>input_sequence_80787
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-------------------------------------------------------------ATGGCACAGCAGGTGAAGA
AGGCGCCGG------------------------------AGC------------CGGAGGTGCAGGACTCGGAGATCCAG
ACACAGCAGGTGAAGAAGGCGCCGGAGCTGCAGGACCCGGAGATCCGGGCAGAGCTGGACCGCCGCGCCCGCGAGGAGGG
CGAGACCGTCATCAAGAGCGGCGCCGGCGGCAAGACCCTCGAGGCGCAGGAGCGCCTCGCAGAAGGTACGTGCGTGCGTT
CATGCGTTGGCGTATCTGG---------------------------------------TGTTGCTCTAACTTTGTGTTGA
TCTGCTTGTGCTGCTGTGCATGCGTGCTGCAGGGCGTAAGAAGGGCGGGCTGAGCCGTGCGACCGGCTCCGGCAACGAGC
GCGCCGAGGGTGAGGGCGGGGTGGTGATCGAGCCGGACGAGAAGAAGCTCGAGGAGGTCAAGAAGGATCTCGGGCGCGAA
TGA-----------------------------------------------------------------------------
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>chr3D_1_TraesCS3D01G149400
AGTTGGCTACTAACACGTAGACCATACTTTGCAAAAGAGTTTCTTAAAACATGCCTCTAACAAAGAGAAGCGTAGTTCAA
AAGAATTCAAATGAAGACATGCGAACATAGACAAACAAAGACCGAATCCAAGCAGATTCACTAAAGGCAACCACCGACCG
AATCCTGTGAGATCCTTCGGAGGCACACCTCCACACGTCCTCCGACGACGGTAGACACTCCACCGGGACAAGGGCTAGAC
GGGAGAACCTTATTCCATCTTTAGGAAGCCGTCGCCGTCTCGTCATCATAAGCATGACACAAACCCTAGCAAATCTTAAA
GAAACATTTGAAAACGAAGTCCTCCCATCGGCAAGGGCCAAAATTCATCACGCCTCATGGCTCTAAGGCC-----AGACG
AGGCAAATCGATGGCACCACCGGTGGTAGGAGGCAGGAACCCTAATCGTGTGTTCACTTGA-GAGGAGAGACGAAGGGGT
AAGTAGTTTTTTTCCCTGCGTCACCTCTATGCAGTTGTGAACAGTTTGTTTATGGAGTAGCTCCAGCAAAAA-ACAAACT
GTCATCCTTGCGCCCGTCATGCTTCACGACCAACGAAAGTACCCAACGTGCTGAAGCCGATGATGCAAAACCAAATGATC
---TACCGACTGCCTCA-GCACACGAAACAGTAGCGTGCAATGT-GCTGGCTAC-CAGAAGG--GCCTCCACGTGAGTCC
CCGGCGCATGAACTTACGGCGACGTTTGACCACGGTCACCGCTACGTGCTCGCCGAGAAATCACTTCCCATCAA-ACGTG
GCGCGCGCCCCATGCATGTTTGCCACGCCGGCCCGGGGTGAAAGGCAGCGGTAACAGCGCACCACGGCCGGCAGCATGCA
CCGTCCACGTAT--ACGGACCGCACCGCCGTTCACGACCTATATAAGTGGCCGGAACTCCGCTCTCCGGTGAAGCAGAGC
ATAGCAGCAGGCTAGCGGAGGCAGACTTCGAAGACTTGTTACGAGC---AGACCGCGAGCAATGGCACAGCAGGTGAAGA
AGGCGCCGG------------------------------AGC------------CGGAGGTGCAGGACTCGGAGATCCAG
ACACAGCAGGTGAAGAAGGCGCCGGAGCTGCAGGACCCGGAGATCCGGGCAGAGCTGGACCGCCGCGCCCGCGAGGAGGG
CGAGACCGTCATCAAGAGCGGCGCCGGCGGCAAGACCCTCGAGGCGCAGGAGCGCCTCGCAGAAGGTACGTGCGTGCGTT
CATGCGTTGGCGTATCTGG---------------------------------------TGTTGCTCTAACTTTGTGTTGA
TCTGCTTGTGCTGCTGTGCATGCGTGCTGCAGGGCGTAAGAAGGGCGGGCTGAGCCGTGCGACCGGCTCCGGCAACGAGC
GCGCCGAGGGTGAGGGCGGGGTGGTGATCGAGCCGGACGAGAAGAAGCTCGAGGAGGTCAAGAAGGATCTCGGGCGCGAA
TGATCGAGCGTGGTAGACGATGTAAGGCCTCACAGGCCGGTCCTCCTATA----------TATCGTACGTGTGTATGTAC
TGCACTGTAGTTAGTACGTAGTGCTATGGATGTACGCGGTAGTAGGCTAGGTTGAAGGATGTAGAGTACGTAGTAGCGTT
