>input_sequence_72990
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-----------------------------------------------ATGGAATTGCAGAAGGATCAGAGGCATCCTCTT
TTGTCCAACAGAACTGATGGCACCAACAACATGAGCCCCACGCAGAAAGCAATCGGACAGGCATACCAGAGCACCGGGCA
CCTCGCCAAACTCCTTCCATCAGGCACCGTGCTTGCCTTCCAGCTGCTGGCTCCAACCATGGCTAAGCACGGCCACTGTG
GTGACTTGGATCGAATGATGACGGGAGGGCTCGTGGTGCTCTGTGCACTCTCATGCTTTGTTCTTAGCTTCACAGATAGC
TTCAGGGATGAGAACGGAAAGGTACGATACGGGTTTGCCACGTTCAAGGGATTGTGGGTCATCGATGGTGGAGTTACTCT
TGATCCACACGCTGCAGTTGAATATAAGATACAATTTCTAGACTTTTTCCATGCAACTGTCTCAGCAACGATCTTTGTTG
CAATCGCCCTGTTTGACCAGAATGTGGCATCTTGCTTTTATCCAATACCATCAGAGGACACAAAGCAAGTTCTCACAACA
GTGCCAGTTGCTATTGGAGTTATTGGAAGCATGCTGTTCGTTAGCTTCCCAACCACCCGCCATGGCATTG-CTTCCCAGT
CACTCCACAATAGTTGGGTCTTCAAAAGATTTGTTCGCTCTAGTTCCTGTTGA---------------------------
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>chr3D_1_TraesCS3D01G245600
CTGATAGATCGATGGTGATTGATGTAGTTGCATTACCACATTTTTTTTTATATAAAGAGCATATTTTATCAACTCATAAT
AAAGTATCAAGGAGATACAAACACGATGAACACACACCTATCCTCTGCATAATTAGGATGAACACAGCTAACACCAACAC
ACACAAAAAGATCATGTCG--ACAGAGCAAAGCCATATAAGGCCAAAATTATGCAAGGGAAAGCATATATTTAGGATTAA
TGCTTGCGAAGAGCCTCGTGCCTTCCATCAGAGGAAATGT---AAGTATAAAAACTATTGCCCACTCAGCAACTCTAGGA
GGTCCCCAAAAGCACATGAACTCTATAATAGCGCCAATTTAGATGCTACGGGGTAAAA----AACATTCTAGCAGATTCT
CTCTATACAGGGTGCTCGAGTCCGGGCATGTTTTTTTTTTCTTTTGCAGAGAAAAAGGAAAAGGGAGTCCCAATGACAAG
TGGGTCCCATGATATGACAGAATTTTAGGAGCTACTCCTACA----------AT--------------------------
-----------------------------------------------------TTTACAATATCTAAGTTTGCGCGACTG
CTTTTGAGCCTCCAAATGATTTCGGAGTGCACTCCAAACCGTTTTTTAGAGGCTGCCTCTTTT-TAGAATCTGTTAGAGT
TGCTTGCTCTTAGGCACA---CTG--------------GTTAGTAACAGCATGCACTTGCGTAATCACCACAAAACATAA
CGGACAAAAAATTAGACACAAAATAAACTATGGTTCCTTC-TGTTACCCAAACGTGCTTTTACAACAGCTAGAACG----
------------------CAACAGAGAAACTGCAGCACCACCAACCCCCCATGTTTTTCTCGCCAGAAACTGCAACCCAG
GATCCGAGCTTGTCTTCAG-TTTTGCTTCTCTTTCTTGCAAGGCAATCCAAAATGGGCGGCAAATAGAAGCCGATCACCA
GCTTCATTCCCTTCAAATCCCTGCTAC---------------------------ACATCCTCAAAGACCTGTTAGAAGGA
AGCAAACAAAGAGGACACCGGCAACAATGACTGCTACACAGCCTGACATGGAATTGCAGAAGGATCAGAGGCATCCTCTT
TTGTCCAACAGAACTGATGGCACCAACAACATGAGCCCCACGCAGAAAGCAATCGGACAGGCATACCAGAGCACCGGGCA
CCTCGCCAAACTCCTTCCATCAGGCACCGTGCTTGCCTTCCAGCTGCTGGCTCCAACCATGGCTAAGCACGGCCACTGTG
GTGACTTGGATCGAATGATGACGGGAGGGCTCGTGGTGCTCTGTGCACTCTCATGCTTTGTTCTTAGCTTCACAGATAGC
TTCAGGGATGAGAACGGAAAGGTACGATACGGGTTTGCCACGTTCAAGGGATTGTGGGTCATCGATGGTGGAGTTACTCT
TGATCCACACGCTGCAGTTGAATATAAGATACAATTTCTAGACTTTTTCCATGCAACTGTCTCAGCAACGATCTTTGTTG
CAATCGCCCTGTTTGACCAGAATGTGGCATCTTGCTTTTATCCAATACCATCAGAGGACACAAAGCAAGTTCTCACAACA
