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# LAST version 1543
#
# a=22 b=1 A=25 B=1 F=0,3,2,6 e=166.503 d=86 x=166 y=43 z=166 D=1e+09 E=30.9637
# R=01 u=2 s=2 S=0 M=0 T=0 m=10 l=1 n=10 K=0 k=1 w=1000 t=4.32027 j=3 Q=0
# Reference sequences=18011 normal letters=16147947
# lambda=0.231467 K=1.69253
#
# AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATA ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT TTA TTC TTG TTT
# A -6 -5 -5 -3 2 2 1 2 -4 -1 -4 -2 -2 -3 -2 -2 -3 -5 -3 -5 -2 -1 -1 0 -2 -3 -3 -2 -5 -4 -3 -4 -3 -4 -3 -4 7 7 6 7 -1 -1 -1 -1 1 2 1 2 -5 -6 -4 -6 2 2 2 2 -4 -3 -6 -3 -4 -5 -3 -6
# C -9 -3 -6 -5 -4 -4 -1 -4 -6 -1 -6 0 -6 -5 -5 -7 -5 -1 -6 -2 -7 -5 -8 -5 -5 1 -6 4 -7 -5 -5 -5 -11 -6 -8 -7 -4 -3 -1 -2 -4 -2 -6 0 -5 -5 -4 -7 -4 0 -2 2 -4 0 -2 0 2 13 2 13 -7 0 -5 -3
# D -2 3 -3 4 -4 -4 -5 -4 -5 -1 -5 1 -9 -9 -8 -9 -2 -1 -2 1 -7 -4 -3 -5 -5 -4 -6 -4 -12 -14 -12 -9 3 10 3 10 -3 -2 -3 -2 -3 2 -2 3 -8 -5 -9 -2 -2 -3 -3 -1 -5 -4 -5 -4 -4 -8 -8 -7 -10 -11 -11 -9
# E 3 -2 2 -2 -3 -4 -3 -4 -2 -2 -1 -3 -5 -8 -6 -6 1 -3 1 -2 -5 -4 -5 -6 0 -3 0 -6 -6 -4 -7 -9 9 3 8 3 -1 -3 -2 -4 0 -4 0 -2 -3 -7 -5 -5 3 -6 1 -7 -4 -5 -5 -5 -2 -9 -6 -8 -6 -10 -6 -10
# F -9 -10 -12 -9 -8 -6 -5 -6 -11 -9 -13 -9 -5 -2 -2 -1 -10 -4 -9 -2 -6 -7 -5 -5 -10 -7 -7 -4 -2 1 0 2 -14 -11 -13 -8 -4 -5 -5 -4 -7 -6 -5 -9 -3 1 -3 -2 -3 4 -4 4 -6 -1 -5 1 -5 -1 0 0 1 10 3 11
# G -4 -1 -5 -1 -4 -5 -5 -6 2 3 1 3 -8 -10 -8 -8 -4 -4 -5 -3 -5 -6 -5 -5 -3 -1 -3 0 -10 -7 -8 -6 0 -1 -2 0 1 -1 0 -2 9 9 9 9 -3 -5 -5 -4 -3 -9 -4 -7 -3 -3 -3 -3 0 -3 -4 -3 -9 -8 -9 -8
# H -3 0 -4 1 -4 -4 -5 -4 -4 -1 -2 -3 -8 -8 -7 -9 2 11 2 11 -1 -2 1 0 -3 3 0 5 -3 -2 -6 -2 -4 -2 -2 -2 -9 -3 -9 -1 -6 -3 -6 -4 -8 -3 -4 -7 0 3 -1 5 -5 -1 -3 -3 -1 -2 -4 0 -2 -4 -7 -5
# I -7 -5 -9 -5 -1 1 1 2 -7 -4 -6 -4 7 9 3 8 -9 -8 -7 -6 -5 -7 -8 -4 -10 -8 -8 -6 1 2 1 2 -9 -10 -9 -10 -3 -3 -4 -3 -8 -9 -6 -9 3 5 3 4 -7 -5 -7 -6 -5 -6 -5 -6 -6 -6 -8 -4 2 -1 2 -1
# K 8 0 8 0 0 -3 0 -3 4 -2 5 -1 -2 -9 -2 -8 3 -2 2 -3 -5 -6 -2 -3 1 3 2 0 -7 -8 -8 -9 0 -3 0 -3 -3 -4 -3 -5 -4 -5 -3 -5 -6 -8 -5 -9 2 -8 1 -7 -4 -7 -6 -5 -1 -6 -4 -7 -8 -12 -8 -12
# L -9 -8 -8 -8 -3 -3 -2 -4 -5 -6 -7 -8 1 1 2 1 -5 -4 -3 -4 -2 -3 0 -3 -4 -3 -4 -2 7 7 7 7 -11 -13 -9 -12 -4 -4 -4 -4 -10 -8 -8 -12 0 0 1 -1 -3 -5 -3 -4 -2 -4 -2 -5 0 -4 -2 -6 7 2 7 1
# M -4 -6 -2 -7 1 -1 5 -1 -1 -5 0 -6 5 1 11 2 -7 -6 -3 -6 -3 -8 -2 -7 -3 -2 -3 -3 2 1 3 0 -7 -7 -6 -9 -1 -3 -1 -3 -8 -9 -4 -6 1 -1 3 -2 -5 -7 -5 -3 -4 -5 -3 -5 -3 -5 -5 -8 2 -3 3 -2
# N 0 10 0 10 -2 0 -3 0 -3 4 -3 4 -6 -5 -7 -3 -2 1 -2 1 -7 -3 -3 -4 -4 -1 -1 -2 -7 -6 -9 -8 -4 2 -3 2 -4 -3 -3 -5 -2 1 -2 1 -8 -8 -4 -5 -2 -3 -4 -3 -4 -5 -4 -2 -3 -5 -7 -4 -9 -11 -10 -9
# P -7 -7 -6 -8 -1 -1 -2 -2 -4 -5 -5 -5 -6 -9 -6 -8 0 -2 -4 -1 10 10 8 10 -5 -1 -2 0 2 -1 -2 1 -6 -7 -6 -5 -1 -2 1 -1 -6 -6 -4 -8 -2 -6 -5 -6 -3 -7 -5 -8 4 2 2 3 -2 -6 -5 -7 -3 -6 -5 -5
# Q 1 -2 1 -2 -3 -5 -3 -4 -1 -2 0 -2 -4 -9 -4 -9 8 3 9 2 0 -3 -1 -4 0 0 3 -1 -2 -4 -3 -5 0 -3 1 -2 -3 -3 0 -4 -4 -3 -4 -4 -3 -7 -5 -8 5 -4 7 -4 -2 -3 -3 -3 0 -7 -1 -5 -5 -8 -4 -8
# R 2 -3 3 -2 -2 -5 -2 -3 8 -1 8 -1 -4 -9 -4 -9 3 3 2 3 -1 -2 2 -3 9 7 8 6 -4 -5 -5 -5 -4 -6 -2 -6 -5 -4 -4 -6 0 -4 -2 -2 -6 -8 -7 -8 1 -3 1 -4 -3 -5 -4 -7 6 2 3 1 -6 -6 -6 -7
# S -4 1 -4 1 1 2 0 2 -2 6 -2 5 -6 -5 -4 -4 -3 -2 -3 -3 0 1 1 1 -4 -1 -2 0 -6 -5 -6 -3 -4 -2 -4 -2 0 1 0 0 -2 -1 -2 0 -6 -4 -4 -4 -2 -5 -2 -3 6 7 7 7 -1 0 -4 0 -1 -2 -2 -3
# T -2 0 -3 -1 7 8 6 7 -2 1 -3 2 2 0 1 0 -5 -4 -3 -4 -2 -1 -1 -1 -2 -2 -3 -4 -4 -3 -3 -3 -4 -4 -4 -2 1 1 0 2 -3 -4 -3 -4 -1 0 -2 0 -4 -7 -6 -6 1 2 2 1 -3 -3 -6 -3 -3 -4 -4 -6
# V -6 -8 -6 -7 0 -1 1 0 -5 -6 -5 -6 4 5 2 5 -4 -6 -6 -5 -5 -4 -6 -3 -8 -5 -7 -7 0 1 1 0 -5 -7 -5 -7 1 0 2 1 -4 -5 -3 -6 8 7 8 7 -7 -8 -6 -4 -5 -4 -3 -5 -7 -5 -6 -4 0 -3 1 -2
# W -7 -11 -9 -9 -6 -10 -9 -8 -5 -6 -1 -6 0 -4 -4 -6 -5 -1 -2 -4 -11 -3 -5 -14 -4 -5 2 -4 -5 -7 -5 -8 -9 -7 -8 -12 -1 -11 -4 -9 -7 -8 0 -6 -6 -3 -8 -7 2 1 9 0 -3 -8 2 -4 9 -1 16 -1 -3 -1 0 1
# Y -8 -3 -9 -2 -8 -6 -5 -9 -10 -3 -10 -4 -7 -6 -6 -7 -6 2 -6 4 -8 -6 -6 -7 -7 -3 -4 2 -6 -5 -5 -4 -10 -4 -9 -3 -10 -4 -4 -6 -9 -6 -10 -4 -7 -4 -8 -6 4 12 4 12 -5 -1 -3 0 -2 3 1 3 -2 4 -4 5
# * -29 -30 -30 -28 -30 -31 -31 -30 -28 -30 -29 -30 -30 -30 -30 -30 -7 -29 -28 -30 -30 -30 -30 -29 2 -31 -27 -30 -29 -30 -29 -30 -27 -31 -30 -29 -30 -30 -29 -30 -28 -30 -31 -30 -27 -31 -28 -30 20 -29 14 -28 -29 -30 -10 -30 18 -30 -19 -29 -25 -30 -29 -30
#
# Coordinates are 0-based. For - strand matches, coordinates
# in the reverse complement of the 2nd sequence are used.
#
# name start alnSize strand seqSize alignment
#
a score=7356.2 EG2=0 E=0
s HERVS71_pol#LTR/ERV1 5 1194 + 1200 LeuGlyProGlnGluProMetValThrAlaThrValGlyGlyGlnProValArgPheLeuValAspThrGlyAlaGluHisSerValLeuGlnThrProLeuGlySerValSerAsnLysLysMetAlaValGlnGlyAlaThrGlyAlaIleGlnGluTyrProValThrHisSerXaaGluValXaaLeuGlyGlnLysArgAlaThrHisSerPheXaaValValProGluCysProPheProLeuLeuGlyArgAspLeuLeuHisLysLeuGlnAlaSerIleSerPheSerAlaGlnXaaAlaHisLeuThrLeuGlyAsnAlaThrSerXaaThrAlaGlnLeuLeuLeuThrThrProLeuSerGluGluTyrLeuLeuValSerProSerXaaSerProGluXaaAsnThrAsnThrLeuLeuLeuXaaXaa------GlnThrLeuPheProArgValTrpAlaGluSerAsnProProGlyLeuAlaLysHishisproproValValValGluLeuLeuAlaThrAlaIleProValGlnValLysGlnTyrProAlaSerGlnGlnAlaArgGluGlyIleAsnProHisIleGlnArgLeuLeuGlnAlaGlyIleLeuThrProCysGlnSerAlaTrpAsnThrProPheLeuProValGlnLysProGlyThrAsnAspTyrArgProValGlnAspLeuArgGluValAsnLysArgThrValThrValHisProThrValProAsnProTyrThrLeuLeuSerLeuLeuProProGluHisThrValCysThrValLeuAspLeuLysAspAlaPhePheAlaIleProLeuAlaProLysSerGlnProIlePheAlaPheGluTrpThrAspProArgSerGlyAspThrThrGlnLeuThrTrpThrGlnLeuProGlnGlyPheLysAsnSerProThrLeuPheGlyGluAlaLeuGlnGlnAspLeuAsnThrPheArgAlaSerHisProAsnCysThrLeuLeuGlnTyrValAspAspIleLeuIleAlaThrGluThrMetAspGlyCysLeuGlnHisThrArgAspLeuLeuTyrLeuLeuGlnGluLeuArgTyrGlyValSerAlaLysLysAlaGlnLeuCysLeuProArgValSerTyrLeuGlyTyrGluIleAsnLysGlyLysArgAlaLeuThrSerAlaArgLysGluAlaIleProArgIleProThrProThrThrLysArgGlnValArgGluXaaLeuGlyAlaMetGlyTyrCysArgXaaTrpIleLeuArgPheAlaGluIleAlaLysProLeuTyrThrAlaThrArgGlyAsnGlyProLeuIleTrpThrAspThrGluGluGlnAlaPheGlnAsnLeuLysLysXaaLeuThrXaaAlaProAlaLeuAlaLeuXaaAsnIleSerLysProPheHisLeuPheValHisGluSerGlnGlyValAlaLysGlyValLeuThrGlnThrLeuGlyProTrpArgArgProValAlaTyrLeuSerLysArgLeuAspProValAlaXaaGlyTrpProSerCysLeuArgAlaIleValAlaThrAlaSerLeuValGlnGluAlaAspLysLeuThrLeuGlyGlnAsnLeuThrLeuThrAlaProHisAlaValGluThrLeuLeuArgSerAlaXaaGlyLysTrpMetSerAsnAlaArgIleLeuGlnTyrGlnSerLeuLeuLeuAspGlnProArgLeuThrPheSerProThrArgCysLeuAsnXaaAlaXaaLeuLeuXaaAspProAspSerXaaThrProValHisAspCysGlnGluLeuLeuGluThrThrGluThrGlyXaaXaa------AspLeuGlnAspValProLeuLysLysAlaAspAlaThrValPheThrAspGlySerSerPheLeuGluGlnGlyValarglysalaglyalaalavalthrthrgluThrAspValLeuTrpSerGlnValLeuProAlaSerThrSerAlaGlnLysAlaGluLeuIleAlaLeuThrGlnAlaLeuArgTrpXaaLysAspLysArgIleAsnIleTyrThrAspSerArgTyrAlaPheAlaThrValHisValHisGlyAlaIleTyrGlnGluArgGlyLeuLeuThrSerAlaGlyLysIleIleLysAsnLysGluGluIleLeuAlaLeuLeuGluAlaValTrpLeuProGlnGlnValAlaValIleHisCysLysGlyHisGlnLysGluAsnThrAlaValAlaArgglyasnglnlysxaaaspseralaAlaArgGluAlaAlaArgProSerValXaaProXaaAsnLeuLeuProAlaValSerPheProGlnProAspLeuProAspAsnProAlaTyrSerAlaGluGluGluLysLeuAlaSerAspLeuArgXaaAsnLysAsnGlnGluGlyTrpTrpIleLeuProAspSerArgIlePheIleProArgAlaLeuGlyGluThrLeuValSerHisLeuHisSerThrThrHisLeuXaaGlyAlaLysLeuAlaGlnLeuLeuArgSerArgPheLysIleProArgXaaGlnSerLeuThrAspGlnAlaAlaLeuTrpCysThrAlaCysAlaGlnValAsnAlaLysGlnGlyProLysProSerProGlyHisArgLeuArgGlyAsnSerProGlyGluLysTrpGluIleAspPheThrGluValLysProHisArgAlaGluTyrLysTyrLeuLeuValLeuValAspThrPheSerGlyTrpThrGluAlaPheAlaThrLysAsnGluThrAlaAsnThrValValLysPheLeuLeuAsnGluIleIleProArgTyrGlyLeuProAlaAlaIleGlySerAspAsnGlyXaaAlaPheThrSerSerIleAlaGlnSerValSerLysAlaLeuAsnIleGlnTrpLysLeuHisCysAlaTyrGlnProGlnSerSerGlyGlnValGluXaaMetAsnHisThrLeuLysAsnThrLeuThrLysLeuIleLeuGluThrGlyGluAsnTrpValXaaLeuLeuProLeuAlaLeuLeuArgValArgCysThrProTyrGlnAlaGlyPheSerProPheGluIleMetTyrGlyArgAlaProProIleLeuProLysLeuLysAspAlaHisLeualagluileserglnalaasnleuleuglntyrleuglnserleuglnglnvalglngluileIleLeuProLeuValArgGlyAlaHisProSerProValProAspGlnMetGlyProCysHisSerPheGlnProGlyAspLeuValPheValLysLysPheGlnArgGluGlyLeuThrProAlaTrpLysGlyProHisThrValIleLeuThrThrProThrAlaLeuLysValAspGlyIleProAlaTrpIleHisHisSerHisIleLysLysAlaAsnLysAlaGlnThrGluThrTrpValProLysProGlySerXaaProLeuLysLeuHisLeuSerArg
