>input_sequence_84874
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---------------------------ATGAAGCCCTGCACGGTGCTGTTCCTCGTAGCCGTGCTCACCGCGTCGGGCGC
---GGTGCGCGGGGCGTCCATGGCAGCGCGCTCGGAGTGCGACCCATGGGCGCTGCGGCCGTGCGCCCCGGTGATCCTCT
GGAGCGCGCCCCCGTCCAGCGCGTGCTGCGCCAGGCTCCGGGAGCAGAGGCGGTGCCTGTGCAGGTACGCCAGGAACCCC
GACCTGGGCAGATACATCAACTCCCAGAACAGCAAGGAGGTCGCGGCTGCGTGTCGCGTGCGGGTTCCTATGTGCTAG--
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>chr3A_1_TraesCS3A01G261600
AGAACAAGAATGGCGCACCTTTCCCTCCCCCCAGGATCCGGTGGATCGACTTGTGCCTGTGGAATGGCCCTGTGACGTGC
GGTCCGTGGTCAGGATTGCTGGGAAAATGTGGCGGCATGACTTCACGCGTTTGGGATGTTCACCTGATTGATTTGTTAGA
TGTCTGATCTGTTTAGTTGCAGAAATTGCGTCTTTATAGGCACCTAAATGCTAGTATGAGCTCTAAAGGGTAAGCCTATG
TTGACAAGGAAAGGATAGCTTGGCCTGTAGGAGGATGAGCAATTGAGGGAGGGGAAT-AAACGGGTGCAGGGCAAGGGTT
TCCTTCAACCAGATGTTTTCTTCGTCAGAGCCCAGACT-GAAGCAAGTTTAGCTGTTTGCCAGTAGTTTATGCCAGAAGC
TTGCCGGAACTGCACCTTGATGCTCTGTGAACATCAATGGGGTTCTGACCGTGACACGCATCAATGTGAACTTGCGACGC
ACCCCAGCGTTTCTGCACTCGCCGTCTCCTACTCAAGTGTGAGAGCTTTTGTGACCCGGTGATGAAGATGCCGTCTTTCT
TACTCCGCATTTCTGACGGCGCTCTCGTCCCAGC------------------AGCCTCCTTATTCCAGAAACAACTATCG
CCATTTCGCCATTGCTCAATGTTGGAAAATCTGTTCAACA----------------------------------------
-AGGCACTTTTATCGGTGTGCTCCACGGTCACCCCACTTCAATTAACAAACGTAATCTGCACAGCAAACCTTGGACATGT
CTCGCTAAGCAGCAGCAGCAGCGTGCTTCACGCGACCCGAGCTCTGAAGCAGTGCCGGAGCCCCAAGCACT-CATTGGAA
TGCCCGTGCTCCACCGTTTACGCAACCGTGCAATGCAAAAGCTTTACG-AAGTTTTAGCGGCACTGTTCCAGATAGAGCA
TGGCGCGGGTGCCGGGTGCGCTGTTCTCTTGCTACAAATAGTATGCCAACCCTCTCTTGTGCTCCCAAAACCACCAGACA
GAGTAATCCTTC----ACTGAGAAGCCATGAAGCCCTGCACGGTGCTGTTCCTCGTAGCCGTGCTCACCGCGTCGGGCGC
---GGTGCGCGGGGCGTCCATGGCAGCGCGCTCGGAGTGCGACCCATGGGCGCTGCGGCCGTGCGCCCCGGTGATCCTCT
GGAGCGCGCCCCCGTCCAGCGCGTGCTGCGCCAGGCTCCGGGAGCAGAGGCGGTGCCTGTGCAGGTACGCCAGGAACCCC
GACCTGGGCAGATACATCAACTCCCAGAACAGCAAGGAGGTCGCGGCTGCGTGTCGCGTGCGGGTTCCTATGTGCTAGGC
TAGCTAGGAATACACGCGCGGCGCGGTTGTGTGAGCGCCGTGCTATTATGCTGTGTTCGTCTTGGCCGTCTCCATTTCTG
ACA-------------------------------------------------TGCTAGCTATTAGCAGTGCTTTGTGTGT
CATTGCCATCAAATGTGCCTGTGGTGTTGATGATCGTGTCTTATTGTTTGGTTTGTTTGTTTTC----------------
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----------AACATATGATTGCACCAACAAGTTATCTGGCACTAAAACCAGTCCTATA-CTGACAATAACGAAATGAAG
TGCTCATGCTACTCCCCTGAAA-CCA--ACACTACACGAATCCAAAAGCAGGTGCATTTCCCTGAACATTGTT------T
ACAACCATGTCTTCTAGTACGCTTCAGGAGGTTCTTCTTGGCAATTCCAGGTCCGCGCTGCTACCCTCCAGCATCTCGAC
GACTCCGCTCATCGACGGGCGACTCGCAGGCGCGGTCTGCGTGCACCACAGCCCGACTATGATCATCTTCCTCACAAGCT
CTCTGGTGTCGCCATTGACGTCCGAAACACTGTTGCAGAACTCATCCAGGTGCTCGTAGAGCCACTGGGCGAAATACTTG
CTGGTGGTGTCAGCACCAACCCTGACGTGTCTCTTTGCCCTGACCATCTCCAGGACCATCACGCCATAGCTGTACACGTC
GGACTTGTTAGTGACCGGCCCGAATCTCCTGGACACCACCTCAGGTGCGTCGTAGCCATCTCTCTCCCTCGCACCACGAG
