>input_sequence_68859
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--------------------------------------ATGGCTGACAATGCTGCCGAGGTGCAGCAGACACCTCAAGGT
GAAC----------ACATTGCCGTTGTTCTTTTCTCGGCACAACATTCAGACTTGACTCAATGAACCTAAGCACATATAT
ATGTATATGTTTTGATCAAACAGTTGTGGAGAAGAGCCAGGCCGCGGAGAAGAGCGAGAAGAAGGCGGAGCTGAAGCCCG
ATGAGGCGAAGAAGCTGATCGAGTTCATGGAGAGTAAGTACGACGAGCACGTGGCGAAGGTGGACTCGTTCGACGACTTC
TACCACGCCATCTACGAGCTCATCCAGTAAGTTTT---CTCCGAACCTTACATGCATTCAGTTCATGTCCATCGTGCATT
CA-----TCATCGCCGCTGAACGAACCCCCCAGGAAGTTCTGCGAGGAGCGCGGGCAGGTGCAGTACAGGATCCCGCCCA
GGGAGAAGCTGCAGGAGGTGTACACGGTGAGTTAGTAGCCGCGTTCTTCAGTCCGGTCAGTACGTGTGGCTTGAATCGAG
GGGGTGCTCATGTTCGT--------GTGG---------------------GCGTGCAGAAGCACCACAAGGCGGGGAGTG
GCGAGGTGAAGCGGGAGGAGTTCGCGAAGATGAGCGGGGAGCTGGTGAAGCGGGACAGCTTCAGCTTCGGCAAGGCGACG
ACGGAGCTGCTCATGTTCCTGTTCGGCGCGCCCATGTGCGCGCTGGTGGCCAAGCGGGTCCTGCCGGGGCTGGGATGGCT
CTCCGACGACACCGTCATTCCGCTCGCCACCTCCGGCGCCGTCGCCTTCCTTGTCCACACCAAAAAGCTCTGA-------
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>chr3A_1_TraesCS3A01G493000
GAATGCGAGATATAGGGGCGCCTCTTAGGATAGCGCGTCATGTGTGGCTTATATGAGAGAAAAAAGGAGTTAAATTCTGA
TAACTATGATTTTTTTTTTGCGGAGATAACTATGATTCTGCTACATCTGTATCTTCATTTTTTGTATTTACAAACAGATA
TTCTGGACTTCTTTTCAGAAAACGGTTGTGATCTTCTGATTATGCA---TATGGAACTACAATGAATGGGTGGATAGCTA
ACGGCAGTGATCCAATAATAGCAAATGTTCCACCATGTTAATGTCCGGGGATGTGATAGAGTAGATAGATATTACGACGC
TGGCACAAAGAATGAAAATGTAGGAAA----------GAAAGAAATAGGCCTATATCAGGCCTCTGTCACATTCCGAATC
TGCTTCACCTAAGCTCAGTGCTTGCGTGCACACATCTTATGCGCGATGCGCCAAGACGACCTCA-TCAAGATTGTGCCAG
GTTCCCACA--GAATTAATTCCATTGTAATCGTACACGCTTGTTCGTCTGGCCCACGTACCATCCATCTGTATTTGCCCA
CTTGTTCCATTTTCTGATGACATTGTTCTTCACCGACAGCTAC------TTGTGAAACTAAGCTTGCATTCCTATTACTT
CTTCAGATTTAGGCGGGAAATATGACGCGTTCGCTCAACATTTCGCTACATT-CCCCACAAGC----TACATATGCATGT
GTGCACGTTCTGTTCCTTCTCTCAG--------------------------------AGAACGGTGTCTGTTTGAAGTCT
GAACCTTGCTTGGTCTGCACCCAAATGCTTGCAGGTGCAGCTTGCAGCTAGCTACGG-------------AATACCGTGC
GACAATGGCCACATGATTCCTGACCTTGGGGGCTCCTTTCCCCCTTGCTCCTGCCCAGCTTTGCTTCCTGCCGAGGCAAT
GCCATTGTCTCTGTCCCACACAAGGAACCTGGCCAGCAGTCTGCCATAATATATACGCAGCAATAGTCTACAC------A
AGGGACCGACCATCCGTTCCTGCATTTCATCGAAGAAGATGGCTGACAATGCTGCCGAGGTGCAGCAGACACCTCAAGGT
GAAC----------ACATTGCCGTTGTTCTTTTCTCGGCACAACATTCAGACTTGACTCAATGAACCTAAGCACATATAT
ATGTATATGTTTTGATCAAACAGTTGTGGAGAAGAGCCAGGCCGCGGAGAAGAGCGAGAAGAAGGCGGAGCTGAAGCCCG
ATGAGGCGAAGAAGCTGATCGAGTTCATGGAGAGTAAGTACGACGAGCACGTGGCGAAGGTGGACTCGTTCGACGACTTC
