>input_sequence_86287
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-----------------------------------------------------------------------ATGGCTTCC
CTCCTGCTGCTGCTGCAAGCCATCATCCGTCGTGCCGACGAGGGACGTCTCGGCACAAGGGAGGTGCCAGAGGAGGTGAA
GCAGCCCAAGATGTTCTCCCCAAACCCTCTGTTGGAGCACAAGGGATGCAGGCTCGACGACGATGATGTGGAAGAAGAAC
GGTGGCTGGTCGCCTGCTTGCAGTGGCCCCGGACCAATCGCCAATCAGCTTGGATGCAGACGATCTGA------------
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>chr3D_1_TraesCS3D01G177800
TCCCACAAAGCCCCCAACGTTTGTCTCTAGTTTACGAGAGAAATCACGTCTGAACCACTCCACGGACCGATACAAGCTTA
CGTTGGATGGTTTTCGCTGTCCGGACAGCGTGGTCCAAACGGATTAGGGAGG-TTTAAGGGTCGGCGTTGAAGATGCCCT
AAGTACCATGCTTACATATAGAGATATATAACAATCTTATGTTC----GTGATTGTTCCAGGTACTGTGTGTAGTTTTGA
TCGAGCAT-GTGATACTGAATTTCCCTCCTCTTCTCAGCTGCTTTTGGTTTCTATCTCTCACGAAAAAACATATCGGAAA
ATAAATAATCAGCTCCAGTGCAAGCTGGGATGCATGATTTCAAAGGCCAAACTGCGTCAGTAACCAACAGATACCTCCGT
CGTGCCCAGAGCAC-----TAGAGTCTAATGAACGGATGAAGATGCACGATCTACTGTATGAGGTTTCTCTAGGGCAGAG
CATACAACAGGTACGTCCAATGAATGGATGAAGACGCACGATCTACG----AGCTAGTGCACTGTACCAAGCCAATCAAC
GGACGAAGA--ATTTGATTAGGTAACAACAGCATATTTACACGCCAAAACCATATGCAGAATAAAGAAGAATCTGCACAC
AAGGTACGTGTTAAAAAAATCTTCCTTTTCGCACCTAAAAGTGTAACCAAAATGTTAGATGACCAAACATTTGACAGGGT
GAAGAGAATTAGCAGTGCGTTTTCCAAAATATCAGTACCAACCACGC----------CTCACCTACAGCCTAACAAAACA
TCACAGCAACCATAACACATATCATAAGCTTTCTGTGATCGAGCAGAAGAGGAAAAGAGTTCCTCCCTCACGAAACAGAT
GTCTTGCAAGAAATGCAAATTCACCTGAAACCAGTAAGAAAAACGAGCACCTGAGTACATGGCTCACTAT----ATGTAC
CTGAGGTTTCAGCATTGTTGCTACCATCATTCCAAAGTAAGCAGCCAGCAGCAGTCCTCAAAAATCTATAGATGGCTTCC
CTCCTGCTGCTGCTGCAAGCCATCATCCGTCGTGCCGACGAGGGACGTCTCGGCACAAGGGAGGTGCCAGAGGAGGTGAA
GCAGCCCAAGATGTTCTCCCCAAACCCTCTGTTGGAGCACAAGGGATGCAGGCTCGACGACGATGATGTGGAAGAAGAAC
GGTGGCTGGTCGCCTGCTTGCAGTGGCCCCGGACCAATCGCCAATCAGCTTGGATGCAGACGATCTGATCTCATTTGATC
ACTTCATATTCATAAATGGAGTGCCTGTCAATCTCGAATGAAGATGGCTGGCTCTGCCTTCCAATGTAGTTCATGCCTAC
ATTGCCTAGGATAATGTATTTTGTGTCTGAACAAATGTTGGTTGATTTCTTGCATGGTTAGTACAAAATGTTCAACATAT
CAGAACTATCTCACTGCCAATAAAACTCTATCTGTATACAGGAAGCAAGCACTTGTTATTGATGAAACTCTATCTGTATA
CAGGAAGCAAGCACTTGTTACTGATGAAATTTCTTTCACACACTTCAATAACCGGTCAAATATACAGCATCCTAAGTGAT
CAACATTTCAGAGAGGTGATGAATCAACCCCAGTCGACAAAAGGAAGCGGAGGATAGCCACCTTCCGGGGGAGGTTGCAG
TGATGGAGGTAAGTTGCCCCAAGAAGTGTGGCCCCTTAGTATGTTCCCTGTGAATTGTGACAGAAATAAATGTAGTCAGG
CCAGTAGCTTCAAATGGAAGCTCATAAAGAGGTTAAGTGCAACGGCGAGTCCAACAGATGGGCTTCAACAGGCTCGAGCC
TGCCCTAGAAAACAAAAAA--TATTACTATAGTACTCCGGGTGAAGCAGCCCTAGAAAAAAAATATTACAAAAGCCCATT
CACCATATAGAAGAGGGAAAGAATGCAGCAGTTAGCCAGGCCAGTAGCTTCACACGCACAAGCACA-----ATGCCCCGC
TACACAGCCAGA-AGCCATGCCGCTGGAGGTACAAGCCGCCAAGTATTTATTTGTCTAATTCTCAGATTACATTGCTAAG
