAAAAAAGGCTGTACCCAAAGTGAGAAATG
+TGGAGAAATGACCACAGTGTTTTCAGTTAGCATGCCTGTCCAATGTGTCTTCCTTCTGGCACCTGCTTTA
+TAATCCCCAAGAGTTCCCACCTGCTGTGTTTCTATGATTTATAGTCATTTCTCTTATTCCTCAGATTCGT
+TCTGGCTACTTTGATGAGAGGTATGTATTGTCTTCAAGAGTCAGAACTGGCCGAAGTATCAGGGGACTCA
+GTCTCCCTCCAGCCTGCACTCGGGCAGAGCGAAGAGAGGTAGAACGTGTTGTGGTGGATGCTCTGAGTGG
+CCTGAAGGGTGACCTGGCTGGACGGTACTATAGGCTCAGTGAGATGACGGAGGCCGAACAGCAGCAGCTT
+ATTGATGTGAGGGCCTTGACAGGGAACGGGATTGTGGAAAAAGAGGTGGAGGGGAGAGTGGACCAGAAAA
+GGTAGATGGCCTGGATGGTACTGTGAGAATTCTTAGACCCAATCCCTTTATTCTCCTCAGGACCATTTTC
+TGTTTGATAAACCTGTGTCCCCATTGCTGACTGCAGCAGGAATGGCTCGAGACTGGCCTGATGCTCGAGG
+GATCTGGTATGGAGCCAACACACTTTTTTGGTTTTTTTTTTCCCCCTTGTATGTGCAAAGTTTTTTCTCC
+ATCTACCCCAGTGCTTGTCTTGCCCACTGATGGCTATACCTATCCTGCCCTCAGGCACAACAATGAGAAG
+AGTTTCTTGATCTGGGTGAATGAGGAGGACCACACACGGGTCATCTCTATGGAGAAAGGCGGCAACATGA
+AGAGAGTGTTTGAAAGATTCTGCCGGGGCCTCAAAGAGGTTGGAGAAGGGTATACCAGGGAGCTAGGGGA
+GAGGAAATGAGAAATACCACACAGCAGCATAGCTAGATCGGCTATATCACTTGTCAGTCAACCCAGAGTA
+TTTCTGATAGTAGAAAGGGTCATTATCATGCTAGGATAATAGTTACAAACCAGGGCCGTCCTTGGNAAAC
+CAGGGCATATAGTTACTCTAAAAATAGAAAGAGTGTCAGTAACCTAAGGAAGGAAATAAAGCATAATCTT
+TGCCAAGTAATGAAAAGAAGGAACCAATGATCAGCAAGCCAGTGCCGGGGTAGGTGGTATGAGGTAGTAT
+GTGCAGTTAAGGAGAACGTTTGAGCCTGGACTGATGGAAGGCGTGAGAGATTGGTTTGTTCATGATACAT
+CACCAAGTTCTGANCAAGGCTCACCTTGGCTCTGGAGATCTGATCCTTGATGTATTTTCTTGTATCTACA
+GTTTTATTTTTGGACTTGTAAAGAAAGGGTGCTTCTCTTTTAGATTCTAGCCAGGAAGCTCACACTATTT
+TCGGCAAGGAATGGATAATGTTCTATGAGTAGCATAGAGAAATACTCTTTAATTATATGACTCTGTTTAT
+TTGTCTATAAAGTTGAGGACTAAATGAAATAATGTAGGCAGAGGAATTGTTCTATAATAAGTGTTAGCTT
+TACGATGTAAAAATCTCCATGCTTGTGATTCCTTCTGAGTTACAGAGCATCATCTTTAGGTAGTGTGGTC
+TTTGTGTCTATTGCTCTGGCAGGCCCCTGTCTCTTCCATCCTAATAGTCATTATGGTGGTCAGGAAAGCA
+AGAACATCTCTTGAAGTCCCCCTCTTCTCACATGTACCTGTGAATCTGGCTTCTCTGCTGTACCTTCTCA
+TGTCTCCCTGCTCTATTATCCATGTTCCTTTTATAGCTAAGAGTAGGCTCTCCTGCCTTAGCACCTCGTT
+TCTGTCCAAAGGGACCCTTTGTCAAAGATGTAATTGATGCATGAGAACTCCCTGTCCTGTTTACTACTTC