GTGCCAGTTGCTATTGGAGTTATTGGAAGCATGCTGTTCGTTAGCTTCCCAACCACCCGCCATGGCATTG-CTTCCCAGT
CACTCCACAATAGTTGGGTCTTCAAAAGATTTGTTCGCTCTAGTTCCTGTTGATCAAACACAGATTCAAAAGCCCCTTAA
GCGGGATAGAGAGAAATATACAGCACCTATTTCTCTAAAATAATATTTATAAGAGTACCTATGGTGGTCTTCGACATGAA
CATGTTTTGTGTATTCAGAAATGAACAGTGCTGGCACCTGGCAGGACAATATATTGGATACGTCTTTGGCACATACCACA
ATTTTTTAAATCTTTCATATG-TACAACTAAGACTTTTGGTTGAATGGTTAAAGCGCCCAACTCATAATTGGTAAATTTG
AGGGTTCAATTCCTACTGGATGCACGTGAACAGGACCGTTCCATAAGTCTACTGGAATTGGTTCTCTATCCACAGAATCT
CATCTATCATGTATATTCATACCATAACATAGGAACAATA----------------------------------------
---------------------------------CGTGGCAGGCACGGAAAAAAGTCTTCATTAATTGGGAAAGAAGCAAT
ATACCAGGAGTCGATAGCTTGTTTTATTCTTGAATCTTCATACATATATGTAGTTAAGTTTTCTATTGTAATTTGCTAGT
TTTTCCAAAATTAACATGTCTAGAAAAGAAGACTTTAAAAATCATATCAGACAGTGCATTCTTGAAGTCATACCACGCAG
CTTTTAAGTCGTCGTGCAATAACCCTGAACAAACATTTTGGTCAACGAAATAAGGAAACAGAAGACACATGACAAGAATA
GAAACGAACTTCAGCAGAGCGCGTGTATGTATCTCTATACATACAAAAACAAGAGATATGGAAGACAACCCCACATCGTA
CCTGAACACTGCCCGCATGCTTGTCACTTCAAAAATTATTCATACAATAAATATTAGTACTTCGCATATCCTGGACATGG
AAGCACTGGAGTTTAAGGGTTTTGGTAGCAACAA-CTCTCTCACTTGTGTAACCCCATGATGGAACAAGTGTGTCGGTTC
ACAATTTTTGCTTGATAAGTCTTAGGCGGATCATGTACCAGCACAGTGTAGCAGGGGGACAGCCTGGTGCATGTAGCTCC
CGCTTGTG
>chr3B_2
-TGATAGATCGACCGTGATTGATGTAGTTACATCGCCACA---TTTTTTTTATAAAGAGCGTATTTTATTAACTCATAAT
AAAGTATCAAGAAGATACAAACACAGTGAACACGCATG--TCCTCTACATAATTAAGATGCACACAGCCAACACCAACAC
ACACAAAAAGATCATGTCGGCAAAGAGCAAAGCCATATAAGACCGAAGCTATGCAAGGGG-AGCATATATTTAGGATTAA
TGCTTGGGAAGAGCCTCTTGCCTGCCATGAGGGGAAATGT---AAGTG--AAAACTATTGCCCACTCAGCAACTCTAGCA
GGTCCACAAAAGCACATGAACTCCATAATAACGCCAATATCGATGCTACGGGGTAG--AAAGAACATTCTAGCAGATTCT
CACTATACAGGGTGCTCGAGTCCCGGCATGGG----TTTTTTCTTCCAGAGAAAAAGGAAAAGGGAATCCCAGTGACAAG
TGGGTCCCATGACATGACAGAATTTTAGAAGCTACCCCCTCGGTAAAGAAATACTCCCTCTGTCCATAATATAAGTGCGT
TTTTATTAATGTAGTGTAAAAAACGCTCTTATACTATGGGAGGGAGGGAGTACTTTACAATATCTAAATTTGCACGACTG
CTTTTGAGCCTCCAAAAGATTTCGGAGTGCACTCCAATCCGTTTT--AGAGGCTGCTTTTTTT-TAGAATCTGCTAGAGT
TGCTTGCTCTTAGGCACACCTCTG--------------GTTAGTAACAGCATGCACTTGCGTAATCACCACAAGGCATAA
CGGACGAAAAATTAGACCCAGAATA-ACTATGGTTCCTTC-TGTTACCTAAACTTGCTTTTACAACAGCTAGAACACAAC
AGAGAAACAGCAGCACCACCAA-----------------------CCCCCATGTTTTTCTCGCCAGAAACTGCAACCCAG
GATCCCAGCTTGCCTTCAGTTTTTGCTTCTTTTTCTTGCAAG-CAATCCAAAATGGGCGGCAAATAGAAGCCGGTCACCG
GCTTCATTCC-TTCAAATCCCTACTACAGGCCCCATCTTCTCTTTCCTCATACTACATCCTCAAAGACCTGTTA-AAGGA
AGCAAACAAAGAGGGCACGAGCAGCAATGACTGCTACACAGCCGGACATGGAATTGCAGAAGGATCAGAGCCATCCGCTT
TTGTCCAACAGAACTGATGGCACTGACAACATGAGCCCCGTGCAGAAAGCAATCAGACAGGCATACCAGAGCACCGGGCA
