>input_sequence_67488
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--ATGATGAGCGGCAACACCCAGCAGCAGCAGTCGGCGGCGG------------CGGCGGAGGAGGAGCAGGAGTTAGCG
CGGAAGCACGCGGCCGCGGTGGCTACGTCGCGGCAATGGTCGTCCCAGACGGAGTCACGGATAGTGCGCGTGTCGCGCGT
CTTCGGCGGCAAGGACCGCCACAGCAAGGTGAAGACCGTCAAGGGTCTCCGCGACCGGCGCGTGCGGCTGTCCGTGCAGA
CGGCGATCCAGCTCTACGACCTGCAGGACCGGCTGGGCCTTAACCAGCCCAGCAAGGTCGTCGACTGGCTGCTCAACGCG
GCCCGCCACGAGATCGACAAGCTGCCGCCGCTCCAGTTCCCGCCGCACCAGGTCGACCTCATGGACCACATGATGACCTC
CTCCTCCATGCCGCTCATGCCGCACGTCGATGACAAGTTCTGCCACTTCGCGTCCACGCTTGCCGGAGATGGTGGCGTCA
AGGCCGGGGCCGACGCAGATGGCGATGGAGCTCACCACAACATGGGGAGGTTCGGCTACCACCGGTTCATGGGGCTCAAT
AACAACTCCCTGGGACTGGTCAACAGCGGGATGCCATACAATTTCACCGGCGAGTCATGGAATAATAGCAGTGTGCACCA
GAGCGGCGGCGCTGGCTCGCCACAGGTCTCGATTGCTGCCGCCGCCGCGGCTCACCACTCGGCATTCCCGTCGTTACTCT
CCTTGGCTCCAAGGTCGCATCAGCTGGTTTACTACTCGTCCGAGGCCGATCAGTTCCCAGTTGATGACCTGGGCTCCCAA
AGCTTATCCTTGAGCTCGGCGAGAGCTTTCCATGACCAGACAGGGAGCTAG-----------------------------
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>chr3A_1_TraesCS3A01G302900
TGGGATTTCTTAATTTT-TGGTGCCTTTTCGTGGTCCTTGATTAGAATTTCATGCGGCAGATCTGGG--AGATTTGTTAA
TCCCTCTCGCTTTGTATACTGATTCTTTGGAATTTTTAAGTCCTT-ATAAGATTATTTTCCTTTCCCACCGAAGTGTTCT
TGTATCGAAACCAAAACTGCACTGGATCCCGAGCTGGAGGACCATTTCTCTTTCTCTCTCTTCT---CCTTTTTCCTTGT
GGGAGCGCCCGATCTGAACCGAATAGTTTGAATTACCCAGTCTCATCGCTTGTAGTACTAATCACTGACACCACAGAC-T
TTTAGTTCAAGAAATCCCAATCGAATCCACGGAATTAATAGTAATTTAGGCTGTATGACAGACAGGCCTGCAGGATTGTG
AAAAGGAAGCAGCTGCTAGCAGCCTAGCACTCAATAC--AAACCCCCTCCCCTCGTTTCACAGAGGCCCAGTG------G
TGAGACTTGTAGGACGACCCCGATTCATAACTTGACTGCAGAACAATCAAAGAGGGCTGA---------------GCCGT
TCATATGTTCAACCATGGAATCATTCTCTTGGGCACCGCATGCAGATCGTGCCGCGTGCGCCTGCGCATCCACAGCGTCC
ATGGGGGGCTCAAGCTGCTGTTGTTCCATTTCCATCTACCCTGCTGCAGCAGTTGCATGCAG-----CTTGAATAAAGCT
GCCGCGCGCGCTCTCCTCTCCCAATCCCA-TCCCCCCGTTGCCGATGGAACAGTACGTACGTACGTGGCGCACATCGACC
GGCCGGTAGACCCCCTGCGCGCCGTTCGGGCACAGTGGTGGACT-----GGTGGTGCATGCTTGATTGGTGGCTTGCTCC
TGTAGAAACACCATTAAATCTCCTTGCTAGCTGCAGGCCTGCAGCTGCATGCGATGTTAATTAATCGAGCTGATGATGTG
ATATGGCAGGTGAAGCTAGCTAGCGCTAGCGGATGATCGAAAGCCGATCGACGATGCGCTTCGTCGTCGGAGGTCACTTG
AAATGATGAGCGGCAACACCCAGCAGCAGCAGTCGGCGGCGG------------CGGCGGAGGAGGAGCAGGAGTTAGCG
CGGAAGCACGCGGCCGCGGTGGCTACGTCGCGGCAATGGTCGTCCCAGACGGAGTCACGGATAGTGCGCGTGTCGCGCGT