TAGATGCTTCGCATAGGTTTGCTACACCAACATCGGATATCTTTGGGCATAGCTCCTGATCCAGCAGAATGTTCCGGGGT
TTGATGCTGATGTTCATGCCGTTAGCACCGTCATCGCCATGGAGATAGTCGAGACCTCGCGCCACGCCCATGGCAATGTC
GAACAGTTTCTCCCAGTACAGCCATAGCGAGTAGTTCTCCTCCACGGAGTCATAGCTGCTGAGAGCATAGCTTTCCAGGG
AGCCATTGGGCATGTACTCGTATATCAGAGCCCTCGTCGGCCC
>chr3B_1
AGAACAAGAACGGCGTACCTTTCCCTCCGCCCAGGATCCGGTGGATCGATTTGTGCCTGTGGAACGGCCTCACGACGTGT
GGCCCGTGGTCAGGATTGCTGGGAAAATGTGGCGGCATGGCTTCACGCGTTTGGGATGTCCACCTGATTGATTTGTTA--
TGTCTGATC-------TTGCATAAATTGCGTCTTTATAGGCACCTAAATGCTAGTATGAGCTCTAAAGGGTAAGCCCATG
TTGACAAGGAAAGGATAGCTTGGCCTATAGGAGGATGAGCCATTGAGGGAGGGGAAT-AAACGGATGCAGGGCAAGGGTT
TCCTTGAACCAGATGTTTTCTTCGTCAGAGCCCAGACTAGAAGCAAGTTTAGCTGTTTGCCAGTAGTTTATGCCAGAAGC
TTGCCGGAACTGCATCTTGATATTCTGTCAACATCAATGTGAACTCGCGA------------------------------
------------CTGCACTCGCTGTCTCCTACTCAAGTG-GAGAGCTTTTGTGACCCGGTGATGAAGATGCCGTCTTTCT
TACTCCGCATTTCTCACGGTGCTCGTCCCAGCCGGCAGCCGTGTTGCTTCTTAGCCTCCTTACCCCAGAAACAACTATCG
CCATTTCGCCATTGCTCAACGTCGGAAAATCTGTTCAACACCTGTGTTATCAACGCTT----GGTTGAGTGTTTATAGAC
CAGACACTTTTATCGGTGTGCTCCGCGGTCACCCCACTTCAATTAGCAAACGTAATCTGCACAGCAAACCTTGGACATGT
CTTGCTACGCAGCAGCAGCAGCGTGCTTCGCGCTACCCGAGCTCCGGAGCAGTGCCGGAGTCCCAAGCACT-CATGGGAA
TGCCCGTGCTCTACCGTTTACGCAACCGTGCAATGCAAAAGCTTTTAGTAAGTTTTAGCAGCACGGTTCCAGATAGAGCA
TGGCGCGGGTGCCGGGTGAGCTGTTCTCTTGCTACAAATAGTATGCCAACCCTCTCTTGTGCTCCCAAAACCAGACAGAG
TCCACTGCAA----------AGAAGCCATGAAGCCCTGCGCGGTGCTGTTCCTCGTAGCCATGCTCGCCGCGTCCGGTGC
GGTGGTGCGCGGGGCGTCCATGGCAGCGCGCTCGGAGTGCGACCCATGGGCGCTGCGGCCGTGCGCCCCGGTGATCCTCT
GGAGCGCGCCCCCGTCCAGCGCGTGCTGCGCCAGGCTCCGGGAGCAGAGGCGGTGCCTGTGCACGTACGCCAGGGACCCC
TACCTGGGCAAATACATCAACTCCCAGACCAGCAAGGAGGTCGCGGCTGCGTGTCGCGTGCGGGTTCCTATGTGCTAGGC
TAGCTAGGAATACACGCGCGGCGTGGTTGTGTTAGCGCCGTGCTATTATGCTGTGTTCGTCTTGGCCGTCTCCGTTTCTG
ACA-------------------------------------------------TGCTAGCTATTAGCAGTGCTTTGTGTGT
CAT-GCCATCAAATGTGCGTGTGGTG------ATCGTGTCTTACTGTTT-----GTTTGTTTTC----------------
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----------AACATATGGTTGCAAGATCAAGTTATCTGACACTGAAACAAGTCCTATT-CTGACAACAACGAAGCGAAA
TGCTCATG-TGCTCTCCTGAAATTTATTACACGACAAAAATCCAGAAGCAGCCGCAGTCCCCTGAACAGCATTTACAAGT
ACACCTATGTCTTT---TACGCTTCATGAGGTTCTTCTCGGCAATTCCAGCTCCGCGCTGCTTCTCTCCAGCATCTCGAC
GACTGCGCTCATCGACGGCCGACTCGCCGGCGCGGTCTGAGAGCACCACAGCCCGACTATGATCATCTTCCTCACAAGCT
CTCTGGTGTCGCCGTTGACGTCCGAAACGCTGTTGCAGAACTCATCCAGGTGCTCGTAGAGCCACTGGGCGAAATACTTG
CTGGTCGTGTCAGCACCAACCTTGACGTGTCTCTTTGCCCTGACCATCTCCAGGACCATCACGCCGTAGCTGTACACGTC
GGACTTGCTAGTGACCGGTCCGAATCTCCTGGACACCACCTCAGGTGCGTCGTAGTCATCTCTCTCCCTCACACCACGAG
TAGATGTTTCGCATAGGTTTGCCACACCAACATCAGATATCTTGGGGCATAGCTCCTGATCCAGCAGAATGTTCCGGGGT
TTGATGCTGATGTGCATGCCGTTAGCACTCTCATCGCCGTGGAGATGGTCAAGACCTCGCGCCACGCCGATGGTGATGTC
