>input_sequence_87385
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--------------------------------------------------------------ATGGAGTACGGGTACCCC
TGCAACAGCT------GCAGCAGCAACAAGGAGAAGAGGCCTCCGCTCAAGAGAGGCCAGCTCAAGCTGCAGATCGCCAG
GACTCTCGGCAGCCTCGTGGTGCCGGGCGCCAAGAGCGGTTTCAGCTTCAGAAGATGA----------------------
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>chr3A_1_TraesCS3A01G353600
TATATTTTTTCGAATTAATAATCATATAAAGGGGTGGAGCACCCCCGAGCCAAAAAAGAAAAAACACATCCCTAATCTAT
CCCAGCACATTGTCAGAATAGTCACGAACAGGAGACCGAGACTCAGCCCAGCCTTACCCACATTCGTACCTTTTACACTT
ATTATGTCATATATAAAACGCAGGTACTCCCTCTGTAAACAAATCTAAAACTCATATACCCA-AATTTAAATGTAAG---
-----ATCTTAGGTTTCCTC-GACGTACTGCCAAAAGAGGCCGTACTACCAACCACATGACACGGTCGAAGTCGATGATT
AATCTAGATTTCTGTTTCCCTTGACATGTTTT-GTTTTGTCACCAGCAAAAAACCCTTGGCCA--------GATACATCG
TT--------CCCATCACTTTAGTTTCGTGTAACCACTTGTAGCACAATAATGCTAGATCTGCTTTAGGTTCTTCAGCCC
TACCTAAGGGCACAGTTGCGTTACTTAACCCAAAAGCACGTCCACTTAGCACTAAACAATGGATTTTGTCCGGGAAAGAC
GCGCTGTAGAATCTAGCGTGCATCTGGCTCCACATGCAGCCGGCCGTCTAATCTGGATTTTGCCACGAGATTAACTGCTC
CCTAATC----------------------------------CCTTCACGGACGCTTCCCTCCCTCCCTCCTCGACGAGTG
TTACGGTGAGAG--------CCGAGAGTGACAAGCGACTCTGCACGCACCCACAGCAGGAGCAAATTTTACCCCACACGA
CTCCAAACAAAGCATACTTATTACTCCCGGCCCCCCAGTAGATGCAGATGCAGATGCAGATGCAGATGCAGGGAGTACTA
-----GTAAACAAAGAAGCACGCGCAATCTAACTAACGGAACGTGCTTAAAAAACCCGCGCTATAAATCAGCTCCGCC--
--TTGCTCACTCTCCATCCACACACCAGCTCTC----GCCTTCCCT-GCAACACA----AGCCACCACT-TGAATCTGAA
AGCACGGAGAGGAGGAGG-------AAGACG-------AGCAAGCAAGCAAAGGGAGGTGCAATGGAGTACGGGTACCCC
TGCAACAGCT------GCAGCAGCAACAAGGAGAAGAGGCCTCCGCTCAAGAGAGGCCAGCTCAAGCTGCAGATCGCCAG
GACTCTCGGCAGCCTCGTGGTGCCGGGCGCCAAGAGCGGTTTCAGCTTCAGAAGATGATGGCTTGAC--------CGGCA
AGGACAAGCAAGCATCTTCTTCGGCCAGT-------CTAGGAGCATGGTGTGGTTCTGGTGC-TTGGTGCGTACAG----
-GGATTGCGTAGATT-----------------------------------------------------------------
-----TAGTCCCTGCTTGATTTGCGGTTTGCTCATTAGATCTCGCTTCCTCGATCGACAATTTTTACGTTGTCCACGAGT
GAAGAAGAAATGTACGGAGATTGGAGCTTCATG----------------------------------------TTCTGAT
TCTGAGATTGGTGCGTC---CCGCTCTTGCTGCATTTGATTTGTCAAACTCTGAAGTCTCTGAACTGAATGAATAGACTG
GCCTGATGGGTGTACTGCGGACGGTACATGCCACAGTGTCAGTTTGCCTGACGCGTGTTTCTTGGTCTCAGCTCCACCAT
GGCGCGGAAGAGTTACCAGCCTCGCGCGTGCGTCCGGCAGTGGTTACCCTTCGCCGCCGATGCAGCGCCATGACACGAGT
CGATCGATCGGGGTTGCCAATTTGCCAATTGATACGATTAAGTAGCAATAGCGCGTTTCCACAAATAAACTCCACAGATA
ACACAAACAGTAAGTACGCTTGCACGCTCGATCTCTTGTTCTTCTCAAAGAAAAGAGCACTCCATCCCATGTTACCAATA
TTTTGAGCTCTCTCTAGCGTTGTTCCCAGTTCCCACCACTTGTGTTTTGCGCAACTACTAGCGGTATTGGAGTATTATTT
TCTTTAAATAATTTATTAGTTGTACCTAACAGCGCAATTTGCATTAGTTGAGTCAAAGGCAGGGCCCCTTAGCGATAACA