CTTCGGCGGCAAGGACCGCCACAGCAAGGTGAAGACCGTCAAGGGTCTCCGCGACCGGCGCGTGCGGCTGTCCGTGCAGA
CGGCGATCCAGCTCTACGACCTGCAGGACCGGCTGGGCCTTAACCAGCCCAGCAAGGTCGTCGACTGGCTGCTCAACGCG
GCCCGCCACGAGATCGACAAGCTGCCGCCGCTCCAGTTCCCGCCGCACCAGGTCGACCTCATGGACCACATGATGACCTC
CTCCTCCATGCCGCTCATGCCGCACGTCGATGACAAGTTCTGCCACTTCGCGTCCACGCTTGCCGGAGATGGTGGCGTCA
AGGCCGGGGCCGACGCAGATGGCGATGGAGCTCACCACAACATGGGGAGGTTCGGCTACCACCGGTTCATGGGGCTCAAT
AACAACTCCCTGGGACTGGTCAACAGCGGGATGCCATACAATTTCACCGGCGAGTCATGGAATAATAGCAGTGTGCACCA
GAGCGGCGGCGCTGGCTCGCCACAGGTCTCGATTGCTGCCGCCGCCGCGGCTCACCACTCGGCATTCCCGTCGTTACTCT
CCTTGGCTCCAAGGTCGCATCAGCTGGTTTACTACTCGTCCGAGGCCGATCAGTTCCCAGTTGATGACCTGGGCTCCCAA
AGCTTATCCTTGAGCTCGGCGAGAGCTTTCCATGACCAGACAGGGAGCTAGCTGCCACCTAGCTAGTTAGTACAACGCTG
GATCGATCGATATCCTGAAGAAGATGGAGCTGATCGATCGGTGGTATGGATTGCAACTTTTATCCTCAAGGTAGGACTTA
ATAATGCTCTCCCAAAGCACAAAATAGCTAGCTAGTAGAAGTGTGTGTGTATGC-----ATTGGTTTTTTTAGATATACT
TCTTCCTATGGGTCAAGCCTAACCGCGGGTTCTAAAAATGTTTTATGC-TTTAAACATATGCTTAATTTGGCTTTGGAAG
TTGAGCAATGCTATCTGGTGGGCTTGCTGTGTGTGCCATACGAATTTGTTACTTCTTTTCATATACAAAGAAGTAAGCTG
TGTAATGGTTTATTGTGCAATAACATTTTTGATTTTTTTAACAT-----TAGTTTATCTAATTAATCTCTCTCTCTCTCT
CTTGCTATGAAACCATGTCCAGGTATGTTATTTGAGTTTTATTGTTACACGT---ACGTGCTACAGCTTTAGCCAGCGGA
AAAAGTCCTGCCCCCGTTCCATTGATTGTACTTTGTCCCACCTTGGGCAGGAACTCTACCATTCGATACAAGTAGAAATT
TAGCAACTAGAGAAAATCCCCATGAAAACTACAAAAATAACAGGTTCACTAGCTACCATATAAACCAGGCCCATTCTGCC
ATAGTGACTAGCCAACACAAACTCAAGACACACCAAGCTCCCACTCAATAAATCTATACTATCTAACAAGAAATCATATA
TGCACGCATCCCAAAGCACATGCAAGTTACAGGCAATGTTAAAGGATATCTAAAATATTGCATCATCTAACTTCTCTAGT
CTAAAATTTTGAAGTTTTATATTAATTCTTAGCATGATATGAAA-TCTGAATTTTGAACCATAGCATCACACATGATTAG
TTGAAGGTGGTTAATTACCAATTCCCCGGCCGTGAGGCTAAT--------------------------------------
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-----------------------------------------------ATTACC---TAAAAACAGCTCATG--TACCTTT
ACATTGTTATATCTCCTGCAGGTTCTCCCTTAAAGC
>chr3D_1
TGGGATTTCTTAAATTTTTGGTGCCTTTTGGTGGTCCTTGATTAGAATTTCATGCGGCGGATCTGAGCTAGATTTGTTAA
TCCGTCTCGCTTTGTATAAAGATTCTTTGGAATTTTTAAGTCCTTGATAAGATTATTTCCCTTTCCCACCGAAGTGTTCT
TGTATCAAAACCTAAACTGCACTGGATCCCGAGCTGGAGTACCATTTCTCTTTCTCTCTCTTCT---CCTTTTTCCTTGT
GGGAGCGCCCGATCTGAACCGAATAGTTTGAATTACCCATTCTCATCGCTTGTAGTACTAATCACTGACACCACAGAC-T
TTTAGTTCAAGAAATCCCAATCGAATCCACGGAATTAGTAGTAATTTAGGCTGTATGACAGACAGGCCTGCAGGATTATG
