>input_sequence_75116
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---------------ATGACGACACCGTCCCTCCTCTCCTCGCTCGCCACGCTCGGCCTCGGCTACTCCATTGCCATCGC
GCTTGGCTTCCTCGTCCTCCTCGCCTCCGTCCTGCTCGCGTCCTACTTCTGCTTCCGACACGGCGAGGGCGCGGGCGGCC
ACTTCGCCGGCGCCATCACGCCCACGTCCAGCTCCAGCCACCCCTCCATCACCGTCCCGCGCGTGCTGTTCGTCGCCGAG
GGGTCCGAGTCCCCCGAGGCCTACTCCTCGGCAGCCGCGGCCGCCTCGTCGCCAGTCGGGCTCGACCTCGCTGCCATCGC
GTCGTATCCCAAGGTCCTCTTCTCCAGGGCCGCGGGCGGCGACGCCATGTGTTCGATCTGCCTGTCCGAGTACATGGACG
GCGTGATGCTACGGCTGATGCCCGAGTGCAGGCACAGGTTCCACGTCATGTGCCTCGACGCCTGGCTGCGCAGGAGCGCG
TCGTGCCCCGTTTGCAGATCGTCCCCCATCCCCACGCCAGTCACCACGCCGCTCGCGACGCCACTCTCGGAGCTCGTCCC
GCTCTCGCAATACGCCGCTGACCGGCGGCGCAGCAGGTGA----------------------------------------
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>chr3A_1_TraesCS3A01G278900
GAGACAGATTAGATGGAGCTTCAGCGCAAATTCCTTCCAGCTCCTCGGAGCAGGGTGGTTAAGGTTCCTTGTCATGCC--
--------ACGGCGTGATTAGGTGCCAGGTTCTTTAGATTGATTCAAGGATTCAAACAGTGACGACTGCGGCTCCGGGGC
CCTAGTTCTTAGGGG--------CACGTGCTTGAAGATTTTTCAGTTGTCATCGGCAAGATTAGGCCGGCCCTGGTGTGA
GAGCCGCGACAGCGGTGCGTCGGTGGCTCGTTCTGGCGGCTGCCTAGTTGTTCGATAGTCCATGGACTTCAATGTAAATT
TTATTACATCTGAGGTGCTTTGTTTGTTTGATGAATCTTTATATAAATCTGATCATGTTTTAGAAAAAACAAACAAACAA
ACAATGGATCATGGAAAAAATAAAGCATTTTACTTAG-TATCAATG----------------------------------
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---------------------------------------------------------------------TTGCATATCAC
CATCACTGATCCATGGTGCCTCAACGACAGGATATCTTCCAAGGAATTGACCCCGCTCTGAGTGGCATTGCTCACCAGCA
TGGCGCTCCAAAGGTCAAACGGAGTGACCTCCAACTCCAACATCCAACATCCCATGCCGCAGCACT-CCAGCAGTGAGCA
CAGGCAGATAGC-CCCCCTCCCACGCTGCCATGCCACGACGCTCCCGTCCTCTCCCTCCCGAAGTCATGACAGCTGAGCC
GAGCAGAGCATCTCCATCCGCCGCCATTACTCCTCGGCCCGTGCCACTTCTCCGGCAATAAATGCAGCCGCTGGCGCCGT
CCACCCACCACCATCAGATCTAGCGCCCCCTCGCCGCGACGGGACGAGAAGGAAACGAAGAAAAATCACCACGCCACCAT
CCACATTTACTCCCTTCCACCCCACTCCACCAGGACTCGACTCTAGCTAGAGCTAGTCGTTCGATCGACC----------
-CACCCCACACGCGCACGCCACCGATGCCATTCCTCCACTTTCCCACTGCAAAATCATCTCGGCCGCCGCCGCCGCCGGT
ACCGCTACCCTCGCCATGACGACACCGTCCCTCCTCTCCTCGCTCGCCACGCTCGGCCTCGGCTACTCCATTGCCATCGC
GCTTGGCTTCCTCGTCCTCCTCGCCTCCGTCCTGCTCGCGTCCTACTTCTGCTTCCGACACGGCGAGGGCGCGGGCGGCC
ACTTCGCCGGCGCCATCACGCCCACGTCCAGCTCCAGCCACCCCTCCATCACCGTCCCGCGCGTGCTGTTCGTCGCCGAG
GGGTCCGAGTCCCCCGAGGCCTACTCCTCGGCAGCCGCGGCCGCCTCGTCGCCAGTCGGGCTCGACCTCGCTGCCATCGC
GTCGTATCCCAAGGTCCTCTTCTCCAGGGCCGCGGGCGGCGACGCCATGTGTTCGATCTGCCTGTCCGAGTACATGGACG
GCGTGATGCTACGGCTGATGCCCGAGTGCAGGCACAGGTTCCACGTCATGTGCCTCGACGCCTGGCTGCGCAGGAGCGCG
