>input_sequence_78463
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------------------------------ATGGAGAAAAGCTCCTTTGCTTCAACCTTTCTCCTGTTGCCCCTTCTGAT
CATTCTACTTTCGACCATTCATAAACCTGCAACATACGGCGAGTGCATACCACCGCCTTGCCAAGGAAGTTAGTATTGCA
CCTGGCACCCTGCTTTGTTCTTACAATTTGCATCATGTCTCCATTTAAC-TTTTTTATTTTGTGTTTGGCCCCAATTTTA
TTTTTTGTTGGAGTTGAACTTTCAATGATCCAAGAAATAACCCGTAATTTCCATTTATTTACCATACAGAACAAAGTTGG
CCAGAGCTCATTGGGAAAGACTCAAACACGGCATACAATTGTATAAGGCACGATAACCCCCAAGTGAATAGCATCACATT
CTTGATTTCTGATGCTCTTCGTCCCAGGGCGGACAATGGCATGTGCTGCAACCATGTGCTTTTGGTGATTGGAAATATCC
CCTCCGGTGGTGATGGTGTCATCAAGGTGCCACATGTTGGATAG------------------------------------
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>chr3D_1_TraesCS3D01G006600
CGAAAGGTGTCACGGATCAAAAATAGCCCAAAGGCAACACGCGCCGTTAATGGACTCAAAGCCATAACGGGCCAAAAATG
GCGCGAAAGCAACACATGCCGTTA-ATGGACCAAAAGGCGCGAATGGGC--CAAAAATGCCCTAGACGCAACACAGTCGT
TAATGGACCGAAAGGTGTGAAGGTCAATAAACGGTCCGGACACAACATGGACAGTTAATGGGCCAAAATACACCATGAGC
CAGACATGGCCAAGACACACGACTGGCCGTAAATGGGCGGAAATATTCCATGGGACGTAAAAAATATCAACGACACTATG
GGTCTTAAACGGATCGGAATACACGAAAGGCCTCAAATCGCCCGGAAACATCACCGGCTGTAATTGGCCTGAAATACGTC
ATGGA----------------------------CAGTGAAAGGCTCGAAAGCAAGTACGGATAAAAATAGAACGAGAGAC
ACACATGAGCCAAAAGTCTCAATGGGCTAGAACCATATTCGATGGCCCACGTGTCGTCGTTCATAGGCGCATATCATCCG
TTGAGTGGCGACCCTTCCAACGAAGAGCTGACGCGTGGTTAAGTTATCGAACGAGAAGCCGACACGTGGAGGATCGTCAT
TTGATGTACCATGATAAAAAAGAGAAATAATGCAGGCGCCCAGCCACTCATTCATCACTATGTGGAACACGTGAATCCAT
GCGGTGTACTAATGAATAATTAATAACAATATCAATTGAATATATCTTATATCTTTCTTCATTCAATAGCCAACATTCAG
TGCATATTGATTTATTGCTAGTCATTACTTTAAATATACAAATCATCAATGGCCGCATTAATTGAAAATATATCCCATTA
ATGCGGCGCTCTATAACTAGAAACCATCAATGGCCGCATTAATTGAAATTATATCCCATTCGCCATTGATTGTC------
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-----------------------------CTTGCTTTGGCGCTCTATAACTAGAAAGCCCCCTCCCCA----AACAATAT
TCTAAACAGGAAAGGTTAAGTTCCAATAAAATGGAGAAAAGCTCCTTTGCTTCAACCTTTCTCCTGTTGCCCCTTCTGAT
CATTCTACTTTCGACCATTCATAAACCTGCAACATACGGCGAGTGCATACCACCGCCTTGCCAAGGAAGTTAGTATTGCA
CCTGGCACCCTGCTTTGTTCTTACAATTTGCATCATGTCTCCATTTAAC-TTTTTTATTTTGTGTTTGGCCCCAATTTTA
TTTTTTGTTGGAGTTGAACTTTCAATGATCCAAGAAATAACCCGTAATTTCCATTTATTTACCATACAGAACAAAGTTGG
CCAGAGCTCATTGGGAAAGACTCAAACACGGCATACAATTGTATAAGGCACGATAACCCCCAAGTGAATAGCATCACATT
CTTGATTTCTGATGCTCTTCGTCCCAGGGCGGACAATGGCATGTGCTGCAACCATGTGCTTTTGGTGATTGGAAATATCC
CCTCCGGTGGTGATGGTGTCATCAAGGTGCCACATGTTGGATAGAACCATTCTCTGCC-TTTTTATTGTAATTTGATCAA
TAAAGTCTTTGCTGTGTTTGCACTTTTCTCCGTTTCATTTCATACAGTTCTTATATAGCCCAAACAACCAACATACTTTC
TCAAACAGGAGACTGAAAGAACATGAAAATATAAGATGC----CTGTTCTGATCCAATCTTGTACATCACATCAAAACCA
AAGGAAGACC----GCATGCTAAAAGGTTAACTATTTAGTATGGGACTGACTATAGGTAAGTCTCCTTATATTTTATTTT
GGTCAAGTCCAATTTGGACCACTCGTTTAGCTTCAACAATTGTTATTCTTTCATCTTTCTCTAGCTTTCTTCCTCCTCGA
ATCGTTCTCCCTCATTTGTTCGCATCCGGGTTGCCTACCATCCCCACCTTCGGGTGGTCTATGGACATGAATGTGATTTT