G----ATGCATGTCCTCGTGTTCGCACGGACATGCGCGCGGTACGTACGTCTGGCTACAAAATTTTGGTCCCCGGATTGT
AGCC-----------------------------------------------------------GCCGTAGCCCCTCTATA
TGTGTAGCTCGATCGTAATCG-ATGTACCCTGGCTGCAAAATTTTGGCATGGATGTACGTTCTGTAGCCAATGATCCCCG
GATATACTTATATAAGTTGATAAATAGTGGTCGTGTCTGCGAAAACTACGCACTAACTTCTTTCCTTTTTTTTTG-AAAG
GGGTTCTCCCCGGCCTCTGCATCAGAGTGATGTATACGGCCCTCTTATTAATGAAAAAAAAGGTTCCAACAAGGTTTCAG
AGTCTCCTACTGAAAAAGTAATAAAACGACAGCTCACACAGAGCTAAAGAGTCTGGACACACAGACTAGCCAAGATAAGA
CGCCACAACCGGCTGGCTAAAGATAGATAGGTAAACTAATTGCCTATCCTATTACATGACCGCCATCCAAACCGGTTGAA
GATATCCCGAGCTACCATCTCCCATTCCCTGACTCCATCG-----------------------------GAGTAGCGACC
ATGTACG-------------------------ACCTGCAAAAAGTGAATACGTGATGTTCTGTTT--------ATCATTT
CTGCAAGTTCAGATAGTCCCCAACAAAGCGCAAACTCCAACACGAATATGTCTCGCTAATTCAGGCTCAATCCCAGTGAG
CCATATCCCAAATAACATAGTGACAGAATTCGGTGGAGTAATATTAAAAGCAATGTGAACCGCCCTTCAAAGTACTCTAG
CAAACGGGCAATCAAAAAAGAGATGTTTGATCGTCTCTTCCCGATCACAGAAGCTACACCTCGTAGGTCCTGTCCAATTA
CGCTTAATCAAGTTATCCTT
>chr3A_142
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-------------------------------------------------------------TAAAGACAACCATCGACCG
AATCCCACAAGGTCCATCGAAGACACACCTTCGCACACCCTCTCACAATGATAGACACACTATCGAGACACAGACAAGGT
GAGACAACGTTATTCTATCTTCAGCAAGCCGTCGCCTTCTCATCGTCATGAACACGACACAAATCCTAGCAAATCTCAAA
-AAAAATATAAAAACGGAGTCCTCTAGTGGATAAGGGCCGAAACTCACCACATCTCACAGCCCTAAGGCCGCAGAAGACG
AGACAGGTCGGTGGCAT-----------GGAGGCAGGAA-CCTAATCGTGTGTTCACTTGGGGAGGAGAGACGAAGGGGT
AAGTCGTTTTTTCCCCTGCGTCACGTCTATACAGCTGTGAACAGTTTGTTTATGGAGTAGCTCCAGCAAAAACACAAACT
GTCATCCTGGCGCCCGTCATGCTTCACGACCAACCAAAGTACCCAACGTGCTGAAGCCGATGATGCAAAACCAAATGATC
ATCTACCGACCGCCTCGTGCACACGGACCAGTAGCGTGCAATGTTGCCGGCTTC-CAGAAGGGAGCCTCCACGTAAGTTC
CCGGCACACGAACTTACGGCAACGTTTGACCACGGTAGCCGCTACGTGCTCGCAGTGAAATCACTTCCCATCAAAACGTG
GCGCGCGCCCCATGCATGTTCGCCACGCCGGCCCGCGGTGAAAGGCCGAGGTAACAGCGCACCACGGCCGGCAGCATGCA
CCGTCCACGTATACACGGACCGCACCGCCGTGCACCACCTATATAAGCGGCC-----TCCGCTCAGTGGTGAAGCAGAGC
ATACCAGCAGGCTAGCGGAGACAGACTTCAAAGACTTGTTACCGAGCAGAGACCGCGAGCAATGGCACAGCAGGAGAAGA
AGGCGCCGG------------------------------AGCTGCAGCAGGACCCGGAGATCCAGGACTCGGAGAACCGG
ACACAGCAGGTGAAGAAGGCGCCGGAGCTGCAGGACCCGGAGATCCGGGCAGAGCTGGACCGCCGCGCCCGCGAGGAGGG
CGAGACCGTCATCAAGAGCGGCGCCGGCGGCAAGACCCTCGAGGCGCAGGAGCGCCTGGCGGAAGGTACGTGCGTGCGTT
CATGCGTTGGCGTATGTGG---------------------------------------TGTTGCTCTAACTTTGTGTTGA
TCTGCTTGTGCTGCTGTGCATGCGTGCTGCAGGGCGTAAGAAGGGCGGGCTGAGCCGTGCGACCGGCTCCGGCAACGAGC