CCAGTAAACTCTAAGTCTCCTTCATGATC---------------------------------------------------
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------------------------------------------------TATTAATTGATTTAGTGTCCAATAAAATTTGC
TCGCAGTCCCA-CAGCAAAGAAAACTTGTT--CAGATTTACAAAAATGAAGAGAAAGAGTACGAGTATGCAATTTTTACA
AGGCCACAAGCAGTTCAGTTATCCCCCCGCCGAACCTGAATTTGCCCCAGCTAATGTG
>chr3A_6
-----CAAAGTCCCCCACGTTTGTCTCCGGTTTACGGGAGAAATCCCGTCAGGACCACCCCACGGATCGATACATGCCCA
CGTTGGATGGATTTCGCTGTCCAGACAGCATGATCCAGACGGATGCGGGAGGTTTTGAGAGTCAGTGTTGGAGATGCTTT
AAGTACAATGCTTATATACAGAGATATATAACAATCTTATGTTCCATAGTAATTGCTCCGGGTACTGC--GTAGTTTCGA
TCGAGCATTGTGATACTGAATTTCCCTCCTCTTCTCAGCTGCTTTTGGTTTCTATCTCTGACAAAAACACATATCGGAAA
ATAAATAATCAGCTCCAGTGCAAGCTGGGATGCATGATTTCAAAGGCCAAACTGCGTCAGTAACCAACAGATACCTCCGT
CGTGCCCAGAGCACTAGTATATAGTGTAATGAACGGATGAAGATGAACGATCTACTGTATGAGGTTTCTCGAGGGCAGGG
CATACAACAGGTACGCCCAATGAACGGATGAAGACGCACGATCTATG----AGCTAGTACACTGTACCAATCCAATCAAC
GGACGAAGAGAATTTGATTAGGTAACAACAGCATATTTACACGCCAAAACCATATGCAGAATAAAGTAGAATCTGCACGT
AAGGTATGTGTT--AAAAATCTTCCTTTTCGAACCTAACAGCGAAACCAAAATGTTAGATGACCAAACATTTGACAGGGT
GAGGAGAATTAGCA--GTGTTTTCCAAAATATCAGCACCAACCACACCCCCAAACGGCTCACCTACAGCCTAACAAAACA
ACACAACAACTGTAACACATATCATAAGCTTTCTGTGATCGAAGGGAAGAGGAAAAGAATTCCTCCCTCACGAAACAGAT
GTCTTGCAAGAAATGCAAATTCACCTGAAACCAGTAAGAAAAACGAGCACCTGAGTACACGGCTCACTATTTATATGTAC
CTGCGGCTTGAGCATTGTTGCTACCATCATTCCAAAGTAACCAGCCAGCAGCAGTCCTCATCGATCTATAGATGGCTTCC
CTCCTGCTGCTGCTGCAAGCCATCATCCGTGGTGCCGACGAGGGGCGTCTCGGCACAAGGGAGGTGCCAGAGGAGGTGAA
GCAGCCCAAGATGTTCTCCCCAAACCCTCTGTTGGAGCACAAGGGATGCAGGCTCGACGACGACGACGTGGAAGAAGAAC
GGTGGCTGGTTGCCTGCTTGCAGTGGCCCCGGACCAATCACCAATCAGCTTGGATGCAGACGATCTGATCTCATC-GATC
ACTT-ATATTCATAAATGGAGTGCCTGTCAATCTCGAATGAAGATGGCTGGCTCTGCCTTCCAATGTAGTTCTTGCCTAC
ATTGCCTAGGATAAAGTATTTTGTGTCTGAACAAATGTTGGTTGATTTCTTGCATGGCTAGTACAAAATGTTCAACATAA
CAGAGCTATCTCACTGCCAATAAAACTCTATCTGTATACAGGAAG-----------------------------------
-------CAAGAACTTGTTATTGGTGAAATTTCTTTCACACATTTCAATGGCCGGTCAAATATACAGCATCCCAAATGAT
CAACATTTCAGACAGGTGGCAATTCAACCCCAGTCGACAAAAGGAAGTGGAGGATAGCCACCTTCAGGGGGAGGTTGCAG
CGATGGAGGTAAGTTGCCCCATGAAGTGTGGCCTGTTAGTATGTTTCCTGTGAAATGTGACAGAAATAAACGTAGCATTA
---------TCAAATGGAAGCTCATAAAGAGGTTAAGTTCAACAGCGAG-CCAACAGGTGGGCTTCAACAGGCTCAAGCC
TGCCCTAGAAAAC-ATTTTTTTATTACTAGAGCACTCCGGTCTGAGCCTAGCTCCCCAGCCCATCT---AAAAGCCCATT
CACCATATAGAAGATGAAAAGAATGCAGCAGTTAGCCAGGCCAATAGCTTCACACGCACAAGCACAGCACCACGCGACTC
GACGCAGCCAGACAGCCACGCCGCTGGAAGGACAAGCCGCCAAATATTTATTTGTCTAATTCTCAAATTACTTTGCTACG
TCAGTAAACTATTAGTCTACTTCATGATC---------------------------------------------------
