>input_sequence_83794
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-----------------------------------------------------------------------ATGAGCTCG
CTGCGATCCAAGCTCGTGGTTGTCGTTCTGGTCATGGCAGTAGCTGCTGCTGGCAGCCTTTCCTTGGTGAGCGTGGAAGA
AAGGCCAGCTCT------ACTCCGTGGCATGGCGCCGTCCACGCCGAACTCAGTGGGGAGCGTCGAATTGCCGTGGCGGC
GCCATGTGCTGCACCGGGGGGAGAAGATCCTGGCCTGGCGGTGGCGCCACAATCCGCCCTCCGGCCCGAGCAGCCGTGGT
CACGCCGTTGTCACCGTCTCGCCGGACGAGGAAGTGAAGAACCAGGGTCCCGCCGAAAACATTGGTCCATCAGTGCCATG
A-------------------------------------------------------------------------------
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-----------------------------------
>chr3D_1_TraesCS3D01G053800
ATATAACGGGCCGGGCTGCTAACGGGCGCCCCGCGCCACCCGAGCCAGGCCGCAGCACGAGATCGACTGACTCAAAACAC
TGGCCAGTCGACGCTAGCTGGCCCATTGAACCGCAGACCGCAATCAAAAAAAGAATAAACAGAACGCATCTCAAAGCAAC
ATCCAACGGACCAGAAATCGACTGACGCAAATGTTAAAACTCAGCTGACTGAGAGGTAGCTATTTCGAAGTTGCTCACAT
ACACGAGCATACACTCACCATATGAACGCACGTGTGCACACACACACACACTACCTCTATGAGCACCTTCGAGGAACTGA
GCCGGCACATCATCTTGAGATTGATGAAGTCACCGCAGACACCTTCGTAGTCGACAGGAACATCTCCTCCCACTTAACGC
TCATCGCCGGAAAGCTGAAAACTCTGATGAGCTGGGGATACCACTGTGCTCCTAACCATACACCACATGTTGATGCGCAG
TTGAAATTTTAACTAATTCGATTAAAAAAGAGAAGCAGGTACGAACAGATCCAACTTTTTTTCAAACTAATAAAAGTCCG
CGACAATAAACAGATGGAAAAAGCCCATTGCATAACCGTAACCTCAAATTCAATATTTTCC---CTTGCCAGTTGCCACG
GCAGATCGAATGTGGTTGCATTGTCCACCACGTATGGGTGCCAACTCTGCAGAGTTCGTTAGTTAGATTTATTGGCCGAA
AGCAGCAGGGCACCACCGCTTTCTCTTCAATTTTCTGGGCTTAATTCGAGTCAGCCATAATCTTCTAACCACCAGCACAT
GCATCCATGCCCGGTAATCAAAAGAAACCATTATTGCCGAGCGCAAGATCTCCTTGGGTGTGCCTATATATGGCCATGGA
GGCA-GAGATCGATCATCCAGTCCATCCACCACACCACATCACAT-------------GCATAACAACCTAGTACGCCAC
AAGAATTAGGCACTCAATATCGATCGCATCGACAATTAATCGGGC--------------AGCTCAATCTCAATGAGCTCG
CTGCGATCCAAGCTCGTGGTTGTCGTTCTGGTCATGGCAGTAGCTGCTGCTGGCAGCCTTTCCTTGGTGAGCGTGGAAGA
AAGGCCAGCTCT------ACTCCGTGGCATGGCGCCGTCCACGCCGAACTCAGTGGGGAGCGTCGAATTGCCGTGGCGGC
GCCATGTGCTGCACCGGGGGGAGAAGATCCTGGCCTGGCGGTGGCGCCACAATCCGCCCTCCGGCCCGAGCAGCCGTGGT
CACGCCGTTGTCACCGTCTCGCCGGACGAGGAAGTGAAGAACCAGGGTCCCGCCGAAAACATTGGTCCATCAGTGCCATG
ACCAACGCACC---------------------------------------------------------------------
-------------------------------------------------------TATGTATATGATTATGAAATATGAA
TACGGTCGATAACATTAATCGCCTATATGTGTATGATAC-TGTACACATGAACGCATCCATTTAAGGACTCATGCATGCA
TTGCATGAGCTGGAGTATGTATTGAGTATAAGGACGGTTTTCCTTACTCATTCTGTATTTTTTGCATTGCATGAGCTGGA
GTATGTATTTAAGTACAAGGTAATGTGCAACGAGCAATCCATTAGTGTTTTGTGTAATTTATTTAGTCTCACAATTTTGT