+TATTCATTTCCCAAGTCACTCTTAATGTATCATTCTCCAAAGCTTCTTCTACGAACAATCTATCTGCCAC
+AATCTTATCAGCATGCATATAATGCAACATCCAAGTGTCCTTCCATGTGCAATGACAATAAGTTTTAACA
+ACAACAAAGAGCATGTCATTCATCGATCGTCAAGTTTCTCGTTGTAGACATAGTTCTAGAATGTCTGTGG
+GGCTAAGAGGGATCCCTCCCTCCCTGATTTTTCACAACAGAACCTCTGTTGACACAGGTGGAGAAGCTGA
+TCCAGGAACGAGGCTGGGAGTTCATGTGGAATGAGCGTTTAGGCTACATCTTGACCTGTCCATCTAACCT
+GGGCACTGGACTTCGGGCAGGAGTCCACATCAAACTGCCACTGCTGAGCAAAGTAAAGGATATGTGGGGC
+TAGAGGGGGTGTAAGAAGGGGGACTTGGAAGGGGGTGGAGGAGACACTCTAAAAAGAGCCAGTCCTAAGG
+GCTTATGGCTAGTGGGCCAAGGGTAGGAGCAGTCTCAGAAACTATTGACATGCCCCTGATCTTTACCTTG
+CATCTAGGATAACCGCTTCCCAAAGATCCTGGAGAACCTAAGACTGCAAAAGCGTGGAACTGGAGGAGTG
+GACACTGCTGCTACAGGCAGCGTCTTTGACATCTCTAATTTGGATCGACTTGGCAAGTCAGAGGTGAGGT
+CTTATGAATCAGGTTAAGAGGTTGAGATAAGGCAGTGAGTGAGCCTCAGGAACATAATAGAATCTGAAGC
+AATGGTCAGGTTGAGTGGGGTAGGGAAGAGAAAACGAGTTTTCAGAGATGGAAGAGCTAAAGAAACTCAG
+GTCAGGCAAGGTGGTCTGTGCTTTTAATACCAGCAGAAGCAAGACAGATCTCTGTGAGTCTCAGGCCAGC
+CAGGGCTACATAATGAGATCCTGTCACAAAAACTGAAAAAAGAAAAAGAAGGAAAAGAAGGAAGGAGGGA
+AGGAAGGAAGGGAGAGAGAGAGAGAGGGAGGGAGAGAGAGGAAGAGAGAGAGATTAAGAGAAGCTCGGGT
+ACACCGGGAAGCAGGGATCAAGGACTGTGTTCTTCAGGTGGAGCTGGTGCAGCTCGTCATCGATGGGGTG
+AACTATTTGATTGACTGTGAACGGCGTCTGGAGAGAGGACAGGATATTCGAATCCCTCCACCTCTTGTCC
+ACAGCAAACATTAACTCCCCATCCCCAGCGGATGAGTCAAGACCCCCAGGACTTCTGCATATTTAACAGT
+GGCCCAGTCTACTTGCCCTGGACCTGCCTCTCTCCCTGTCCTAGTAAAGACTCCACATTATGTTGCAGCT
+GTCTGTGTTATTTCTATTGGTGTGGTGAGGAGGAAGTAGGAAATGAAAAGAAACAGTGAGGTTATTCATG
+ATGGCAAGAGGCGTATATGCCAGGAGCACAGTTCTCAGGTGGGTGGAATGCATTGGAATTTTACCCACAA
+TCCTCATCCACTTACTGAGAATAATTAGTATGCACTTCCATTTACAAGTTGTTCAGTATGATGTAAATTT
+TCTCCCTCAACTGAAGGAACAGTTATCATAATAGGTGGCCAAAAAAAATGCTGACGGGGCAATGCCAGGG
+CCCAGGAGGCTTGGAACCAGTCGTAGAGACCCCAGGCTGAGTTTCGACCTAGAATGAGACAAGGAATGGG
+AGGAAAAAAAATCACAGTTCCGTTCCCCAGGAGCCTTTGATGTTTCAAATTTAGCTCTGTGTATAGATCC
+CTCTACTCCAGAGATTCTCCTGTGTGGGGTCTGAGGACCAGACAGCACCAAGTTAGGACTTAGATGGACT
+CTGGGTCAGATGACAGCTTATCAAACTATGCAGTTGGTAACGTACCCAGCTGCTCTGGGATCTCCTTCCC
+TTCGTGTTGGGCCC

