>input_sequence_87342
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-----------------------------------------------------------------ATGACTCCTCTGGAA
TTACAACCTTCACCACAATGTTGTCGTCCATGGATCAAATCATTTTGTGCATTGGATTTCACTTGCTTCTCTACGGTTCC
ATTGCGTGTGCTTGGGATAGGTATTCTATATAAATGTTTCGCCGTATTATTATGTATTCTCCTTTAG-------------
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>chr4D_1_TraesCS4D01G072900
TTAGGTTTTTTTTTCATCGTCTATACATAGCTTTGGTCTTATTTGACTTTGCTATTCGCTGACGAATTTTTGTGTGTGTG
TGTGTTGGTGTTGGCTGTGTGCATTCTAGCTATGCAGAGGCCGGGTGTGTGCTCTTTGTGTTTGTATCCTCTTGATACTC
CATTCCAAGCCAATAAAATCCACCCTTTATCAAAAAATGTTTACAATATACTCTATATATCTATTGCTCGTGTCTTTGAA
GGCAACCGCCATCTTCAAATTGATCCTCG--GACTTATGAAATCGTTGTATTTTAGATATTTATCACATATAATTGAGGG
TGATTTTAGAGAACATGGTTGATTCTCTCGTGGGAACTGGGAAATGGGTTAGCATT-GTCATGTGATCAGTATCGCCCAA
GGAACCGCTCCTAACCCCTCGGTACATCTTCTGGCCATATATTTATGGAATTATGCCGAACATACATGATAGATGGCCCT
CTAAATTTAAAGGAAGATGGTACCTGCAATTAAGAAAAAGGAATTTGTAAAAATAATTGTTGTTGAATAATGCCAAATAA
AATCTAAAAGAATATCCAAAAATCCAACACTAAAAAGAGAGTGAAATATTCAATCCAATAAGAGAAGAAAGGGGGTCAAT
ACTTAGTTTTTGTGCCCAAGCGAATCTCATCCAATCATTTATGCATGGAATGAATC--------GGTTTAATATCAATCT
TGTAATCGAGAACCATGGACCAACTTTCACAACTTGCCAACGGTTATCGTTGTCCTGCGAGTTACAACTATTATGTTTTT
GGTGTTTTTGCTACTTAATATAATTGTGTAGACATATGTTCTATTACACAC---------CAGGTGTAGATCGGATATAA
CACAATGGCGCATGTTCATGCGCACACATTTTGATTAGGATCGTACTCTATGGTTACGATTCTG-----TATGTCTTTTG
AATCCGTCGAAATACTATTTTACGGTATAGATGCTTATGACCTCCCTCTCTATGCCTTTGCGGTAATGACTCCTCTGGAA
TTACAACCTTCACCACAATGTTGTCGTCCATGGATCAAATCATTTTGTGCATTGGATTTCACTTGCTTCTCTACGGTTCC
ATTGCGTGTGCTTGGGATAGGTATTCTATATAAATGTTTCGCCGTATTATTATGTATTCTCCTTTAGTT-TT-TCATCTA
TATAGAAGTGAAATAAAATAACCCGATTGAAGGGTAATGCTCATATGCTTGTAATGCACTGTATAGTAGGCTATTGCACA
ATATTCTTTTTCACTTCAATGATTTTTTTTGTAATTCATTGATATTACAAAAATATGTATTGAAAATATGATAGCCAATT
TACTTGCTAATTTGAATCCGACTGA-------------------------AAGTACAAAGTTCAAGCCTCTTGACTCTTC
ACACACTTTCTCGCAAATAGGTTTAAAATATATTATTGTTTTCTATTATATTAGAGTTTTTTCCTT-TTTTTTACCTGTC
AATGAATATTCTAATGTGAATG------------GAATT---------------------------TCATAGTATGGAAA
GAGAATAATTCGCAATTCGGGCTGCAGATTGCATGAAGTCCATCAAGGCGTGGAGCCTTTAAAGTGCCAATATCAAATAG
ATCCCTACA----------------------AACATCCTTGGAAAAATAAGGAGCTAGGAGAGCATTGTTACTTTCGTCA
GAAACCCTCCTCCCAACAAGGGATAAGACATCCTGAT-CTGATTCCAAAACTCCTTCGTGTATCTTTCTATTTCGATTCC
AAAACACCTTAGTGTATTTCTCTATTCCGGCATCCCCGTGACTAACACCGC-----------------------------
------AATATCGAGTGGG-CCAGAGGGTATCTCTACATCGCCGAAGGGTCAAATCTCATTGTTGACATATCATGTACCT
CATAATACTTCCATTTCACCTCCAGCGAGGTAGCTATCTAATTCGATCCGGAGTCGGAGCTAAAAGGCCCTCCACTCGGA
TCGATCAAGTTTCTTCTATGCCTCTAATGGCTACATAGCAGCAAGCCGTGGCATCCCCGTTTCGGACATAATCTTAGCGA
CTAGCGAGGCCTTGCCGAGGCCGCCACTTCCAATTTACACCTAATCCCTCCAATTCATATTATTTGTCGCTCAAACGGAT
GTATTAGACGTATTTTAGTGCTAGGCACATCCATTTGAGCGGCTAATAATATGTGGATCGGAGGGAGTACATT
>chr4A_225
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----------------------------------------------------------------TGCTGGTGTCTTTGGT
GGTAACCGCCATCTTCAAATGGATCCCCGTAGACTTATGGAATCGATGTCTTCTAAATATTTATCACATATAATTGAGGG
CGATTTTAGAGAATATGATTGATTCCCTAGTGGGAACTGGGAAATGGGTTAGCAACCGTCATGTGATCGGTAGCGCCCAA
GGAACTGGTCCTAACCCCTTGGTACATCTTTTGGCCATATATTTGTGGAATTATGCCCAACATCCATGATACATGGCCCT
