>input_sequence_77419
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--------ATGAAGCGGACCAGGGCGCAGAACCCCAAGGCCCAGGACCCGGAGCCGCAGGACCCCGCC------GCCGCC
GGGAGCAACCCCAACCCGAAGCCGCAGCGCCGCGCGAAGCAGCCCCGGCAGCCCAAGGCGGCGGCGACGGCGGGCAAGAA
GACGGCCGCGGCGCGCGATGCCGCCGCGGTGGCCGCGACCGCTGCCGCTGCTGCTGCCACCTCCGTCGCCGCAGCGTCCC
CTGCTGCGGAGATGGCGCCCGTCGTCCCCGACGTGTGCGTCGCCGCCGGCGGAGGAGGAGGTGGGGAGGTGGCGTGCGGC
CTGCCGGCTGAGTGGGACGAGATGGACGGCGCGAACGGGTCGCCGTGGTGGACGTTCGGGGTGGAGGAGGAGAAGCTGCT
GGGGTGGTTCCCGTTCGTGGAGGAGGACTTCCTGTCCGT---CGGCGGCGTCGGCCCCGCCGCCGCCGAGCCCTCGGTCT
TCGACGACGACATCTGGCGGATCCACCAGATCTACGAGATCCCCAGCTACGCCGCCAAGTGA------------------
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>chr3A_1_TraesCS3A01G041900
CGACATACGGGCAGCCTCATGTCGGCCCCTTAAAGTAAAGTACTAATAGC-----CCCCTCGTCGATCGCTTTAATGCCG
AGATACGACCGGTGGTGGTACCGCTGC--ACCACG-CCACCGGCTCAGTACACGTACACGTACGTACTACGAACCAGTGT
TATCGAGCTACATTTA------ATTATGATGAGATGAGACGATGATATGATAGTAGTAGAAATCCGGTGGAATTTGGGCG
CTTGCAGGTTCTAGTAATGAGTAGCATGCATTGTTGGACGCCG-------------ATCTCTTAATTATGCTTCACGGTG
TCGGCATGCGGTCTGCACATGCACATGCACGCCGCCCTCGGCGATCACCTTCCCGAGCCGAGCCCCCGGCGCCTCCACGT
GAGCCGCGACGGGATCGGCGCGA--------------CGCACGCCGGCGGCACATGTCGTGCAACACGGGC---------
--------GCGATCTCCGTCTATGC------------------------GTACGTGCAATAACTCGTACTAGCATACTAG
AC-ACAAGCAAAAGGGTGAATTTGTCACGGAATGC-------ACGGATCGCGATTTACCATTGCCATCGATGCGTCGCCT
TGTCGACCGGACCGGAAGGCCAAGAAGAACAGCGACGTGGCCGGCCGCGCCGCGCGGGTCGCCACCAGGCCCAGTTGCGT
TGCATGCACATCCACCCGAGTCGCCGTCACGGGGCCGGGTC---GACGGATGGACCCGGTGCGG----CGTACGCACGCG
GCCAGCGCTGAAGGCGGCTGTGTA--------------------GCGGCGGCGTGCACGCTGCGACCAGGCCAGCAATGC
CCAGCACACCGCTGAACCGAACCGGTGTCGACCAAGTGG----CTCGCCGCACCGCCAAAAGGGCGACCCGGACCCGAAC
CCCGCCCCGCCGCTGCGAGTACAAAAGGGCCGCAAAGCCCAAGCACCATCGTATCA-------CCCCAGCCCCACCCCCA
CACTCCCCCGGCGCTCTCACTCTCCCCTCGCCGCCTCCCCTGCACCAGAGCTAGCAGAGGAGGGCTCTCCGGACTCTAGC
CGGGCGCCATGAAGCGGACCAGGGCGCAGAACCCCAAGGCCCAGGACCCGGAGCCGCAGGACCCCGCC------GCCGCC
GGGAGCAACCCCAACCCGAAGCCGCAGCGCCGCGCGAAGCAGCCCCGGCAGCCCAAGGCGGCGGCGACGGCGGGCAAGAA
GACGGCCGCGGCGCGCGATGCCGCCGCGGTGGCCGCGACCGCTGCCGCTGCTGCTGCCACCTCCGTCGCCGCAGCGTCCC
CTGCTGCGGAGATGGCGCCCGTCGTCCCCGACGTGTGCGTCGCCGCCGGCGGAGGAGGAGGTGGGGAGGTGGCGTGCGGC
CTGCCGGCTGAGTGGGACGAGATGGACGGCGCGAACGGGTCGCCGTGGTGGACGTTCGGGGTGGAGGAGGAGAAGCTGCT