TACCACGCCATCTACGAGCTCATCCAGTAAGTTTT---CTCCGAACCTTACATGCATTCAGTTCATGTCCATCGTGCATT
CA-----TCATCGCCGCTGAACGAACCCCCCAGGAAGTTCTGCGAGGAGCGCGGGCAGGTGCAGTACAGGATCCCGCCCA
GGGAGAAGCTGCAGGAGGTGTACACGGTGAGTTAGTAGCCGCGTTCTTCAGTCCGGTCAGTACGTGTGGCTTGAATCGAG
GGGGTGCTCATGTTCGT--------GTGG---------------------GCGTGCAGAAGCACCACAAGGCGGGGAGTG
GCGAGGTGAAGCGGGAGGAGTTCGCGAAGATGAGCGGGGAGCTGGTGAAGCGGGACAGCTTCAGCTTCGGCAAGGCGACG
ACGGAGCTGCTCATGTTCCTGTTCGGCGCGCCCATGTGCGCGCTGGTGGCCAAGCGGGTCCTGCCGGGGCTGGGATGGCT
CTCCGACGACACCGTCATTCCGCTCGCCACCTCCGGCGCCGTCGCCTTCCTTGTCCACACCAAAAAGCTCTGATCGATCG
ATCATGTCTCAACCGAGTGATTGTATATGGATATATGTGGCAGTAAAATAATGCGATGGCT--CGGCTCAAATACTGATG
CGAGAACAAATTCAACTGCAGTAATTGAC--------------------TAGTAAACAAGAGTATCAGACTGCTGGGTTT
TTTCTA-CGTATTTGTAATAAAAAGAATGGCGGCCAACGAAGGTTA-GCTGGACGGGTAGAATAGTAATACTCCAAAGGC
AAGGCACAAACACACGGGGAACCCAGGGGAGTGGCGTGTCCAACCACCGAAAATAGAGACCAGGAAGAAAAAAGGCACAC
CACTCTATATTTAAAAAATATAGTACTTACATACAAAGTTAAAACATTCTGAAAATGTTTTTGAACAAACCTGACCTTCT
ATTGTACTTGTTTAAAAAATCACAAAAATAAAACTCCCGTTGACAAAATTCTCAGTCAAAATAGTGTGAATAGTGACCTA
TAATGGCAATAAATTTTATTTTTTTGCCCTAAAGTCAACACTGGTTTTTTATTCATGAAAATTTAAATAGTAGTACAAAA
GAAAGTCAAGTTTATTCTAAAACAACCTCTCAACTTGTTTTGCTTTTATTTTACGAGAATGCTATTTTCCTGCCGACTGG
CAATTAGCGACAGGCACGT-------ACGAGCCGTTGGATCCGCTTCTCGCGCTCGATAAACCGCTTGTTCAGTTCTAGC
GCGTGAAAAAAGCTACCGAAAAATAAAATGAAGCACCAATAGGAGTCGAACCCACAACCAATTGGATGAAGCCCTCTGCA
CACAACCAACCGGTACATATAAATGTTCTG--------------------------------------------------
---------------------------------------------------------------------------TTTTC
CTACTAGTTTAACAGGATTTTATACCTTATTTAATGAGAGTGGGAAAGAAAAACAACATTGCCTTTGACCTAGAGACAAA
ACCATCTAGTCCAGGTTTTGTAAGGACTGATGCATCATGTTGTATTTATCTCTCTTTTTGTAGTGATGAACATTTTTCTA
GTGAAATAAACATTCCGCTCACATAGAAT
>chr3B_105
GATGAAG-------------------------------------------------------------------------
------------------------------TATGATTCTGCTACAAAAGCATCTTCCTTTTTTAG--TTACAAACAGATA
TTCTGGACTTCTTTTCAGTAAACGGTTGTGA---TCTGATTATACATACTATGTAACTACAATGAACGGGTGGGCAGTTA
ACGGTAGTGATCCAATAATAGCAAAGGTTCCACTATGCCAATGCCC--GGATGTGATAGAATAGATAGACATCCCAACGC
TGCCACAAGAAAAGAAAATACTCCACACATCTCATGTGAAAGAAATAGGCCTATCTCAGGCCTGTGTCACTGTCCGAATC
TGCTTCCGCTAAGTGCAGTGCTTGCGTGCACACATCTTATGTGCGATCGATGCGCCAACATGAGCTCAAGACCATGCCAG
GTTCCCACACAGAATCAATTCCATTGGAGTCGGACACGCTTGTTCGTCTGCTACACGTACCAGCCATGTGTATTTGTCCA
CCTGCTCCATTTTCTGACGACATTGCTCTCCACTGACAGCTACTCCTACTTGTGAAACTAAGCCTGCATTCCTGTTAGTT
