>input_sequence_87387
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---------------------------ATGGGGAAGATGTGCTGCAGCCAGGAGGAGGACGAGGCGGGGTTCAACCTGCT
GCCGCTGGTGATGGCCGCCTTCGTCATCATGCTGCTCTTCGTCGTCTGCTCGCCGCCGCCCCGGCGCAGGCGCTGCGTCG
TCGTCCCGTGCTACTGA---------------------------------------------------------------
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>chr3B_1_TraesCS3B01G506900
GATCA---------------------------------------------------------------------------
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-------AGGTCGTACGCTGACAGCAAGT-TGTTCTCGGTATGAAAAT------ATACTACTCATGCGCGTATCGGTGCC
CAAATTTTCGTAGAGTAATCGCCACTTGCGTGCCC----AATCATGCGTACATACCA-GCTTTCAGTGCAAATGTCAATG
ATATCTA-TA-----CATGCAATCACGCTGA-TTGCTGAACAGCACGCATTAAACAGA-------GCAGCAAAAAACAAA
GTCATGTCTTATTTCACCATCACGGAATTTTCAGTAGAGGCAGCGGCTCCTTCCAGCCATGC-TTTCACCGGCGTCCAAA
TCAACCGAGGTTTAGACTAATCGCCAGGCGATAATGACACTACGTACGGATCTACTGTCAACTACAGTACCAAAACAGAG
GAGAAGACGCATTGACCAGACTACTTGTACTGTCAGTTACTTAGTAATTAACTAACTAAA-----GCATGCTGAATTCCT
ACGT----------------------------------------------------------------------------
---------AGCGACCTGCTGCCCGTAGCAACCCCATCGT------------GATCTGTTGGTAGTGGGCTAGCTCTGGA
TCCGTCCTCGCGGTGGGTGCGCGCGGGCGCGTAGGTGATTGATTGATGGATTGGTCGACTCGACTCAATTGTCGCGTCCC
CAACCAGACGGTCCCAACAAGCGAAAAGAAATCCCATCATGGAAGAGGAATAGAAGAGCTCGACGGCGACGCCGCAACCA
CCGCTCCCACCCCACCCCACATGATGCCACAAAGCACGCAAGCGGGCGAACAGGGGAGAGGAGACCCTTCCATTCACATC
ACAACTTCAGAAGTGCCATAGGGAAATAGTGTAGAAGTTTCATCCAGAGACGACCGACCGACCCACCGGACGCGGAGAGG
GGGAGGGAAAGAG-GGAGAGTGGTCTAT-----AGATAGATACAGCTGAAATCCCACTGCCCCAAGAAAGAA---CTTCT
TCCCTTCTTCCTCGTCTCGTCTCCTCCTTCCTCCTCGTCCTCCAAGCCAAG-----AAACTCCTCA--TCTCCACCGTCC
GCCCGTGAAGGAAGGAGGCGATCGGCCATGGGGAAGATGTGCTGCAGCCAGGAGGAGGACGAGGCGGGGTTCAACCTGCT
GCCGCTGGTGATGGCCGCCTTCGTCATCATGCTGCTCTTCGTCGTCTGCTCGCCGCCGCCCCGGCGCAGGCGCTGCGTCG
TCGTCCCGTGCTACTGACCTGACCTGACCTCATGGTGGCCGGGTGGTGGGAGCCT------CGATCGGCGGCGCTGCAGG
CAGGCAAGTGGCTGGTGCTGTGGTAGGCGTTTGTTTGGTTGGTGTCTGAA-TTTTCTGACTGATGCGT-----GTTGGGC
GGAAGAATAATCTCAATTTCTGCTGAATTCGATCGGACTGTAAAGCTAAAGTCATTCTCTTGTTGCAAGTCTGTCTTGTT
GTTAATAATTACTCGTG---TGATTGATGTGCGTGCCGTCCGTTGATTCATCTGCATGCGTGCGGCCTGAATCGATCGAC
TCATCTTGATTCGGTCCCGGAATTCTCGATCAGTTTAATCAGAGCGTCGATCGAAGCAGCACAGGGCTCATTTCTGTCTG
CGGGGAGAGAACAAAATGCTACTAGTACCAGTATTCCTCTGCACTGCACAGAAAGATTGCACCCGTGTATCAACATGTTC
ACAACAAGTTCAGCCGTTTCACCAATGTATCATCAGAGAGATTGTCGAGTGAGTGCCGTGCAGGCCGTTGTGAAACTGTT
GTAGATAAGAATTTGCGCACAATCCCATGTTTAGGATCGGTGAACTAACGCGCACAACGAAGCAAGCAGAAACGCTTGCA
GCAGAAGATCGGGGCGCACAAGTGCATGTGCGGTGGGTATCGTCTTGCTTAGTTTCGCCGTTTAGATTTTAGAACGGGGC
TACCTGTAGCTGGTAGGACTGTTCAGTCGGTCAGCACGTGGGAGCAGCAAAGCAAGACTTGGAACCTTGCATTGGGACCG