GGGGTGGTTCCCGTTCGTGGAGGAGGACTTCCTGTCCGT---CGGCGGCGTCGGCCCCGCCGCCGCCGAGCCCTCGGTCT
TCGACGACGACATCTGGCGGATCCACCAGATCTACGAGATCCCCAGCTACGCCGCCAAGTGAAGCGAAGCGACGGACGTC
GCAAAATGCGGGCGGGCGGGCGGCATTCGGCGTGGAGGCCTTCCGCTTCGAGAG---AGAAATTAGATAGGAGCTGCTAC
CACT-----------------------------ACTAGTGCTTTTGCGGTACAGGAAC-GGGGAACGGACTAATCGAGGA
GG----------CCACTAATGTCACCTTAGGCGAGCGAGCTAGTTAACCAGATGTTATGCAA---GCAAGCAAAAGAAGA
AGAAAAATTGCGACGGCGATGCGATTTCACGTGCCCTCTTCTTGTGCCCTGCGTCTTGATTTTA--GCCGTGTTGTTGCG
CGATTAGCTTCCATTCTCATGTGCGTTCTCCGGTAACGTGGCTCGTCACCGGAGTAGTTCTTGGTATTAGGACTTGCATT
CCATCACAGCAACGCACAAACGAGGGCTCCTGTCCTGTGGGTGGCAAACTGCACAGTGCAGTGCAGTTGGTTCCATCGTT
TCAATGGAGCGGGACGACAAGCCTGCCTCTGCCTGTTGCCTCCAGAAAGAGACCAAAATTTGGG----------------
----CGGGTTTGCGCGCGCAAACGGAGCAAGAACGGCGCGGAGAAAGGAAGCGGCGCTCCTGAATTTCTGGAGGTGGAGG
TGGAGTGCGTTCCCA----TGTCAGCAAATGCCAGAATCGCGTCGTTTCTGTAACTCTGTTTTCCGTGAACCACGGCGCG
TTCCCATGTCAGCAAATGTGGCTGAATCGCGTTGCTTGTCTCCGTTTCCGTGGAACAGCTGTTGCACTTCGTAAGAGTAT
GTAATGTACGTTCAGTTGCAGCACGCGCAAGGTTGAAATATAAAACCGCAGAATGCTACTTTCAAGCCCTAATGTGGTTT
TGTACGATTTTTATAGGACATGATTTCTAATTTTTTTTCTATATAAAGCCCTTTGATTTTGTATAGTGGATTCATGTCTT
CCATCACATATCAAAGAGCAAAATATTAGGCCGGACCTAATGATGAAAAAGAAAACAATAAACCAAGCAACATCTGTTTC
CTACAAGAAGTGAT
>chr3D_1
CGACATACGGGCAGCGTCATGTCGGCCCCTTAAAGTGAAGTGGTAGGAGTACTAGCCCCTCGTCGATCGCTTTAATGCCG
AGATACGACCGGTGGT---ACGTGCCGCAACCACT-CCACCGGCTCAGTACACGTACGTACGAACAAGTA----CTGTAT
TATCGAGTTAGATATT------TTAATTACGAGATGAT----GA------------TAGAAAACCGGTGGAACTTGTGCA
CTTGCAGCTTCTAGCAGCAT---GCATGCATTGTTGGACGTTACATACACGAGCGAATCTCTGAACTACGCTTCACGGTG
TCGGCATGCGGTC------TGCACATGCACGCCGCCCTCGGCGCTCACCTTCCCG---------------GCCTCCACGT
GAGCCGCGACGGGATCAGCGCGA--------------CGC-----------GCATGTCGTGCAACACGGAG---------
--------GCGATCTCCGTCTGTGC------------------------GTACGTGCAACAATTAGT-------------
AC-ACAAGCAAAAGGGTGAATTTGTCACGAAACGC-------ACGGACCGCGATTTACCATTGCCATCGCTGCGTCGCCT
TGTCGACCGGACCGGAAGGCCAGGAAGAACAGCGACGTGG------------------------CCAGGCCCAGTTGCGT
TGCATGCACATCCACAAGAGTAGCCGTCACGGGGTCAGGTC---GACGGA----CCCGGTGCAG----CGTACGCACGCA
GCCAGCGCTGAAGGCGGCTGGCGGCAGCCGCATGTGTTTCGGCGGCGACGGCGTGCAAGCTGCGACCAGGCT--------
-CAGCCCACCGCTGAACCGAACCGGTGCCGATCAAGTGG----CTCGCCGCACCGCCAAAAAGGCGACCCGGACCCGACC
CCCACCCCGCCCTA-CGAGTACAAAAGGGCCGCAAAGCCCAAGCACCATCGTATCACCCTAG------CCCCCACCCCCA