AC-------CATCTTGTGAGTTAGATTTTGTATTTGTTTGTGTTTGACTGCGCGAAAAAATGATGACGCAGAAGACGATA
GAGAAATATAAGGCGAAGCCGGTCGATTAGTTAGAAGCTAAGCAAGC---------------------------------
-----ACAGGCATACTTTGGTGCGGTGCTAATGCTACTACGGCTCTTTTTCTTCTTCTTGAGATGATG------------
-----------------------------TACTAGGCTACTAGC----ATCCTGTATGCAACCAGACATGATGACATATT
ATTGCATGCAAGCGAGGTAATTTGTTTTCATTCGAAA--------------TATGGTACCACAGTTCATAACCGAGCTTG
TACATCCAGGTCACTGCCACCGTGCATTGCTCCACTGCACATCTAGTCTAAAGAAGAGGCACACGTCACCAAACACCTAC
CA--AACTAAATGCCATGTGTAGAATCCGTGTGATCAGATGATGTA-CTGATCCATCAGAAAAGCAAAAGCAGGCGACAT
GTCACTCTTCTCTTGATATTCGTACGCTGATTTTAGGTGGGTAGTTTCGCTGTATAAACTACTATCTCTGTACCGAAATA
CTTGTAGTT--GAGATCTTATACAGAGAGAGTACAACTTGTGTAAACACGTGCTAAAGTAGATAACCTGGTGTCGTGGAT
AAATCAAGGGGGTTAACCATGATGAGCTGTCATGCTGACGACGTGACAAACATGCAAAAATTATTGATGTATACATGAGT
TGCATGGATTTTTAAAAATAGTGTGTTGCAGCTGT
>chr3B_578
AAAAAG--------------------------------------------------------------------------
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----------------------GCCCATTGCATAACCGTAAGCTCAACTTCAATATTATTTCCGCTTGGCAGTTGCCACC
GCAGATCGAATGCGGTTGCGTTGTCCACGAC----GGGTGCCAACTGTGCAAAGTTCGTTCGCTGGCTTTATTGACCGAA
AGCATCTCGGCACCACCGCTTTCTCTTCAATTTTCTGGGCTTAACTCGATTCAGCCATTACCTTCTAACCACTAGCACAT
GCACGCATGACCGGTAATCAAAACAAAACATTATTGCCGAGCGCTAGATCTCCTTGGGTGTGCCTATATATGGCCATGGA
GGCAAGAGATCGACCATCCAATCCATCTAC----------CACAT-------------GCATAACAACGTAGTACACCAC
AAGAATTAGGCACTCAATATCGATCGCATCGACAATTAATCGGGCAGCCCAGCTAGGCCAGCTCAATCTCAATGAGCTTG
CTGCGATCGAAGCTCGTGGCTGTCGTTCTGGTCATGACAGTAGCTGCTGCTGGCGGCCTATCCTTGCTGAGCGCGGAAGA
AAGGCCAGCTCTATCTCTACTCCGTGGCATGGCGCCGTCAACGCCGAACTCGGTGGGGGCCGTCGAGTTGCCGTGGCGGC
GCCATGTGCTGCGCCGGGGACAGAAGATCCTGGCCTGGCGGTGGCGCCACAATCCGCCCTCCGGCCCGAGCAGCCGTGGT
CACGCCGTTGTCACCGTCTCGCCGGACGACGAGGAGAAGAAACAGGGTCCCGCAGAAAGCATTGGTCCATCAGTGCCATG
ACCAACACACGTACTCCCTCCGTTCCGAATTACTTGTCTTGGATTTGTCTAGATACGGATGTATCTAGACTCATTTTAGT
GCTAATACATCCGTATCTAGACAAATTTAAGATAAGTAATTCGGAACAGAGGGAGTATGTGTATGATTATGAAATATGAA
TACGGTCGATAATATGAATCACGTATA--TGTATGATAC-TGTACACATGAACGCATCCATTTAAGGACTCATGCATGCA
TTGCATGAGCTGGAGTATGTATTGAGTATGCGGACGGTCTCCTTATATAAATACTAC-----------------------
-------------TACAAGGTAATGTACAACGAGCAACCCATTAGTATTTTGTGTAATTTATTTAGTCTCACAATTTTGT
ACTAGCATGCATCTTGTGAGTTAGATTTCGTATTTGTTTGTGTTTGACTACGCG-AAAAACCATGATGCAGACAACGATA
GAGAAAATTAAGGCG----------------------------AAGC---------------------------------
-----ACAAGCATGCTTTTGTGCAGTGCTAATGCTACTAGGGCTCTTCCTTTTGTTCTAGAGATGAATGCTACTACTAGG