s HERVS71A 3493 3582 + 8946 CTTGGCCCCCGGGAGCCCATGGTGACCGCCACAGTGGGGGGCCAGCCTGTACGCTTCCTAATNGACACCGGGGCGGAACACTCGGTACTGCAGACACCCTTGGGCAGTGTCTCTAATAAAAAGGTGGCTGTACAAGGGGCTACTGGAGCTATTCAGGAATATCCTGTCACCCACTCACGAGAGGTGAGTTTGGGACAGAAAAGAGTAACCCACTCATTTCTCGTGGTCCCAGAGTGCCCCTTTCCCCTCCTCGGACGAGACCTGCTCCATAAGCTACAGGCGTCTATCTCCTTCTCGGCCCAACAAGCTCACCTCACGTTAGGGGACACAACGCCCCCTACTGCCCAGCTCCTGCTAACCACCCCTCTGTCGGAGGAATATCTCTTAGTTTCACCCTCACAACCGCTGGAGAATAAAACTAATCCTCTCCTACTG------GATTTACAGACTCTCTTTCCTCGAGTCTGGGCCGAGTCAAACCCCCCGGGACTGGCAAAGCACCATCCGCCAGTAGTTGTAGAACTCCTGGCCACCGCCCTGCCAGTCCAGGTAAAACAATATCCTATGAGTCAGCGGGCTAGAGAGGGAATCAATCCCCATATTCAGCGACTGTTACAAGCTGGCATACTCACACCATGTCAGTCCGCCTGGAATACTCCATTTTTGCCGGTCCAGAAACCCGGAACAAATGATTACCAGCCTGTACAGGACTTGCGGGAAGTTAACAAGCGGACAGTCACCGTCCATCCAACTGTCCCTAACCCTTATACTTTACTCAGCCTGCTCCCGCCAGAACATACAGTATACACTGTCCTTGACTTAAAGGATGCTTTCTTTGCTATTCCTCTGGCCCCCAAAAGCCAACCTATCTTTGCTTTTGAATGGACAGATCCTGGCTCGGGAGACACCACCCAATTAACCTGGACTCGGTTACcccagggttttaaaaattcccccaccctttttggggaaGCCCTCCAACAGGATCTTATACCATTCCGAGCCAGTCACCCTAACTGCACTCTTCTCCAGTACGTGGACGACCTTTTATTGGCTACTGAAACTACTGACAGCTGCCTGCAACATACTAGGGACCTACTTTACCTCCTTCAGGAACTCGGGTATCGGGTCTCAGCCAAGAAGGCCCAGCTTTGTCTTCCCAGAGTTTCCTACCTAGGGTACGAGATAAACAAAGGAAAAAGGGCACTCACCAGTGCTCGAAAGGAAGCCATCCTGCGAATCCCCACTCCCACCACCAAGAGACAGGTACGTGAATTCCTGGGGGCCGTGGGATACTGTCGCCTATGGATATTGGGGTTCGCGGAAATCGCCAAGCCCCTGTACACCGCTACCGGAGGGAATGGCCCGCTAGTTTGGACTGACACAGAAGAACAGGCTTTTCAAAACCTGAAAAAGGCATTAACTGAGGCCCCTGCTCTAGCCCTCCCAAATATCTCAAAACCATTTCACCTTTTTGTTCATGAAAGCCAGGGAGTCGCTAAAGGGGTACTCACTCAGACTTTGGGGCCATGGCGACGCCCAGTGGCCTATTTGTCTAAGAGACTGGACcctgtggcctccgggtggccaagttgtctgcgagCCGTAGCGGCAACAGCAAGCCTGGTCCAGGAGGCTGATAAACTGACTCTGGGCCAGAATTTAACCCTTACGGCTCCTCATGCCGTAGAGACTTTGCTACGAAGTGCTTCTGGCAAATGGATGTCGAATGCTCGCATCCTGCAGTATCAGAGTTTACTGTTAGATCAGCCTCGTTTAACTTTCTCTCCCACAAGGTGTTTAAATCCAGCTACCTTGCTCCCTGATCCAGACCTCACCACACCTGTCCATGACTGCCAGGAACTGTTAGAGACTACGGAAACTGGC------CGACCTGATCTCCAAGATGTGCCTCTAAAGGAGGCGGACGCCACCGTGTTTACAGACGGTAGCAGCTTCCTCGAACAGGGAGTACGAAAGGCTGGTGCGGCCGTTACTACGGAGACGGATATACTGTGGGCCCAGGCGCTGCCGGCAGGTACCTCGGCACAGAGGGCTGAATTGGTCGCCCTCACTCAGGCTCTCCGATGGGGTAAGGACAAACGTATTAACATTTACACTGACAGCAGGTATGCTTTTGCTACTGTGCATGTACACGGAGCCATCTATCAAGAGCGNGGGCTACTCACCTCAGCAGGAAAGACTATCAAAAACAAAGAAGAAATTTTGGCCCTGCTTGAAGCCGTTTGGCTCCCTCAGCAGGTGGCTGTAATTCACTGCAAAGGACATCAAAGAGAAGACACGGCCATTGCCCGTGGTAACCAaagagcagaCTCTGCAGCTCGAGAGGCAGCTCGGCTCCCGGTCGCGCCTTTGACCCTGCTGCCCGCNGTGTCCTTTCCGCAACCTGACTTGCCAGACCACCCAGAATACTCCCCAGAGGAAGAAAAACAGGCTTCGGATCTTCAGGCCAGTAAAAATCAGGAAGGTTGGTGGATTCTTCCTGATTCCAGAATCTTCATGCCCCGAGCCCTCGGGGAAACTTTAATCAGTCGTCTGCATTCTACCACCCATTTGGGAGGAGTAAAACTGGCCCAGCTTCTAAGGAGCCGTTTCAAGATCCCCCACCTTCAGGACTTAGCTAACCAAGCAGCTCTCCGGTGTACGGCTTGTGCTCAGGTAAACGCCAAGCAAGGTCCTAAACCCAGCCCAGGCCACCGCCTCCGGGGAGACTCGCCAGGAGAAAGGTGGGAAATTGACTTTACAGAGATAAAACCACACCGGGCAGGGTATAAATACCTCCTGGTGCTAGTAGACACCTTTTCCGGATGGACTGAGGCATTTGCCACCAAAAACGAGACTGCCACCACGGTAGTTAGGCTTTTACTCAATGAAATCATCCCTCGACATGGGCTGCCTGCTGCCATAGGGTCTGATAATGGACCGGCCTTCACCTCGTCCATAGCTCAGTCGGTCAGTAAGGCATTAAACATTCAATGGAAACTCCATTGTGCCTATCGACCCCAGAGCTCTGGACAGGTAGAACGCATGAACCGCACCCTAAAAAGTACTCTTACAAAATTAATCCTAGAGACCGGTGAGAATTGGGTAAGGCTCCTTCCTTTAGCCCTTCTTAGAGTAAGATGCACCCCTTACCGGGCTGGGTTTTCACCTTTTGAAATCATGTATGGGAGGGCTCCGCCTATCTTGCCTAAGCTAAGGGATACCCATTTAGCAGAAATCTCACAAGCTAATTTGTTACAGTACCTGCAGTCTCTCCAACAGGTACGAGACATCATCCAGCCACTTGTCCGGGGAGCNCATCCCAATCCAGTTCCTGACCAGACGGGGCCCTGCCACTCTTTCCAGCCGGGTGACCTGGTGTATGTTAAAAAGTTCCAGAAAGAAGGACTCACTCCTGCCTGGAAAGGACCTCATACTGTCATCCTCACCACGCCGACGGCTCTGAAGGTGGACGGCATTCCTGCTTGGATTCATCACTCTCGCATCAAAAAGGCCAACAAAGCCCAGCAAGAAACATGGGTCCCCAAGCCTGGGCCAGGCCCCTTAAAACTGCGCCTAAGTCGA
# Query sequences=1 normal letters=8923
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