>input_sequence_80865
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--ATGCTGGAAGGGAAGGCGACGGTGGAGGACACCGACATGCCGGCCAAGATGCAGCTGCAGGCTACGTCGGCGGCGTCC
AGGGCGCTCGACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCGGCGCACATCAAGAAGGTGAGAAA-CATGCCAATCC
CGCC-CCCAAATCTATAAGCTGCTGAATCTGCAAGTAACAAGCTAG-GACAGTGCAAGTGCTGCCGAATGATTGGATCTG
ATTTGGACGGCTGCACTGCAGGAGTTCGACACGATCCATGGCCCGGGGTGGCAGTGCGTGGTCGGCTGCAGCTTCGGCTG
CTACTTCACGCACAGCAAGGGGAGCTTCATATACTTCAAGCTCGAGTCGCTCCGGTTCCTCGTCTTCAAAGGCATGGCGG
ATGAGCAACCGCTGCCGTGCTGA---------------------------------------------------------
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>chr3B_1_TraesCS3B01G330900
TTTCATAATATAAAAACGTTTTTGACATTAGTCACTCTTATATTATACTCACACCGTCCAAAAATATTTATCAAAAAAAT
AGATGTATCTAGACATATTTAAATTCTAGTACCACCTTTTTGACACATGTACTGCCGGTACACCACGGCTGGACCGCAGG
AGACCTGCCGCATCTCCGATTATTAACATAAACTATTCCAACAGGGCCATAGCTCCAGAAAAAATATATTATCTCCGGAT
CAAATTAGCAAGAGCTCTTCCCTTTCACATGGAGCTGCTCGCTTTCGCTTATCCCATCCGTTTCTGCTTGTTCCGGTCCA
AGAATACATGA---ATGACTGGACCACGAGGATGGATTGAACAGCAAAGTTCACTGTAACCCACACATGCCTTAATAATA
CGTAATAATGAAAGTAGTAAAAACGCGGCTGGTGACCGCACTTATACTCTCTATATACATACACTCGGAGATCCGATCAG
GTCGGAGACTTTTCAGCCTCCAGCTTACGTGGAGTGCTAATTAACCCATCTGGTGG----------ATATCTTCCAACAA
AAATATCGATCGAGCCAGCAGAACTACTCAGGACAGGCGCCCAGCCCAGCCAGAACGCCAACCATTTTAAATTCAATCGA
AAGGAGAAAAGAACGAACTCAGCAGGCAA---CAGCAGCATCTCCATTTTCAAAGCCAGCCGGAGG-------CCGGAGC
GGCTGTGCCTCAGGTGCTCTATCTATCCGGGAAGGGAACTCGCCGCTGGCTGGAGGTGGTCGTTAGCATGTCAAGTTG--
TTTTCTT--TCGAGCTCTCGTTAGCACGTCACGTTGACGTGGACGCCCGAGCGTGAACTCCGTAGCTATCCGAGCATCCG
CCTACAAAAGGGGCA-AAGCGGTGCCCGGAGCTGCTCCATCCATCATCATCTCCTCTACCCAGCCAGACCTGTCCC----
----------GAGCCAATCATACAGTGCGGCGCGTGCGACTGCGAGCAGAGCTTCTAGCAGAGGAGGGAAGGAGCGAGCG
GGATGCTGGAAGGGAAGGCGACGGTGGAGGACACCGACATGCCGGCCAAGATGCAGCTGCAGGCTACGTCGGCGGCGTCC
AGGGCGCTCGACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCGGCGCACATCAAGAAGGTGAGAAA-CATGCCAATCC
CGCC-CCCAAATCTATAAGCTGCTGAATCTGCAAGTAACAAGCTAG-GACAGTGCAAGTGCTGCCGAATGATTGGATCTG
ATTTGGACGGCTGCACTGCAGGAGTTCGACACGATCCATGGCCCGGGGTGGCAGTGCGTGGTCGGCTGCAGCTTCGGCTG
CTACTTCACGCACAGCAAGGGGAGCTTCATATACTTCAAGCTCGAGTCGCTCCGGTTCCTCGTCTTCAAAGGCATGGCGG