GCGCAGAGGGCGAGGGCGGGGTGGTGATCGAGCCGGACGAGAAGAAGCTCAAGGAGGTCAAGAAGGATCTCGGGCGCGAA
TGATCGAGCGAGGTAGACGATGTACGGCCTCACAGGCCGGCCCTCCTATATATATATATATATCGTACGTGTGGATGTAC
TGTA----AGTTAGTACGTAGTGCTATGGGTGTACGTGGTAGTAGGCTAGGTTGAAGGATGCAGCTTACGTAGTAGCGTT
GATGCATGCATGTCTTCGTGCTCGCACGGACATGGC----GTACGTACGGCTGGCTACAAAATTTTGGTCCCTGGATTGT
AGCC-----------------------------------------------------------GCCGTAGCCCCTCTATA
TATGTAGCTCGATCGTAATCC-ATGTACCCTGGCTGCAAAATTTTGGCATGTATGTACGTTCTGTAGCCAATGATCCCCG
GATATATGAGTTGATAA--ATAAATAGTGGCCGTGTCTGCGAAAACTCCACACTAACTTCTATTC---------------
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>chr3B_598
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--------------------------------------------AACGTGCTGAAACCGATGATGCAAAACCAAATGATC
---TACCGACTGCCTCA-GCACACGAAACAGTAGCGTGCAATGT-GCTGCCTGGGCAGAAGG--GCCTCCACGTGAGTCC
CCGGCGCATGAACTTACGGCAACGTTTGACTATGGTCATTGCTACTTGCTCTTCGTGAAATCACTTCCCATC-AAACGTG
GCGCGCACCCCATGCATGTTGGCCACGCCGGCCATCGGTGAAAGGCCGAGGTAACAGCGCACCACGGCCGGCAGCATGCA
CCGTCCACGTAT--CCGGACCGCACCGCCGTTCACGACCTATATAAGTGGCC-----TCCGCTCTCGGGTGAAGCAGAGC
ATATCAGCAGGCTAGCGGAGACAGACTTCGAGGACGTGTTACGAGC---AGACCGCGAGCAATGGCACAGCAGGGGAAGA
AGGCGACGGAGATGCAGGACCCGGAGATCAGGGCAGAGCAGGTGAAGAAGGCGCCGGAGCTGCAGGACTCGGAGACCCGG
ACACAGCAGGTGAAGAAGGCGCCGGAGCTGCAGGACCCGGAGATCCGGGCAGAGCTGGACCGCCGCGCCCGCGAGGAGGG
CGAGACCGTCATCAAGAGCGGCGCCGGCGGCAAGACCCTCGAGGCGCAGGAGCGCCTGGCAGAAGGTACGTGCGC-----
-------TGGCGTATGCGTATATATATACCAGTTGTTCTAACTTGTTTCTTGAGCCATTGATGTGCTAACCTTGTGTTGA
TACGCTTG--------------CGTGCTGCAGGGCGTAAGAAGGGCGGGCTGAGCCGTGCGACTGGCTCCGGCAACGAGC
GCGCCGAGGACGAGGGCGGGGTGGTGATCGAGCCGGACGAGAAGAAGCTCGAGGAGGTCAAGAAGGATCTCGGGCGCGAA
TGATCGAGCGTGGTAGACGATGTACGGCCTCACAGTCCGGTCCTCCTATA----------TATCGTACGTGTGTATGA--
------------AGGATGTAGTGCTATGGATGTACGCAGTAGCAGGCTAGGTTGAAGGATGTAGCGTACGTAGTAGCGTT
GATGCAC----GTCTTCGTGTTCGCACGGACATGCGCG--GTACGTATGGCTGGCTACAAAATTTTGGTCCCGGGATTGT
ATATATGTAGCTCGATCGTAATCTATGTACCCTGGCTACAAAATTTTGGCATGTATGTACGTAGCCGTAGCCCCTCTATA
TATGTAGCTCCATCGTAAATCTATGTACCCTGGCTGCAAAATTTTGGCATGTATGTACGTTCTGTAGCCAATGATCCCTG
GATATATGAGTTGAT------AAATAGTGGCCGTGTCTGCGAAAACTCCACACGAACTTCTTTCCT--------------
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>chr7D_1810
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-----------------------------------------------------------------TTTTTTTTTG-AAAG
GGGATCTCCCCGGCCTCTGCATCAGAGTGATGCATACGGCCATCTTATTAACGAAATAAAAGATTCCAACAAGGTTTCAA
AGTCTCCGACTGAAAA-GTAATAAAAAGACAGCTCACACAGAGCTAAAGAGGCTGGACACACAGACTGGCCAAGATAAGA