src/blat/mCrea.mrna

+>mCreaMrna
+TGCTCTGGCTGGCTCCTTGCTTCGCTGCGCTTCTCCTGCAGCCTGGTAGGCACCGGCTGCCACTTCAGCT
+tcagccttcatcgtgacccctattttggctccagtctccgacccagctccgtcctctctctacccggttg
+CATCTTCCCTCCTAGTTCCTGACTTGCACCAGATCCTGCTCTGAATCTTTGTAGCCGCATCCCCAAGCCA
+tggctggtcccttctcccgtctgctgtctgcccgccctggactcaggctcctggctttggctggagctgg
+GTCTCTCACCGCCGGGATTCTGCTCCGCCCGGAATCTGTAGGAGCTGCCGCTGCTGAACGGAGGAGACTG
+tatcccccgagcgctgagtacccagacctccgaaagcacaacaactgcatggccagtcacctgaccccag
+CAGTCTATGCACGGCTCTGCGACAAGACCACACCCACTGGTTGGACACTAGATCAGTGCATCCAGACTGG
+agtggacaaccctggccaccccttcatcaagactgtgggcatggtggctggagatgaggagacctatgag
+GTATTTGCTGAACTGTTTGACCCTGTGATCCAAGAGCGGCATAATGGATATGACCCCAGAACAATGAAGC
+acaccactgaccttgatgccagtaaaattcgttctggctactttgatgagaggtatgtattgtcttcaag
+AGTCAGAACTGGCCGAAGTATCAGGGGACTCAGTCTCCCTCCAGCCTGCACTCGGGCAGAGCGAAGAGAG
+gtagaacgtgttgtggtggatgctctgagtggcctgaagggtgacctggctggacggtactataggctca
+GTGAGATGACGGAGGCCGAACAGCAGCAGCTTATTGATGACCATTTTCTGTTTGATAAACCTGTGTCCCC
+attgctgactgcagcaggaatggctcgagactggcctgatgctcgagggatctggcacaacaatgagaag
+AGTTTCTTGATCTGGGTGAATGAGGAGGACCACACACGGGTCATCTCTATGGAGAAAGGCGGCAACATGA
+agagagtgtttgaaagattctgccggggcctcaaagaggtggagaagctgatccaggaacgaggctggga
+GTTCATGTGGAATGAGCGTTTAGGCTACATCTTGACCTGTCCATCTAACCTGGGCACTGGACTTCGGGCA
+ggagtccacatcaaactgccactgctgagcaaagataaccgcttcccaaagatcctggagaacctaagac
+TGCAAAAGCGTGGAACTGGAGGAGTGGACACTGCTGCTACAGGCAGCGTCTTTGACATCTCTAATTTGGA
+tcgacttggcaagtcagaggtggagctggtgcagctcgtcatcgatggggtgaactatttgattgactgt
+GAACGGCGTCTGGAGAGAGGACAGGATATTCGAATCCCTCCACCTCTTGTCCACAGCAAACATTAACTCC
+ccatccccagcggatgagtcaagacccccaggacttctgcatatttaacagtggcccagtctacttgccc
+TGGACCTGCCTCTCTCCCTGTCCTAGTAAAGACTCCACATTATGTTGCAaaaaaaaaaaaaaaaaa