CGGGGTTTCAAAGAACGCAGTACCTGCTATTAA-AAAAAGAAATTTGTAAAAATAATTGTTGTTGAATAGTGCCAAATCA
AATCTAAAAATAT---CAAAAATCCAACACTAAAAAGAAAGTGAAGTAATTAATACAATAAGAGAAGAAAGGGGGCCGAT
ACTTAGTTTTCATGCCCAAGCGAATCCCATTCAATCATTTACTCATGGAATGAATCAGTTCAAAGGTTTAATATCAATCT
TGTAATCGGGAGCCATGGACCAACTTTCACGACTTGCTAATGATTATCATTGTCTTGCAACTTACAACCGTTATGTTCCC
GGTGTTTCTTCTACTTAATAAAATTGTGTAGACATGTGTTCTATTAAACAAAGTTCACAGCACGTGTAGATGGGATATAA
CACAATGACTCATGCTCATGAGCACG------GATTAGAATCGTACTCTATGGTTACGATTCTACTAGATATGTCTTTTG
AATCCGTTGAAAAACTATTTTACAGTATAGGCGCTTATGACCTCCCTATCTATGCCTT-GCGGTAATGACTCCTCTGGAA
TTACAATCTTCACGACAACGGTGTCCTTCATGGATCAAATTATTTCGTGAATTGGATTTCACTTGCCTGTCTACGGTTCC
CTTGCGTGTGCTTGGGATAGGTGTTCTATATAAATGTTTCGTCGTATTATTATGTATTCTTCTTTAGTTGTT-TCATCTA
TATAGAAGTGGAATAGAATAACCCGGTTGAAGAGTAATGATCATACGCCTGTAATGCACTGTATAGCAGGCTATTGCATA
ATATTCTTTTTCAGTTAAATAAAG--TTTTGTAATTCGTTGATATTGCAATAATTTATATTGAAAATATGATAGCCAATT
TACTTGCTAATTTGAATCTGACTGGACAAATCGTAAAATTCTTATTG---AAGTCCAACGTTCAAGCCTCTTGGCTCTTC
TCACACTTAATCACAAATGGATAAAAAATAGATTATTGTTTTCTATTATATTAGAGCTTTCC---T-TTTTTTACTTGTC
GATGAATGTTCTAATGGGAATG------------GAATT---------------------------TCATAGTATTGAAA
GAGAATATCTCACAGTTCGGAATGGAAATTACATGAAGTCCATCAAGGCCCGGAGCCTTTAAAGCACCAATATCAAATAG
AGCCCTACGCAATATCAAATAGAGCCCTACGAACATCCTTAAAAAAATAAGGGGCTAGGAGAGCATTGTTCCCTTCGTGA
GAAACCCTCCTCCGAACAAGGGATAATGCATCTTGAT-TTGATTCCAAAACTCCACAGTGTATCT---------------
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>chr4B_1042
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--------------------------TCGATGGATCACATTATCTCGTGGATTGGATTTCACCTGACTGTCTATGGCTCC
CTTGCATGTGCTTGGGATAGGCGTTTTGTATAAATGTTTCATTGTATTATTACGTATTCTCCTTTATTT-TT-TTATATG
TATAGAAGTGGAATAGAATAACCCAGTTGAAGGGCAATGATCATACGCCTACAATGCACTATATAGTAGGCTATTGCATA
GTATTCTTAGATATTGCAATTTGA-----------------ATGTTGCAATAATTGATATTAAAAAAA-GATAGGCAATT
TACTTGCTAATTTGAATCCGACTATACAAATCGTAAAATTCTTATTGTTGAAGTCCAAAGTTCAAGTCTCTTAGCTCTTC
TCAAGCTTTCTCACAAATGGGTTT-AAATAGATTATTATTTTCTATTATATTAGAGTTTTCC----CTTTTTTACATGTT
AATGAATATTCATAGTATTATTATTTTTACAGAAGAATT---------------------------TCATAGTATTGAAA
GAGAACATGCCGCAATTCGGAATGCAAATTACATGACATCCATCAAGGCCCGGAACCTTTAAAGCACCAATATCAAATAG
AGTCATACGG----------------------ACATCCTTGCCAAAATAAGGGGCTAGGAGAGCATTGTTTCTTTCATTA
GAAACCCTCCTACAAACAAGGGATAAGACATCCTGATTTTGATTCCAAAACTCCTTAGTGTACC----------------
------------------TCTCTATTCCGGTATCCCCGCGACTAACACCTTAGTCACTATACCTGGCATACGATGTTGGA
TACCGTAATATCGGGTGGGCCCAGAGTGTATCTCTCCATCGCCGAAGGGTCAAATCTCAGTCTTGATC----GTGTACCA
CATAATAGTTCCCTTCCACCTCCGGCGAGGTAGCTATCTAATTCGAGCAGGAGTCGGAGCTAAAAGGCCCTCCAATCACG
TTGATCAAGTTTCTTCTCTGTCTCTGCTGGCTACACGGCAACAAGCCATGTCATTCCCATTACGGACGTAGTCTTAGCGA
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>chr6A_1045
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-----------------------------ATGGATTAAATTATTTCGTGGATTGGATTTCACTTGCCCGTCTATGTTTCC
CTTGCGTGTGCTTGGTATAGGTGTTC--TATAAATGTTTCACTGTATTATTATGTATTCTCTTTTAGTT-TTTTTATATG
TATAGAGGTGGAATCGAATAACCTGCTTGATGGGTAATGATCATACGCCTGTAATGCACTT-------------------
------TTTTTCACTTAAATGAA---TTTTGTAATTCATAGATATTGCAATACTTTATATTAAAAATAAGACAACCAATT
TACTTGCTAATTTCAATCCGACTATACAAATCGTA-AATTCTTATTGTTCAAGTCAAAATTTCAAGTCTCTTAGT-----
TCACGCTTTCTCGCAAATGGGTT-AAAATAGATTATTATTTTCTATCATATTAGAGCTTTCC---TCTTTTTTACATGTC