CACTCCCCCAGCGCTCTCACTCTCCCCTCGCA-----------GCAGAGCTTGCTCGCAAGAAGCAGAGCAAGTGGCCGG
CGGCGA-CATGAAGCGGACCAGGGCGCAGAACCCCAAGGCCCAGGACCCGGAGCCGCAGGACCCCGCG------GCCGCC
GGGAGCAACCCCACCCCGAAGCCGCAGCGCCGCGCGAAGCAGCCCCGGCAGCCCAAGGCGGCGACGGCGGGTGGCAAGAA
GACCGCCGCGGCTCGCGAGGCCGCTGCGGTGACCGCGACGGCAGCCGCTGCTG------CCTCCGTCGCCGCAGCGTCCC
CCGCAGCGGAGACGGCGCCGGTCGTCCCCGACGTCTGCGTCGGCGCGGGAGGAGGAGGG---GAT---GTGGCGTGCGGC
CTGCCGGCGGAGTGGGACGAGATGGACG---------GGTCGCCGTGGTGGACGTTCGGGGTGGAGGAGGAGAAGCTGCT
GGGGTGGTTCCCGTTCGTGGAGGAGGACTTCCTGTCCGTCGGCAGCGGCGTCGGCCCCGCCGCCGCCGAGCC------CT
TCGACGACGACATCTGGCGGATCCACCAGATCTACGAGATCCCCAGCTACGCCGCCAAGTGAAG--AAGCGACGGACGCA
AAAT-------GCGGGCGGCATTCCA----------------CCACTTGGAGAG---AGAAACTACTACTAATCTATGAG
GTTACCATCTCATAGATTTGTGCTACCAGCAGCAGTAGTGCTTTTGCGGTACAGGAACAGGGGAACGGACTAATCTATGA
GGTTACCATCTACTACTAATCCCAGTTTAGGCGAGTGAGCGAAGCTAGTTTTAACGCCTTGTTATGCAAGCAAAGAACAA
AGAAAAATTTCGACGGCGATGCAGTTTCACGTGCCCTCTTCTTGTGCCCTGCGTCTTGATTTT-----------------
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>chr3B_47
TAGCCCCTCAT--------------------------------------------------GTCGATCGCTTTAATGCCG
AGATACGACTGGTGGT---ACCGCTAC--TCCACCACCACCGGTGCAGTACACGTA-GTACGAACGAGTA----GTATAT
CATCGAGTTAGATACGTACGTGTTAATTATGAGACATGACACGA------------TAGAAAACCGGTGGGATTTGGGCA
CTTGCAGGTTCTAGTAGCAT---GCATTTACATGAA-----------------CGAATCTCTTAATTATGCTCCACGGTG
TCGGCATGCGGCC------TGCACATGCACGCCGCCCTCGGCGCTCACCTTCCCGAGT-----CCCCGGCGTTTTCACGT
GAGCACGCCGGCGGCCGCGTCATGGGCGGCTGCCACGCGC-----------ACATGTCGTGCAACACGGGCACGGCTACG
TGGCCGACGCGATCTCCCTCAGGCCTCAGCCCAACCACTCGTGTGTGGAGTACGTACAATACAATGATCGTACACGTATA
CTGACAAGCAGAAGGGTGAAGTTTCTTGGGGGAAAACGTAGTACGGATGGTGATTCACCATTGCCATCACTGCGTCGCCA
TGTCGACCGGGAGGGT-----AAGAAGAACAGCGACGTGG------------------------CCACCAGGTCCA--GT
TGCATGCACATCCACACGGGTCGCCGTCACGGGTCGGGTCGACGGACGGA----CCCGGTGCGACGGACGCACGCACGCG
GCCAGCGCGGAAGGCGGCTGCATGTGTCGCTG-------CGGCGGCGGCGGCGTGCAAGCTGCGACCGTG----------
CCAGCCCACCGCTGAACGGAACCGGTGTTGATCAAGTGGCTGGCTCGCCGCACCGCCAAAAAGGCGACCCGGACCCGAGC
CCCGACCCCGCCCAGCGAGTACAAAAGGGCCGCAAAGCCCAAGCAGCATCGTATCAGCCCCAGCCCCACCCCCACCCCCA
CACTCCCC-AGCGCTCTCACTCTCCGCTCGCCGTCTTCCTCCCGCAGAGCGCGCTCGCAAGAGGCAGAGCACGA-----G
CGGCGG-CATGAAGCGGACCAGGGCGCAGAACCCCAAGGCCCAGGACACGGAGCCGCAGGACCCCGCGGCCGCAGCCGCC