src/blat/mCrea.pep

+>mCreaPep
+MAGPFSRLLSARPGLRLLALAGAGSLTAGILLRPESVGAAAAERRRLYPPSAEYPDLRKHNNCMASHLTP
+AVYARLCDKTTPTGWTLDQCIQTGVDNPGHPFIKTVGMVAGDEETYEVFAELFDPVIQERHNGYDPRTMK
+HTTDLDASKIRSGYFDERYVLSSRVRTGRSIRGLSLPPACTRAERREVERVVVDALSGLKGDLAGRYYRL
+SEMTEAEQQQLIDDHFLFDKPVSPLLTAAGMARDWPDARGIWHNNEKSFLIWVNEEDHTRVISMEKGGNM
+KRVFERFCRGLKEVEKLIQERGWEFMWNERLGYILTCPSNLGTGLRAGVHIKLPLLSKDNRFPKILENLR
+LQKRGTGGVDTAATGSVFDISNLDRLGKSEVELVQLVIDGVNYLIDCERRLERGQDIRIPPPLVHSKH

src/blat/makefile

+kentSrc = ..
+include ../inc/common.mk
+
+L += -lm $(SOCKETLIB) -lz
+MYLIBDIR = ../lib/$(MACHTYPE)
+MYLIBS =  $(MYLIBDIR)/jkOwnLib.a $(MYLIBDIR)/jkweb.a 
+
+O = blat.o
+
+blat: $O $(MYLIBS)
+	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/blat $O $(MYLIBS) $L
+	${STRIP} ${DESTDIR}${BINDIR}/blat${EXE}
+
+all:
+	cd ../lib && ${MAKE}
+	make
+tags:
+	ctags *.c *.h ../lib/*.c ../inc/*.h
+
+test::
+	blat -verbose=0 hCrea.geno hCrea.mrna testRna.psl
+	cmp testRna.psl refRna.psl
+	blat -verbose=0 -prot hCrea.pep mCrea.pep testProt.psl
+	cmp testProt.psl refProt.psl
+	blat -verbose=0 -t=dnax -q=prot hCrea.geno mCrea.pep testProtX.psl
+	cmp testProtX.psl refProtX.psl
+	blat -verbose=0 -t=dnax -q=rnax hCrea.geno mCrea.mrna testRnaX.psl
+	cmp testRnaX.psl refRnaX.psl
+	blat -verbose=0 -fine hCrea.geno hCrea.mrna testFine.psl
+	cmp testFine.psl refFine.psl
+	cd test && ${MAKE}
+
+clean::
+	rm -f testRna.psl testProt.psl testProtX.psl testRnaX.psl \
+	testFine.psl $(O) blat

src/blat/refFine.psl

+psLayout version 3
+
+match	mis- 	rep. 	N's	Q gap	Q gap	T gap	T gap	strand	Q        	Q   	Q    	Q  	T        	T   	T    	T  	block	blockSizes 	qStarts	 tStarts
+     	match	match	   	count	bases	count	bases	      	name     	size	start	end	name     	size	start	end	count
+---------------------------------------------------------------------------------------------------------------------------------------------------------------
+1531	0	0	0	0	0	8	3802	+	hCreaMrna	1540	0	1531	hCreaGeno	6896	240	5573	9	312,199,96,222,86,124,135,126,231,	0,312,511,607,829,915,1039,1174,1300,	240,1156,1558,2040,2391,2592,4377,5013,5342,

src/blat/refProt.psl

+psLayout version 3
+
+match	mis- 	rep. 	N's	Q gap	Q gap	T gap	T gap	strand	Q        	Q   	Q    	Q  	T        	T   	T    	T  	block	blockSizes 	qStarts	 tStarts
+     	match	match	   	count	bases	count	bases	      	name     	size	start	end	name     	size	start	end	count
+---------------------------------------------------------------------------------------------------------------------------------------------------------------
+370	9	0	0	0	0	0	0	+	mCreaPep	418	39	418	hCreaPep	417	38	417	1	379,	39,	38,
+38	7	0	0	0	0	0	0	+	mCreaPep	418	0	45	hCreaPep	417	0	45	1	45,	0,	0,

