>input_sequence_75902
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-----ATGAGGACACAAGCTGTCGTGCTCGCCTACTCGCTGTTGGCATCCGCGCTGCTGTGCAGGTGCGCCGCGGCCTCG
CCGGCGTTCATCGTCGGGAAGCTCGTCATGGGCGGTGAGTATTCAGTGCCTGTTCGGTACTTCTCCCATTTCAAAACTCC
ACTCCGTGCGAGGAGCTGGGTCTGTGCGATTGCGCTATCGCTCCCTCCGCTCCGAGAGTTGCAGCTGTGGAGCGGAGTGG
ATCCGAGCAGGGCTTCAGTACGCCAACAGCTGGCCAATTGGTTTGAGTACGATCGACTAGCGTACTTACACATGTGTTTG
TGTATTGCAGGGGCGGAGTTACGCCGTCCCATGATCGACACCATGACGGCGAATCAATCAGCACCACTGCAACTTTCGAC
GGCGGCGAGCGATGGAAATGTAGACGGACTCCATCCGAACAGGTTCTCCTTGCTCCCGGAAATAACCTCACCGCTGGACC
GGAACCATCCCTTTGGCGAACAAGGGATAGTGCTCGATCACTTGCTCGTGTTTTTGGTGCTCTTTGTTGTGTACATCTTC
CGCTGA--------------------------------------------------------------------------
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>chr3D_1_TraesCS3D01G246400
ATGCATGTGCCATGGATCTGTGCCTTTGCTCGCAATCTATTTTCTTTTAAATAGAAGTATATTAAT----AAAACGACTA
AAACAAAAAGTTGGTTGACAAATTGACAGG-AAAAAA---TCATGAGTGTAATACGCACATAGTGCTACCTGGGCCGCGG
CCGTGTCAGTTCTAATTCTGTCATGCAGGACACATGATCCGACCAAACATTACAGGCAGGCCTACTTTGTTGAAAAAAGA
CAGGGCAATTTATTACAGCAATACTATCTTATATTATCTTATTTTTATTTAATA---TAGATTAGTCTTAGGTCTTGTAT
-GACCCGTGAAAGACTCTCTTTGTTGAAAATTCTGTTCCCAAAATTCATAAAATAAAAGGAAAAATATTTTCACTTTCCT
AAACTAAGGACGGGAAATAAAAAGGCGAGCATATCTTCTAAATTAATCATACTCAACTCGGCCCTTCCTAGAATGGGGCA
TTATCTGTCCC---------------------------------------------------------------------
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----------------------------------------GATAAATAATTTCAGGAGTAATAAATAGGACTATTTTTTG
TGGGAGCTGACCACAAATACATCAGGCCATCATTTTTGACAAAGCTGACGACAAATACATCACACATTAGTTGTGGCGTG
CGCTAGTAGCTGGCCTGCTCCCCTGCCTGCCGGGCAGCGTGCATCCTTTGACAA-AATCATTCCGCCGGATAAATCCGGA
TGGTGGCCAACCGGGACAGACTTCCTCAACAGCC---CTTCCCGCCGCTCATCTGCCCTGCCGCGGCAAATCCAACGGCC
CATACCTGCACACGTCATAGCACGAGTAAGAAAATACAGCAGACCCAGGAACCGCACGGCACTCGGTCAGAAGCGGCTTG
CTGATGAATCAAGTCCGGTCAGCGGGATAGACTTCAGACACAAAAACAAAGCCGCACCAATTCCCGCCTCTTTATAAACC
CGACGCGAGTGAGCCACCAAATCACGCAGTTCTGTCATCGCGGCCTACAACCGGGGAAAGCACAAACAAGCCGAGCGCCA
ACACCATGAGGACACAAGCTGTCGTGCTCGCCTACTCGCTGTTGGCATCCGCGCTGCTGTGCAGGTGCGCCGCGGCCTCG
CCGGCGTTCATCGTCGGGAAGCTCGTCATGGGCGGTGAGTATTCAGTGCCTGTTCGGTACTTCTCCCATTTCAAAACTCC
ACTCCGTGCGAGGAGCTGGGTCTGTGCGATTGCGCTATCGCTCCCTCCGCTCCGAGAGTTGCAGCTGTGGAGCGGAGTGG
ATCCGAGCAGGGCTTCAGTACGCCAACAGCTGGCCAATTGGTTTGAGTACGATCGACTAGCGTACTTACACATGTGTTTG
TGTATTGCAGGGGCGGAGTTACGCCGTCCCATGATCGACACCATGACGGCGAATCAATCAGCACCACTGCAACTTTCGAC
