>input_sequence_83880
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-----------------------------------------------------ATGGATGGATGCTTGCAGGTGGTGGAG
TTGAAGGTCGGGATGCACTGCGACAGGTGCATCAAGTCGATCAAGAAGGCGATCAAAACGATCGATGGTACGA---AAGC
CTCTGATCCACTCGACAAAACACAGCCTCACTTTCCATACTTTGCA-------GTATATGGTTAATTATTAACCCTGGTT
TGTGCGTGCGTATGCGCAGACATGGAGAGCTACCAGCTCGAGAAGGAGACGAACAAGGTGACCGTGACGGGGAATATCAC
CCCGGAGGAAGTGGTGAAGGCTCTGCAGAAGATCGGGAAGACGGTAACTTACTGGGGTGAGTGA----------------
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>chr3D_1_TraesCS3D01G341000
TCATTAGTTAGTCCAGTTTTATTCAGATCAGCTACCTTGACACTCCAACAGATGTCATCTTTCATCGATTCTTTTCGTAT
TGCACGTTACTGGAAGAAGAAGAAGAAAGC--------------------------------------------------
-------------------CTCTCGTGATTATTTTGAGAGGCTCCTACTATGACGATGATGATGCAATATAAAATCATGC
GTAAGCCTCTGGGCAAAGAATAAGGGCATGTACAATGATGGCATATGGATACAGATGCCCCATGACAAAAAGTAGTTTGA
GGCATCTACATTTATTTTTTCTCCTCAATGCAAGCTACCATTAGTGGGCCTCATTAAGAAATAGAAAATAAAGACTTTAG
TACACATGCATCTCTATTTTTCACTCCAACCTTTTCAGCTTTTGATCCCGGACCACACTTTTCCTCTCCAAGCACCTGCC
TCCTCGAGAGGATCCCGCTTTCCTATCCGAACCTACTTTACGTCATATCCGATCCTACATGGCATGCGAGGCATCACCCT
GAGGCTATGCATTGTACATGCCCTAATGTACCATGTCATCTAGTGTGTTCCAGTAACTCCAGAAAGATTTAGCTGGACCC
AGTTCAAAAGTAGATTCTTGCGCGTTTCATGGTAGCCTTGGGCAACCTGTGGAGTCCCTCTCCGAGTGTGAAAGAAATGC
TCAAACGCCCTGCCTTCACGATGACAGCTTTAAAGCGAACCGATGCTATGTGCTTTGTCGTTCACGGTGGAGAACAAAAG
TTCGCCGTTGCTTGTGGAAAAGAGAAAGGTTCAGACGCAGTATATAAGCTCCAGGATACAGAGAGACTGTGAAACCTCTC
CACTTCAGACTTCAGAGCTGCCTGGGAAGTGGTGGCTGCACCTGCACAGTAGCAGTCTCCTGTTCAGTTCTACTCGCCGA
GAAACCAAGCCATGGCTGTAAGTTACTGGTCAGATCTTCTGTTTATTCAACAGTATGTATGC------------------
------ATGTATCTGAAGAACTACTGTGCGTATAGAAATGGAAAGTTGATTTCATGGATGGATGCTTGCAGGTGGTGGAG
TTGAAGGTCGGGATGCACTGCGACAGGTGCATCAAGTCGATCAAGAAGGCGATCAAAACGATCGATGGTACGA---AAGC
CTCTGATCCACTCGACAAAACACAGCCTCACTTTCCATACTTTGCA-------GTATATGGTTAATTATTAACCCTGGTT
TGTGCGTGCGTATGCGCAGACATGGAGAGCTACCAGCTCGAGAAGGAGACGAACAAGGTGACCGTGACGGGGAATATCAC
CCCGGAGGAAGTGGTGAAGGCTCTGCAGAAGATCGGGAAGACGGTAACTTACTGGGGTGAGTGAAGAACAGAGCCCAGAG
GAAGACGAGCCACACGGTAACAACTTATTGTTACTGGGAGTGCGGACTATAGAGCCCACGTAGTTAGCTAGCTAGTTAGT
ATTAGCTCATGTGCTTACCATGGGATATCAGGAGCTATTTATACTGCAGATCGGGTAATTCTGGTGAGTTTCTTTGAACT
GGTAGATGTTGGTTCTTCCCTCGCTTGATCCCATATTGACCGCGGCGTCGTCGTGTTGGG-TTAACTCTTCTGTATTGCG
TATACTGAACTCATGGCAAAGTCTTGTAGAGGATGAACCCAACTTTTGTACGTTTTCACGGGGAATATATGTATGAAAGG
AGTGATATAACTGTCAGGATTAGTTTCAGACTTCCAGTTTTCATCTTAA-CGAACAG--ATGTCTCAGCTGGACTGGCTG
ACCGTGCTAACGTTGATTGATTGATTGATACTACGAGTAGCAAGCAAGCCACC---------------------------
CCTTATCCATTCAGCAATCATACAGATACAGTTGCATCGTAACAGCAAGATCGGTCCTTCGTCGACATCGATCCAACTAT
ATAC--TACTAGTGTCCATAGTCAATAAAGGGTACCCTTTTTCAGAAAATAAAAAAAGTTAAAGATCGAATACATCTATC
AGTACGCAATTCAAACGGCTTCGTTTTTAGATCTTTCTTTA-AGTTTTGTTAGGGGTTTTTGTCCTGATCAGGAAGTTGA
GATAGTGACGGCT-CTCTGAAGATAAAATAAGGTTCTTTTTGTCTAGCCCATGTTTTGGTGATGCGTCTAGCATCATCGG
TAAACGTGTGAAGGTGTGTCTCCGCTGGATCTATCTTTGGTGGATCCTTCCAATCAACGCTACTCTTTATCGGCGGCGGT
TGCTGCTTTGGTGCGCTGGTCTTATAATGCTTTAGCATGACGATTTTTCGACTGTCTACTACAATAAGTTTTGTCCGGCT