src/blat/refProtX.psl

+psLayout version 3
+
+match	mis- 	rep. 	N's	Q gap	Q gap	T gap	T gap	strand	Q        	Q   	Q    	Q  	T        	T   	T    	T  	block	blockSizes 	qStarts	 tStarts
+     	match	match	   	count	bases	count	bases	      	name     	size	start	end	name     	size	start	end	count
+---------------------------------------------------------------------------------------------------------------------------------------------------------------
+399	15	0	0	1	4	8	3811	++	mCreaPep	418	0	418	hCreaGeno	6896	403	5456	9	45,68,32,74,29,41,45,42,38,	0,49,117,149,223,252,293,338,380,	403,1151,1558,2040,2391,2593,4377,5013,5342,

src/blat/refRna.psl

+psLayout version 3
+
+match	mis- 	rep. 	N's	Q gap	Q gap	T gap	T gap	strand	Q        	Q   	Q    	Q  	T        	T   	T    	T  	block	blockSizes 	qStarts	 tStarts
+     	match	match	   	count	bases	count	bases	      	name     	size	start	end	name     	size	start	end	count
+---------------------------------------------------------------------------------------------------------------------------------------------------------------
+1531	0	0	0	0	0	8	3802	+	hCreaMrna	1540	0	1531	hCreaGeno	6896	240	5573	9	312,199,96,222,86,124,135,126,231,	0,312,511,607,829,915,1039,1174,1300,	240,1156,1558,2040,2391,2592,4377,5013,5342,

src/blat/refRnaX.psl

+psLayout version 3
+
+match	mis- 	rep. 	N's	Q gap	Q gap	T gap	T gap	strand	Q        	Q   	Q    	Q  	T        	T   	T    	T  	block	blockSizes 	qStarts	 tStarts
+     	match	match	   	count	bases	count	bases	      	name     	size	start	end	name     	size	start	end	count
+---------------------------------------------------------------------------------------------------------------------------------------------------------------
+1219	114	0	0	2	56	9	3865	++	mCreaMrna	1606	200	1589	hCreaGeno	6896	394	5592	10	145,205,96,222,82,128,135,126,167,27,	200,355,560,656,878,960,1088,1223,1349,1562,	394,1150,1558,2040,2391,2588,4377,5013,5342,5565,