ATGAGCAACCGCTGCCGTGCTGATCCGCTCCGCGC----ATATTTTCACGGCCTGCTGGACTACTACTTGATTACGGGGC
GGCGG-------CTAGTAGTGTGAAACAGTTCCATGAAATGCGCCAATATGGATAAGATGTAAGCT-------TTTGCAT
-CGCAATTCGCGAGTGTGGTCTAAAACTCTGAATGCGTT-GAAT-GGTGGAATTGATCTTCAAATATGATGTTCCGCC-T
TGATTCAGACGAATACAGATAAATTGTTTCAGTAT---------------------------------------------
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-------------------TTTTTGGTCGAAAGATGCTCCT-AGTGTAACTCGCCTGTAAGTGACTAATCCTTTCTGGCT
GGAAGAATAAACAAAAAAAATCATCAATGATAAATTTTTTTGTC----------------TCCGACCTACCGGATTCGAA
CCAGTGACCTAAGGATTTATCTGTAAATACTACAGTCCTCCGCTCTACCAACTGAGCTAAGGTCGGGTTACA--------
----TATTAACATCTTATTAACGGCAACACCAGTTTTGTGTTGGTGATATCCATCGAGTCAAACTTCACATTAACATGAA
CACCAACTGAGTTCAATTGGTTAAACTTGTTTTATGCTCGAAAAATTTACTGCTTCAAAAAACTCTTTTATTCGATGGGA
GGGTGTTGATGAAGAGGCTAAACGAGTACCTAACACAAAGGC-AATTCAATAAGGACCTACTATCATAACAAACCGTGAC
ACTGATTGGAACAACCACATAGGCAAGGACAT-ACCTAGGTTGAGATACAATTCTAGAAAAGGCAAAGTTCAACTTTGTT
TCCTCTCTTCCCGCAAAAAAAAAAAA--TCCTCTCTACTTTGGTACCCAAAACCTTCTTCCTCTTCTGGGGACACAGAGT
GAAATTGTTTGGAATTTCGGGAACCGGCCTGTAGACGACGAGATGCTCATGTACTATGCTTAGGGCATCTTCAACGGCGA
CCCGCAAATTTTCTCCCGCGTTCGTCCGCAGACAGGACGGGACCAGTCTGATGGATGCGGAAGGCCGTCATCCAACCGTA
GCCATAAATGTTCGTCTCTGCT
>chr3D_1
TTTCATAATATAAAAGCGTTTTTGACACTAGTCGCTTTTATATCATATTCATTCCGTCCTAAAATACCTGTCCAAAAAAT
AGAAGCATTCAGACATATTTTAATTCTAGTACCACCTTTT-GGCACATGTACTGCTGGTACACCACGGCTGGACCGCAGA
AGACCTGCCGCATCTCCGATTATTAACATAAACTATTCCAACTGGGCCATAGCTCCGGAAAAATTATATTATCTCCGGAT
CAAACTAGCAAGAGCTCTTCCCTTTCACATGTAGCTGCTCGCTTTCGCTTATCCCATCCGTTTCTGCTTGTTCCGATCCA
AGAATACATAGTATATGACTGGACCACGAGGATGGATTTGGA--CAAAGTTCACTGTAACCCACACATGTCTTAACAATA
-------ATGAAAGCAGTAAAAACGCAGCTAGTGACCGTACTTATACTCTCTATATACATATACTCGGAGATCCGATCAG
GTCGGAGACTTTTCAGCCTCCAGCTTACGTGGAGTGCTAATTAACCCATCTGGTGG----------ATATCCTCCAACAA
AAATATCGATCGAGCCACCAGAAT---TCAGGACAGGCGCCCAGCTCAGCCAGAACGCCAACCATTTTAAATTCAATCAA
AAGGAGAAAAGAAAGAACTCAACAGCAGCAGGCAACAGCATCTCCACTTTCAAAACCAGCCGGAGGCCGGAGGCCGGAGC
GCCTGTGCCTCAAGTGCTCTATCTATCCGGGAA-----CTCGCCGCTGGGTCGAGGTGGTCGTTAGCACGTCAAGTTGTT
TTCTCTT--TCGACTTCTCGTTAGCGCGTCACGTTGACGTGGACGCCCGAGCGTGAACTCCGTAGCTATCCGGGCATCCG
CCTACAAAAGGGGCATAAGTGGTGCCCGGAGCTGCTCCATCCATCATCACCTCCTCTACCCAGCCAGACCTGTCCC----