GGGAGCAACCCCAACCCGAAGCCGCAGCGCCGGGCCAAGCAGCCGAGGCAGCCCAAGGCGGGGGCAACGGGGGGCAAGAA
GACGGCCGCGGCTCGCGAGGCCGCCGCGATGGCCGCGACGGCTGCCGCTGCCGCTTCT---TCCATCGCCGTAGCCTCCC
CTGCTGCGGATATGGCGCCGGTCGTCCCCGACGTCTGCGTCGCCGGCGTCGGAGGAGGG---GGGGAGGTGGCGTGCGGC
CTGCCGGCGGAGTGGGACGAGATGGACG---------GGTCGCCGTGGTGGACGTTCGGGGTGGAGGAGGAGAAGCTGCT
GGGGTGGTTCCCGTTCGTGGAGGAGGACTTCCTGTCCGTCGGCGGCGGCGCCGGCCCCGCCGCCGCCGAGCC------CT
TCGACGACGACATCTGGCGGATCCACCAGATCTACGAGATCCCCAGCTACGCCGCCAAGTGAAG--AAGCGACGGGCGCA
AAAT-------GCGGGCGGGCGGCATTCGGCGTGGACGCCTTCCACCACTTCCGAGAAGAAACTAGATAGGAGCCGCTAC
CACT-----------------------------AGTAGTGCTTTTGCGGTACAGGAAC-GGGGAACGGACTAATCGAGGA
GGTTACCATCCACTACTAATGTCAATTTAGGCGAGTGAGCGAAGCTAG-TTTAACGCCTTGTTATGCAAGCAAAGAACAA
AGAAAA-TTGCGACGGCGATGCAATCTCTCGTTGC--CTTCTTGTGCCCGGCGCCTTGATTTCTCGGCCGTGTTGTTGCG
CGATTAGACACCATTCTCATTTGCGTTCTTCGGCAATGCGGCTCGTCGCCGGAGTTGTTGCTGGGATTAACT--------
-------------------------------------------------------GTGCAGTGCAGTTGGTTTCGTCGTT
TCAATGGAGCGGGACGATGAGCCTGCCTGTGCCTGTTGCCTCCGGAAGGAGGCCGAAATTTGGGGTTGGGCGGCGCTGGA
GCGCCGGGTTTTCGCGGGCGAACCAAGCAACAACGGCGCGGAGAAAGGCAGCGGCGCTCCTGAATTTCTGGAGCTGGAGG
TGGAGTGCGTGCGTTCCCGTGTCAGCAAATGCCAGAATCTCGTCGTTTCTGTAACTCTGTTCT-CGTGAACCACGGTGCG
TTCCCATGTCAGCAAAC--GGCTGAATCGCGTTCCCTTTCTGTGTTTCCGTGAACCACGA-TTGCACTTCGAAAGCGTCT
GTGATGCACGTTCAGTTGCATTCGT---AAGGTTGAAATATAAAACCGCAGAATGCTACTGTCAAGGCCTTCTTTGGTTT
GTAC----------------------------------------------------------------------------
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>SNPs
---------------S--------------------S----SS--SS--S------------------------------
----------------SSS------S--------S----------------------SSSSSSSS-SSSSSSSS-S--S-
-------S--S--S-S------S-S--S------------SSSSSSSSSSSSSSSS------S----------------S
----------------SSSSSSS-----------------SSS-------------------------------------
-------------SSSSSS------------------------S-------------SSSSSS-----------------
----------------------------------------SSSSSSSSSSS-----------------------------
---------------------S----------------------------------------S-S--S-SSS--SSSSSS
--------------------------------S------------------------------------S----------
----------------------------------------SSSSSSSSSSSSSSSSSSSSSSSS----------------