CGACGAGCAAAGTTGGGATGGAGATGGCACAGCAGATCACCGCCGAATGGTGACAGAGTCCCGTCCCAGTCGGGCGACTC
GGGCCGCACCAGCGAGCGGGCGACTAGCATGGCGCACCACAGCGTCCACAAGGCACAAGGGTGCGTGGGCGCGCATGCAC
ACGACCAGCGCTGCACGCCGTCGACAGCAGACGCGCGCGCGTGGCCTGGTGCGCTGCGCTCCGCCGCCCTCT
>chr3D_1
ACGATGGTTCCTGAACAACACGCATTAAACAGAGCAGCAAAAAACTAAGTCGGGTCTTTCACCATCACGGAATTTTCAGT
AGAACCAGCAGCGGCCTCAGCCATGCTTTTCACCGGTGTCTGAATCAACCGAGGTTTAGACTAATTCCCAGGCGATAATG
ACACTACGTACGGCTGTACTATCAACTACAGTAGCAAGCAGACGAGTAAACGCATTGACCAGACTACTTGTACTGTCATT
TACTCCATCCGTCCCATGATATATAAGATCGTTTTTTATACTACCCTAATGTCAAAAACGCTCTTATATTGTGAGACGAG
GGGAGTAGTAATTAACTAACTAAACCATGATAGATGCCCGGCTGTAGATGCTCTTATGCGAGATAGGGCTACTCGGGTGT
AGTTTGGCTTAGCGAGGTTACCCTGCATCCCATATACTGCATCGAACACTTCTTGGAGGAACGCCACAACGATGCGGCAT
TTTTTTTACGAGAAAACTTTCGATATATTAAACTTTAATCACGGCAGTACAATAAACATCATAAATAATAAAATTTACAT
CCAGATTCATAGACCATCTAGCGACGACTATAAGCACTGAAGCGAGCCGAAGGTGTGCCGCCGTCATCGCCCCTCCCTCA
CCAAAGCCGGACAAAATTTATTGTAGTAGGCAGTCGGAAAATCGTCGTGCTAAGGCCCCATAGGACCGATGCATCAGAAC
AGCAACCATCGCCATTGAAGTGTAGCGTAGATCGAAACGATCAAACCAGTATACACATGAATAAAGACCCAAAAAATGGA
TCCAAGCAAATCCACCAAAGACCAGCACGACCGAATCTTGCGGGATCGTTTGAAGACACACCTCCACATGATCACCATCG
GTGCTAAACACATCATCGGAACGAGGGCTGGGCGAGGAGAACCTTATTCTATCTTCAGGAAACCGACACCGCCTCCTGAG
CAGGACACAAACCCTAAACGAACTCACAAACCTAAAAACGAAGGAAGATCCCTCCCGCTAGCAAGGGCCAGGGTCCACCG
CGCCTCCATGGTACTAGGGCCACCGGCGACAAGGCGGATCGGCAACGGCGGAAGGCAGAGGAACTCTAACTTTTTCTTGA
ATAGGAGAGATGGCGGCTACATCTGGTGGAGGAAAACGATTCCCTGAATCCGATAAAAGTGGAATTAACTCTAACTCTAT
AAAGTATTGTACAATTGCTTAAGCTATTTGAGAAAATAATATACAATTAATAGGCAGAAATGTTCTGGTAAATTGGGAAG
TGATTCTAGATGAAACTAGATTATGTCATGTGCACTACCACGGGAACCGTGTTAAAACAAACGCGTGAATGGGTGCTTAA
AAACAACTAAAACTAGTAAGAAAATAATGCATGAATGTTCCGATAAAAGAGTGCTCTCAATTTATATTTGAAAAATAATA
AAACCTATGAAGTATGTGACCAAATGATGAATAAAAAGAGAAAACTATTGAACTGAACTTAACATGACACCATCTTTTAA
CCAAAATGTGAAGTATATGAATTATACATATTTCCTCCAACCTGTACCATCCACTATCACACAAAAATAAACGAAAAAAG
TAAGTCCCACTTTCTAGCACCCTCATTTGTCATTTTTGATAGAAATTACACTCCCTAAAAAAATAGAAATCACACCAGCT
TGACAGAACATACTGAAAAAAAGGGTAAAATGCGGCACACATTTCATTAAATGAATTAAAATTCCTTAAATGGCGTCATT
CCTGTCAAAGATACAAACAGGTGCAAAAGGAGGGGGTGAAATTCCTTAAATATAATAACCGAACTTGAAATGTTGGGGGC
CCCACACGCACAGAGAAAAAGAGTGGCAAATGCAGTTTTTTTTTTTAAATTTAGGTCGGCATGTACCTTTGCGGTGCACG
TCAGCTTCTCCTTTTCTAAAAACGAATAAATGCATGGCAATACAATGATGCATCAGGAGTAGTAGCATTGCCGTCTCAAT
CATCGGGAATTCGCGATGTTATGCATGTTTACATTAGGATTTAGTAAGGTGGGAGACCCTGACCTAGTCGCGGCAAGCAC
CCGATCAAGGTCGTACACTGACAGCAAGT-TGTTCTTGGTATGAAAATGAAAGTATACGATCCATGCGCGCATCAGTGCC
CAAATTGTCGTAGAGTAATCGCCACTTGCGTGCTCAATTAATCATGCACACATACCATGCTTTCAGTGCAAATGTCAATG
ATATCTACTATACTGCACAGAATCATGCTGG-TTGCTGAACAACACGCATTAAAACTTAAACGGGGCAGCATAAACACAA
AGTCGGGCC--TTTCACCATCACGGAATTTTCAGTAGAGCCGGCGGCTGCTTGCAGCCATGTTTTTCACCGGCGTCCAAA