GGCGGCGAGCGATGGAAATGTAGACGGACTCCATCCGAACAGGTTCTCCTTGCTCCCGGAAATAACCTCACCGCTGGACC
GGAACCATCCCTTTGGCGAACAAGGGATAGTGCTCGATCACTTGCTCGTGTTTTTGGTGCTCTTTGTTGTGTACATCTTC
CGCTGATTTCGAGGCAGTTCCAAATCTTCTCCGGATTACACTCAGAT-----GTATTATATATGCTGTGTACTATATTTA
ATGTCCTGCGCAAGCAGTAGAACTAATAAT---CTGATACTTCCTACGTTTCTTTATATAAGGTATATTTGTTTTTTAAT
AAAATTTCACAATATAAGGTGCATTTCTTGTAACTCCTCAACATTTCGTTTTTAGCGCTCTTGAAAAAAAGAAAAATATC
TCTTCCC-GATTGCATGTATTTCTCTTTTTAAAGAAAAAAAGGAAAGTGTCTCGGTTCTGATTGCATGTATCTCTTACTA
CTTTTCAAGCATAAATGATTAATTGCTACTAATCAATGATTTAGCCAAGGTTATTTTTGTCCTAACTTGTGTATAATTAC
GTGTCTTGGTCACCGTGCCAAAATTATACACATTAAATAAAGGAATGGAGGGAGTATGTTAAGAGCAACTCCAGCACATG
TATCCATTTCGTCCGCCGCCGTCCGTTTGGGTCGCCGCGGACAAAAGTGCTGACCCAACGCGCCGACCCATTCCCAAAAT
GTCTTCGCTTCGCGTCCGCGCGGACCCATTTCTGGCCCAAATTTGCAGCTGAAATGCGTCGGCGCGGATGCG--------
---CCGCGCG--TCCTCGGTCTCCGCCGCGTCCCCACCTAGCAGCCGCCCAACTACCGAGGTCGTCTTTATTAATGACGA
CCGCCAATCGC-GGCCCACGCATCAGCGACGGCGGTCGACCTTTTTTAATCTGAGCGTGCAGTGGGGCGGCGTCCTCATC
CACTTCCAGACGCCCTCGTCCTCATCTCGCCACTCACTGTGCTCCCCCGTCGGCGCTAAAACCTAGCCATCGCCATGGGC
TTCTTCTCCGGCAAGGGCAAGGCCCCCGC-------CGCCCCTCCTCCCGCCTTCGCCGGCGTCTTCTCGCCGGCCTCAG
CTGCGCATCAACTGTTGGGGAACGTAGTAATTTCAAAAAAACATCCTACGCACACGCAAGATCATGGTGATGCATA
>chr3B_1
ATGCATGTGCCATGGATCTATGCCTTTGCTCGCAATCTATTTGTTTTTATATAGAAGTATATTAACCGAAAAAATGATTA
AAACAAAAGGTTGGTTGATAAATTGACTGAGAAGAAAATATCATGAGT--AAAACGCACATAATGCTACATGGGCCGCAC
CCTTGTCAGTTCTAATTCTGTCATGTAGGACACATGATCCGACCAAACATTACAGGCAGGCCTACTTTGTTGAAAAAAGA
CAGGGCAATTTATTATAACAATAA----------TATCTTATTTTTATTTAATA---TAGATTAGTCTTAGGTCTTGTTT
-GACCTGTGAATGACTCCCTTTGTTGAAACTTCTGTTCCC-AAATTCATAAAATAAAAGGGAAAATATTTTCACTTTCCT
AAACTAAGGACGGGAAATAAGAAGGCGAGCATATCTTCTAAATTAGTCATACTCAACTCGGGAAAAAAATTATATGAGAC
CAGGTCTCATATAAAGCAGGTGAGACCCGCCCTGATGGATGACACGTGGCATTCACAAATCACAAAGCATCTAATCTCTC
CCCCCCTGATTTCAGGTGGGGGGTGGGGTGGATGCTTTGTGATTTGTGGATGCCACGTGTCATCCATCAGGGCGGGTCTC
ACCTGTTAACCCGTGAGACCTGGTCTCATAGAATTCTGCGGATAAATAATTTCAGGAGTATTTA-----------TTTTG
CGGGAGCTGACCACAAATACATCAGGCCATCATTTTTGACAAAGCTGACGACAAATACATCACACATTAGTTGTGGCGTG
CGCTAGTAGCTGGCCTGCTTCCCTGCCTGCCGGGCAGCGTGCATCCTTTGACAA-AATCATTCCGCCGGATAAATCCGGA
TGGTGGCCAACCGTGACAGACTTCCTCAACAGCCGCCCTTCCCGCCGCTCATCTGCCCTGCCGCCGCAAATCCAACGGCC
CATACCTGCACACGTCATAGCACGAGTAAGAAAATACAGCGAACCCAGGAACCGCACGGCACTCGGTCAGAAGCGGCTTG
CTGATGAATCAAGTCCGGTCAGCGGGGCAGACTCCGGACACGAAAACAAAGCAGCACCAATTCCCGCCTCTTTATAAACC
CGACGCGAGTGAGCCACCAAATCACACAGTTCTGTCGTCGCGGCCTACAACCGGGGAAAGCACAAACAAGCCGAGCGCCA