AATGAATATTCTAATGGGAATG------------GAATTTCATAGTATTTTTTTATGGAAAAAAAATCATAGCATTGAAA
GAGAATAGGTCGCAATTCAGATTGCAAATTACATAAAGCCCATCAAGTTCCAAAACCTTTAAAGCACCAATATCAAATAG
AGCCATACG----------------------AACATCCTTGGCAAAATAAGGGGCTAGTAGAGCATTGTTCCTTTCGTCA
GAAACCCTCCTACAAACAAGGGATACGACATCCTGATTTTGATTCTAAAACTCCTTAGTGTATC----------------
------------------TCTCTATCCCGGTATCCTCGCGACTAACACCTTAGTCACTATACCTGCCACACGATGTTGGA
TACCGTAATATTGAGTGGGCCCAGAGTGTATCTCTCCATTGCCGAAGGGTCAAATCTCAGCCTTGACATATTGTGTACCG
CATAATATTTCCATTCCACCTCCAGCGAGGTAGCTATCTAATCCGAGTGGGAGCCGGAGCTAAAAGGCCATCCACTCGCG
TCGATCAAGTTTCTTCTCTTTCTCTACTGGCTACACGGCTGCAAGCCATGTCATCCCCGTTTCGGACGTAGTCTTAGCGA
GTAGCGAGGCCTTGCCGGGGCCGCCACTTCCAATTTACACCTAATCCCTCCCATTCATATTATGTGTTGCTCAAACAGAT
ATATTAGATGTATTTTAGTGCTAGACATATTCATTTGAGCAACTAATAATA----------------------
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----S---------SS
--S-----------------S-----S------------S-----S---S--S--S------------------------
S------------S---S-------S--S-------------------------SS------------S---S-------
-----S-S-----------S----------S-------------S------------S-----S-------S--------
-SSSS---S--S---SSSS--------S-----S------S----------------------------S--------S-
---------SS--SSS----------------------S------S--S-S---S--------------------S-S--
----------SS--------------S---S----------SS-------------------------------------
--------S--S------------------S------S--S-S-----S-----S---S-S-------SS-------SSS
-------S-S----------S--------------S----------S---S-----------S--------S--------
-------S-S----S-----S----SSSSSSS------S------------------------S----------------
-------S----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--------------------S---S---S-S-----------------------
------------------------S-----------------------------S------------------S------
S-----------------S-----------S-----------------------------SSSSS----------S----
----------------S----------------------------------------------------------S----
-------SS-----------SS----S---S------------------SS-------------SS--------------
-S------S-------------------------------------------S-----------------S---------
-------------S------------------------S-----------------S--------SSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSS------------S-------S----------SS-----------------------------
--------------------------S--------S-----------------------S-S---------SS------S
-------S-------S------------------------------S-S-----------------------------SS
-----------------S--S-----S--------SS----------S--S----------------S--S---------
S----------------S---------------------------------S-----------S---S--------S---
S-------S---------------S--S--S---------SS---------SSSSSSSSSSSSSSSSSSSSSS
>forward_97
-----------------------------------------------------------------------------GTG
TGTGTTGGTGTTGGCTG---------------------------------------------------------------
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>reverse_1956
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-----------------------------------ACATCGCCGAAGGGTCAAAT-------------------------
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