CTTTTTTTTTTTTTGAGGGAAAGGAATGCTACTAGGTTACTAGC----ATTCTGTATGCAG-------------------
-----------GCGAGGTAATTTGTTTTCTTCGAAAATAGGCCCAAGGTGGTATGGTACCACAGTT--TAACCGAGCTTG
TACATCCAGGTCACTGCCACCGTGCATTGCTCCACTGCACATC-AGTCTAAATAAGAGGCGCACGTCACCAAACACCTAC
CAGGAACTAAATGCCATGTATAAAATCCGTGTGATCAAATGATGCA-CTGATCCATCAAAAAAGCAAAAGTGGGCGACAT
GTCACTCTTCTCTTGATATTCGTATGCTGATTTTAGGTGGGTAGTTTCGTTGTATAAATTACTACCTCTGTACCGAAATA
CTTGTAGTTCGGAGAACTTGTACAGAGGGAGTACAAGTTGTGCAAACACGTGCTAAAGTAGTTAACCTGATGTCATGGAT
AAATCAAGGGGGTTAACCATGATGAGCTGTCCTGCTGATGAGGTGACAAACATGCAAAACTTATTGATGTATAGATGAGT
TGCATGGATTTAAAAAAATAGTGTGTTGCAGC---
>chr3B_578
AAAAAG--------------------------------------------------------------------------
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----------------------GCCCATTGCATAACCGTAAGCTCAACTTCAATATTATTTCCGCTTGGCAGTTGCCACC
GCAGATCGAATGCGGTTGCGTTGTCCACGAC----GGGTGCCAACTGTGCAAAGTTCGTTCGCTGGCTTTATTGACCGAA
AGCATCTCGGCACCACCGCTTTCTCTTCAATTTTCTGAGCTTAACTCGATTCAGCCATTACCTTCTAACCACTAGCACAT
GCACGCATGACCGGTAATCAAAACAAAACATTATTGCCGAGCGCTAGATCTCCTTGGGTGTGCCTATATATGGCCATGGA
GGCAAGAGATCGACCATCCAATCCATCTAC----------CACAT-------------GCATAACAACGTAGTACACCAC
AAGAATTAGGCACTCAATATCGATCGCATCGACAATTAATCGGGCAGCCCAGCTAGGCCAGCTCAATCTCAATGAGCTTG
CTGCGATCGAAGCTCGTGGCTGTCGTTCTGGTCATGACAGTAGCTGCTGCTGGCGGCCTATCCTTGCTGAGCGCGGAAGA
AAGGCCAGCTCTATCTCTACTCCGTGGCATGGCGCCGTCAACGCCGAACTCGGTGGGGGCCGTCGAGTTGCCGTGGCGGC
GCCATGTGCTGCGCCGGGGACAGAAGATCCTGGCCTGGCGGTGGCGCCACAATCCGCCCTCCGGCCCGAGCAGCCGTGGT
CACGCCGTTGTCACCGTCTCGCCGGACGACGAGGAGAAGAAACAGGGTCCCGCAGAAAGCATTGGTCCATCAGTGCCATG
ACCAACACACGTACTCCATCCGTTCCGAATTACTTGTCTTGGATTTGTCTAGATACGGATGTATCTAGACTCATTTTAGT
GCTAATACATCCGTATCTAGACAAATTTAAGATAAGTAATTCGGAACAGAGGGAGTATGTGTATGATTATGAAATATGAA
TACGGTCGATAATATGAATCGCGTATA--TGTATGATAC-TGTACACATGAACGCATCCATTTAAGGACTCATGCATGCA
TTGCATGAGCTGGAGTATGTATTGAGTATGCGGACGGTCTCCTTATATAAATACTAC-----------------------
-------------TACAAGGTAATGTACAACGAGCAACCCATTAGTATTTTGTGTAATTTATTTAGTCTCACAATTTTGT
ACTAGCATGCATCTTGTGAGTTAGATTTCGTATTTGTTTGTGTTTGACTACGCG-AAAAACCATGATGCAGACAACGATA
GAGAAAATTAAGGCG----------------------------AAGC---------------------------------
-----ACAAGCATGCTTTTGTGCAGTGCTAATGCTACTAGGGCTCTTCCTTTTGTTCTAGAGATGAATGCTACTACTAGG
CTTTTTT--TTTTTGAGGGAAAGGAATGCTACTAGGTTACTAGC----ATTCTGTATGCAG-------------------
-----------GCGAGGTAATTTGTTTTCTTCGAAAATAGGCCCAAGGTGGTATGGTACCACAGTT--TAACCGAGCTTG
TACATCCAGGTCACTGCCACCGTGCATTGCTCCACTGCACATC-AGTCTAAATAAGAGGCGCACGTCACCAAACACCTAC
CAGGAACTAAATGCCATGTATAAAATCCGTGTGATCAAATGATGCA-CTGATCCATCAAAAAAGCAAAAGTGGGCGACAT