CCTCGCCAAACTCCTTCCATCAGGCACCGTGCTTGCCTTCCAGCTGCTGGCTCCAACCATGGCTAAACAAGGCCACTGTG
GTGACTTGGATCGGATGATGACGGGAGGGCTTGTGGTGCTCTGTGCACTCTCGTTCTTTGTTGTTACCTTCACAGATAGC
TTCAGGGATGAGAACGGAAAGGTACGACACGGGTTTGCCACGTTCAAGGGATTGTGGC-CATTGATGGTGGAGTTACTCT
TGATCCACACGCTGCGGTTGAATATAAGATAACATTTCTAGACTTTTTCCATGCAACTGTCTCAGCAGTGATTTTTGTTG
CAATCGCCCTATTTGACCAGAATGTGGCATCTTGCTTTTATCCAATACCATCAGAGGACACAAAGCAAGTTCTCACAACA
TTGCCAGTTGCTATTGGAGTTATTGGAAGCATGCTGTTTGTTAGCTTCCCAACCACCCACCATGGCATTGGCTTCCCAGT
CTCTCCACAGTAGCTGGGTCTTCAAAAGATTTGGTTGCTCTAATTCCTGTTGATCAAACACAGAGTCGAAAACCCCTTAA
GTGGGATAGAGAGAAATATACAGCACCTATTTC-CTAAAATAATATTTATAAGAGTACCTATGGTGGCCTTCGACATGAA
CATGTTTTGTGTATTCAGAAATGAACAGTGCTGGCAACTGGCAGGATAATATATTGGATACATCTTTGGCACATACCACA
ATTTTTTAAATCTTTCATATGATACAACTAAGACTTTTGGTTGAATGGTTAAAGCGCCCAACTCATAATTGGTAAATTTG
AGGGTTCAATTCCTACTGGATGCACGTGAACAGGAACGTTCCATAAGTCTACTGGAATTGGCTCTCTATCCACGGAACCT
CATCCATCATGTATATTTATACCATAACATAGGAACAATATGAACTCGTATTCTTATTGATACTCGAACTCAGAGCATAG
GAGGGAAAGTCGATACATGGATGGAATCAAATACGCGGCAGGCATGGAAAAAAGTCTTCATTAATTGGGAAAGAAGCAAT
ATACCAGGAGTCGATAGCTTGTTTTTGTCTTGAATCTTCATACATATATGTAGTTAAGTTTTGTATTGTAATTTGCTAGT
TTTTCCAAAATTAACATGTCTAGGAAAGGAGACTTTAAAAATCATATCAGACAGTGTATTCTTGAAGTCATACCACGCAG
CTTTTAAGTCGTCATGCAATAACCCTGAACAAACATTTTGGTCGACGAAATAAGGAAACAGAAGACACATGACAAGAATA
GAAATGAACTTCAGCAGAGCGCGTGTATGTATCTCTATACATACAAAAACAAGAGATATGGAAGACAACCCCACATCGTA
CCTGAACACTGCCCGCATGCTTGTCACTTCAAAAATTATTCATACAATAAATATTAGTACTTCGCATATCCTGGACATGG
AAGCACTGGAGTTTAAGGGGTTTGGTAGCAA-AA-CTCTCTCACTTGTGCAACCCCATGACGGAACAAGTGTGTCGGTTC
ACAATTTTTGCTTGATAAGTCTTAGGCGGATCATGTACCAGCACAGTGTAGCAGGGGGACAGCCTGGTGCATGTGGTCCC
GCTT----
>chr3A_2
-TGATAGATCGCCGGTGATTGATGTAGTTACATCGCCACA---TTTTTTTAGTAAAGGGCGTACTTTATTAACTCATAAT
AAAGTATTAAGAAGATACAAACCCAGTGAATACACAC--ATCATCTGCATAATTAAAATGCACATAGCTGACACCA--AC
ACACAAAAAGATCATGTCGGTAAAGAGCAAAGCCGTGTAAGACCGAAGCTATGCAAGGGGAAGCATATATTTTGGATTAA
TGCTTGGGAAGAGCCTCTTGCCTGCCATCGGAGGAAATGTTGTAAGTATAAAAACTATTGCCCACTCAGCAACTCTAGCA
GGTCC-CAAAAACACATGAACTCCATA------------TAGATTCTACGGGGTAAAAAAAGAACATTCTAGCAGATTCT
CTCTATACAGGGTGCTCGAGTCCGGGCATGGG----TTTTTTCTTGCAGAGAAAAAGGAAAAGAGAGTCCCAACGACGAG
TGGGTCCCATGATATGGCAGAATTTTAGAAGCTACCCCCTCGGTAAAGAAGTAT--------------------------
-----------------------------------------------------TTTACAGTATCTAAATTTGCACGACTG
CTTTTGAGCCTCCAAATGATTTCGGTGTGCACTCCAACCCGTTTC--AGAGGCTGCCTTTTCTCTAGAATCTGCTAGAGT
TGCTTGCTCTTAGGCACACCTCTGGTTAGTAACAGGCTGTTACTAACAGCATGCACTTGCGTAATAACCACAAGGCATAA
CGGACAAAAAATTAGACCCAGAATA-ACTATGGTTCCTTCTTGTTACCTAAACGTGCTTTTACAACAGCTAGAACG----
------------------CCAA-----------------------CCCCCATGTTTTTCTCGCCAGAAACTGCAACCCAG