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------------------------------------------------TATTAATTGATTTAGTGTCCAATATAATTTGT
TCGCAGTCCCCTCAATAAAGAAAACTTGTTCGCAGATTTACAAAAATGAAGAGAAAGAGTATGAGCATGCACAA--TTTT
TA--CACAAGCAGTTCAGTTATACCCTTGCCGAACCTGAATTTGCCCCAGCTAATGTG
>chr3B_461
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-----------------------------------------------------------------------AGGGCAGGG
CATACAGCATGTACGTCCAATGAACGGATGAAGGCGCACGATCTATCAATCAGCTAGTGCACTGTACCAATCCAATCAAC
GGACGAC--GAATTTGATTAGGCAACAACAGCATATTTACACGCGAAAACCATATGCGGAATAAAGTAGAATCTGCACAC
AAGGTTTGTGTT-AAAAATTCTTCCTTTTCGCACCTAAAAGCGTAACCAAAATGTTAGATGACCAAACATTTGACAGGGT
GAAGAGAATTAGCAGTGTGTTTTCCAAAATATCAGTACCAACCACGC----------CTCACCTACAGCCTAACAAAACA
TCACAGCAACCATAACACATATCATAAGCTTTCTGTGATCGAACAGAAGAGGAAAAGAATTCCTCCCTCACGAAACAGAT
GTCTTGCAAGAAATGCAAATTCACCTGAAACCAGTAAGAAAAACGAGCACCTGAGTGCATGGCTCGC----TATATGTAC
CTGAGGCTTCAGCGTTGTTGCTACCATCATTCCAAAGTAACCAGCCAGCAGCAGTCCTCAAAAATCTATAGATGGCTTCC
CTCCTGCTGCTGCTGAAAGCCATCGTCCGTGGTGCCGACGAGGGGCTTCTCGGCACAAGGGAGGTGCCAGAGGAGGTGAA
GCAGCCCAAGATGTTCTCCCCAAACCCTCTGTTGGAGAACAAGGGATGTAGGCTCGACGACGACGATGTGGAAGAAGAAC
GGTGGCTGGTCGCCTGCTTGCAGTGGCCCCGGATCAATCGCCAATCAGCTTGGATGCAGACGATCTGATCTCATC-GATC
ACTTCATATTCATAAATGGAGTGCCTGTCAATCTTGAATGAAGATGGCTGGCTCTGCCTTCCAATGTAGTTCTTGCCTAC
ACTGCCTAGGATAAAGTATTTTGTGTCTGAACAAATGTTGGTTGATTTCTTGCATGCCTAGTACAAAATGTTCAACATAA
CAGAACTATCTCACTGCCAATAAAACTCTATCTTAATACAGGAAG-----------------------------------
-------CAAGCACTTGTTATTGGTGAAATTTCTTTCACACATTTCAATGGCCGGTCAAATATACAGCATCCCAAATGAT
CAACATTTCAGACAGGTGACAGTTCAACCCCAGTCGACAAAAGGAAGCGGAGGATAGCCACCTTCGGGGGGAGGTTATAG
CGATGGAGGTAAGTTGCCCCAAGAAGTGTGGCCCCTTAGTATGTTCCCTGTGAATTGTGAAAGAAATAAACGTAGCATTA
---------TCAAATGGAAGCTCATAAAGAGGTTAAGTGCAACGGCGAGTCCAACAGGTGGGATTCAACAGGCTCAAGCC
TGCCCTAGGAAACAATTTTTTTATTACTATAGTACTCCGATCTGAGCCTAACTCACCAGCCCATCT---AAAAGCCCATT
CACCGTATAGAAGAGGAAAAGAATGCAGCAGTTAGCCAGGCCAGTAGCTGCACGCGCACAAGCACAGCACCGCA-----C
GACGCAGCCAGCCAGCCACACCGCTGGAGGGATAAGCCACCAAGTATTTATTTGTCTAATTCTCAAATTACT---CTAAG
TCAGTAAAATATTAGTCTACTTTATGATATACTCCCTCCGATCCTTTTTACTCTGCATATTAGGTTTGTCTGAAGTCAAT
CTCATCCAACTTTGACCAAGTTTATATAAAAAATTATTGACATTTACATAACAACACCAACATCATTAGATTCATCTCGG
AATATATTTTCATATTATATTTATTAGATATTATAGATGCTAATAATTTCTAATATAAATTTGGTCAAACTTAACTAAGT
TTGACTTCCGGCAAATCCAATGTGCAGAGTAAAAAGGACCGGAGGGAGTATTAATTGATTTATTGTCCAATATAATTTGT
TCGAAGTCCCCTCAACAAAGAAAACTTGTTCGCAGATTTACAAAAATGAAGAGAAATAGTACGAGCATGCACTTTTTTTT
TA--CACAAGCAGTTCAGTTATACCCCCACCGAACCTGAATTTGCCCCAGCTAATGTG
>SNPs
SSSSS-----S----S-----------SS-------S--------S----S-S-----S-------S-------S--SS-
----------S-----------S------S--S----S------SS----------S--S---S-S----S------SS-