GTCACTCTTCTCTTGATATTCGTATGCTGATTTTAGGTGGGTAGTTTCGTTGTATAAATTACTACCTCTGTACCGAAATA
CTTGTAGTTCGGAGAACTTGTACAGAGGGAGTACAAGTTGTGCAAACACGTGCTAAAGTAGTTAACCTGATGTCATGGAT
AAATCAAGGGGGTTAACCATGATGAGCTGTCCTGCTGATGAGGTGACAAACATGCAAAACTTATTGATGTATAGATGAGT
TGCATGGATTTAAAAAAATAGTGTGTTGCAGC---
>chr3A_614
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-----------------------------------------------------TATTTTCC---CTTGCCAGTTGCCACG
GCAGATCGAATGCGGTTGCGTTGTCCATCAC----GGGTGCCAACTCTGCAAAGTTCGTTCGCTAGCTTAATTGACCGAA
AGCAGCACGGCACCACCGCTTTCTCTTCAATTTTCTGGGCTTAATTCGAGTCAGCCATTACCTTCTAACCACCAGCACAT
GCATCCATGCCCGGTAATCAAAAGAAACCATTATTGCCGAGCTCTAAATCTCCTTGGATGTGCCTATATATGGCCATGGA
GGC-AGAGATCGATCACCCAGTCCATCCAC----------CACGCCAAATCGTCACACGCATAACAACCTAGTACGCCAC
AAGAATTAGGCACTCAATATCGATCACATCGACAATTAATCGGGCAGCCCAGCTAGGCCAGCTCAATCTCAATGAGCTCG
CTGCGATCCCAGCTCGTGGTTGTCA-------------------------------------------------------
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-----------------------------------------------------CCGTCTTCCGGCCCGAGCAGCCGAGGT
CACGCCGTTGTCACCGTCTCGCCGGACGAGGAGGAGAAGAACCAGGGTCCCGCCCAAAACATTGGTCCATCAGTGCCATG
ACCAACGCACGTATGTAC--------------------------------------------------------------
-----------------------------------------------------------TATATGATTATGAAATATGAA
TACGGTCGATAACGTGAATCGCCTATA--TGTATATATGATGTACGCATGAACGCATGCATCTAAAGACTCATGCATGCA
TTGCATGAGCTGGAGTATGTATTGTGTATACCGACGGTCTCCTTATATGTA-----------------------------
-------------TACAAGGTAATGTGCAACGAGCAATCCATTAGTATTTTATGTAATTTATTTAGTCTCACAATTTTGT
AC-------CATCTTGTGAATTAGACTTTGTATTTGTTTGTGTTTGACTACACGTAAAACCGATGATGGAGACAACGATA
GAGAAATATAAGGCG----------------------------AAGCCGGTCGATTAGTTTAGCAGGCTGGGAAGCTAAG
CAAGCACAGGCATACTTTGGTGCGGTGCTAATGCTACTAGGGCTCTTT-TTTTCTTCTTGAGATGATG------------
-----------------------------TACTAGGCTACTAGCTAGCATTCTGTATGCTACCAGATATGATGACATATT
ATTGCATGCAAGCGAGGTAATTTGTTTTCATTCGAAA--------------TATGGTACCACAGTTCATAACCGAGCTTG
TATATCCAGGTCACTGCCACCGTGCATTGCTCCACTGCACATCTAGTCTAAAGAAGAGGCGCACGTCACCAAACACCTAA
CAGGAACTAAATGCCATGTGTAGAATCCGTGTGATCAAATGATGTACCTGATCCATCAGAAAAGCAAAAGCGGGCGACAT
GTCACTCTTCTCTTGATATCCGTACGCTGATTTTAGATGGGTAGTTTCGCTGTTTAAACTACTATCTCTGTACCAAAATA
CTTGTAATTGGGAGAACTTGTACAGAGGGAGTACCAGTTGTGTAAACACGTGCTAAAGTAGATAACCTGATGTCGTGGAT
AAATCAAGGAAGTTAACCATGATGAACTGTCATGCTGATGACGTGACAAACATGCAAAACTTATTGATGTATAGATGACT
TGCATGGATTTAAAAATATAGTGTGTTGCAGCT--
>SNPs