src/blat/test/badSplice/small2.fa

+>Y14441 1
+gctggctcgagcctctcctgctcagcaccatggctaagacccctagtgac
+catctgctgtccaccctggaggagctggtgccctatgacttcgagaagtt
+caagttcaagctgcagaacaccagtgtgcagaaggagcactccaggatcc
+cccggagccagatccagagagccaggccggtgaagatggccactctgctg
+gtcacctactatggggaagagtacgccgtgcagctcaccctgcaggtcct
+gcgggccatcaaccagcgcctgctggccgaggagctccacagggcagcca
+ttcaggaatattccacacaagaaaacggcacagatgattccgcagcgtcc
+agctccctgggggagaacaagcccaggagcctgaagactccagaccaccc
+cgaggggaacgaggggaacggccctcggccgtacgggggcggagctgcca
+gcctgcggtgcagccagcccgaggccgggagggggctgtcgaggaagccc
+ctgagcaaacgcagagagaaggcctcggagggcctggacgcgcagggcaa
+gcctcggacccggagcccggccctgccgggcgggagaagccccggcccct
+gcagggcgctagaggggggccaggccgaggtccggctgcgcagaaacgcc
+agctccgcggggaggctgcaggggctggcggggggcgccccggggcagaa
+ggagtgcaggcccttcgaagtgtacctgccctcgggaaagatgcgaccta
+gaagccttgaggtcaccatttctacaggggagaaggcgcccgcaaatcca
+gaaattctcctgactctagaggaaaagacagctgcgaatctggactcggc
+aacagaaccccgggcaaggcccactccggatggaggggcatctgcggacc
+tgaaggaaggccctggaaatccagaacattcggtcaccggaaggccacca
+gacacggctgcgagtccccgctgccacgcccaggaaggagacccagttga
+cggtacctgtgtgcgtgattcctgcagcttccccgaggcagtttctgggc
+acccccaggcctcaggcagccgctcacctggctgcccccggtgccaggac
+tcccatgaaaggaagagcccgggaagcctaagcccccagcccctgccaca
+gtgtaagcgccacctgaagcaggtccagctgctcttctgtgaggatcacg
+atgagcccatctgcctcatctgcagtctgagtcaggagcaccaaggccac
+cgggtgcgccccattgaggaggtcgccctggaacacaagaagaaaattca
+gaagcagctggagcatctgaagaagctgagaaaatcaggggaggagcagc
+gatcctatggggaggagaaggcagtgagctttctgaaacaaactgaagcg
+ctgaagcagcgggtgcagaggaagctggagcaggtgtactacttcctgga
+gcagcaagagcatttctttgtggcctcactggaggacgtgggccagatgg
+ttgggcagatcaggaaggcatatgacacccgcgtatcccaggacatcgcc
+ctgctcgatgcgctgattggggaactggaggccaaggagtgccagtcaga
+atgggaacttctgcaggacattggagacatcttgcacagggctaagacag
+tgcctgtccctgaaaagtggaccactcctcaagagataaaacaaaagatc
+caactcctccaccagaagtcagagtttgtggagaagagcacaaagtactt
+ctcagaaaccctgcgttcagaaatggaaatgttcaatgttccagagctga
+ttggcgctcaggcacatgctgttaatgtgattctggatgcagaaaccgct
+taccccaacctcatcttctctgatgatctgaagagtgttagacttggaaa
+caagtgggagaggctgcctgatggcccgcaaagatttgacagctgtatca
+ttgttctgggctctccgagtttcctctctggccgccgttactgggaagtg
+gaggttggagacaaaacagcatggatcctgggagcctgcaagacatccat
+aagcaggaaagggaacatgactctgtcgccagagaatggctactgggtgg
+tgataatgatgaaggaaaatgagtaccaggcgtccagcgttcccccgacc
+cgcctgctaataaaggagcctcccaagcgtgtgggcatcttcgtggacta
+cagagttggaagcatctccttttacaatgtgacagccagatcccacatct
+atacattcgccagctgctctttctctgggccccttcaacctatcttcagc
+cctgggacacgtgatggagggaagaacacagctcctctgactatctgtcc
+agtgggtggtcaggggcctgactgaatgcccaacactgcatctctcttcc
+tgcttctggccttgtatcttgcattcacactcaatagtcacggaatgccg
+actaggtgctagctgctatgggaaatgcaaaaataacaaaatagttactg
+tgcccacggagcctacccgattatagcagaggtaagttaggaacgaacat
+gttagtcaatccgggtgaagacatgtactgatgacacaccatggatttca
