>input_sequence_74499
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--ATGGATCGCCGCCGCCATCACCAAGCCAGAGAATTCGGTCGGTAAT----CTCATGCTCCTCCTCTTATCTTCTCCGC
CTCA---------TCCATGT---ATCAGCTAGCAAGCAACCGAGTCA---TAGCAATT-CAAACTTGA------ATGAAT
GAATGAATCAACCAATCGATCGATC----ATTCGCAGTGGCGGACGTGGTGCTGTGGCGGCGAGGCCGGGCGGACCTGAC
CGCGCTGCTGCTAGCGGCCACCGTCGCCTCCTGGATCCTCT---TCAACCGCGCCTCCGGATACACGGCCGTCTCACTGG
CTGCCGACGTGCTGCTCCTCCTGCTGGTGGTGCTCTACGCATGGTCCAGGGCCGCGCGCCTCCTCGGCCGCCCCGCCCCG
TCCAT---CCCCGACCTGCAGCCGGCGGCCGACGAGCTCGTCGCGCTGGTCCGCTCCGGCCTCGCCCGCCTCGCCTCCGC
CTTCCGCCGCGTCGCGCAGGGCCAACCCGGCTCCGGGCGCGTCTTCGCCTGCCTCGCCGCTGCCGCCCTGCCCGGCGGCC
TCGCGCGCGACCTCCCCACCCTTTTCATAGCAGGAACTGGAATCTGTGTGTTCGGGCGGTTTGCTCTATCCCTCTCGTAA
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>chr4A_1_TraesCS4A01G493100
CCACAAGAAGGCTGAGGAAACGGTGGAGCGTGCAATTGATATGCTTCCCAACCGTGTCAGTCATTATATCAAAACAAGGG
ATAGCGGGTATCTAAGTGTAAATTTATCTATCCGTCACTATATCGGCACAATGGATATAAGGCTGGTCATAATGGGCAAA
AACTTAGGAGTAACTTAGACTAGTGTCATGCATATGACACTAGTCTAACTTACTACCTTCGTAGTGCAAAATAATATAGT
AGTAGTGTCATAGATTGTTTCATTTATTAGCTCATAGACTCATTTTGACTCGGGAAACGCTATGTTACAGTAACATATAT
TATGTTACCACAAACACCTCTTTCCTCATTAAATACTTGCCACATAAGCAAAATTGTATTGGAATGTGTTAAGTTACTAC
CTAAGGCTAGCCATAGTGGGAGTAACTTAGGTAGTAACATAGCACATCCCAAGAAAAAATTGCTTATGTGGCATGGAGTT
AATGAGAAAAGAGATGCTTGTGGTAACATAATATGTTACTGTAACATAATACACCCCAAGGTAAAATGAGTCTATATATC
AATTAATGAAGGCTTGCATGTTACCATCCATATGTTACTACCCACTATGAAGGTAGTAACATAGACTAGTAACATATGCA
TGTTACTAGTCTAAGTTACTCCCCACTATGACCAGCCTAATCGAGTGGACTGGGAGGTACGTAACTAACGCTGCAAGTGG
GACTGTTCCTGGGAATCCCACCTTGATCCACCTAGTCCCAACACGGCTTGATGGAAAAGTAGTGGACGTCCCATCAAAAC
TAGCGCATATTAGGTGGGAATAAGTGGGATCCCACTTAACAGATACATCATATGCATAACTGA-----------------
------------------GAAAAATTGCAATTTGCAGCA---TTTGGGAAAGTGAATTGCACGCCTCCCTCCTTTGATCA
TT----CATCAAACAAATTCCAACCCGGCCAGTACCAAACCCTCTCCTCTCGGCCTGCCTCGAATCATCCATGGACATGC
ACATGGATCGCCGCCGCCATCACCAAGCCAGAGAATTCGGTCGGTAAT----CTCATGCTCCTCCTCTTATCTTCTCCGC
CTCA---------TCCATGT---ATCAGCTAGCAAGCAACCGAGTCA---TAGCAATT-CAAACTTGA------ATGAAT
GAATGAATCAACCAATCGATCGATC----ATTCGCAGTGGCGGACGTGGTGCTGTGGCGGCGAGGCCGGGCGGACCTGAC
CGCGCTGCTGCTAGCGGCCACCGTCGCCTCCTGGATCCTCT---TCAACCGCGCCTCCGGATACACGGCCGTCTCACTGG
CTGCCGACGTGCTGCTCCTCCTGCTGGTGGTGCTCTACGCATGGTCCAGGGCCGCGCGCCTCCTCGGCCGCCCCGCCCCG
TCCAT---CCCCGACCTGCAGCCGGCGGCCGACGAGCTCGTCGCGCTGGTCCGCTCCGGCCTCGCCCGCCTCGCCTCCGC
CTTCCGCCGCGTCGCGCAGGGCCAACCCGGCTCCGGGCGCGTCTTCGCCTGCCTCGCCGCTGCCGCCCTGCCCGGCGGCC
TCGCGCGCGACCTCCCCACCCTTTTCATAGCAGGAACTGGAATCTGTGTGTTCGGGCGGTTTGCTCTATCCCTCTCGTAA
CAAGTGGGGTTTGGATGGGTTCCAATGGGCTAATAGGGGGGTTAGCCCACTTAATATTCTGCCCGTCCAGTGGGAATCCA
CTAATGCAATTTAAGTGGGATGGGATTCTTAATCCCACTTATTCCCACCCC-ACCTGCAATGTGACTTCTACTCCCTCCG