AAAAGGAAGCAGCTGCTAGCAGCCTAGCACTCAGTAC--AAACCCCCTCCCCTCGTTTCACAGAGGCCCAGA------AG
TGAGACTTGTAGCACGACCCCGATTCATAACTCGACTGCAGAACAATCAAAGAGGTCTGATGGCGGGGCTGGCGGCG-GT
TCATATGTTCAACCATGGAATCATTCTCTTGG-CACCGCATGCAGATCGTGCCGCGCGGGCCTGCGCATCCACAGCGTCC
ATGGGGGGCTCAAGCTGCTGTTGTTCCATTTCCATCTACCCTGCTGCAGCAGTTGCATGCAG-----CTTGAATAAAGCT
GCCGCGCGCGCTCTCCTCTCCCAATCCCATTCCCCCCGTTGCCGATGGAACAGTACGTACGT----GGCGCACATCGACC
GGTAGA-----CCCCTGCGCGCCGTTCGGGCACAGTGGTGGACT-----GCTGGTGCATGCTTGATTGGTGGCTTGCTCC
TGTACAAACACCATTAAATCTCCCTGCTAGCTGCAGGCCTGCAGCTGCATGCGATGTTAATTAATCGAGCTGATGATGTG
ATATGGCAGGTGAAGCTAGCTAGCGGAC------GATCGAAAGCCGATCGACGATGCGCCTCGTCGTCGGAGGTCACTTG
AGATGATGAGCGGCAACAACCAGCAGCAGCAGTC------GG------------CGGCGGAGGAGGAGCAGGAGCTAGCG
CGGAAGCACGCGGCAGCGGTGGCTACGTCGCGGCAATGGTCGTCGCAGACGGAGTCACGGATAGTGCGCGTGTCGCGCGT
CTTCGGCGGCAAGGACCGCCACAGCAAGGTGAAGACCGTCAAGGGTCTCCGCGACCGGCGCGTGCGGCTGTCCGTGCAGA
CGGCGATCCAGCTCTACGACCTGCAGGACCGGCTGGGCCTTAACCAGCCCAGCAAGGTCGTCGACTGGCTGCTCAACGCG
GCCCGCCACGAGATCGACAAGCTGCCGCCGCTCCAGTTCCCGCCGCACCAGGTCGACCTCATGGACCACATGATGACCTC
CTCCTCCATGCCGCTCATGCCGCACGTCGATGACAAGTTCTGTCACTTCGCGTCCACCCTCGCCGGAGATGGTGGCGTCA
AGGCCGGGGCCGACGCAGACGGCGGTGGAGCTCACCACAACATGGGGAGGTTCGGCTACCACCGGTTCATGGGGCTCAAC
AACAACCTC---GGACTGGTCAACAGCGGGATACCATACAATTTCACCGGCGAGTCATGGAATAACAGCAGTGTGCACCA
GAGCGGCGGCGCTGGCTCGGCGCAGGTCTCGATCGCTGCCGCCGCCGCGGCTCACCACTCGGCATTCCCATCGTTACTCT
CCTTGGCTCCAAGGTCGCATCAGCTGGTTTACTACTCGTCCGAGGCCGATCAGTTCCCAGTTGATGACCTGGGCTCCCAA
AGCTTATCCTTGAGCTCGGCGAGAGCTTTCCATGACCAGACAGGAAGCTAGCTGCCACCTAGCTAGCTAGTACAACGCTG
GATCGATCGATATCCTGAAGAAGATGGAGCTGATCGATCGGTGGTATGGATTGCAACTTTTATCCTCAAGGTAGGACTTA
ATAATGCTCTCCCAAAGCGCAAAATAGCTAGCTAGTAGAAGTGTGTGTGT--GC-----ATTGGTTTTTTCAGATATACT
TCTTCCTATGGGACAAGCCTAACCGCGCGTTCTAAAAATGTTTTATGCTTTTAAACATATGCTTAATTTGGCTTTGGAGG
TTGAGCAATGCTAGCTGGCGGGCTTGCTGTGTGTGCCATACGAATTTGTTACTTCTTTTCATATACAAAGAAGTAAGCGG
TGTAATGGTTTATTGTGCAATAATATTTTTGATTTTTTTTTAACAATAGTAGTTTAGCTAATTAATCTCTCTCTTATA--
----TTATGAAACCATGTCCAGGTATGTTATTTGAGTTTTGTTGTTACTTGTTACACGTGCTACAGCTTTAGCCAGCGGA
AAAAGTCCAGCCCCCGTTCCATTGATTGTACTTTCTCGCACCTTGGGCAGGAACTCTACCATTCGATACAAGTAGAAATT
TAGCAACTAGAGAAAATCCCCACGAAAACTACAAAAATAACAGGTTCACTAGCTACCATCTAAACTACACCCATTCTGCC