CTTCAAATTAAGGCGGGAAATATGATGCGTTCGCTCCACATTTCGCTACATTCCCCCACAAGCTACTTACATATGCATGT
ATACACGTTCTATTTCTTCTCTCAGGAATCAGGATTCAGGAGTAAGGGCAAAGCTAGAGAGCGGTGTCCATCTGAAGTCT
GAACCTTGCTTTGTATGCACCCATATGCTTGCAGGTGCAGCTTGCAGCTTGCAGCTAGCTGCGGAATACCAATACCGTGC
GACAATGGCCACATGATTCCTGACCTTGGGTTCTCCTTTTCCCCTTGCT----------------TCCTGTCGAGGCGAT
GCCATTGTCACTCTCCTACACAAGGAACATGGACAGCAGCCTGCCATAATATATACGCAGCAATAGTCTACACAAACACA
AGGGACCAACCATCAGTTCCTGCATTTCATCGAAGAAGATGGCTGACAATGCTGCGGAGGTGAAGCAGAAACCTCAAGGT
GAGGTGAAACCAGATGAGGGTC----------------------------------------------------------
--------------------------------AGAGCCAGGCCGCGGAGAAGAGCGAGAAGAAGGCGGAGCTGAAGCCCG
ATGAGGCGAAGAAGCTGATCGAGTTCATGGCGAAGAAGTACGACGAGCACGTGGCGAAGGTGGACTCGTTCGACGACTTC
TACCACGCCATCTACGAGCTCATCCAGTAAGTTTCTTCCTCCGAACCTTACGTGCATTCAGTTCATCTCCATCGTTGATT
CA-----CCATCACCGCTGAACGATCCTT-CAGGAAGTTCTGCGAGGAGCGCGGGCAGGTGCAGTACAGGATCCCGCCCA
GGGAGAAGCTGCAGGAGGTGTACAAGGTGA----GTGGCCGCGTTCCTTTCTTCCTTATCGGCAATCTTCAGTAAATGAG
AGGGTGGACGTCTCACATTTGTGTCTGGATCGTCGGAATGGATGGCGGGAGCATGCAGAAGCACCACACGTCCGGG---G
GCGAGGTGAAGCGGGAGGAGTTCGCGAAGATGAGCGGGGAGCTGGTGAAGCGGGACAGCTTCAGCTTCGGCAAGGCGACC
ACGGAGCTGCTCATGTTCCTGTTCGGCGCGCCCATGTGCGCGCTGGTGGCCAAGCGGGTCCTGCCGGGGCTGGGCTGGGT
CTCCGACGACACCGTCATCCCGCTCGCCACCTCCGGCGCCGTCGCCTACCTCGTCCACTCCAAGAAGCTCTGATCGATCC
ATCATGTCTGAACCGAGTGACTGTATACGGATAT--GTGGCAGTAGATTAATGCGATGGCC--GGGCTCAAATATTGCAG
CGAGCACAAATTTAACTGCAGTAATTGAC--------------------TA-------------TCAGACTGCTGGGTTA
TTTTTA-CGTATTTGTAATAAAAAGAATGGCGG-----------------------------------------------
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>chr3D_717
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-----------------------AG--------------------------------AGAACGATGTCTGTCTGAAGTCT
GAACCTTGCTTTGCCTGCACCCAAATGCTT--------------------GCAGCTAGCTGCGGAATACCAATACCGTGC
GACAATGGCCACATGATTCCTGACGTTGGGTGCTCCTTTTACACTTGCTCCTGCTCGGCCTTGCTTCCTGCCGAGGCAAT
GCCATGGTCACTGCCCTACACAAGGAACCTGGCCAGCAGCCTGCCATAATATATACGCAGCAATAGTCCACT------CA
AGGGACCAACTATCCGTTCCTGCAATTCATCGAAGAAGATGGCAGAAAATGCTGCTGAGGTGAAGCAGACACCTCAAGCT
CAAGGTGAGCTCAAACATTTCCGTTGTTCTTTTCTCAGCACAACATTCAGGCTTGACTCAATAAACCTAAGCACATATAT
ATA------TTTGGATCAAATAGTTGGGGAGAAGAACCAGGCCGCCGAGAAGAGCGAGAAGAAGGCGGAGCTGAAGCCGG
ATGAGGCGAAGAAGCTCATCGAGTTCATGGAGAAGAAGTACGACGACCACGTGGCGAAGGTGGACTCCTTCGACGACTTC
TACCACGCCATCTACGAGCTCATCCAGTAAGTTTCTCT----GAACCTTATGTGTATCCAGTTCATTTCCATCGTTCATT