TTCGAAATTACTTGTCGCGAAAATGGATGTATCTAGACGTATTTTAGTTCTAGATACATTCATTTTCGAGATAAGTAATT
CCGAACGGAGGGAATAGTATATAGAAACAGGGTGCAAAAGGAAAACGCGGTATACAGTTTCTTTTTGAATAGTTTGGATT
GCCTACCACAGGTGGTCCACAGTTTTTACGAGGAACATAGTTTGGGTCTACTTCTACG-GGCAGATAAGAGGACCGTATC
TACTTAAAGTAGCTAAACATCACAGCTCAACTACATAGTACTAGTACTTCCAGTCAAAAAAAAAAAACTACATAGTACTA
CATCATTAAAAGAAATAGGACCGTATCACTTATCACAAATATTCAGTATG---------CACACTCCACAAATATTATCA
CAAATATTCAGTGTGCACACTCCACAAATATTATCACAAATATTCAGCTTCCGTATTGCTTATCACTTGAATAGATTTAT
TTAACTCGAGGAATTTTACCATGTGCTAGAACAAAAATTACATCTGTGCATACACATT---AAAAAAAGGATTTGCTAGA
GCAGAATCAGCCGCTTG-AAAAAAAATGACTCTAATCGCAACCGAATTTTGGTGGCCGTCCGATCAGTGCGGGCATTCAC
GCGAGCACACATGGCACTGGGCCGTGGGCGTCTCTCCGGAACAGAGGAGGCGTGAGAGAAAGATGTGCCGGAGAGACGGC
GAGCCAATGTTTCTGCGGTTGGGCGGTGGTGCGGTGGTCACCCAACGCCGGCGCCGTCCCGTCCTTGGGCTGGAGTGGAG
TCGTCGCAGCTTGTTCTCTGTAAGTTTTCGATCTGTAGCTC-AAGCTAGGGTTCCT
>chr6A_167
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------GGAGTAATTTATACTAGTGTCATCCATATAACACTAGTCTAAGTTACTACCTCCATAGTGCAAAGTAAGTAAGT
AGTAGTATCATAGATGGTTTCATTTATTAGCTCATAGACTTATTTTGCCTCGGGAAACGCTATGTTACAGTAACATA--T
TATGTTACCACAAGCACCTCTTTCCTCATTAAATACTTGCCACATAAGCAAAATTGTTTTGGGATGTGTTAAGTTACTAC
GTAAGACTACGCACAGTGGGAGTAACATAGGTGGTAACATCACATTTATCTAGGCAATG------ATGTGGCATGTAATT
AATGAAGAAAGAGAGGCAAGTAGTAA------------------------------------------------------
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------------------------------------------------------CATAACTAGTTA--------------
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----------------CTGTAACATCACACATATCAAAAAAAGATGAGTCTACAACCT-AATAAATGA------AGTGAT
GCATGATACAACACATATGTTACTACTCATTGTAGGGGTAGTAACATAAATTAGTAACATATG-----------------
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-------CATGTTACTCCTCTAAGTTACTACCCACTATGACTAGTCTAA-------------------------------
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>chr7B_706
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-----------------------------------------------------------------TAACGCTGCAAGTGG
GACTGTTCCTGGGAATCCCACCTTGATCCACCTAGTCCCAACACGGCTTGATGGAAAAGAAGTGGATGTCCCATCAAAAC
TAGCGCATAATAGGTGGGAATAAGTGGGATCCCACTTAACAGATGCATCATATGCATAACTGAGAAAAATTGCAATTTCC
GGTTTCTTTCTTTCCAGCGAAAAATTGCAATTTGCAGCA---TTTGGGAAAGTGAATTGCACGTCTCCCTCCTTTGAGCG
TT----CATCAAACAAATTCCAACCCGGCCAGTACCAAACCCTCTCCTCTCGGTCTGCCTCGAATCATCC------ATGG
ACATGGATCTTCGCCGCCATCACCACGCTGGAGAATTCGGTCGGTAATTAACCTCATGCTCCTCCTCTTATCTTCTCCGC
CTCA---------TCCATGT---ATCAGCTAGCAAGCAACCGAGTCA---TAGCAATCGCAAACTTGA------ATGAAT
GAATGAATCAACCAATCGATCGATC----ATTCGCAGTGGCGGACGTGGTGCTGTGGCGGCGAGGCCGGGCGAACCTGAG
TGCGCTGCTGCTGGCGGCCGCCGTCGCCTCCTGGATCCTCT---TCAACCGCGCCTCCGGATACACGGCCGTCTCGCTGG