CTGGTGATGTAGGGGCGATGACGGCGGCGCGCCTTCGGCTCTCTTCAGTGCTTCTAGTC
>chr3A_1
TCATTAGTTAGTCCAGTTTTATTCAGAACAGCTACCTTGACACTCCAACAGATGTCATCTTTCATCGATTCTTTTCGTGT
TGCACGTTACTAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGA
AGAAGAAGAAGAAGAAAGTCTCTCGTGATTATTTTGAGAGGCTCCTACTATGACGACGATGATGAAATATAAAATCATGT
GTAAGCCTCTGGTTAAAGAA------------------------------------------------------------
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-----------------------TAATGTACTAGGTCAGCTAGTGTGTTCCAGTAACTTCAGAAAGATTTAGCTGGAGCC
GGTTCAAAAGTAGATTCTTGCGCGTTACATGGTAACCTTGGGCAACCTGTGGAGTCCCTCTCCGAGTGTGAAAGAAATGC
TCCAATGCCCTGCCTATGCGATGACAGCTTTAAAGCGAACCGATGCTATGTGCTTTGTCATTCACGGTGGAGAACAAAAG
TTTGCCGTTGCTTGTGGAAAAGAGAAAGGTTCAGACGCAGTATATAAGCTCCAGGATACAGAGAGACTGAAAC----CTC
TACTTCAGACTTCAGAGCTGCCTGGGAAGTGGTGGCTGCACCTGCACAGTACCAGTCTCCTGTTCAGTTCTGCTCGCCGA
GAAGCCAAGCCATGGCTGTAAGTTATTAGTCAGATCTTCTGTTTATTCGACAGTATGTATGTATGTATGTATGTATGTAT
GTATGTATGTATGTGAAGAACTACTGTGCTTATGGAAATGGAAAGTTGATTTCATGGATGGATGCTTGCAGGTGGTGGAG
CTGAAGGTCGGGATGCACTGCGACAGGTGCATCAAGTCGATCAAGAAGGCGATCAAGACGATCGATGGTACGACGAAAGC
CTTCGATCCACTCGACATAAAACAGTCTCACTTTCTGCAG-TTGCA-------GTATATGATTAA--ATTAACCCTGGTT
TGTGCGTGCGTATGCGCAGACATGGAGAGCTACCAGCTCGAGAAGGAGACGAACAAGGTGACCGTGACGGGGAACATCAC
CGCGGAGGAAGTGGTGAAGGCTCTGCAGAAGATCGGGAAGACGGTAACTTACTGGGGTGAGTGAAGAACAGAGCCCAGAG
GAAGGCGAGCCACACGGTAACAGATTATTGTTACTGGGAGTGCGGACTACAGAGCCCACGTAGTTAGCTAGCTAGTTAGT
ATTAGCTTATGTGCTTACCATGGGATATCAGGAGCTACTTGTACTGCAGATTGGGTAATTTTGGGGAGTTTCTTTGAACT
GGTTGATGCTGGCTCTTCCCTCGCTTCATCC--TATTGACCGCGGGGTCCTCGTGTTGCGTTTAACTGCTCTGTATTGCG
TA--CTGAACTCATGGCAAAATCTTGTAGAGGATGAACCCAACTTCTATACGTTTTCACGGGGAATATATGTATGAAAAG
AGTGATATAGCTGTCAGGATTTGTTTCAGACTTTCAGTTTTGATCTTAAACGAACAGATATGTCTCAGCTGGACTGGCTG
ACCGTGCTAACGTTGATTGATTGATTGATACTACGAGTAGCAAGCAAGCCACT---------------------------
CCTTATCCATTGAGCAATCACACAGATACAGTTGCATCGTAACAGCAAGATCGGTCCTTCGTCGACATCGATCCAACTAT
ATGCTATACTAGTATCCAAAGTCAATAAAGGGTACCCTTTTTCAGAAAACAAAAAAAGTTACAGATCAAACACATCTATT
AGTACGCGATTCAACCGGCCCCGTCTATAGTTTTTTTTTTTGAGTTTTGTTAGT-GTTTGTGTCATCTTCAGGAAATCAA
GACGGCGGCGACTCCTCTAAAAATGAAATAAGGTACTTCTTGTTTAGAATCCATTCCGATGGTGCGTCTAGCATCATCGT
TAGGCGTGTGGAGGTGTGTCTTCTATCGATCTGTCTTT------------------------------------------
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>chr3B_1
TCATTACTTAGTCCAGTTTTATTCAGATCATCTACCTTGACACTCCAACAGATGTCATCTTTCATTGATTCTTTTTGTAT
TGCACGTTACTAG-------------------------------------------------------------------
--AAGAAGAAGAAGAAAGTCTCTCTTGATTATTTTGAGAGGCACCTACTATGACGATGATGATGAAATATGAAATCATGT
GTAAGCCTCTGGTTAAAGAA------------------------------------------------------------
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-----------------------TAATGTACCATGTCAGCTAGTGTGTTCCAGTAACTTCAGAAAGATTTAGCTGGAGCC
AGTTCAAAAGTGGATTCTTGCGCGTTTCATGGTAGCCTTGGGCAACCTGTAGAGTCCCTCTCCAAGTGTGAAAGAAATGC
TCCAATGCCCTGCCTTCACGATGACAGCTTTAAAGCGAACCGATGCTGTGTGCTTTGTCATTCACGGTGGAGAACAAAAG