ATAGTGACTAGCCAACACAAACTCAAGACACACCAAGCCCCCACTTAATAAATCTA---TATCTGACAAGAAATCATATT
TGCACGCATCCCAAGGCACATGCAAGTTACAGGCAATGTTAAAGGATATGAAAAATATTGCATCATCTAACTTCTCTAGT
CTAAATTTTTGATGTTTTATATTAATTCTTAGCATGATATGAAAATCTGAATTTTGAATCATAACATCACACATGATTAG
TTGAAGGTGGTTAATTACCAATTCCCCGGCCGTGAGGCTAAT--------------------------------------
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-----------------------------------------------ATTACCTAATAAAAGCAGCTCCTGGGTACCTTT
ACATTGTTATATCTCCTGCAGGTTCTCCCTTAA---
>chr3B_1
TGGGATTTCTTAAATTTTTGGTGCCTTTTGGTGGTCCTTGATTAGAATTTCATGCGGCGGATCTGAGCTAGATTTGTTAA
TCCGTCTCGCTTTGTATACAGATTCTTTGGAATTTTGAAGTCCTTGATAAAATTATTTTCCTTTCCC-CCGAAGTGTTCT
TGTATCAAAACCAAAACTGCACTGGATCCCGAGCTGGAGGACCATTTCTCTTTCTCTCTCTTCTTCTCCTTTTTCCTTGT
GGGAGCGCCCGATCTGAACCGAATAGTTTGAATTACCCATTCTCATCGCTTGTAGTACTAATCACTGACACCACAGACTT
TTTAGTTCAAGAAATCCCAATTGAATCTACGGAATTT---GTAATTTAGGGTGTATGACAGACAGGCCTGCAGGATTATG
AAAAGGAAGCAGCTGCTAGCGGCCTAGCACTCAATACAAAAACCCCCTCCCCTCGTTTCACAGAGGCCCAGTGGTGAGAG
TGAGACTTGTAGCACGACCCCGATTCATAACTCGACTGCAGAACAATCAAAGAGGTCTGATGGCGGGGCTGGCCGGCCAT
TCATATGTTCAACCATGGAATCATTCTCTTGGT-ACCGCATGCAGATCGTGCCGCGCGGGCCTGCGCATCCACAGATGCC
GTTA-------------------TTCCATTTCCATCTACCCTGCTGCAGCAGTTGCATGCAGTTTAGCTTGAATAAAGCT
GCCGCGCAAGCTCTCCTCTCCCAATCCCATTCCCCCCGTTGCCGATGGAACAGTACGTACGT----GGCGCACATCGACC
GGTAGA-----CCCCTGCGCGCCGTTCGGGCACAGTGGTGGACTCTGGTGGTGGTGCATGCTTGATTGGTGGCTTGCTCC
TGTACAAACACCATTAAATCTCCCTGCTAGCTGCAGGCCTGCAGCTGCATGCGATGTTAATTAATCGAGTTGATGATGTG
ATATGGCAGGTGAAGCTAGCTAGCGGAC------GATCGAAAGCCGATCGACGATGCGCCTCGTCGTCGGAGGTCACGTG
AGATGATGAGCGGCAACAACCAGCACCAGCAGTC------GGCGGCGGCGGCGGCGGCGGAGGAGGAGCAGGAGCTAGCG
CGGAAGCACGCGGCCGCGGTGGCTACGTCGCGGCAATGGTCGTCGCAGACGGAGTCACGGATAGTGCGCGTGTCGCGCGT
CTTCGGCGGCAAGGACCGCCACAGCAAGGTGAAGACCGTCAAGGGTCTCCGCGACCGGCGCGTGCGGCTGTCCGTGCAGA
CGGCGATCCAGCTCTACGACCTGCAGGACCGGCTGGGCCTTAACCAGCCCAGCAAGGTCGTCGACTGGCTGCTCAACGCG
GCCCGCCACGAGATCGACAAGCTGCCGCCGCTCCAGTTCCCGCCGCACCAGGTCGACCTCATGGACCACATGATGACCTC
CTCCTCCATGCCACTCATGCCGCACGTCGATGACAAGTTCTGCCACTTTGCGTCCACGCTCGCCCGAGATGGTGGCGTCA
AGGCCGGGGCCGACGCTGACGGCGGTGGAGCTCACCACAACATTGGGAGGTTCGGCTACCACCGGTTCATGGGGCTCAAC
AACAACTCCCTGGGACTGGTCAACAGCGGGATGCCATACAATTTCACCGGCGAGTCATGGAATAACAGCAGTGTGGACCA
GAGCAGCGGCGCTGGCTCGCCACAGGTCTCCATAGCTGCCGCCGCCGCGGCTCACCACTCGGCATTCCCGTCGTTACTCT
