>input_sequence_74661
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---------ATGTCCCAAGCGCCGAACGCCGAGCCCGACGAGCGCGACGGCTTCACCTGCGGCACGCTGTTCACGTGCCT
CTGCCTCCCAGGACTCTCCAAGAAGAAGCCCGAGGAAACCGGCAACTCCGGCAAGAGCCA------GCAGCCAGCGGCGC
CGGAACAAGACCAGCGCACGGAGCAGGAACCGCCGCAGGTGCTGCTAACCCGTGCGGCGTCCCTGGAGAAGCTCGAGTGC
TCCTCGCTCTACTCCGGCAGCAACATCGTCTTCGACTTCCTGGTGGAGCCTGGGGGAAGGGACGACCGTGGCGCC-----
-GTCCATGGATACTGCCCGTCGCCGTGCTTCGACCTGCCGGTGGAGCTGATACGGGCCGGCGAACGATGCGGGGCTGTAG
CAAGCGACGCGCCGGTCACGTCCGCCTTCGTGTTCGACGGCCACCGAGATGGCGCAGCTCTGAAGAGGATAGCGTCGTGC
CTGGCGTCCAGCGTGCCTACAGGCGGCGAGGCGCGGCCAACGCATCTCGTGAGGTTCCTGTCCGCGTCGGGTTGTGCCGT
GCCGGTGCGGTCTCCCGTGACGTCTTTCGGTGGCCCGGCAAATGGGGGCGGCGGTTGA----------------------
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>chr3B_1_TraesCS3B01G358600
GAGTAATTTCCACGCCAAGCAGCTGAGCAATGGCGGCGAGCTGCTCACCGTCGTCTGGTTCTTGATGACGCACCTGGGGA
TGGGCGAGCAATACAGGATAGAGGCTGGGCATGCAAGAGCTAAACTAATTGTAGAGAAGAAC------TGAGAAGATCAC
CAAACGGTTGTGTACTCTGTAC-------TCTGTACTACCTTCAAAAATTCTTAGGTAATATGTGCGCTTTCAAGTAACT
TGAACTGATCTGGTCAGTTTGGTGAATTGGAATGTATTGGCAATACGGATTTACTCCCTAGGTTCCACTGAAACCAGTAC
AGTACGAGGTGGAAATATCATATGACACCACACTTCACATGACAACATGGTACCACTCCTCAAACTTCAAATTTGCAAGT
CTCCGCAAAATTCGATAAAAGTTGTGAACGTTCAACAAGATATG-TTTACACACTCCCTTAAATTTTCAGACCCAAATTC
GAAATATACAATGAGAAACAAAAGGATCAAACCTAGCATGAACAGTGTCACAAAAAGACAAATAGCA-------------
----------CTATTCACAATTGAATTTGTCTTCTTTGTTTCTCTGTGTGCATTTCGAATTTGGGATTGAAAATTTTAGA
GATTGTAGACTCATATGTTGTGAACATTTAGAGTTTTGTTTTTCATTTTTTAAAA--AAACTTGAAAATTTGAATTTTGA
GGA-GTTGTATCATGTTATCTCGATCATGCAGAGCATGCACAACATAGG-----AAGGAAGTCGAGTC-AACGAACCAAG
CGCCATACGGCTAGATCTACGCAGAACGAGTATGTAAGTGGGTCCCGACGACTAAGTTAAGCCAGGAAATCATGAAACAC
ACGATCTAGCGGGCTGACCGGCGGTGTGCCCCTCCACTCCGCCACCACCCGCCACCGCGACCTTACCCGGCCACCTCACT
ATATACCGGTACTGCGCTAGCTAGACGTAC---GTCCTCCCCGTTCCCTCCAAGGCGTTCGAATTTGTGTGCACCGGCCG
GCGAGCGCTATGTCCCAAGCGCCGAACGCCGAGCCCGACGAGCGCGACGGCTTCACCTGCGGCACGCTGTTCACGTGCCT
CTGCCTCCCAGGACTCTCCAAGAAGAAGCCCGAGGAAACCGGCAACTCCGGCAAGAGCCA------GCAGCCAGCGGCGC
CGGAACAAGACCAGCGCACGGAGCAGGAACCGCCGCAGGTGCTGCTAACCCGTGCGGCGTCCCTGGAGAAGCTCGAGTGC
TCCTCGCTCTACTCCGGCAGCAACATCGTCTTCGACTTCCTGGTGGAGCCTGGGGGAAGGGACGACCGTGGCGCC-----
-GTCCATGGATACTGCCCGTCGCCGTGCTTCGACCTGCCGGTGGAGCTGATACGGGCCGGCGAACGATGCGGGGCTGTAG
CAAGCGACGCGCCGGTCACGTCCGCCTTCGTGTTCGACGGCCACCGAGATGGCGCAGCTCTGAAGAGGATAGCGTCGTGC
CTGGCGTCCAGCGTGCCTACAGGCGGCGAGGCGCGGCCAACGCATCTCGTGAGGTTCCTGTCCGCGTCGGGTTGTGCCGT