AATCCCAGCTTGCCTTCAGTTTTTGCTTCTTTTTCTTGCAAGGCAATCCAAAACAGGCGGCAAATAGAAGCCGGTCACCG
GCTTCATTCCCTTCAAATCCCTACTACA----------------------------------------------------
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>chr3A_963
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---------AGAGGGCACCAGCAGCAATGACTGCTACACAGCCGGACATGGAATTGCAGAAGGATCAGAGGCATCCTCTT
TTGTCCAACAGAACTGATGGCACTGACAACATGAGCCCCGTGCAGAAAGCAATCAGACAGGCATACCAGAGCACCGGGCA
CCTCGCCAAACTCCTTCCATCAGGCACCGTGCTTGCCTTCCAGCTGCTGGCTCCAACCATGGCTAAACAAGGCCACTGTG
GTGACTTGGATCGGATGATGATGGGAGGGCTTGTGGTGCTCTGTGCACTCTCGTGCTTTGTTGTTACCTTCACAGATAGC
TTCAGGGATGAGAACGGAAAGGTACAATACGGGTTTGCCACGTTCAAGGGATTGTGGGTCATTGATGGTGGAGTTACTCT
TGATCCACACGCTGCGGTTGAATATAAGATGACATTTCTAGACTTTTTCCATGCAGCTGTCTCAGCAGTGATTTTTGTTG
CAATCGCCCTATTTGACCAGAATGTGGCATCTTGCTTTTATCCAATACCATCAGAGGACACAAAGCAAGTTCTCACAACA
TTGCCAGTTGCTATTGGAGTTATTGGAAGCATGCTGTTTGTTAGCTTCCCAACCACCCGCCATGGCTTTGGCTTCCCAGT
CTCTCCACAGTACCTGGGTCTTCAAAAGATTTGTTTGCTCTAATTCCTGTTGATCAAACACAGAGTCGAAAACCCCTTAA
GCGGGATAGAGAGAAATATACAGCAC-TATTTCTCTAAAATAATATTTATAAGAGTACCTATGGTGGCCTTCGACATGAA
CATGTTTTGTGTATTCATAAATGAACAGTGCTGGCACCTGGGAGGACAATATATTGGATACGTCTTTGGCACATACCACA
ATTTTTTAAATCTTTCATATGATACAACTAAGACTTCTGGTTGAATGGTTAAAGCGCCGAACTCATAATTGGTAAATTTG
AGGGTTCAATTCCTACTGGATGCACGTGAACAGGAACGTTCCATAAGTCTACTGGAATTGGCTCTCTATCCACGGAATCT
CATCCATCATGTATATTCATACCATAACATAGGAACAATATGAACTCGAATTCTTATTGATACTCGAACTCAGAGCATAG
GAGGGAAAGTCGATACATGGATGGAATCAAACACTAGGCAGGCACGGAAAAAAGTCTTCATTAATTGTGAAAGAAGCAAT
ATACCAGGAGTTGATAGCTTGTTTTTGCCTTGAATCTTCATACATATATGTAGTTAAGTTTTGTATTGTAATTTGCTAGT
TTTTCCAAAATTAACATGTCTAGAAAAGAAGACTTTAAAAATCATATCAGAC--TGCATTCTTGAAGTCATACCACACAG
CTTTTAAGTCGTCGTGCAATAA-CCTGAACAAACATTTTGGTCAACGAAATAAGGAAACAGAAGACACATGACAAGAATA
GAAATGAACTTCAGCAGAGCGCGTGTATGTATCTTTATACATACAAAAACAAGAGATATGGAAGACAACCCCACATCGTA
CCTGAACAGTGCCCGCATGCTTGTCACTTCAAAAATTATTCATACAATAAATATTAGTACTTCGCATATCCTGGACATGG
AAGCACTGGAGTTTAAGGGTTTTGGTGGCAGAACTCTCTCTCACTTGTGCAACCGCATGATGGAACGAGTGTGTCGGTTC
ACAATTTTTGCTTGATAAGTCTTAGGCAGATCATGTACCAGCACAGTCTAGCAGGGGGACAGCCTGGTGCATGTAGCTCC
CGCTTGTG
>SNPs
S-----------S----------------S---SS-----SSS------S----------S--------S----------
-----------S------------SS-----------SS----------------S----S-------------------
----------------------S------------------S--S--SS----------S--------------------
------S----------S-----S------------------------------------------------------S-
-----S-----------------S------S-------S-----------------------------------------
------------------------------SSSSSS----S-S-------------------------------------