TCAACCGAGGTTCAGACTAATCGCCAGGCGATAATGACACTACGTACGATTGTACTGTCAACCACAGTACCAACACAGAG
GAAC--ACGCATTGACCAGACTACTTGTGCTGTCAGTTG----GTAATTAACTAACTAAACTAAAGCATGCTGCATTCCT
ACGT----------------------------------------------------------------------------
---------AGCTACCTGCTGCCAATAGCAACCGCATCCGGCCATCCTGATCGATCTGTTGGTAGTGGGCTAGCTCTGGG
TCTGCCCTCGCGGT----------GGGTGCGTAGGTGATTGATTGATTGGC---------CGACTCTATTGTCGCGTCCC
CAACCAGACGGTCCCAACAAGCGAAAAGAAATCCCATCATGGAAGCGGAATAGAAGAGGTCGACGGCGACGTCGCAACTA
--------------------------CCACAAAGCACGCAAGCGAGCGAGCA-GGGAGAGGAGACCCTTTCATTCACATC
ACA--------------ATAGGGAAATAGTGTAGAAGTTTCATTCAGAGACGACCGACCGACCCACCGGACGCGGAGAGG
GGGAGAGAGGTCTTTA-----------------AGATAGATGCAGCAGAAATCCCACTGCCCCAAGAAAGAA---CAACT
TCTTC-----------------CCTTCTTCCTCCTCGTCCTCCAAGCCAAGCCAAGAAACTCCTCGTCTCTCCACCCTCC
GTCCGTGAAGGAAGGAGGCAATCGGGTATGGGGAAGATGTGCTGCAGCCAGGAGGAGGACGAGGCGGGGTTCAACCTGCT
GCCGCTGGTGATGGCCGCCTTCGTCATCATGCTGCTGTTCGTCGTCTGCTCGCCGCAGCCCCGGCGCAGGCGCTGCGTCG
TCGTCCCGTGCTACTGACCTGACCTGGCATCATGGCGGTGCGGTGGTGGGAGCCTCGACCACGATCGGCGGCTCTGAAGG
CAGGCAAGTGGTT----CTGTGGTGGTAGGC-GTTTGGTTGGTGTCTGAA-TTTTCTGACTGATGCGT-----GTTGGGT
GGAAGAATAATCTCAATTTCTGCTGAATTCGATCGGACTGTAAAGCTAAAGTCATTCTCTTGTTGCAAGTCTCTCTTGTT
GTTGTTAATTATACCCGTGTTGATTGATGTGTGTGCCGTTGATTGTTCTACGAGTGCGGGCCTGA---------ATCGA-
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>chr3A_1
GATCA---------------------------------------------------------------------------
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-------AGGTCGTACCCTGACAGCAAAGGTGTTCTTGGTATA------AAAGTATACTATCCATGCGCGTATCGGTGCC
CAAATTGGCGTAGAGTAATCGCCACTTGCGTGCTCAATTAATCATGCATACATACCATGCTTTCAGTGCAAATGTCAATG
ATATCTA-TATACTGCATACAATCATGCTGATTTGCTGAACAACACGCATTAAACAGA-------GCAGCAAAAACACAA
AGTCGGGTC--TTTCACCATCACGGAATTTTCAGTAGAGCCGGCGGCTGCTTCCAGCCATGCTTTTCACCGGCGTCCAAA
TCAACCGAGGTTTAGACTAATCGCCTGACGATAATGACAGTACGTACGATTGTACTATCAACAACAGTACCAACACAGAG
GAGAAGACGCATTGACCAGACCTGCAG---TGTCAGTTG----GTAATTAACTAACTAAACTAAAGCATGCTGCACTCCT
ACGTACTCCCTCCGTTCGGAATTACTTGCCTTGGAAATGGATGTACCCTCCGTTCGGAATTACTTGTCTCGAAAATGGAT
GTATTTAGAAGCTACCTGCTGCCCGTAGCAGGCCCACCCAAGCGTCCTGATCGATCTGTTGGTAGTGGGCTAGCTCTGGG
TCTGTCCTCGCGGT----------GGGTGCGTAGGTGATTGATTGATGGATTGGTGGACTCGACTCTATTGTCGCGTCCC
CAACCAGACGGTCCCAACAAGCGAAAAGAAATCCCATCATGGAAGCGGAATAGAAGAGCTCGACGGCGACGCCGCAACCA
CCGCCACATG---------CATGATGCCACAAACCACGCAAGCGAGC---------------------------------
-CAACTTCACAAGTGCCATAGGGAAATAGTGTAGAAGTTTCATTCAGAGAC-----------CCACCGGACGCGGAGAGG
GGGAGGAAGAGAGAGGGGAGTGGTCTTTAAGACAGATAGATACAGCAGAAATCCCACTGCACCACGAAAGAAGGACTTCT
TCCCTTGTTCCTCGCCCAGTCTCCTTGT---------TCCTCCAAGCCAAG-----AAACTGCTCTGTCTGTGAGAAAAG
CGAGCG----------GGCGATCGGCCATGGGGAAGATGTGCTGCAGCCAGGAGGAGGAGGAGGCGGGGTTCAACCTGCT