TTTGCCGTTGCTTGTAGAAATGAGAAAGGTACAGACGCATTATATAAGCTCCAGGATACAGAGAC----TGAAACCTCTC
TACTCCCGAGCTCACCGAGAAGT---AAGTGGTGGCTGCACCTCCACAGTAGCAGTCTCCTGTTCAGTTCTGCTCGCCGA
GAAGCCAAGCCATGGCTGTAAGTTACTGGTCAGATCTTCTGTTTATTCAACAGTATGTATGTATGTATCC----------
--------------GAAGAACTACTGTGCCTATGGACATGGAAAGTTGATTTTATGGATGGATGCTGGCAGGTGGTGGAG
CTCAAGGTCGGGATGCACTGCGACAGGTGCATCAAGTCGATCAAGAAGGCGATCAAGACGATCGATGGTACGA---AAGC
CTCTGACCCACTCGACAAAAGACAGTCTCACTTTCCATACTTGCAGTATATCTGTATATGATTAATTATTAA-CCTGGTT
TGTGCGTGCGTATGTGCAGACATGGAGAGCTACCAGCTCGAGAAAGAAACGAACAAGGTGACCGTGACGGGGAACATCAC
CCCGGAGGAAGTGGTGAAGGCTCTGCAGAAGATCGGGAAGACGGTAACTTACTGGGGCGAGTGAAGAACAGAGCCCAGAG
GAAGAGGGAACAGACGGTAACATAGTGCTGCTGGGGCGAAGAC------TAAAGCGCACGGAATCAGCTAGCTAGCTAGT
TACTGTAT------TTACCATGGGATATCAGGAGCTATTTGTACTGCAGATCGGGTAATTGTGGTGAGTTTCTTTGAACT
GCTAGATGTTGGTTCTTCCCTCGCTTGATCATATATTGACCGCGGCGTCGTCGTGTTGGGTTAGCTCAT-----------
----CTGTACTCATGGCAAAATCTTGTAGAGGATGAACCCAATTTTTGTACGTTTTCACGGGGAATATATGTATGAAAAG
AGTGATAT--------------GTTTCAGACTTTCAGTTTTCATCTTAA-CGAACAGATATGTCTCAGCTGGACTGGCTG
ACCGTGCTAACGTTGATTGG----TTGATACTAGCTATTCCCGTCTTCTTTGGTGGCTACCTGGAAGGAACCATGCCACG
CCTTATCCATTCAGCAATCATACAGATACAGTTGCATCGTAA--------------------------------------
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>SNPs
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-----------S---------------SSS--------------------------------------------------
----------------------------------------------------------------S--------------S
------------SS------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSS---------------S-------------------S------------------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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----------------------SS--------------------------------------------------------
-------S--------------------------------S-------------------S-------------------
-------------------------------S-----------------------------------S------------
--SS----------------S---------------------------------------------------------S-
---------S-----------S-----------S----------------------------------------------
----------------------------------------------------S---------------------------
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--S----------S----S------------------------------S-----------S-----S--S--------S
-------S------S----SS---S-S---S-S---S---S------------SS----S----S-SS-------S-SS-
--SS-S-S--S-------S--S--S---------S---S----S---SSSSSS--SS-S--S-----------------S
--SS------S----------S-SS-S-----S-----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_502
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--CTCGAGAGGATCCCGCTTTC----------------------------------------------------------
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>reverse_2297
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--------------------------------------------------------ACGCTACTCTTTATCGGCGG----
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