GAACAGTTTCTCCCAGTACAGCCATAGCGAGTAGTTCTCATCTACGGAATCGTCGCTGCTGAGAGCATAGCTTTCCAGGG
AGCCGTTGGGCATGTACTCGTATATCAGGGCCCTCGT------
>chr3D_60
-----------------------------------------------------------TGGAATGGCCCTGCGGCGTGC
AGTCTGTGGTCAAGATTGCTGGGGAAATGAGGCGGCATGACTTCACGCGTTTGGAATGTTCACCTGATTGATTTGTTAGA
TGTCTGATCTGTTTAGTTGCCGAAATTGCGTCTTTATAGGCACCTAAATGCTAGTATGAGCTCTAAAGGGTAAGCCTATG
TTGACAAGGAAAGGATAGCTTGGCCTATAGGAGGACGAGCAATTGAGGGAGGGGAATAAAACGGATGCAGGGCAAGGGTT
TCCTTCAACCAGATGTTTTCTTGGTCAGAGCCTAGACTAGAAGCAAGTTTAGCTGTTTGCCAGTAGTTTATGCCAGAAGC
TTACACGAACTCTCCGACG-------------------------------------------------------------
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----------------------------------------GTGTTGCCTCTTAGCCTCCATATTGCAGAAACTACT----
-----TCGCCATTGCTCAACATTTGAAAATCTGTTCAACACCGGTCACTAGGCTCGACACTAGGTTGAGTGTTTACAGAC
CAGACACTTTTATCGGTGTGCAGCACATTATTAA---------TAACAAACATAATCT----------------------
-TTGCTAGGCGGCAGCAGCAGC----TTCACGCTACCCGAGCTCCGAAGCAGTGCCGGAGTCCCAAGCACTCCATGGGAA
TGCCCATGCTCCACCGTTTACGCAACCGTGTAATTCAAAAGCCTTA---AAATTTTAGCGGCACAATTTCAGAC--AGCA
TGGCACGGGTGACGGC-------TTCTCTTGCTACAAATAGTACACCAAGCCTCACTTGTGCTCCCAAAACCAAACAGAG
TCCACTGCAATCCGTGACTGAGAAGCCATGAAGCCCTGCGCGGTGCTGTTCCTCGTAGCCGTGCTCACCACGTCCAGCGC
---GGTGCGCGGGGCATCCATGGCAGCGCGCTCGGAGTGCGACCCGTGGGCGCTGCGGCCGTGCGCCCCGGTGATCCTCT
GGAGCGCGCCCCCGTCCAGCAAGTGCTGCGCCAAGCTCCGGGAGCAGAGGCGGTGCCTGTGCAGGTACGCCAGGAACCCC
GACCTGGGCAAATACATCAACTCCCAGAACAGCAAGGAGGTCGCGGCTGCGTGTCGCGTGCGGGTTCCTATGTGCTAGGC
TAGCTAGGAATACACGCGCGGCGTGGTTGTGTTAGCGCCGTGCTATTATGCTGTGTTCGTCTTGGCCGTCTCCGTTTCTG
ACTGCCGGGTGATGTGGTGTCAGACAAGAAGAGTTGTGATAACGGACGGCCTTGTTAGCCATTAGCAGTGCTTTGTGTGT
CAT-GCCATCAAATGTGCGTGCGGTG------ATCGTGTCTTATTGTGC-----GTTTGTTTTCCTGTGGGGTTGCGGTG
GCATAATTTGACGAAGTTGTTGTTCTTCGCCTTCATGCTCACCAGGCACCTTAATTTGAGCGTCTCGAGATATTTGTGTG
TCTCAACAACAACATGTGATTGCATGAATAAGTTATCTGTCAC------CAGTCCTATACCTGACAATAACAAAATGAAG
TTCTCATGTTGCTCTCCTGAAATCCA--ACACTACACAAATCCAAAAGCAGGTGCATGTCCCTGAACATTGTC------T
ACAACCATGTCTTCTA---CGCTTCAGGGGATTCTTCTTGGCAATTCCAGCTCCGCGCTGCTACCCTCCAGCATCTCGAC
GACTCCGCTCATCGACGGCCGACTCGCAGGCGCCGTCTGCGAGCACCACAGCCCGACTATGATCATCTTCCTCACAAGCT
CTCTGGTGTCGCCATTGACGTCCGAAACACTGTTGCAGAACTCATCCAGGTGCTCGTAGAGCCACTGGGCGAAATACTTG
CTGGTCGTGTCAGCACCAACCTTGACGTGTCTCTTTGCTCTCACCATCTCCAGGACCATCACGCCGTAGCTGTACACGTC
GGACTTGCTAGTGACCGGTCCGAATCTCCTGGACACCACCTCAGGTGCGTCGTAGCCATCTCTCTCCCTTGCACCGCGAG
TGGATGTCTCGCATAGGTTTGCTACACCAACATCAGATATCTTTGGGCAGAGCTCATGATCCAGCAGAATGTTCCGGGGT
TTGATGCTGATGTTCATGCCATTAGCACCGTCATCGCCGTGGAGATAGTCGAGACCTCGCGCCACACCGATGGCGATGTC
AAACAGTTTCTCCCAGTACAGCCATAGCGAGTAGTTCTCCTCTACGGAATCGTCGCTGCTGAGAGCATAGCTTTCAAGGG
AGCCGTTGGGCATGTACTCATATATCAGAGCCCTTGTTGGCCC
>SNPs