---------------S----------------------------------SSSS--------------------------
--------------------SS-S---------------------------------S-------------SSSSSSSSS
-----S-------------------------S-----------------------------S----------------S-
-----------S-S------------------------------------------------------S-----------
---------S-----------------------S--S--SSS-S-SSSSSS-SSSS-SSSSS---SSSS-SSSSSSSS-S
---SS-S------------------------------------------------------------S------------
----------------------------------------------------------------------S---------
------------S-----S--------------------S---------------S-SS---------------------
-------------------S--------------S-----------------------SSSS------------------
--------S-------------------SSSSSSSSS-------------------------------------------
------------------------------------------------------------------------SSSSSS--
----------------------------------------------------------------SS------------SS
SS-SSSSSSSS-------------------------S-------S-----------------S-----------------
----------------------------------S---------------------------------------------
-------------S----------SS---------S----S-SSSS-SSSSSSSSSSSSSSS------------SS-SS-
----------------------S----------------------------------------S----------------
-------SSS----------S--------S---S--S-S--------S-------S---SS---S----SSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----------------S-S-----
-----------------SS---------S--------------S---S---S--S-------------------------
-----------S----S--S---SS-----S-----------------S------------------------S------
----------S-SSS------------------------S---------------------S-S------------S---
----------------SSS--------------S-S-S---SS---------S-S--SSSS----------S---S--S-
--S---S-------------SSSSSSSS--------------------------------S-----S---SS-S------
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSS
>forward_281
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---------------------TAGCATGCATTGTTGGACGC---------------------------------------
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>reverse_2134
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-----------------------------------------------------CAGTGCAGTGCAGTTGGTTC-------
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