CCGCCGACGTGCTGCTCCTCCTGCTGGCGGTGCTCTGCGCGTGGTCCAGGGCCGCGCGCCTCCTCGGCCGCCCCGCCCAT
CCCCGAGACCCCGACCTGCAGCCGGCGGCCGACGAGCTCGCCGCGATGGTCCGCTCCGGCCTTGCCGGCCTCACCTCCGC
CTCCCGCCGCGTCACGCAGGGCCAGCCCGGCTCCGGGCGCGTCTTCGCCTGCCTCGCCGCCGCCGCCCTGCTCGGCCGCC
TCGCGCGCGACCTCCCCACCCTTTTCATAGCAGGAACTGGAATCTGTGCGCTCGGGCGGGTTGCTCTATCC-TCTCGTAA
CAAGTGGGGTTAGGGTGGGTTCCAATGGGCTAATA---GGGTTAGCCCACTTAATATTCTGCCGGTCCAGTGGAAATCCA
CTAATGCAATTTAAGTGGGATGGGATTCTTAGTCCCACTTATTCCCACCCCCACCTGCA---------------------
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>chr6B_706
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-----------------------------------------------------------------TAACGCTGCAAGTGG
GACTGTTCCTGGGAATCCCACCTTGATCCACCTAGTCCCAACACGGCTTGATGGAAAAGAAGTGGATGTCCCATCAAAAC
TAGCGCATAATAGGTGGGAATAAGTGGGATCCCACTTAACAGATGCATCATATGCATAACTGAGAAAAATTGCGATTTCC
GGTTTCTTTCTTTCCAGCGAAAAATTGCAATTTGCAGCA---TTTGGGAAAGTGAATTGCACGTCTCCCTCCTTTGATCA
TT----CATCAAACAAATTCCAACCCGGCCAGTACCAAACCCTCTCCTCTCGGTCTGCCTCGAATCATCC------ATGG
ACATGGATCGCCGCCGCCATCACCACGCCGGACAATTCGGTCGGTAATTAACCTCATGCTCCTCCTCTTATCTTCTCCGC
CTCA---------TCCATGT---ATCAGCTAGCAAGCAACCGAGTCA---TAGCAATCGCAAACTTGA------ATGAAT
GAATGAATCAACCAATCGATCGATC----ATTCGCATTGGCGGACGTGGTGCTGTGGCGGCGAGGCCGGGCGAACCTGAG
CGCGCTGCTGCTGGCGGCCGCCGTCGCCTCCTGGATCCTCT---TCAACCGCGCCTCCGGATACACGGCCGTCTCGCTGG
CCGCCGACGTGCTGCTCCTCCTGTTGGCGGTGCTCTGCGCGTGGTCCAGGGCCGCGCGCCTCCTCGGCCGCCCCGCCCCG
CCCAT---CCCCGACTTGCAGCCGGCGGCCGACGAGCTCGCCGCGCTGGTCCGCTCCGGCCTTGCCGGCCTCACCTCCGC
CTCCCGCCACGTCACGCAGGGCCAGCCCGGCTCCGGGCGCGTCTTCGCCTGCCTTGCCGCCGCCGCCCTGCTCGGCCGCC
TCGCGCGCGACCTCCGCACCCTTTTCATAGCAGGAACTGGAATTTGTGCGCTCGGGCGGGTTGCTCTATCC-TCTCATAA
CAAGTGGGGTTAGGGTGGGTTCCAATGGGCTAATA---GGGTTAGCCCACTTAATATTCTGCCGGTCCAGTGGAAATCCA
CTAATGCAATTTAAGTGGGATGGGATTCTTAGTCCCAC------------------------------------------
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>chr1D_864
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------------------GAAAAATTGCAATTTGCAGCAGCATTTGGGAAAGTGAAGTGCACGTCTCCCTCCTTTGATCA
TTCATTCATCAAACAAATTCCAATCCAGCAAGTACCAAACCCTCTCTCGCGGCCAATC----------------------
-CATGGATCGCCGCCGCCAGCACCACGCCGGAGAATTCGGTCGGTAAC----CTCCTCGTCTCTCTCTCTCTCTCTCTCT
CTCTCTCTCTCTCTCTCTGTATCATCAGCTAGCAAGCAACCGCAGACC---------------------------TGAAT
GAATGAATCAACCAATGGATCCATC----ATTCGCAGTGACGGACGTGGTGCTGTGGCGGCGAGGCCGGGCGGAGCTGAG
CGCGCTGCTGCTGGCGGCCGCCGTCGCCTCCTGGATCCTCT---TCCACGGAGCCTCGGGTTACACGGCCGTCTCGCTGG
CCGCCGACGTGCTCCTCCTGCTGCTGGCGGTGCTGTACGCGTGGTCCAGGGCCGCGCGCCTCCTCGGCCGCCCCGCCCCG
CCCAT---CCCCGACCTGCAGCCGGCGGCCGACGAGCTCGCCGCGCTGATTCATTCGTGCCTCGCCGACCTCGCCTCCGC
CTTCCGCCGCGTCGCGCAGGGCCAGCCCGGCTCCGGCCAGGTGTTCCTCTGCCTCGCCGCCGCCGCCCTGCTGGGCCGCC