CATTTCATCATCACCGCTGAACCTTCATT-CAGGAAGTTCTGCGAGGAGCGCGGGCAGGTGCAGTACAGGATCCCGCCCA
GGGAGAAGCTGCAGGAGGTGTACACGGTGA----GTGGTCGCGTTCTTACTTACT-----GGCAATCTTCAGTAAATGAG
AGGGTGTGCGTCTCACCTTTGTATCGTGG---------------------GTGTGCAGAAGCACCACAAGGCGGGGAGCG
GCGAGGTGAAGCGGGAGGAGTTCGCGAAGATGAGCGGGGAGCTGGTGAAGCGGGACAGCTTCAGCTTCGGCAAGGCGACG
ACGGAGCTGCTCATGTTCCTGTTCGGCGCGCCCATGTGTGCGCTGGTGGCCAAGCGGGTCCTGCCGGGGCTGGGGTGGCT
CTCCGACGACACCGTCATCCCGCTCGCCACCTCCGGCGCCGTCGCCTTCCTCGTACACACCAAGAAGCTCTGATCGATGA
AGC----CTGAACCGAGTGATTGTATATGGATAT--GTGGCAGTAAAATAATGCGACGGCTCGGGGCTCAAATACTGAAG
CGAGCACAGATTTAACTGCACTAGTTGACAAGTACTACATCAGAGTATATA-------------TCAGACTGCTGGTTGT
TTTTCTTCGTACTTGTAATAAAAAGAATGGCCGGTAACGAAGGTTAGGCTGGACGGGTAGAATAATAATACTCCAAAGGC
AAGGCACAAACACACGGGGAAGCCAGGGGAGTGGCGTGTTGAACCACCGAAAATAGAGACCAGGAGG-AAAAAGGCACAC
CACCCTATATTTTAAATAATTAGTAATTACATACAAAGTTAAAAAATTCTGAAAATGTTTTTAAATAA------------
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>chr6A_2387
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-------------------------------------------------------AGAATGCTATTTTCCTGCCGATTGG
CAGTTAGCGACAGGCACGTACGACTCACGAGCCGCTGGATCCACTTCTCACACTCGATAAACCGCTTGTTCAGTTCTAGC
GTGTGAAAAAAGCTACCGAAAAATAAAATGAAGCGCCAATAGGAGTCGAACCCACGACCGATTGGGTGAAGCCCACTGCG
CGCAACCAACTGGTACATATATCTGTTCTACTCCCTCTGTTCCGAATTACTTGTCTTGGATTTGTCTAGATACGGATGTA
TCTAGACTCATTTTAGTGCTAGATACCTCCGTATCTAAAAAAATCTAAGACAAGTAATTCGGAACGGAGGGAGTATTTTC
CTACCAGTTTAACAGGATTTTATACCTTATTTAATGAGAATGGGAAAGAAAAACAACATTGCCTTTGACCTAGAGACAAA
ACCATCTAGTCCAGGTTTTGTAAGGAATGATGCATCATGTTGTACTTATCTCTCTTTTTGTAGTGATGAACATTTTTCTA
GTGAAATAAACATTCCGCTCACATAGAAT
>SNPs
--SSSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSS---------------SSS-S------S------SSSS-------------
------------------S------------SSS---------S---------S------------S------SS--S--
----S--------------------S-------S---SS----S--SS------------S--------S--SS-S----
--S-----SS--S------SSSSS-S----------------------------S--------S------SS--------
------SS-----SS--------------------------S-----SSSSSSSSSSSSSSSSS-------SSS------
---------------S----------S-S---S-----------------SSS---------S----S--------S---
-S--S------------S-------S---S---S-----------------------------S---------S---S--
-----S---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-------------S-----------S-----------------
--SSSSSSS---S-------S-----S-----------------------------------------------------