----------S----S------------S--------------------S----------------------S-------
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--------------------------S-------------------------------------S---------------
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---------------------SS-----S----------S-SSSSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSS----------S----------------S----------------------------------------
--------------S----S----SSSS-SSSSS----------------------------------------------
-------------------S------------------------------------------------------------
---S----------------------------------------------------------------------------
--S----S-------------------------S----------S---------------S--------------S----
----------------------------------------------S-----------------S---------------
------------------S------------------------------------------------------SSSSSSS
SSSSSSS-SS-----------------------------S----------------------------------S-----
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----------S---------------------------------------------------------------------
-----------------------S--------S----------------------------------------S------
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---S--------------S-------SSSSSS-----------------SSSSS--------------------------
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------------------------SS-------------S----S-----------------------------------
--------S-S---S----------------------S------------------------------------------
----------------S---------------------------------S-----------------------------
------------------S----------------------S--------------------------------------
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-----S---------------S-------------------------------------------S--------------
-------S----------S-------------------------------------------------------------
------S---------------------------S---------------------------------------------
--------------------------------------S-----------------------------S-----S-----
------------------------------------------S-----S--S-S--------------------------
----S--------------------------------S-----
>forward_482
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--------------------------------------------------------------AATGTGAACTTGCGACGC
AC------------------------------------------------------------------------------
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>reverse_2102
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---------------------CTGACGTGTCTCTTTGCCCT---------------------------------------
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