TATTGCTTATGGTGTTCTTTGTACCACCTTGATAGATAATGAAT-GATCAGAAGTTTTCAACAACAAAAAATACTTTTGG
GAACAGTGGTTATGTTAATTAAGGTGAACTGGCTAAACAAGTTGTTAGCTTGCCCATCACCCTTGTAAATACTGATATCC
GCAATAGTTTGGTTGTCATGGAAGTTGGTGAGGATTTGCTCAATCCTAGTGAGTATGAGGTATTCTTTGGAATCAACATA
GTCATCATATCCCCATCTGTCCACACGCCAAGAGAATGATTAGTAACTTGAAGATGCGTGATATCTGCATTATAAATCAT
CGTATACGAAATTGCGCATGCCAAACTGAAAAA------AAAGATAGAAGGTTAAAAAAATCAGCATATTTT-----TTT
ATAGAAGGTAAACTTGCATACTAAAACACGTCCATGGCTATTTTTAATCTACATAACTTGCAAAATATCCAAAGGGATAC
TATAAATCTAAAGTGAGCATCTACAACCGGACCACTCATATCCTCCCCAATCGTCCAGCCGGACAGCCCGATCATTGTCT
GGCATAGGAGAGAGAAGAGAAAGGC
>chr3B_1
CGAATGGTGTGACGGATCAAAAATAGCCCAAAAGCAACACGGGCTGTTAATGGACTCAAAGCCGTAATGGGCCAAAAATG
GCGCGAATGTAACACATGCTGTTAAATGGAACAAAAGGCACGAGTGGGCAACAAAAATGCCCTAGACGCAACACAC-CGG
TAATGGAGCAAAAGGTGCGAATGCCCAAAAACGGTCTGGACATAACATAGATAGTAAATGGGCCAAAATACACCACGGGA
CAGAAATGGCCAAGACACACGACAGACTGTAAATGGGTGCAAATATTCCACGGGACGTAAAAAGTATTAACGGCACTATG
GGTCTTAAACGGATCGGAATACACAAAAGGCCTGAAATGGCCCGGAAACATCACATTCTTTAATTGGCCCAAAATACATC
ATGGGTCGTAAAAGGTCCGTGAAGCAGCATGGGCAGTGAAAAGCTCGAAAGCAAGTACCGGTCAAAAAAGAACGAAAGGC
TCGAAAGTATGT--------------------------------------------------------------------
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--------------------------------------------------------ACTATGTGGAACACGTGAATCCAT
GCGGTGTACCAATGAATAATTAATAACAACATCAATTGAATATATCTTATATCTTTCTTCATTCAATAGCCTACATTCAG
TGCATATTGATTTATTGCTTGTTATTAGTGTAAATACACAAACAATCAATGGACGCATTAATTAAAAATATATCCCATTA
ATGCAGTGCTCTATAACTAGAAACAATCAATGACAGCATTAATTGAAAACATATCCCATTCGCAATTGATTGTC------
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-----------------------------CTTGCTTTGGCGATCTATAACTAGAAAGCCCCCTCCCCA----GACAATAT
TCTAAACAGGAAAGATTAAGTTCTAGTAAAATGGCGAAAATCTCCTTTGCTTCAACCTTTCTCCTGTTGCCCCTTCTGAT
CATTCTACTTTCAACCATTCATAAACCTACAACATATGCCAAGTGTATACCACCGCCTTGCCAAGGAAGTTAGTATTGCA
CCTAGCACCCTTCTTTGTTCTTACAATTTGCATCATATCCCCATTGAACTTTTTTTATTTTGTGTTTGGACCCATTTTTA
TTTTTTGTTGGAGTTGAACTTTCAATTATCCAAGAAATAACCCATAATTTCCATTTCTTTACCATACAGAACAAAGTTGG
CCAGAGCTCATTGGGAAAGACTCAAACACGGCGTACAATTGTATAAGGCGCGAGAACCCCCAAGTGAATAATATCACGTT
CTTGATTTCTGATGCTCTTCGTCCTAGGGCGGACAATGGCATGTGTTGCAACCATGTGCTTTTGGTGATAGGAAATATCC
CCTCCGGTGGTGATGGTGTCATCAAGGTGCCACATGTTGGATAGTACCATTCTCTACTTTTTTTATTGTAATTTGATCAA
TAAAGTCTTTGGTGTGTATGCACTTTTCTCCATTTCATTTCATACAATTCTTATATATCCCAAACAACCAAATTACTTTC
TCAAACAGGAGACTGAAAGAACATGAAAATATA----AGAAGGTTGTTCTAATCCAATATTGTACATCAAATCAAAACCA
AAGGAAGATCGCAGGCATGCTAAAAGGTTAACTATTTAGTATGGGCCTGACTATAGGTAAGCCTCCTTATATTTTATTTT
TGTCAAGTCCAATTTGGACCATTGGATTAGCTTCAACAATCGTTATTCTTCCATCTTTCTCTAGCTTTCTTCCTTCTCGA
ATCGTTCTTCCTCCACTGTTCGCCTCCGAGTTTCCTACCATCCCCTCCTTCGAGTGGTCTATAGACCTGAATGTGATTTT
TATTGCTTATGTTGTTCTTTGTACCGCCTTGATAGATAATGAATATATCAGAAGTTCTCAACAACAAAAA--ACTTTTGG