CGCCACAACCGGCTGACTAAAGATAGATAGGTAAACTAATTGCCTATCCTATTACATGACCGCCATCCAAACCGGTTGAA
GATATCCCGAGCTACCATCTCCCAGCGGATAGATCTAGTAACCAAATGCTCCCTGGCCTCCATCGGAGTGAGTAGCGACC
ATGAACGGATCACGGCCGTGGCTCGGAAAATAACCTGCAAAAAGTGAATACGTGATGTTCTGTTAAAAACCAAATCATTT
CTGCAAGTCCAGATAGTCCACAACAAAGCGCAAACTCCAACACGAATATGTCTCGCTAATTCAGGCTCAATCCCAGTGAG
CCATGTCCCAAATAACGTAGTGACAGAATTCGGTGGAGTAATATTAAAAGCAATGTGAACCGTCCGCCAAAGTACTCTGG
CAAACGGGCAATCAAAAAAGAGATGTTTGATCGTCTCGTCCCGATCACAGAAGCTACACCTCGTAGGTCCTGTCCAATTA
CGCTTAATCAAGTTATCCTT
>chr4D_1810
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-----------------------------------------------------------------TTTTTTTTTGAAAAG
GGGATCTCCCCGGCCTCTGCATCAGAGTGATGCATACGGCCATCTTATTAACGAAATAAAAGGTTCCAACAAGGTTCCAA
AGTCTCCGACTGAAAA-GTAATAAAAAGACAGCTCACACAGAGCTAAAGAGGCTGGACACACAGACTAGCCAAGATAAGA
CGCCACAACCGGCTGGCTAAAGATAGATAGGTAAACTAATTGCCTATCCTATTACATGACCGCCATCCAAACCGGTTGAA
GATATCCCGAGCTACCATCTCCCAGCGGATAGATCCAGTAACCAAATGCTCCCTGGCCTCCATCGGAGTGAGTAGCGACC
ATGAACGGATCACGGCCGTGGCTCGGAAAATAACCTGGAAAAAGTGAATACGTGATGTTCTGTTAAAAACCAAATCATTT
CTGCAAGTCCAGATAGTCCACAACAAAGCGCAAACTCCAACACGAATATGTCTCGCTAATTCAGGCTCAATCCCAGTGAG
CCATGTCCCAAATAACGTAGTGACAGAATTCGGTGGAGTAATATTAAAAGCAATGTGAACCGTCCGCCAAAGTACTCTGG
CAAACGGGCAATCAAAAAAGAGATGTTTGATCGTCTCGTCCCGATCACAGAAGCTACACCTCGTAGGTCCTGTCCAATTA
CGCTTAATCAAGTTATCCTT
>chr6D_1820
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----------------------------------------------------------------------------AAAG
GGGTTCTCCCCGGCCTCTGCATCAGAGTGATGCATACGGCCCTCGTATTAACGAAA-AAAAGGTTCCAACAAGGTTTCAA
AGTCTCCTACTGAAAAAGTAATAAAACGACAGCTCACACAGAGCTAAAGAGGCTGGACACACAGACTAGCCAAGATAAGA
CGCCACAACCGGCTGGCTAAAAATAGATAGGTAAACTAATTGCCTATCCTATTACATGACCGTCATCCAAACCGGTTGAA
GATATCCCGAGCTACCATCTCCCAGCGGATAGATCCAGTAACCAAAAGCTCCCTGGCCTCCATCGGAGTGAGTAGCGACC
ATGAACGGATCACAGCCGTGGCTCGGAAAATAACCTGCAAAAAGTGAATACGTGATGTTCTGTTAAAAACCAAATCATTT
CTGCAAGTCCAGATAGTCCACAACAAAGCGCAAACTCCAACGCGAATATGTCTCGCTAATTCAGGCTCAATCCCAGTGAG
CCATATCCCAAATAACGTAGTGACATAATTCGGTGGAGTAATATTAAAAGCAATGTGAACCGTCCTCCAAAGTACTCTAG
CAAACGGGCAATCAAAAAAGAGATGTTTGATCGTCTCTTCCCGATCACAGAAGCTACACCTCGTAGGTCCTGTCCAATTA
CGCTTAATCAAGTTATCCTT
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----S------S------
-----SSSS--S---S---S--S-------S-S---SS----SS--S-S-S-------S-S-S--S----SS-S-S--SS
-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---SS----SS--S------------------
--S--SS---S-----SSSSSSSSSSSS-----------S--------------------S-------------------
----S-------S-----------S-----S---S---------------------------------------------
--------S-------------------------S---------------------------------------------
----------------------------------------------------S---------------------------
--------------------S----------------------------------S------------------------
--------------------S--------------S----------S-S-------------------------------
----------------------------------------------------SSSSS---------S-------------
---S----------------S-----------------------------------------------------S-----
-----------------------------------------------------------S---------------S--S-
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---------------------------------------------------------S----------------------
---------------S----------------------------------------------------------------
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----------S---------------------------------------------------------------------
------------------------S-------------------------------------------------------
--S-SSSS--------------------------------------------------------S---------------
--------------S-----------------------SS---------S----------------------S-------
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-S------------------S------------------------------S----------------------------
------SSSS-SS-SSSSS-----------S----------------S-S------------------------------
--------------------------------S------------------S----S----------------------S
---------------------------------------------------S----------------------------
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------------------------SSSSS-SSS----SSS----------------------------------------
---S------------------------------------------------------------S---------------
--------S----------S------------------------------------------------------------
----------------S---------------------------------------------S---S-------------
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>forward_223
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-------------------------------------------GACGACGGTAGACACTCCAC-----------------
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>reverse_1719
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--------------------------------------CGGTACGTACGTCTGGCTAC----------------------
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