AATTAACAATAGATCCCTACATTATCCTGAGAATGCTACAAGGTAAGACCGGCCGGCATGTCTATCTTGCATACATGTAT
TATCACGGGGAGCAGATTTGATGTTCCTAGGTGCTTCT-------TAAACATATATTCTCTGGTGTTGAGACGGCGCTCT
GAAGGTGAGCAGCTTGTAAAACTGACCTGTGGGTGTCTGTTTACCATAGAATACACAGCTCTGCAGTCTCCATTCTTGT
>chr3D_73
------------------------------------------------------------------------TAATCTAT
CCTAGTACATTGCCAAAATAATCAGGAACAGGAGACCGAGACTCAGCCCAGCCTCACCCACATTCATGCCTTTTACACTA
ATT---TCGTATATAAAACACACGTATTCCCTCAGTAAACAAATAGTATAAAACACACGTACTAATTTACATGTAAGAAC
CGCAAATCTTAGGGTTCCAC-GACCCACTGCCAAAAGAGGCCGTACTGCCAACCACGTGACATGGTCGAGGGCGATGAAT
AATCTGGAATTCTGTTTCCCTT-ACATGTTTT-GTTTTGTCACCAGCGATAAACCCTTGGCTG--------GATACGTTG
TTTGTTCCCACCACTTTAGCT------GTGTAACCACCGGTAGGACAATAATGCTAGATCTGCTTTAGGTTCCTCAGTTC
CACCTAACGGCACAGTTGCATTACTTAACTCAAAAGCATGTCCACTTGGCACTAA-CAACAGATTAAGTCCGAGAAAGAC
GCGCTCAAGAATCTAGCGTGCATCTGGCTCCACAGGCAGCCGGCCGTCTAATCTAA---TTGCCACGAGATTAATCGCTC
CCTGATC----------------------------------CCTTCACGGATGCTTCCCTT--------CTCGACGAGTG
T--CAGTGAGAG--------CCGAGAGTGACAAGTGACTCCGCACGCACCCACAACAGGAGCAAATGTTACCCCACACGA
CTCCAAATAAAGCGAACTTATT---CCCGGACCCCA-------------------GCAGATGCAGATGCAGGGAGTACTA
CACTAGTAAACAAAAAAGCACGCGCAACCTAACTAACGAAACGTGCCTAAAAAACTCGCACTATAAATCAGCTCCGCC--
--TTGCACACTCTCCATCCACAAACCAGCTCCC----GCCTTCCCT-GCAACACAAGCTAGCCACAGCT-TGAATCTGAA
AGCACGGAGAGGAGGAGG-------AGGAAGACGAGCAAGCAAGCAAGCAAAGGGAGGAGCAATGGAGTACGGGTACCCC
TGCAACAGCT------GCAGCAGCAACAAGGAGAGGAGGCCGCCGCTCAAGAGAGGCCAGCTCAAGCTGCAGATCGCCAG
GGCTCTGGGCAGCCTCGTGGCGCCGGGCGCCAAGACCAGCTTCAGCTTCAGAAGATGATGGAGC----------------
-------------------------------------------------ATGG-TGTGGTGC-TTGATGTGAACA-----
GAGATTGTGCAGGTCGAAGAAGAGTTGTTTTAGTT-AGGTGTGCTTCTAATTTGTGTCCAGTTCCCCCCCTTCCACGGTT
CCACCTAGCCCCTGCTCGCTTTGAGGTTTGCTGATTAGATCTCGCTTCCTCGATCGACAATTT--ACGTTGTCCACGAGT
GAAGA---CATGTACGGAGATTGCAGATCCATGCTTGTTCAGAATGCACTGTAGCTTCTAATGGGAATTACAATCCTGAT
TCTGAGATTGATGCGTCTCCCCGCTCTCACTCCATTTGATTTGTCCAACTCTGAAGTCTCTGAACTGAATGAACAAACCG
GCATAATGGGTGTACTGCGGACGGTACATGCCACATTGTCAGTTTGCCTGACGCGTGCTTC-------------------
------------TTACCAGCCTCGCGCGTGCGTCCGGCAGTTGTTACCGA------------------------------
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----------------------------------------------------TCAAAGGCAGGGCCCCTTAGCGATAACA
AATTGACAATAGATCCATACGTTATCCTGAGAGTGCTGCAAGGTAAGACCGGCCGGCATGTCTATCTTGCATCCATACAT
TATCACGGGGAGCAGATTTGATGTTCCTAGGTGCTTCTTAATTCTTAAACATATATTCTCTGGTGTTGAGACG-------
-------------------------------------------------------------------------------
>chr3B_106
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-------------------------GAAGAGGAGACCGAGACTCAGCCCAGCCTCACCCACATTCATGCCTTCTACACTT