TCGTGCCCCGTTTGCAGATCGTCCCCCATCCCCACGCCAGTCACCACGCCGCTCGCGACGCCACTCTCGGAGCTCGTCCC
GCTCTCGCAATACGCCGCTGACCGGCGGCGCAGCAGGTGACGGATACTCTACATGGGTGCACCTCGC------TGATCTT
CATTGTTACTCCTTTTTTT------TTGCGTTG-------AAGGGTTCTGTAAATTTGTGGATTGTTTGATTGGTAAGGA
TACATGAGGGGTTTTAGGTGCTAGTACGACTGATGGAGTGCTTAGGATTTGTAAAGAGTTGCTTGGTTCC-ATTACTATT
ACTTCGAGAAAATTTTGTAATGTAGAAGTAG---ATGGGTTTCTCGAAAAAAAAGTAGATGTTGGAGCAAGGCATAGTTG
TGAAGAGCAGTGCTATACGGACGATAAAACACAGACGATTCACGCACGACAGTGAAATCCAGCCACACATGCAGGTGTAC
AGGAGAGCAACGGCCGCTGGATACTTAGTCGTCTTCACATCGTGTACGCTTTTATCGTGTGTAGAGCAGTTTCGAGTTGT
GAATACAGTGTTGCTGGTTTGCCTTATTGAGAAAT--GTTATGATTAGTATTGTCTACTGCTACATAAGG----------
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--------------------------TTTACTTTGCATTTCATTTTTCTATCGTGATCATGATGTGGTCGCTTTAATTGT
ATGAACTCTATATCTTGAAGATTTGTCTAGTGTTT------TCTGTCTTGTTGCAATGTTTTTATTTTCA----TTTTTT
TTCTA---------------------------------------------------------------------------
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-------------------------------------------------------------ATAACTACTTCTAGCATGA
AGAAACCCTTGCATGGCTTCGTCTTGCATGGCCTTTACAGGCGCTGTGGATCCCGGTGGATCCCGGTCCTTGCTGGTGGG
AGGGCCCCTGTTTTGTTTTTAGGTGTTTTTTTTGTT-CGTTTAGGGTTTGTGTCCTGCTCAAAAACACATAAAGACAAGA
AGGCGGCGGTGGCTCCCTGAAGTTGAAATAAGGTTCTTCCCGTCTAGCCTCCATTATTATGGTGTTTCTAGCGCCATCGG
AAGGTGTGTGGACGTGTGTCTCTGACGGATCTCGTGGGATTCGGTCGGCGTTTATTTTTTGTGGTTCTACTTGGATCTGG
TGTTCGCTCGTTTGTGCTTGTGTGTTTTCAGGTTGGATTCTTCTGATC
>chr3B_3
--GACAGATTAGATGGAGCTTCAGCGCAGATTCCTCCCAGCTCCTCAGAGCGGGGTGGTTAAGGTTTCTTGTCATGCATA
TGTACGCTACGGCGAGATTAGGTGCCAGGTTCTTTAGATTGATTCAAGGATTCAAACAGTGACGACTGCGGCTCTCGGGC
CCTAGTTCTTAGGGGCAGAGGGGCACGTGCACGAAGACTTTTCAATTGTCATCGACAAGATTAGGCCGGCTCCGGTGTGA
GAGCCACGACAACGGTGCGTCGGCGGCTCGTTCTGGCGGTTGCCTGGTCGTTCGATAGTCCATGAACTTCAATGTAATTT
TTATTACGTCTGAGGTGCTTTGTTCGTTCGATGAATCTTTATATAAATCTGATCATTTTCTAGAAAAAACAAACAAACAA
ACAATGGATCATGGAAAGAATAAAGCATTTTACTTAGGTATCAATG----------------------------------
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---------------------------------------------------------------------TTGCATATCAC
CATCACCGGCCCATGGTGCCTCAGCGACAGGATATCTTCCAAGGAATTGACCCCGCTATGAGTGGCATTGCTCACCAGCA
TGGCGCTCCAAAGGTCAAAC-GAGTGACCTCCAACT-------CCAACATCCCATGCCGCAGCACTTCCAGCAGTGAGCA
CAGGCAGATAGC-CCCCCTCCCACGCTGCCATGCCGCGACGCTCCCGTCCTCTCCCTCCCGAAGTCATGACAGCGGAGCC
GAGCAGAGCATCTCCATCAGCCGCCATTACTCCTCGGCCCGTGCCACTTCTCCGGCAATAAATGCAGCTGCTGGCGCCGT
CCACCCACCACCA-CAGATCTAGCACCCCCTCGCCGCGACGGGACGAGAAGGAAACGAAGAAAAATCACCA-GCCACCAT