GCCGCTGGTGATGGCCGCCTTCGTCATCATGCTGCTGTTCGTCGTCTGCTCGCCGCAGCCCCGGCGCAGGCGCTGCGTCG
TCGTCCCGTGCTACTGACGTGGCATCATGG--TGGTGGTGCGGTGGTGGGAGCCTCGACCTCGATCGGCGGCGCTCAAGG
CAGGCAAGTGGCTGCTACTGTGGTGGTAGGC-GTTTGGTTGGTGTCTGGATTTTTCTGACTGATGCGTGTTGGGTTGGGT
GGAAGAATAATCTCAATTTCTGCTGAATTCCATCGGACTGTAAAGCTAAAGTCATTCTCTTGTTGCAAGTCTATCTTGTT
---GTTAATTATACCCGTGTTGATCGATGTGCGTGCCGTTGATTATTCTCCGAGTGCGGGCCTGA---------ATCCAC
TCACCTTGATTTGGTGCCTGAATT--------------------------------------------------------
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>SNPs
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----------------S-------------------S-----------------------SS------------------
------S--------------------------S-------------S--------------------------------
------------------S------S----------------S--------------------------------SSS--
SSSSS-S-SSS----------------------------S-S------S-------------------------------
------------------------------------------------SS-S----------S----------S------
----------------------------S---------SSSSS------------------------------S------
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------------S-------------------------SS---------------------------------------S
--S-----------SSSSSSSSSS---S---------------------------S----------S-------------
---------------------------------------------S----------------------------------
----SS-SSSSSSSSSSSS-------------------------S----S--S----------------S----------
---------S---------------------------------S------------------------------------
--------S-------S---------S-------------------S---------------------------------
------S-------S-SS-------S---------------------------------------S----------S---
-S------------------------------------------------------------------------------
------------------------------------S-------------------S-----------------------
----------------------------S---------SSS-----------------------------------S---
--------------S-S-------S-SS-SSS-----------------------------------------------S
------------------------------------------------------------------------S-------
---SS------SS-SS-----------------------SSS---S-SS-SSS-SSS-S-SSS-SSSSSSSSSS------
---S-------S---S--S-----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_2720
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------------------------------------------------------------GGTAGTGGGCTAGCTCTGGA
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>reverse_3972
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---------------------------------------------------GCACAACGAAGCAAGCAGAA---------
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