ATT---CCGTATATAAAACACACGTACACGCTCTGTAAATAAATAAAG-----CACACGTACTAATTTACAGGTAAGAAC
CGTAAATCTTAGGTTTCCCTTGACGTACTGCCAAAAGAGGCCGTACTAGCAACCATGTGACACGGTCGAGGGCGATGATT
AATCTGGAGCTCTGTTTCCCTTGACATGTTTT-GTTTTGTCACCAGCAATAAACCCTTGGCTGTCTGGCTGGATACGTTG
TT--------CCCGCCACTTTAGTTTCGTGTAACCACTGGTA-------------------GCTTTAGATTCTCCAGCTC
CACCTAACGGCACAGTTGCATTAATCAACTCAAAAGCATGTCCACTTAGCACTAA-CAATGGATTTAGTCCGAGAAAGAC
GCGCTGCAGAATCCAGCGTGCATCTGGCTCCACAGGCAGCCGGCCGTCTAATCTAA---TTGCCACGAGATTAACTGCTC
CCTAATC----------------------------------CCTTCACGGATGCTTCCCTCCCTCCCTCCTCGACGAGTG
T--CAGTGAGAG--------CCGAGAGTGACAGGTGACTCTGCACGCACCCACAATAGGAGCAAAATTTACCCCACACGA
CTCCAAAAAAAGCGAACTTATT---CCCGGACCCCA-------------------GCAGATGCAGG-AGTAACC------
-------AAACAAAGAAGCACGCGCAATCTAACTAACGGAACGTGCCTAAAAACCCCGCCCTATAAATCAGCTCCGCC--
--TTGCTCACT--CCATCCCCAAACCAGC--TC----GCCTTCCCT-GCAACACA----AGGCACCACT-TGGATCTGAA
AGC-------------------------ACG-------AGCAAGCAAGCAAAGGGAGGTGCAATGGAGCACGGGTACCCC
TGCAACAGCAATAGCAGCAGCAGCAACAAGGAGAAGAGGCCTCCGCTCAAGAGAGGCCAGCTCAAGCTGCACATCGCCAG
GACCCTGGGCAGCCTCGTGGCGCCGGCCGCCAAGAGCGGCTTCAGCTTCAGAAGATGATGGCTTGAC--------CGGCC
GCGACAAGCAAGCAAGCACCTTCTCGACCAATCTAGCTAGGAGCATGGTGTGATTCTGGTGG-TTGATGTGTACAGTGTA
GGGATTGTGCAGGTTGAAGAGGAGTTGTTTTAGTT-AGGTGTGCTTCTAATTTGTGTCCAGTTTCCCCCCTTCCACGGTT
CCACCTAGCCCCTGTTCGCTTTGAGGTTTGCTGATGAGATCTCGCTTCCTTGATCGACAATTTTTACGTTGTCCACGAGT
GAGGG---CATGTACGGAGATTGCAGATCCATGCTTTTTCAGAATGCACTGTAGCTTCTAATGGGAATTACAGTTCTGTT
TCTGAGATTGATGCGTCTCCCCGCTCTCACTCCATTTGATTTGTCCAACTCTGAAGTCTCTGAACTGAATGAATAGACCG
GCATAATGGGTGTACTGCGGACGGTACATACCACATTGTCAGTTTGCCTGACGCGTGTTTC-------------------
------------TTACCAGCCTCGCGCGTGCGTCCGGCAGTGGTTAC---------------------------------
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>chr3D_260
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-----------------------------GCCAAAAGAGGCCGTACTACCAACCACGTGACACGGTCGAGGGCG----TT
AATCTGAATCTCTCTTCCTCTCTCGATCGACAGGTCTTGTCACCAGCAATAAACCC-TGGCTG--------GATCCGTTG
TTTGTTCCGACCCACCACTTTTGTTTCGTGTAACCACTTGTAGCACAATAATGCTAGATCTGCTTTAGATTCTTCAGCCC
TACCTAACGGCACAGTTGCATTACTTAACTCAAAAGCATGCCCACTTAGCACTAA-CGATAGATTTAGTCCGGGAAAGAC
GCGCTCAAGAATCTAGCGTGCATCTGGCTCCACAGGCAGCCGGCCGTCTAATCTAA---TTGCCACGTGATTAACTGCTC
CCTAATCTGGCTCGTGATTTATCATTAGTCGCTATGTATGTCCTTCACGGATGCTTCCCTCCCTCGCTCCTCGACGAGTG
T--CAGTGACAAGTGA------------------TGACTCTGCACGCACCCACAACAGGAGCAAATTTTACCCCACACGA
CTCCAAACAAAGCAAACTTATTATTTCCGGACCCCCAGCACGGGA----------------------AGTAAAC------
-------AAACAAAGAAGCACGCGCAATCTGACTAACGGAACGTGCTTAAAAAACTCGCACTATAAATCAGCTCCGCC--
--TG---CACACTCCATCCACAACCCTTCTATC----GCCTTCCCT-GCGACACA----AGCCACCACT-TGAATCTCAA