------S-------S---S-------------------------------S----S---S-------SSS-------S--
-----------------------------------------------------------S--S----S------------
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---------------------S---S-------------------S------------------------S-------S-
------------------------S--------------------S------------------------S---------
------------------------------------------------------------------S-------------
------S-----S----------------------------S--------------------------------------
-----------------S--------------------------------------------------------------
------------------------------------------S---------------S---------------------
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------S---------------------------------S---------------------------------------
------------------------------S-------------S-----------------------------------
---------------------------------------------------------------S----------------
--------------------------------------------------------------------------SS----
------------------------------------------------------------------------S-------
--------------S------------------------------------------S---------------------S
---------------------------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSS-------------S--S------------------S------SS---------------------S--S----
------------S------SS-S------------------------------------------S--------------
S---------------------------------------------------------------------S----SSSSS
SSSSSSSSS------------------------------------------------S-----------------S----
---------------SSSS---------------------SSSS---SSSS--SSSS-SSSS--S-SSS-----------
----------------S-------------------------------------------------------S--SS-S-
S--S--------------S-----------S----------------------------------S-----S--------
S---------S-S-----S-------------------------------------------------------------
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------------------------------------------------------------------------S------S
----------S---S--------------------------------------------------S-----S-----SSS
SSSS------------------S-----------------------------------
>forward_29
---------GCCCCCAACGTTTGTCTCTA---------------------------------------------------
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>reverse_1681
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TGATGGAGGTAAGTTGCCCC------------------------------------------------------------
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