TCGCGCGCGACCTCCCCACCCTGTGCTACGCAGG----------------------------------------------
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>chr6B_995
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----------------------------------------------------------------------------ATGG
ACATGGATCGCCGTCGCCATCACCACGCCGGAGAATTCGGTCGGTA----ACCTCATGCTCCTCCTCTTATCTTCTCCGC
CTCA---------TCCATGT---ATCAGCTAGCAAGCAACCGAGTCA---TAGCAAACGCAAACTTGA------ATGAAT
GAATGAATCAACCAATCGATCGATC----ATTCGCGGTGGCGGACGTGGTGCTGTGGCGGCGAGGCCGGGTGAACCTGAG
CGCGCTGCTGCTGGCAGCCGCCGTCGCCTCCTGGATCCTCT---TCAACCGCGCCTCCGGATACATGGCCGTCTCGCTGG
CCGCCGACGTGCTGCTCCTCCTGCTGACGGTGCTCTACGCGTGGTCCAGGGCCGCGCGCCTCCTCGGCCGCCCCGCCCCG
CCCAT---CCCCGACCTGCAGCCGGCGGCCGACGAGCTCGCCGCGCTGGTCCGCTCCGGCCTTGCCGGCCTCACCTCCGC
CTCCCGCCGCGTCACGCAGGGCCAGCCCGGCTCCGGGCGCGTCTTCGCCTGCCTCGCCGCCGCCGCCCTGCTCGGCCGCC
TCGCGCGCGACCTCCCCACCCTTTTCATAGCTGGAACTGGAATCTGTGCGCTCGGGCGGGTTGCTCTATCC-TCTCATAA
CAAGTGGGGTTAGGGTGGGTTCCAATGGGCTAATA---GGGTTAGCCCACTTAATATTCTGCCGGTCCAGTGGAAATCCA
CTAATGCAATTTAAATGGGATGGGATTCTTAGTCCCACTTATTCCCACCCCCACCTGCAGCGTGAC--------------
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>chr1B_1005
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------ATCGCCGCTGCCATCACCACGCCGGAGAATTCGGTCAGTA----ACCTC----------------CTCCTCCTT
CTCT---------TCTCTGT---ATCAGCAAGCAAGCAA-------------GCAACCGCAGACCTGAATGAGTATGAAT
CAATGAATCAACCAATCGATCGATCGATCATTCGCAGTGGCGGACGTGGTGCTGTGGCGCCGAGGCCGGGCCGACCTTAG
CGCGCTGCTGCTGGCGGCCGCCGTCGCCTCCTGGATCCTCTTCTTCCACGGCGCCTCGGGTTACACGGCCGTGTCGCTGG
CCGCCGACGTGCTGCTCCTGCTGCTGGCGGTGCTGTACGCGTGGTCCAGGGCCGCGCGCCTCCTCGGCCGCCCCGCCCCG
CCCAT---CCCGGACCTGCAGCCGGCGGCGGAGGAGCTCGCCGCGCTGGTCCGCTCCGGCCTCGCCGGCCTCGCCTCCGC
CTTCCGCCGCGTCGCGCAGGGCCAGCCCGGCTCCGGGCGCGTCTTCGCCTGCCTCGCCGCCGCCGCCCTGCTCGGCCGCG
TCGCGCGCGACCTCCCCACCCTCTGCTACGCAGG----------------------------------------------
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>chr4A_1955
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---------------------------------AACATAGTTTGGGTCTACTTCTACGAGGCGGCTAAGATCACCGTATC
TACTTAAAGTAGCTAAACATCACAGCTCAACTACATAGTCA---------------------------------------
-ATCATTAAAAGAAATAGGACCGTATCACTTATCACAAATATTCAGTGTGCAACTTAACCACACTCCACAAATATTATCA
CAAATATTCAGTGTGCAACTTAGCCACACTC---CACACATATTCAGCTTCCGTGTCGCTTATCACTTGAATAGATTTAT
TTAACTCGAGGAATTTTACCATGTGCTAGAACAAAAATTACATCTGTGCGCATACACAGTAAAAAAAAGGATTTGCTAGA
GCAGAGTCAGCCGCTTGAAAAAAAAATGACTCTAATCGCAACCGAATTTTGGTGGCTGTCCGATCAGTGCGGCGATG---
-----------TGGCACTGGGCCGTGGGCGTCTCTCCGGAGCAGAGGAGGCGTGAGAGAAAGATGTGCCGGAGAGGCGGC
GAGCCAATGTTTCTGCCGTTGGCCGGTGGTGCGGTGGTCACCCAACGCCGGCGTCGT--CGTCCTTGGGCTCGAGTGGAG