GAACAGTGGTTATGTTCGTTAAGGTGAACTGGCTTAACAAGTTGTTAGCTTGGCC--CACCCTTGTAAAGACTGATATCG
ACAAAAGTCCGATTGTCATGGAAGCCGGTGAGGATTTGCTCAATCCTAGTGAGTATGAGGTATTCTTTGGAATCAACATA
GTCATCGTATCCTCATCTGTCCACACGCCAAGAGAATGATGAGTAACTTGAAGATGCTTGTTGTCTGCATTATAAATCAT
CGTATACAAAATTGCGCACCCCAAACT-AAATA------AATGATAGAAGGTTAAAGTAATTAGCAGATTTT-----TTT
ATAGAAGGTACACTTGCATAATAAAACACACACATTG-TTATTTTAATCTACATAACTTGCATAATATCGAAAGGGATAC
TATAAATTTAAAGTGAGCATCTACAGCCAGACCACTCATATCCTCCGCAAACGTCCGGACGGACAGCCTGGTCATTGTTC
GTAC-AGGAGAGGGAGAAGAAAAA-
>chr3A_668
TATA----------------------------------------------------------------------------
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--------------------------------------------------------------TGGAAGACATGAATCCAT
ACGGTGTACCAACGAATAATTAATAACAATATCAATTGAATATATCTAGTATATTTCTTCATTCAATAGCCAACATTCAG
TGCACATTGATTTATTGCTAGTTATTGTAGATACACGGAC---CATCAATGGGCGCATTAATTGAAAATATGTCACATTA
ATTAAAGATAAATTATCCTTGATTTTTTTTTGCGGGAAAGGAACTTTTCATTGATCAACTATGATGATTACATTCAGATT
CAACAATGCTAGCTATCTCCCTAGGGGAATTCCGGAGCCAGCATGCCGTGCGCTGTTGCGAGCGACCCATACAAGCTAGG
GTGTGGCTCGCCAAATTTGCGTGCCTGCTGATCTTAGCTAGACTAATGTTCCTTTCTTGAGCCAGAACTCTTCTGATCTC
ATTAACCCGGTACGCATACCTCGACCGGTCTTGATTTGGGGTTCTATAACTAGAAAGCCCGCCCCCTTCCCCAACAGTAT
TCTTAACAAGAAAGATTAAGTTCTAGTAAAATGACGAAAATCTCCTTTGCTTCATCCTTTCTGCTGTTGCCCCTTCTGAT
CATTCTACTTTCGACCATTCATAAACCTACAACATATGCCGAGTGTACTCCACCGCCTTGCCAAGGAAGTTAGTATTACA
CCTAGCACCCTTCTTTGTTCTTACAATTTGTGCCATGTCTCCATTGAAC-TTT-TTATTTTGTGTTTGGCCCCAAATTTA
TTTTTTATTGGAGTTGAAC-TTCAATGGTCCAAGAAATAACTGATAATCTGCATTTCATAC----ACAGAACAAAGTTGG
CCAGAGCTCGTCGGGAAAGACCCAAACACGGCGTACAATTGTATAAGGCATGATAACCCCCAAGTGAATAACATCACATT
CTTGATTTCTGATGCTCTTCGTCCCAGGGCGGACAATGGCATGTGCTGCAACCATGTGCTTTTGGTGATTGGAAATATCC
CCTCTGGTGGGGATGGCATCATCAAGGTGCCACATGTTGGATAGAATCATTCTCTACTTTTTTTATTGTAATTTGATCAA
TAAATT------------------------------ATTTCATACAATTATTATATAACCAAAACAACCAAAGTATTTTC
TCGAATAGAAGACTGAAAGACCATGAAAATATAATTAAGAAGGCTATTCTGATCCAATCTTATACATCGAATGAAAACCA
AAGTAAGATCACGGTCATGCTAAAAGGTTAATTATTTAGTATGGGTCTGACTATAGGTAAATCGCCTTATATTTTATTTT
GGTCAAGTCCATTTGGGACCATTGGATTAGCTTCAATGATCGTTATTCTTCCACCTTTCTCTAGATTTCTTCCTTCTCGA
ATCGTTCCTCCTCCACTGTTCACCTCCGGGTTGCCTCCCATCCCCTCCTTTGGGTGGTCTACGAACCCGAATGTAATTTT
TATTACTTATGGTGTTCTTTGTACCGGCTTGGTAGATGATGAATAGATCAAAAGTTTTCATTTTTT-----TACTTTTGG
GGATAGTGGTTATGGTCATTAAGGTGAACTAGCTAAACAAGTTGTAAGCTTGCACATCACCCTTGTAAAGACTTATATCG
GCAAAAGTCCGGTTGTCATGGAAACTGGTGAGGATTTGCTATTCCCTAGTGGGTGTGGGGTATTCTTTGGGATCACGATA
GTCATTGTATCCCTATCTGTCCACACCA-AAGAGAATGTGGAGTCACTTGAAGATGTTTGATACCTGCATGATACAGTTC
G----AAGAAATTATGCACACCAAACT-GAAAAAAGTACAATGATAGAAGGTTAAATTTTTTTAGCAGAAAAAAAAATTA
ATAGAAGGTAAACTTGCATACTGAAATACGCCCATGGATTTTTTTAATCCACATAACTTGCATGATATCAAAAGGGGTAA
TATGAAGGTAAAGTGAGCATCTACAACCGGACCACTCATATCCTCCCTAGACGTCTGGCCGGACAGGCCGATCATTGCCC