CCACATTTACTCCCTTCCACCCCACCCCACAGGACTACTCT-----------CTAGTCGTTCGATCGACCCACCCCATCC
CCACCCCACACGCGCACGCCACCGATGCCATTCCTCCACTTCCCCACTGCAAAATCGTATCG------GCCGCCGCCGTT
ACCGCTACCGTCGCCATGACAACACCGTCCCTCCTCTCCTCGCTCGCCACGCTCGGCCTCGGCTACTCCATCGCCATCGC
GCTTGGCTTCCTCGTCCTCCTCGCTTCCGTCCTGCTTGCGTCCTACTTCTGCTTCCGACACGGCGAGAGCGCGGGCGGCC
ACTTCGCCGGCGCCATCACGCCCACGTCCAGCTCCAGCCACCTGTCCATCACCGTGCCGCGCGTGCTGTTCGTCGCCGAG
GGGTCCGAGTCCCCCGAGGCCTACTCCTCGGCAGCCGCGGCCGCCTCGTCGCCAGTCGGGCTCGACCCCGCTGCCATCGC
GTCGTATCCCAAGGCCCCCTTCTCCAGGGCCGCGGGCGGCGACGCCATGTGTTCGATCTGCCTCTCCGAGTACATGGACG
GCGAGATGCTACGGCTGATGCCCGAGTGCAGGCACAGGTTCCACGTCATGTGCCTCGACGCCTGGCTGCGCAGGAGCGCG
TCGTGCCCCGTTTGCAGATCGTCCCCAATCCCCACGCCCGTCACCACGCCGCTCGCGACGCCACTCTAGGAGCTCGTCCC
GCTCTCGCAATACGCCGCTGACCGGCGGCGCAGCAGGTGACGGGTAGTCTACATGGGTGCACCTCGC------TGCTCTT
CATTGTTACTCCTCTTTTT------TCTTTTTGCGTTGAAAAGGGTTCTGTAAATTTGTCGATTGTATGATTGGTAAGGA
CACATAAGGAGTTTTAGGTGCTAGTACGACTGGTGGTGTGCTTAGGATTTGTAAAGAGTTGCTTGGTTCCCATTACTATT
ACTTCGAGAAAATTTTGTAATGTAGAAGTAGATGACGGGTTTCTCGAAAAAAAAGTAGATGTTGGAGCAAGGCATA----
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---------------------------------------------------------------------------GTTGT
GAATACAGTGTTGCTGGTTTGCCTTATTGTGAAATGTTAA---ATTAGTATTGCCTACCGCTACATAAGGCCGGTCACAG
TAGGGAGGAACTTAGGAGTAACATCACATACTCCAATACAACTTTGCTTATGTGGCACGTATTTAATAAAAAGAGAGGTG
TTTGTGGTAACTAACTAAGTTACCGGAACATCACACACTCCAACAAACAATGAGTCTATAACCTAATAAATACATCGTTG
CATGACACTACATAGATGTTCCTACCCACTATGGAGGTAGTAACATAGTCTAGGGAAGTGTGTAAGTTACTAGCTTATGT
TCTTGCTCATTGTGACCAGCCTAAGGTTTACTTTGTATTTCATTTTTCTATTGTGATCATGACGTGGTCGCTTTAATTGT
ATGAACTCGATATCTTGAAGATTTGTCTAGTGTTTCGGTTTTCTATCTCGTTGCAACGTTTTTAATTTCTTACTCCTCCA
TTCCACTAAGCCCGCGCTTTTCAAGGTCTAACTTTGACCATAAATTTATCCAACGAGACCGACTGCGGTGGAAGAAAAAA
ATTATATAATTGAAAACTTATTTTAAATACAAATTCACTGATATAACTTTTGCTCCCACCGTAGTCGGTCTTGTTGGTTA
AATTTATGATCAAAGTTGAACTATGGGAAGAAAGCACTACATTATGAAACGAAGGGAGTATATAACTACTTCTAGCATGA
AGAAACCCTTGCATGACTTCGTCTTCTATGGCCTTGCGGTAATGGAGGCAT---GGTGGATCCCAGTCCTTGCCGACGTG
AGGGCTCCTGTTTTGTTTTTAGGTGTTCGTTTATATCCATTTAGGGTTCTTGTCTTGTTCA-------------------
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>chr3D_3
--GACGGATTAGATGGAGCTTCAGCGTCGTTTCCTCCCAGCTCCTCGGAGCGGGGTGGTTAAGATTTATCGTCATGC---
-GTACGCAACGACGAGATTAGGTGCTAGGTTCTTTAGATTGATTCAAGGATTCAAACAGTGATGAGTGGGGCTCT-GGGC
CCTAGTTCTTAGGGGCA--------CGTGCACGTAGACTTTTCAGTTGTCATCGACAAGATTAGGCTGACTCCGGTGTGA
GAGCCGCGGCAACGGTGCGTCGGCAGCTCGTTTTGGCGGCTGCCTGGTTGTTAGATAGTCCATGGACTTCAATGTATTTT
TTATTACTTTTGAGGTGCTTTGTTCGGTCGATGAATCTTTGTGTAAATCTGATCATTTAAAAAAA-------------AA