-GCGCGGAGAGGAGGAA----------G----------------------AAGAGAGGAGCAATGGAGTACGGGCACCCC
TGCAACAGCT------GCAGCAGCAACAAGGAGAAGAGGCCTCCGCTCAAGAGAGGCCAGCTCAAGCTGCAGATCGCCAG
GACTCTCGGCAGCCTCGTGGTGCCGGGCGCCAAGAGCAGCTTCAGCTTCAGAAGATGATCACCTGAGCAGCCACTCAATC
AGGGCAAGC-----AGCATTTTCTCAGCCAATCTAC----GAGTATCGTATGG-TCTGGTGC-TTGATGTATACC-----
GGGATTG-------------------------------------------------------------------------
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>chr3B_260
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-----------------------------GCCAAAAGAAGCCGTACTACCAACCACGTGACACGGTCGAGGGCG----TT
AATCTGAATCTCTCTCTCGACAGG-----------TTTGTCACCAGCAATCAACCACC------CTGGCTGGATGCGTTG
TT--------CCCACCACTTTTGTTTCGTGTAACCACTGGTAGCACAATAATGCTAGATCTGCTA-AGATTCTTCAGCCC
TACCTAACGGCACAGTTGCATTACTTAACTCAAAAGCATGGCCACTTAGCACTAA-CGATAGATTTAGTCCGGGAAAGAC
GCGCTCAAGAATCTAGCGTGCATCTGGCTCCACAGGCAGCCAGCCGTCTAATCTAA---TTGCCACGAGATTAACTGCTC
CCTAATCTGGCTGATGGTCATCGTTTGTGCA----GTATGGCCTTAACGGATGCTTCCCTCCCTC----CTCGACGAGTG
TTACAGTGAGAGCCGAGAGCCCGAGAGTGACAAGTGACTCCGCACGCACCCACAAGAGGAGCAAATTTTACCCCACACGA
CTCCAAATAAAGCGAACTTATT---CCCGGACCCCA-------------------GCAGATGCAGGGAGTAAAC------
-------AAGCAAAGGAGCACGCGCAATCTAATTAACGGAACGTGCCTAAAAAACCCGCGCTATAAAGCAGCTCCGCC--
--TTGCACACT--CCATCCCCAAACCATC--TCCCTCGCCTTCCTCAGCAACACA----AGCCACCGCT-AGAATCTCAA
-GCGCGGAGAGGAGGAAGACAAGCAAGG----------------------AAGAGCGGAGCAATGGAGTACGGGTCCCCC
TGCAACAGCT------GCAGCCGCAACAAGGAGAAGAGGCCTCCGCTCAAGAGAGGCCAGCTCAAGCTGCAGATCGCCAG
GACTCTGGGCAGCCTCGTGGTGCCGGGCGCCAAGAGCAGCTTCAGCTTCAGAAGATGATCAATTGAGCAGCCACTCAGCC
AGGGCAAGC-----AGCATTTTCTCGACCAATCTAG----GA-----GTATGG-TCTGGTGC-TTGATGTGTACC-----
GGGATTGCGCAGGTT-----------------------------------------------------------------
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>chr3A_869
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--------------------------------------------------------------ATAAATCAGCTCCGCCCG
CCTTGCACACTCTCCATCCACAAACCAGCTCTC----GCCTTCCTCAGCAACACA----GGCCACCACTTTGAATCTCAA
-GCGCGGAGAGGAGGAGG-------AGG----------------------AAGAGAGGAGCAATGGAGTACGGGCACCCC
TGCAGCAGCT------GCAGCAGCAGCAAGGAGAAGAGGCCTCCGCTCAAGAGAGGCCAGCTCAAGCTGCAGATCGCAAG
GACCCTCGGCAGCCTCGTGGCGCCGGGCGCCAAGACCGGCTTCAGCTTCAGAAGATGATC-------------CTCAGCC
AGGGCAAGC-----AGCATTTTCTCGACCAATCTA---AGGAGTATCGTATGG-CCTGGTGCTTTGATGTGTACC-----
GGGATTGTGTAGGTTGAACAAGAGTTGCTTTAGTTTAGGTGTGCTTCTTTGTAGTATCGAGTTCTCCCCGTAAGG-----
---CCCAGCCCCTGCATGCCTTGAGGTTTGCCGATCAGATCTCGCTTCCTCGATCGACAATTTTTACGTTGTCCACGAGT
GAAGA---AATGTACGGTGATTGGAGATGG----------------------------TAATGGGAATTACAGTTCTGAT