GGAG-AGGAGAGAGAAGGAAA----
>SNPs
----S-----S---------------------S--------S--S------------------S---S------------
-------S-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-S----------S------------S---S----S-------
------------------------S--------S----S---------------SSS--S---------SS------S--
----S------------------------------------S----------------S-S-S----S-------S--S-
S-SS-S-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------------------------
---------S----------------------------------------------------------------------
----------------------S----S-S------S-----S---------S---------------------------
----S-S-----------------S-------S-S-------------SS-------------S----------------
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-----------------------------------------S--------------------------------------
--------------S--------S-S--------S-----S---------------------------------------
----------------------------S-------S-S------S----------------------------------
---S-------S---------------------------------S----------------------------------
-------------------------------------------S------------S-----------------------
--------------------------------S-------------------------------------S---------
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-------------------------------------------------------S-S----------------------
-----------S-----S-------------S--------------S----------S-------------SS-------
----------------------------------SSSSS------------------------------S----------
--------S------------------------------------S----------------------------------
---------------------S-S-S--------------S---------S-----------------------S-----
--------S----SSS-------S---------------------S--------------------S-------------
-------------------------S--------------------------------------------S---------
----------------S----------------------------------------------------S---------S
----S---SS--------------S-------------------------------------------------------
------S---------------------------------S----------------S----------------------
------------------SS-------S-------------S--------------SS---S----S-------------
------------------------------S------S-S----------------------S------S----------
-------S------------------------------------------S-----S----------------------S
--SSS-----------------SSS
>forward_683
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-----------------------GAAATAATGCAGGCGCCCAG-------------------------------------
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>reverse_2089
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--------CCCTCATTTGTTCGCATCCG----------------------------------------------------
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