----------------------------S------S--SS-S--------------------------------------
-------------------------------------------------------------------S-----S------
-------------------------------------S-------SS-----------S--------------S------
-------------------------------------------------------------------------SS-----
-----------------S--S----S----------------------S-------------------------------
-------------------S-SSSSSSSSSSSSSSSSSSSSSSSS-----------------------------------
-----S------S-----------------S------------------------------------------S-----S
----------------------S---------------------------------------------------S-----
--------------S----S---S-------------------S------------------------------------
-----------------------SS--------------SS-------------S-------------------------
------------------------------------------------------------------S--S----------
-------------S-----------------S--------------------S---------S---S-------------
--------------------------------------------------------------S-----------------
---------------S---------------SS----------------------------------SS---S-------
----------S---------------------------------------------------------------------
S-------------------------------------S-----------------------------------------
-S-------S---S---------------------S------S---------------------S--S---S--------
-------------------------------------------------------------------S------------
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-----------------------------------S-------------------------S-----------S------
----S---------------------------------------------------------------------------
-----------------------------------S--------------------------------------------
-------------------------SS-----------------------------------S-----------------
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----S---------------------------------------------------------------------------
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-------------------------------S-----------------S------------------------------
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>forward_1144
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----AACAAAGAGGACACCGGCAA--------------------------------------------------------
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>reverse_2565
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----CGAACTTCAGCAGAGCGC----------------------------------------------------------
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