TCTGAGATTGATGCGTCTCCAAACTGTCCTTTCATTGGATTTGTCCAGCTCTGAAGTCTCTCAACTGAAT----------
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>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS--------
--S--S------S--S----S---S-----------------------------S----------S-S------------
---SSS--S----------S--S---------------------SS--S-SSSSSSSSSSSS-------S----------
------------------S-------------------------------------S------------S-S--------
-----S-------------------------------------------S-----------SS-------------S-S-
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-------S-----------S---------S--------S----------------S----------S-------------
------S---------------------------S-------------------SSSSS---------------------
---------------------------------------------------S----------------------------
----S-----------------------------S-------------------S-------------------------
--------------S--------S------S-------S-SSS-SSSSSSSSSSS-------------------------
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----------------------S---------------------------------------------------------
--------------------------S-----------------------------------------------------
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---------------------------------------S---------------------------------------S
--------------SSSS---SSS-S-SS-------------------------------------S--S----------
------------S-------------------------------------------------------------------
--------S---------S----S--------S-----------------------------------------------
-----SSS------------------S-S---------------------------------------------------
----------S----------------SS--S-------------S--------------------------------S-
--S-S------------------------------S-------------------------SSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSS------------------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----------------------------
----S-----------S---S-----------S----S----------------------------------S---SS--
-------------------------------------------------------------------------SSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_725
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-----------------------------------------------------------------CCTCCTCGACGAGTG
TTACG---------------------------------------------------------------------------
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>reverse_2015
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--------------TAGCGTTGTTCCCAGTTCCC----------------------------------------------
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