+gaggaggaagtacggagtcgttgcataatccgcccctggtgggtggcact
+ctcaggtgctcctgaacagaagatttggccctcattttccctcagaaccc
+cacggcaaggatatatgtccccttgttctctctgcttctgtcttgaggat
+atgggaagcctagagaaacgcaagcagactggattgggatagaagtattt
+gtgtacctggattaatgaactatga
+>BC101511 1
+gctcgagcctctcctgctcagcaccatggctaagacccctagtgaccatc
+tgctgtccaccctggaggagctggtgccctatgacttcgagaagttcaag
+ttcaagctgcagaacaccagtgtgcagaaggagcactccaggatcccccg
+gagccagatccagagagccaggccggtgaagatggccactctgctggtca
+cctactatggggaagagtacgccgtgcagctcaccctgcaggtcctgcgg
+gccatcaaccagcgcctgctggccgaggagctccacagggcagccattca
+ggaatattccacacaagaaaacggcacagacgattccgcagcgtccagct
+ccctgggggagaacaagcccaggagcctgaagactccagaccaccccgag
+gggaacgaggggaacggccctcggccgtacgggggcggggctgccagcct
+gcggtgcagccagcccgaggccgggagggggctgtcgaggaagcccctga
+gcaaacgcagagagaaggcatcggagggcctggacgcgcagggcaagcct
+cggacccggagcccggccctgccgggcgggagaagccccggcccctgcag
+ggcgctagaggggggccaggccgaggtccagctgcgcagaaacgccagct
+ccgcggggaggctgcaggggctggcggggggcgccccggggcagaaggag
+tgcaggcccttcgaagtgtacctgccctcgggaaagatgcgacctagaag
+ccttgaggtcaccatttctacaggggagaaggcgcccgcaaatccagaaa
+ttctcctgactctagaggaaaagacagctgcgaatctggactcggcaaca
+gaaccccgggcaaggcccactccggatggaggggcatctgcggacctgaa
+ggaaggccctggaaatccagaacattcggtcaccggaaggccaccagaca
+cggctgcgagtccccgttgccacgcccaggaaggagacccagttgacggt
+acctgtgtgcgtgattcctgcagcttccccgaggcagtttctgggcaccc
+ccaggcctcaggcagccgctcacctggctgcccccggtgccaggactccc
+atgaaaggaagagcccgggaagcctaagcccccagcccctgccacagtgt
+aagcgccacctgaagcaggtccagctgctcttctgtgaggatcacgatga
+gcccatctgcctcatctgcagtctgagtcaggagcaccaaggccaccggg
+tgcgccccattgaggaggtcgccctggaacacaagaagaaaattcagaag
+cagctggagcatctgaagaagctgagaaaatcaggggaggagcagcgatc
+ctatggggaggagaaggcagtgagctttctgaaacaaactgaagcgctga
+agcagcgggtgcagaggaagctggagcaggtgtactacttcctggaacag
+caggagcatttctttgtggcctcactggaggacgtgggccagatggttgg
+gcagatcaggaaggcatatgacacccgcgtatcccaggacatcgccctgc
+tcgacgcgctgattggggaactggaggccaaggagtgccagtcagaatgg
+gaacttctgcaggacattggagacatcttgcacagggctaagacagtgcc
+tgtccctgaaaagtggaccactcctcaagagataaaacaaaagatccaac
+tcctccaccagaagtcagagtttgtggagaagagcacaaagtacttctca
+gaaaccctgcgttcagaaatggaaatgttcaatgttccggagctgattgg
+cgctcaggcacatgctgttaatgtgattctggatgcagaaaccgcttacc
+ccaacctcatcttctctgatgatctgaagagtgttagacttggaaacaag
+tgggagaggctgcctgatggcccgcaaagatttgacagctgtatcattgt
+tctgggctctccgagtttcctctctggccgccgttactgggaggtggagg
+ttggagacaagacagcatggatcctgggagcctgcaagacatccataagc
+aggaaagggaacatgactctgtcgccagagaatggctactgggtggtgat
+aatgatgaaggaaaatgagtaccaggcgtccagcgttcccccgacccgcc
+tgctaataaaggagcctcccaagcgtgtgggcatcttcgtggactacaga
+gttggaagcatctccttttacaatgtgacagccagatcccacatctatac
+attcgccagctgctctttctctgggccccttcaacctatcttcagccctg
+ggacacgtgatggagggaagaacacagctcctctgactatctgtccagtg
+ggtggtcaggggcctgactgaatgcccaacactgcatctctcttcctgct
+tctggccttgtatcttgcattcacactcaatagtcacggaatgccgac
+