-S-S-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSS-------------------S-----S--------------------------------
------------S------S-----------SSSS----------------S--------S-S---S-------S-----
-------S--------------------------------------------------S-S-------------------
--------------------------------------------S-----------------------------------
------------------------------SSSSSSSSSS----------------------------------------
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------------------------------------S-----------------S----S------S------S------
---------------------------------------S-----------S------SS------S-------------
------------S------SS-----------------------------------------------------------
--------------------------------S-S---------------------------------------------
----------S---------------------------------------------------------------------
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---------------S-----------SS---------------------------------------------------
------------------------------S-------S-S-S-SSS-S-S-SSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSS---------------------------------S---------------------------------
-------------------------------------------------S----S-----S-----S-----SS------
---------------SSSSSSSSSSSSSSSSSSSSSSSSSSSS-------------------------------------
---------------------------------------S--------S-S-----------------------------
--------------------------------------------------S---------------S-------------
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------------------------------------------------------------S-------------------
-------------------------------------S---------------------------------S--------
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---------------S---S-------S--------S--------------------------------S----------
--------------------------------------S--------------------S-------------S------
-----------SS--------------------SS
>forward_692
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--------------------------------TATGGGTGCCAACTCTGCAG----------------------------
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>reverse_1663
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--------------------------------------------------------------TGCATTGCATGAGCTGGA
GT------------------------------------------------------------------------------
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-----------------------------------