GCCGGTGCGGTCTCCCGTGACGTCTTTCGGTGGCCCGGCAAATGGGGGCGGCGGTTGACGACTCGTGCCCGCGGTGGCAT
ACAACTTGAAGCCGAAAACGATGCGAGAGGGGAACCGTCG-TTGCAAGAAGTTGGTGTCGCATTTGGTTTTCACACTTTT
AACAACAGAAATCCAATTCCATTTTTAACGCAACGCAACACTCATATATACGTGCATACATTCATCCCTATGCATACTTT
ATCTCTATGAGCATCTTTAAGAGACCGAGTCGGCATATCATTTTGAGATTGTATAAAGTAATCGTAGACGTCTCGTAGTG
GATGAAAATGTCTCCTCCCACAAAACACACATCGCTGAAAATTCTGAAATAAATCCAGGATATTCGCAAGCACCAGGACT
TTAACCCTGGTGGGCTAGAGATACCACTATCCTCCTAACCATCCAAATACAGATTGGTTCGCCCCTAGAGCATCTTTAAG
GGCAATGCTCAAATCGCATCCCCTATTCATCTAGTACTTACATAAAGTAACAAATGATGTTCTATGTATCGTTGAAGGAG
CTGAAAGTGCCAAATCGATAAATGACCAATCCTGGTTCTCATTCCTAAAGTACTAAACCCTTCAACTTTATTTCAATTCC
ATCCTCTCAGCCTGTGCAATGTACTCTATAAGACCGCTTTAAAGGTAGTGGTAATTCTCTCAGACATTATTTCAAAGGAG
CAATCAACTTTTGTTTCTAGACACTTAATAACGGATAAGTTGAAGTTAGATATGGCAAAGCCTATGACCGAGTTGGGTGA
AGTTATCTTCAGGCAATCATGGAAAAGTTGGGTTTTAATCCTCAGTGGATCTCCATTGTTATGGGTATGATAAGCTCGGT
TTCTTTTTTCTGTGATTTTTAATGGAACAAAGTTGGACAATTTTAAGGCTTCACGAGTAATCCATTAGGGAGATCTTTCA
ACTTATCTTTCTTGTTAGTAGCAGAGGGCCTCTCGCGCCTATTGAAAGCTAGTGGTAGTCATCGTACCTTTCTGAATTAA
AGTGGCTCAAACGCTCCGG
>chr3A_1
GAGCAACTTCCACGCCAAGCAGCTGAGCAACGGCGGCGAGCTGCTCACCGTCGTCTGGTTCTTGATGACGCACCTGGGGA
TGGGTGAGCAGTACCGGATAGAGGCTGGGCATGCAAGAGCTAAACTAATTGTAGAGAAGAACTGAGATTGAGAAGATCAC
CAAAGGGTGGTGTACTCTGTAGACTGTAGTCTGTGCTATCTTCAAAAATTCTTAGGTGATATGTGCGCTTTCAAATAACT
TGAATTGATCTTGTCAGTTTGGTGAATTGGAATGTATTGGCAATACGGATGTACTCCCTCGGTTCCACTGAAACCAGTAT
AGTACGAGGTGGGAATATCACATGATACCACACTTCACATGACAACATGGCACCACTCCTCAAACTTCAAATTTGCAAGT
CTCCACAAAATTCT-----------------------AGATATG-TTTATACAATACCTTAAATTTTCAGACCCAAATTC
GAAATATACAATGAGAAACAAAGGGGGCAAATCTAGCATGAA-----------------------CA-------------
----------CCATTCACAATTGAATTTGTCTTCTTTGTTTCTCCGTGTGCATTTCGAATTTGGGATTGTAAATTTTAGA
GATTGTAGACTCATATGTTGTTAACATTCAGATTTTT--TTCTCATTTTTTGTTTAGAAACTTGCAAATTTGAATTTTTT
AGCGGTTGTATCATGGTATCGCGATCATGCAGAGCATGCATAGCACATG-----AACGAAGTCGAGTCAAACGAACCAAG
CGCCATACGGCTAGATCTACGCAGAACGAGTATGTAAGTGGGCCCCGACGACTAAGTTAAGCCAGCAAATCATGAAACAC
ACGATCTAGCGGGCTGACCGGCGGTGTGCCCCTCCACTCCACCACCACCCGCCACCGTGACCTGACG----CACCTCACT
ATATACCGGTACTGCGCTGGGCTGACAT--------CTCCCTATCCCCTCCAAGGCGTTCGAACTTGTGTGTACCTGCCG
GCGAGCGCCATGTCCCAAGTGCCGAACGCCGAGC---------GCGACGGCTTCACCTGCGGCACGCTGTTCACGTGCCT
CTGCCTCCCAGGACTCTCCAAGAAGAAGCCGGAGGAAACCGGCG---------AGAGTCG------GCAGCCAGCGGCGC
CGGAACAGGACCGGCGCACGGAGCAGGAACCCCCGCAGGTGCTGCTAACCCGCGCGGCGTCCCTGGAGAAGCTCGAGTGC