ACAATGGATCATGGAAAAAATAAAGCATTTTACTTAGGTATCAATTTTGCATACAATTTGTCTAATTTACATCTAGATGT
ACGGATGTCACATTTAAACTCTCGCAATAAGGCAGTAACAAGAAACAAAAAAAAAGTTAGGATAAAAAAATAAACCATAA
ACATAGTGGATATCAGGTTAGATGTGTGATATAGTTATGTCACATCTAGATGGGTGCAAGACAGACCTTTTGCATATCAC
CATCACCGGTGGATGGTGCCTCAACTACAGGATATCTTCCAAGGAATTGACCCCGCTCTGAGTGGCATTGCTCACTAGCA
TGGCGCTCCG-AGGTCAAAC-GAGTGACCTCCAACT-------CCAACATCCCATGCCGCAGCACT-CCAGTACTGAGCA
CCGGCAGATAGCCCCCCCTCCTACGCTGCCATGGCACGACGCTCCCGTCCTCTCCCTCCCGAAGTCATGACAGCGGAGCC
GAGCAGAGCATCTCCATCCGCCGCCATTACTCCTCGGCCCGTGCCACTTCTCCGGCAATAAATGCAGCCGCTGGCGCCGT
CCAGCCACCACCACCAGATCTAGCGCCCCCTCGCCGCGACGGGACGAGAAGGAAACGAAGAAAAATCACCACGCCACCAT
CCACATTTACTCCCACC---------CCACCAGGACTCGACTCTAGCTAG------TCGCTCGATCGACCCACCCCATCC
CCACCCCACACGCGCACGCCACCGATGCCATTCCTCCACTTCCCCGCTGCAAAATCATCTCGGCCGCCGCCGCCGCCGTT
ACCGCTACCGTCGCCATGACGACACCGTCCCTCCTCTCCTCGCTCGCCACGCTCGGCCTCGGCTACTCCATCGCCATCGC
GCTTGGCTTCCTCGTCCTCCTCGCTTCCGTCCTGCTCGCCTCCTACTTCTGCTTCCGACACGGCGAGGGCGCGGGCGGCC
ACTTCGCCGGCGCCATCACGCCCACGTCCAGCTCCAGCCACCTCTCCATCACCGTGCCGCGCGTGCTGTTCGTCGCCGAG
GGGTCCGAGTCCCCCGAGGCCTACTCCTCGGCAGCCGCGGCCGCCTCGTCGCCAGTCGGGCTCGACCCGGCTGCCATCGC
GTCGTATCCCAAGGCCCCCTTCTCCGGGGCCGCGGGCGGCGACGCCATGTGTTCGATCTGCCTCTCCGAGTACATGGACG
GCGAGATGCTACGGCTGATGCCCGAGTGCAGGCACAGGTTCCACGTCATGTGCCTCGACGCCTGGCTGCGCAGGAGCGCG
TCGTGCCCCGTTTGCAGGTCGTCCCCAATCCCCACGCCCGTCACCACGCCGCTCGCGACGCCACTCTCGGAGCTCGTCCC
GCTCTCGCAATACGCCGCTGACCGGCGGCGCAGCAGGTGACGGATACTCTACATGGGTGCACCTCGCTGACGCTGCTCTT
CATTGTTACTCCTCTTTTTTTCTTTTTGCGTTG-------AAGGGTTCTGTAAATTTGTCGATTGTTTGATTGGTAAGGA
CACATGAGGAGTTTTAGGTGCTAGTACGACTGGTGGTGTGCTTAGGATTTGTAAAGAGTTGCTTGGTTCCCATTACTATT
ACTTCGAGAAAATTTTGTAATGTAGAAGTAGATGATGGGTTTCTTGAAAAAAATTTAGATGTTGGAGCAAGGCATA----
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---------------------------------------------------------------------------GTTGT
GAATACAGTGTTGCTGGTTTGCCTTATCGTGAAATGTGTTATGATTAGTATTGGCTACTGCTACATAAGG----------
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--------------------------TTTACTTTGCATTTCATTTTTCTATTGTGATCATGATGTGGTCGCTTTGATTGT
ATGAACTAGATATCTTGAAGATTTGTCTAGTGTTT------TCTGTCTCGTTGCAATGTTTTTATTTTCTTATCTTTTTT
TTCAA---------------------------------------------------------------------------
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-------------------------------------------------------------ACAACTACTTCTAGCATGA
AGAAACCCTTGCATGGCTTCGTCTTCCATGGCCTTACCTCCATGGAGGCGT---GGTAGGCCCATGCCTT------CGGG
AGGGCCCCTGTTTTGTTTTTAGGTGTTCTTTTGTGTTTGTTTAG------------------------------------
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>SNPs
SS--------------------------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---------------SSSSSSS-------------------------------------
--------------------------------------------------------------------------S-----
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-------------S------------------------------------------------------------------
-------------------------S------------------------SS----------------------------
-----------------------------------------S------------------------------------S-
---------S-------------------------------------------------------------S--------
------------------------S-------------------------------------------------------
------------------------------------------S------------S------------------------
-------------------------------------------------------------------S------------
--------------S--S---------------------------------------------S----------------
---S----------------------------------------------------------------------------
--------------------------S-----------S-----------------------------------------
---------------------------------------------------------------------------S----
-------------S---------------------------------------------S--------------------
S--------S----------------------S---S-------------------------------------------
----------------------------------------------------------------------------SSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----
-----------------------------S-----------------------S--------------------------
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---------------------------------------------------S----------------------------
--------S---------------------------------------S--------------------S----------
---S----------------------------------------------------------------------------
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-------------------------S---------SS-SSSSSSSSS-S--SSS----------S--------S-SS---
---------------------------S----SSS-------------SS----S--S---SSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_1066
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------TTACTCCCTTCCACCCCACT------------------------------------------------------
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>reverse_3281
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TGTTCGCTCGTTTGTGCTTG----------------------------