CCTTGGCTCCAAGGTCGCATCAGCTGGTTTACTACTCGTCGGAGGCCGATCAGTTCCCAGTTGATGACCTGGGCTCCCAA
AGCTTATCCTTGAGCTCGGCGAGAGCTTTCCATGACCAGACAGGAAGCTAGCTGCCACCTAGCTAGCTAGTACAACGCTG
GATCGATCGATATGCTGAAGAAGATGGAGCTGATCGATCGGTGGTATGGATTGCAACTTTTATCCTCAAGGTAGGACTTA
ATAATGCTCTCCCAAAGCACAAAATAGCTAGCTAGTAGAAGTGTGTGTGT--GTGCATTATTGGTTTTTTCAGATATACT
TCTTCCTATGGGACAAGCCTAACCGCGGGTTCTAAAAATGTTTTATGC-TTTAAACATATGCTTAATTTGGCTTTGGAAG
TTGAGCAATACTAGCTGGTGGGCTTGCTGTGTGTGCCATACAAATTTGTAACTTCTTTTCATATACAAAGAAGTAAGCGG
TGTAATGGTTTATTGTGCAATAACATTTTTA--TTTTTTTGAACAATAATAGTTCAGCTAATTAATCTCTCTCTT-----
-TTGTTATGAAACCATGTCCAGGTATGTTATCTGAGTTTTG-------TTGTTACACGTGCTACAGCTTTAGCCAGCGGA
AAAAGTCCTGCCCCCGTTCCATTGATTGTACTTTCTCCCATCTTGGGCAGGAACTCTACCATTCGATACAAGTAGAAATT
TAGCAACTAGAGAAAATCCCCACGAAAACTACAAAAATAACAGGTTCACTAGCTACCATCTAAACTAGACCCATTCTGCC
ATAGTGACTAGCCAACGCAAACTCAAGACACACCAAGCCCCCACTCAATAAATCTA---TATCTGACAAGAAATCATATT
TGCACGCATCCCAAAGCACATGCATGTTACAGACAGTGTTAAAGGATATGAAAAATATTGCATCATCTAACTTCTCTAGT
TTAAAATTTTGATGTTTTATATTAATTCTTAGCATGATATG-AAATCTGAATTTTGAATCATAGCATCACACATGATTAG
TTGAAGGTGGTTAATTACCAATTCCCAGGCCGTGGGGCTAATTAATACTTCCTCCGTTCCTAAATGTAAGTCTTTGTAGA
GATTCCACTATAAACCGCATACGGATGTATATAGATGCATTTTAAGTTTAGATTCATTCGTTTTGCTCCGTATGTAGTCC
ACCTAGTAGAATCTCTACAAAGACTTATATTTAGGAACGGAGGGAGTATTACC---TAAAAACAGTTCATGGGTGCCTTT
ACATTGTTATATCTCCTGCAGGTTCTCTCTTAA---
>SNPs
-------------S---------------S----------------------------S------S--------------
---S---------------S------------------------------------------------------------
------S-------------------------------------------------------------------------
---------------------------------------S----------------------------------------
-------------------------------------S---------------------------------------S--
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------------S-------------------S----------------------S------------------------
--------------------------------S-----------------------S-S---------------------
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--------------------------------------------------------------SSSS--------------
--SS-SSSSSS---------------------------------------------------------------------
----S------------------S--------------------------------------------------------
-------------------------SSSSSSSSS-------------------------S--------------------
-S----------------S---------------SSSSSS----------------------------------S-----
--------------------------------------------S-----------------------------------
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------------------------------------------------------------S-------------------
-------------------S----S------------------------------------------------------S
-----------------------------------------------------------------S--------------
---------------------------------S----------------------------------------------
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--------------------------------------------S---------------------S-------------
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--------------------------------------------------SS------------------S---------
------------S-------------------------------------------------------------------
-------------S----------------------------------------------------------------S-
---------------------------------------SSS-S------------S-----------------SSSSSS
S---S-----------------------------------S-------SS------------------------------
----------------------------------S---------------------------------------------
----------------------S------------------------------------S-----S--S-----------
--------------------------------------S-----------------SSS-----S--------------S
-------------------------------------------------SS-----------------------------
------------S---------------------------------------------S---------------------
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---------------------------------SSS
>forward_885
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-----------------------------------------------------------------TTGGTGGCTTGCTCC
TGTAG---------------------------------------------------------------------------
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>reverse_2549
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--------------------------------------------------------------------GCCCATTCTGCC
ATAGTGACT-----------------------------------------------------------------------
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