TCCTCGCTCTACTCCGGCAGCAACATCGTCTTCGACTTCCTGGTGGAGCCGGGGGGAAGGGACGACCGTGGCGCC-----
-GTCCATGGATACTGCCCGTCGCCGTGCTTCGACCTGCCGGTGGAGCTGATAGGGGCCGGCGAACGATGCGGCGTCGTCG
CCAACGACGCGCCGGTCACGTCCGCCTTCGTGTTCGACGGCCACCGAGATGGCGCAGCTCTGAAGAGGATGGCGTCGTGC
CTGGCGTCCAGCGTACCGACGGGCGGCGAGGCGCGGCCGACGCATCTCGTGAGGTTCCTGTCCGCGTCGGGTTGTGCCGT
GCCGGTGCGGCCTCCCGTGACGTCTTTCGGTGGCCCGGCAAAGGGGGGCGGCGGTTGACGAGTCGTGCCCGCGGTGGCAT
ACAACGTGAAGCCGAAAACGATGCGAGAGGAAAACCGTCGTTTGCATGAAGTTGGTGTCGCATTTG--------------
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>chr3D_1
GAGCAACTTCCACGCCAAGCAGCTGAGCAACGGCGGCGAGCTGCTCACCGTCGTCTGGTTCTTGATGACGCACCTGGGGA
TGGGCGAGCAGTACCGGATAGAGGCTGGACATGCAAGAGCTAAACTAATTGTGGAGAAGAACTGAGATTGAGAAGATCAC
CAAACGGTGGTGTACTCTGTAG-------TCTGTGCTACCTTC-AAAATTCTTAGGTAATATGTGCGCTTTCAAGGAACT
TGAACTGATC-TGTCAGTTTGGTGAATTGGAATGCGATGGCAATACGGATGTACTCCCTCGGTTCCACTGAAACCACTAC
AGTACGAGG--------------GATACCACACTTCACATGATACCACGGTACCACTCCTCAAATTTCAAATTTGCAAGT
CTCCACAAATTTCGATAAAAGTTGTGAACGTTCAACAAGATATGTTTTATACCATCCCTTAAATTTTCAGACCCAAATCC
GAAATATACAATGAGAAACAAAAGGGACAAATCTAGCATGAA-----------------------CAGTGTCACAAAAAG
ACAAATAGCACTATTCACAATTGAATTTGTCTTCTTTGTTTCTCTGTGCGCATTTCGAATTTGGGATTGAAAATTTTGGA
GATTGTAGACTC--ATGTTGTGAACATTCAGAGTTTTATGTTTTCA----------------------------------
-----TTGTATCATGGTATGACGATCATGCAGAGCATGCATGCACAGCACAGGAAACGAAGTCGAGTC-AACGAACCAAG
CGCCATACGGCTAGATCTACGCAGAACGAGTATGTAAGTGGGCCCCGACGACTAAGTTAAGCCAGGAAATCATGAAACAC
ACGATCTAGCGGGCTGACCGGCGGTGTGCCCCTCCACTCCACCACCACCCGCCACCGCGACCTTACCCGGCCACCTCACT
ATATACCGGTACTGCGCTAGCTAGACGTACTACGTCCTCCCCATTCGCTCCAAGGCGTTCGAATTTGTGTGCACCGGCCG
GCGAGCGCCATGTCCCAAGCGCCGGACGCCGAGCCCGACGAGCGCACCGGCTTCACCTGCGGCACGCTGCTCACGTGCTT
CTGCCTCCCAGGATTCTCCAAGAAGAAGCCGGAGGAAACCGGCG---------AGAGCCAGCAGGAGCATCCAGCGGCGC
CGGAACAAGACCGGCGCACGGAGCAGGAACCCCCGCAGGTGCTGCTAAGCCGCGCGGCGTCCCTGGAGAAGCTCGAGTGC
TCCTCGCTCTACTCCGGCAGCAACATCGTCTTCGACTTCCTGGTGGAGGCGGGGGAAGGGGACGACCGTGGCGCCCGGGC
GGTCCATGGATACTGCCCGTCGCCGTGCTTCGACCTGCCGGTGGAGCTGATACGGGCCGGCGAGCGATGCGGGGCCGTCG
CCAGCGACGCGCCGGTCACGTCCGCCTTCGTGTTCGACGGCCACCGAGATGGCGCAACTCTGAAGAGGATGGCGTCGTGC
CTGGCGTCCAGCGTGCCGACGGGCGGCGAGGGGCGGCCAACGCATCTCGTGAGGTTCCTGTCCGCGTCGGGTTGTGCCTT
GCCGGTGCGGCCTCCCGTGACGTCTTTCGGTGGCCCGGCAAAGGGGGGCGGCGGTTGACGAGTCGTGCCCGCGGTGGCAT
ACAACGTGAAGCCGAAAACGATGCGAGAGGGAAGCCGTCG-TTGCATGAAGTTGGTGTCGCATTTGGTTTTCACAATTTT
GACATAAGAAATCCAATTCCTTT---------------------------------------------------------
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>SNPs