---------------------------------SS---------------------------------------------
----------------------------------S----------------S--------------S--------S----
------------S-----------S--SSS--------------------------------------------------
------------------------------SSSS--S-----------SSS-S-SS-SSSSS-SSSSSS-SSS--SS---
S-----SS-S-S-SSSS-------------------------------------------------------------S-
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--------------------------------------------------------------------------S-----
------------------S--------------------------------S-----------S---------------S
---------S------------------------SS---------------------------S--------------S-
----S-------S--------------------------------------SSSSSSSSSSSSS----------------
---S-----------------------------SS-----------------------------S---------------
---------------------S-----------------SS------------------------S-S------------
---S--------S---S-SS-----S------------------S-----------------S--S--SSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS---------------------S---
--S-------------------------------S-------S------S-S----------------------------
-S--------------------------------S--------------------S---S-----S--------S----S
-S--------S----------SS------S--------------------------------------------------
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----S----------------------------------S----------------------------------------
--------------------------S-----------------S-----------------------------------
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>forward_31
-----------ATAGGGGCGCCTCTTAGGAT-------------------------------------------------
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>reverse_1575
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------------------------------------------------------GGTCAGTACGTGTGGCTTGA------
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>forward_1573
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---------------------------------AGTAGCCGCGTTCTTCAGTC---------------------------
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>reverse_2706
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-----------------------------------------------------------------ATGAAGCCCTCTGCA
CACAA---------------------------------------------------------------------------
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