src/blat/test/badSplice/test

+blat -q=rna -fine chr16part.fa small2.fa small2.psl > small2.log
+pslReps -nohead small2.psl smallBest2.psl /dev/null
+awk '{print $10,$19}' smallBest2.psl
+echo 'see also small2.log'

src/blat/test/dupeTargetName/q.fa

+>USI-EAS376_1_PE_FC30MJEAAXX:3:45:469:751-chr6-32656004
+GTTGGCTGAAGTCCAGAGTGTCCTTTCTGATTCCTGAAGTAGATGAACAGCCCGGCCCCAAGGAAGAGCAGGCCC

src/blat/test/dupeTargetName/t.fa

+>hg18_refGene_NR_001298 range=chr6:32628468-32635757 5'pad=0 3'pad=0 strand=- repeatMasking=none
+GAATACAGAATGTGGGCAAACTCGCTTCTGTGCCGGCCGCCAGAAGGTTT
+GCTGAGGGCAATCACTCCCTGGTGCCGGGCTCCTTGAGGTTATGCACTGG
+GACATCTAGAGCCTATTGTTTGAGGAATGCAGTCTTGCAAGCCTGCTCTG
+GATCAAGCCACAGACTGAAACACCCCCGAAGAGCAAGCACGTTTCTTGGA
+GCAGGCTAAGTGTGAGTGTCATATCTTCAATGGGATGAAGCGGGTGCAGT
+ACCTGAACAGATACATCCATAAACGGGAGGAGAACCTGCGCTTCGACAGC
+AACGTGGAGGAGTTCCAGGCAGTTACGGAACTGGGGCGGCCTGTCGCAGA
+GAACTGGAACAGCCAGAAGGGCATCCCGGAGGAGAAGCGGGACAAGATGG
+ACGACTACTGCAGATACAATTACGGGGTTTTTTGAGAGCTTCACAGTGCA
+GCCGCGAGTCCATCCTAAGGTGACTGTGTATCCTGCAAAGACCCAGCCCC
+TGCATCACCGCAACCCCCTGGTCGGCTCTGTGAGTGGTTTCTATCCAGGC
+AGCATTAAAGTCAGGTGGTTCCAGAATGGTCAGGAAGAGAAGGCTGCGGT
+GGTCTCCATAGGCCTGATCCAGAATGGAGATTGGACCTTCCAGACCCTGG
+TGATGCTGGAAACAGTTCCTCGGAGTGGAGAGGTTTACACCTGCCAAGTG
+GAGCATCCAAGCGTGACGAGCCCTCTCACAGTGGAATGGAGTACACGGAC
+TGAATCTGCACAGAGCAAGATGCTGAGTGGAGTCGGGGGCTTTGTGCTGG
+GCCTGCTCTTCCTTGGGACAGGGCTGTTCATCTACTTCAGGAATCAGAAA
+GGACACTCTGGACTTCAGCCAACAGGACTCCTGCGCTGGACTCCTGAGCT
+GAAGTGCACATGACCACATTCAAGGAAGAACCTTCTGCCACAGCTTTGCA
+GGATGAAAAGCTTTCCCACTTGGCTCTTATTCTTCCACAAGAGCTCTCTC
+AGGACCAGGTTGTTACTCGTTCAGCAACTCTGCAGAAAATGCCCTCCCTT
+GTGGCTTCCTCAGCTCCTGTTCTTGGCCTGAAACCCCACAGCCTTGATGG
+CAGCGCCTCGTCTTCAACTTTTGTGCTTCCTTTTACCTAAATTTTCCTGC
+CTCCCCTGGGTCTGTATTCCCCTTGTGCCACAAACACATTGCATTATTCA
+ATGTTTCTCAAACATGGAGTTAAAAATTATCTGGT
+>hg18_refGene_NR_001298 range=chr6_qbl_hap2:3714100-3715251 5'pad=0 3'pad=0 strand=- repeatMasking=none
+AGTCCAACCTAAGGGGACTATGTATCCTGCAAAGACCCAGCCCCTGCCTC
+ACAGCAACCTCCTGGTCTGCTGTGTGAGTGGTTTCTATCCAGGCAGCATT
+GAAGTCAGGTGGTTCCGGAATGGTCAGGAAGAGAAGGCTGCGGTGGTCTC
+CATAGGCCTGATCCAGAATGGAGACTGGACTTTCCAGACCCTGGTGATGC
+TGGAAACAGTTCCTCGGAGTGGAGCACGGTCTGAATCTGCACAGAGCAAG
+ATGCTGAGTGGAGTCGGGGGCTTCGTGCTGGGCCTGCTCTTCCTTGGGAC
+GGGGCTGTTCATCTACTTCAAGAATCAGAAAGG

src/blat/test/intron50k/expected/test1.psl

+psLayout version 3
+
+match	mis- 	rep. 	N's	Q gap	Q gap	T gap	T gap	strand	Q        	Q   	Q    	Q  	T        	T   	T    	T  	block	blockSizes 	qStarts	 tStarts
+     	match	match	   	count	bases	count	bases	      	name     	size	start	end	name     	size	start	end	count
+---------------------------------------------------------------------------------------------------------------------------------------------------------------
+600	0	0	0	0	0	2	60200	+	query	600	0	600	chr16part	100000	10000	70800	3	200,199,201,	0,200,399,	10000,60200,70599,