ACACCATGAGGACACAAGCTGTCGTGCTCGCCTACTCGCTGTTGGCATCCGCGCTGCTGTGCAGGTGCGCCGCGGCCTCG
CCGGCGTTCATCGTCGGGAAGCTCGTCATGGGCGGTGAGTATTCAGTC--------------------------------
--------------------------------------------------------------------------------
-----------------GTACACTGAGAACTGACCAATCAGTTTGGGTACGATCGACTAGCGTACTTACACATGTGTTTG
TGTTTTGCAGGGGTGGAGTTACGCCGTCCCATGATCGACACCATGACGGCGAATCAGTCTGCACCACTGCAACTTTCGAT
GGCGGCGAGCGATGGGCATGTGAATGGACTCCAGCTGAACTGGTTCTCCTTGCTCCCGGAAATAACCTCACAGCTGGGCC
GGAGCCATCCTCTTGCGGAACAAGGGATAGTGCTCGATCACCTGCTCGTGTTTTTGGTGCTCTTCGTTGTGTACATTTTC
CGCTGATTTCGAGGCAGTTCCAAATCTTCTCCGGTTTATACTCAGAT-----GTATTATATGTGCTGTGTACTATATTTA
ATGTCCTGCGCAAGCAGTAGAACTAATAATAATCTGATACTCCCG----TTTTTTATATAAAGCGTATTTATTTTTTAAT
AAAATTTCACAATGTAAGATGCATTTCTTCTAACTCCTCAACATTTTATTTCTAGCGCTCTAGAGAAAAGGAAAAATATC
TTTCCCCTGATTGCATGTATTTCTCTTTTTAAAGAAAAAAAGGAAAATGTCTCGGTTTTGATTGCGTGTATCTCTTACTA
CTTTCCAAGCATAAATGATTAATTGCTACTAATCAATGATTTAGCCAAGGTTATTTTTGTCCTAACTTGTGTATAATTAC
GTGTCTTGGTCACCGTGCCAAAATTATACATCTTAAATAAAGGAATGGACGGAGTATGTTAAGAGCAACTCCAGCACATG
TATCCATTTCGTTCGCCGCCGTCCGTTTGGATCGCCGCGGACAAAAGTGCTGACCCCACGCGCTGACCCATTCCCAAAAT
GTCTTCACTTCACGTCAGCGCGAACCCATTTTCGGCCCAAATTTGCGGCTGAAATGCATCGGCGCGGATGCGAAGCGGAT
GCGCCGCGCA--CTCTCGGTCTCCGTCGCGTCCCCACCTGGCAGTCGCCCAACTATCGAGGTCGTCTTTATTAATGACGA
CCGCCGACCACGGGCCCACGCATCAGCGACGGCGGTCGACCTTTTTTAATCCGAGCGTGCAGTGGGGCGGCGTCCTCATC
CGCTTCCAGACGCCCTTGTCCTCATCTCGCCACTCACTGTGCTCCCCCGTCGGCGATAAAACCTAGCCATCGCCATGGGC
TTCTTATCCGACAAGGGCAAGGGCAAGGCCTCCATCGCCCCTTCCCCCCACCTCTGTCGGCATCTTCCCGCCGGCCTCAG
TTGCGCATCAAC----------------------------------------------------------------
>chr3A_1
ATGCATGTGCCATGGATCTGTGCCTTTGCTTGCAATCTATTTTTTCTAAAATAGAAGTATATTAAT----AAAACGACTA
AAACAAAAGATTGGTTGATAAATTGACAGA-AAAAAAATATCATGAGTGTAATACGCACATAGTGCTACATGGGTCGCGG
CCGTGTCAGTTCTAATTCTGTCATGCGGGACACATGATCCGAC-AAACATTACCGGCGGGCCTACTTTGTTGAAAAAAGA
CAGGGCGATTTATTACAGCAATAATGTCTTATATTATCTTATTTTTATTTAATACTATAGATTAGTCTCAGGTCTTGTTT
TGACTGGTGATAGACTCCCTTTGTTGAAAATTTTGTTCCTAAAATTCATAAAATAAAAGGAAAAATATTTTCACTT----
AAACTAAGGATGGGAAATAAAAAGGCGCGAATATCTTCTAAATT-ATCATACTCAACTCGGCCCTTCCTAGAATGGGGTA
TTATCTGTCCC---------------------------------------------------------------------
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----------------------------------------GATAAATAATTCCAGGAGTAATAAATAGGTCC-TTTTTTG
CGGGAGCTGACCACGAACATATCAGGCCATCATTTTTGACAAAGCTGACGACAAATACATCACACATTAGTTGTGGCGTG