TCGTCGCAGCTTGTTCTCTGTAAGTTTTGGATCTGTAGCTAGAAACTAGGGTTCCT
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSS-------S---S-----------S-----S------------S---------S-S---------S---SSS---
------S--------S------------------------S------S-----------------------------SS-
-------------S-------------------------------------------S----S-----------------
S----S---SS--S------------S-----S-------SS--SS-SS-S--SS--SSSSSSSS----------S-S--
-----SS-------S--SS--S----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS---------------
-----------------------------------------------------------S------S-------------
---------S----------------------------------S-----------------------------------
---------------------------------------------------------------S----------------
----------------------------------------------------------------------SSSSSS---S
-------------------------S---S--------------------------------------------------
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-------------------------------------------------------------------------------S
------------S------S-------------------------------------------------------S----
-S-------------------------S------------S---------------------------------------
S---------------------------------------S-------------------------S-------------
------------------------S-----------------------------------S----------S----S---
------------------------------------------------S-S--------S-----------S--------
-----------S--S--------------------SSS-------------------------S---------S------
-------------------------------S---------------------------SS-----SSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----------------------------S-S-----SS--------
---------------------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
S----------------------------------------------S--------------------------------
-----------------SSS-SSS--S-SSSSSS----S---------------S-S-----------------------
-------------------------------------------------SS-S---SS----------------------
-----S--------------------------------------------------S---------------SS--SSSS
SSSSSSSSSSS-----------------------------S----------------------------------S----
----------------S-----S------------------------------S---SS------------S--------
----------------------------S-----------S---S-----------
>forward_25
-----AGAAGGCTGAGGAAACGGTG-------------------------------------------------------
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>reverse_1949
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----------------------------AGGGTGCAAAAGGAAAACGC--------------------------------
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