---S--S-----------------------S-------------------------------------------------
----------S---S-----------------------------------------------------------------
--------S------------S------------S---------------------------------------------
-----------S--------------------------------------S--------S--------------------
------------S-------S----S------------------------------------------------------
----S--------------------------------------------S---S--------------------------
-------------------------SS----S----------SSSSSSSSSSSSSSSSSSSSSSS---------------
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----------------------------S--------S-------------SSSS---------S-------------SS
S-S------------S----S-------------------S-S--S-S--------S-----------------------
------------------------------------------S-------------------------------------
----------------------------------------S---------------------------------------
------------------------------------------S-------------------------------------
--------S-----------------------------------------------------------------------
------------------------------S------------SSSSSSSSSS---------------------------
------------S------------------S--------------------S---------------------------
--------------------------------------------------S-----------------------------
---------------------------------------------------------------------------S--S-
-S--------------------------------------------------------------------S---------
-----------------S--S-----------------------------------------------------------
----------S-------------------------------S------------------S------------------
-----S-------------------------S--------------S----------------------------S----
S---SS--------------S--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSS
>forward_333
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------------------------------------------------------------------------ACCAGTAC
AGTACGAGGTGGA-------------------------------------------------------------------
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>reverse_2240
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-------------------------------------------------------------------------------C
ATCCTCTCAGCCTGTGCAA-------------------------------------------------------------
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