CGCTAGTAGCTGGCCTGCTTCCCAGCCTGCCGGGCAGCGTGCATCCTTTGACAAAAATCATTCCGCCGGATAAATCCGGA
TGGTGGCCAACCGTGACAGACTTCCTCAACG---GCCCTTCCCGCCGCTCATCTGCCCTGCTGCGGCAAATCCAACGGCC
CATACCTGCACACGTCATAGCACGAGTAGGAAAATACAGCAGACCCAGGAACCGCATGGCACTTGGTCAGAAGCGGCTTG
CTGGTGAATCAAGTCCGGTCAGCGGGACAGACTTCTGACACGAAAACAAAGCAGCACCAATTCCCGCCTCTTTATAAACC
CGACGCGAGTGAGCCACCAAATCAT--------------GCAGCCTACAACCTGGGAAAGCACAAGCAAGCCAAGCGACA
ACACCATGAGGGCACAAGCTGTCGTGCTCGCCTACTCGCTGTTGGCGTCCGCGCTGCTGTGCCGGAGAGCCGCGGCCTCG
CCGGCGTTCATCGTCGGGAAGCTCGTCATGGGCGGTGAGTATTCAATC--------------------------------
--------------------------------------------------------------------------------
-----------------GTACACCAAGAGCTGGCCAATCGGTTTGAGTACGATCGACTAGCGTACTTACACATGTGTTTG
TGTTTTGCAGGGCTGGAGTTACGCCGTCCCGTGATGGACACCATGACGGCGAATCAGTCAACACCACTGCAACTTTCGAC
GGCGGCGAGCGATGGAAATGTGGACGGACTCCATCCGAACTGGTTGTCTTTGCTCCCGGAAATAACCTCACCGCTGGACC
GGAACCATCCCTTTGGCGAACAAGGGATCGTGCTCGATCACTTGCTCGTGTTTTTGGTGCTCTTTGTTGTGTACATCTTC
CGCTGATTTCGAGGCAGTTCCAAATCTTCTCCGGATTACACTCAGATCAGACGTATTATATGTACTGTGTACTATAGTTA
ATGTCCTGCGCAAGCAGTAGAAATAATAAT---CTGATA-----------------------------------------
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>chr1A_2002
ATGTA---------------------------------------------------------------------------
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-------------------------------------------------------------AGAGCAAATCCAATGCACG
TACCCATTTTGTCTGCCGCCATCTGTTTGGATTGCCGCGGACAAATGTATTGGCCCAACACACCGACCCATTCCCAAAAC
GCGTCCACGA-----------GGACCCATTTGAGGCCCAAATTTGCGGCTGAAATGCGTCAGCACAGACGTGAAGTGGAC
GCGCCGCACGTCCTCTCGTTGTCCATCGTGTCCCCACCTGGCAGCCATTCAACTACCGCGGTCGTCTTTATTAATGAGGA
CCGCCGACCGTAGGTTGACGTGTTAGCGACGGCAGTCAGCCTTTTTTAATCCGAGCATGTGGTGAGGGACCGTCCTCATC
TGCTTCGAGATGCCCACATC--CATCTCGCCACCCACAGTGCTCCCTCATCGGCGACAAACCCTAGCCACCACCATGGGC
TTCTTCTCCGGCAAGGGCAAGGCCCCCGCACCCCTTCCCCCTGCCCCCCTCCTCCGCCGGCATCTTTCCACCGGCCGCGG
CAACACATCAATGT--------------------------------------------------------------
>SNPs
-------------------------------------------S------------------------------------
--------S---------S----------S---------------------------------------S----------
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-----------------------S-S----------------------------------------------------S-
-----S-----------S--------------------------------------------------------------
------------------------------------------------------------------------------S-
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---------------------------------------------------------------------S-SS-------
S-------------------------------------------------------------------------------
-------------------S------------------------------------------------------------
-------------S------------------------------------------------------------------
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---------------------------S-------S-----S----------S---------------------------
-------------------------S----------S-------------------------------------------
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-----------------------------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSS----S----S-----------S-----------------------------------------
---S---------S------------------------------------------S-----------------------
---------------------S------------------S---------------------------------------
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-------------------------------------------------------------S------------------
-----------------------------------------S--SSSSS--S---------S-SS-----S---------
-------------S----S----------S----------------SS---S---------S--S----S----------
-S-S------------------------------------------S----------S-------S--------------
----S---------------------------------------------------------------------------
------------------------------SS-----------------S------------------------------
------------------------------S-------------------------------------------------
------S----S----S--------------SS-------------S---------------------------------
------------SS-----------S-------------S----------------------------------------
-----S-S-------------------------------------------S----------------------------
-S-----------------------------------------------------S------------------------
-------------------------------------S---S---S---S---S-------S-----S------------
------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_1146
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------GAGTGAGCCACCAAATCACG------------------------------------------------------
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>reverse_2770
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-------------------------------------------------GCACACGCAAGATCATGGTG-------