----------GAGCCAATCATACAGTGCGGCGCGTGCGACTGCGAGCAGAGCTTCTAGCAGAGAAGGGAGGGAGTGAGCG
GGATGCTGGAAGGGAAGGCGACGGTGGAGGACACCGACATGCCGGCCAAGATGCAGCTGCAGGCCACCTCGGCGGCGTCC
AGGGCGCTCGACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCGGCGCACATCAAGAAGGTGAGAAACT-TGCCAATCC
CGCC-CCCAAATCTACAAATT-CTGAATCTGCAAGTAACAAGCTAGAGACGGTGCAAGTGCTGCGGAATGATTGGATCTG
ATTTGGATGGCTGCACTGCAGGAGTTCGACACGATCTATGGCCCGGGGTGGCAGTGCGTGGTGGGCTGCAGCTTCGGCTG
CTACTTCACGCACAGCAAGGGGAGCTTCATATACTTCAAGCTCGAGTCGCTCAGGTTCCTCGTGTTCAAAGGCATGGCGG
ATGAGCAGCCACTGCCGTGCTGATCTGCTGCGCCC----CTGTTTTAACGGCCGTGTGGACTACTCGATGATTACGGGGC
GGCAGTTACTGCCTACTAGTCTGAAACAGTTCCGTGAAATGCACCAATATGATATGCTGTAACTTGATTCAGCTTTTGCA
CCGCAATTCGCGAGTGTGGTCTGAAACTCTGAATGCGTTGAATGGTGTGGAAATGATCTTCAAACATGATGTTCCAC-TT
TGATTCAGATGAATACAGATAGGTTAATTCAGTATATTGGTGAAGAATTGCTGCAGAATCAGTTGGTTTTTGGCCGAAAG
ATGCTCTTCAATGTAACTTGCCTGTAAACGTGGTCCTTTTCGGCTGGACGAAAGATATAAAAAAAGATAAAAAAATAAAC
GACGAAAAAAGTAAACGTGAAATGCACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCGTGAAATGCACCA
ATATGATATGCTGTAACTTGATTCAGCTTTTGCACCGCAATTCGCGAGTGTGGTCTGAAACTCTGAATGCGTTGAATGGT
GTGGAAATGATCTTCAAACATGATGTTCCACTTTGATTCAGATGAATACAGATAGGTTAATTCAGTATATTGGTGAAGAA
TTGCTGCAGAATCAGTTGGTTTTTGGCCGAAAGATGCTCTTCAATGTAACTTGCCTGTAAACG--TGGTCCTTTTCGGCT
GGACGAAAGATATAAAAAAAGACAAAAAAAGATAAAAAAATAAACGACGAAAAAAGAATATCCGACCTACCGGATTCGAA
CCAGTGACCTAAGGATTGATCTGCAAATACTACAGTCCTCCGCTCTACCAACTGAGCTAAGGTCGGGTTGGTGTTGCTGA
AACGTATTAATATGCTATTAACGGTAGCACCAGTTTTGTGTTCATGATATCCATCGTGTCAAACTTTACATTAACATGAA
CACGAACTGAGTTCAATTGGTTAAACTTGTTTTATGCACGAAAAAAGTATTGCTTC-AAAAAATCTTTTATTCGATGCGA
GGGTGTTGATGAAGAGGCTAAACGAGTACCTAACACAGAGGCAAATTCAATGAGGACCTACAGCCATAACAAACCGTGAC
ACTGATTGGAACAACCACATCAGCAAGGACATTACCTAGGTTGAGATCAAATTCTAGAAAAGGCAAAGTTCAACTATGTT
TCCTCTCTTCCCGCAAAAAAAAAAAGTTTCCTCCCTACTTTGGTACCCAAAACCTTCCTCCTCTTCCGGCGACATAGAGT
GAAACTGTTTGGAATTTTGGGAACCGGCCTGCAGAAGATGAGATGCTCATGTATTATGCTT-------------------
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>chr3A_117
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------------------------------------TTTTTGGCTCATGTACTGTTGGTACACCACGGGTGGACCGCAGG
AGACCTGCCGCATCCG-----ATTAGCATAAACTATTCCAACTGGGCCACAGCTCCAGAAAAGATATATTATCTCCGGAT
CAAACTAGCAAGAGCTCTCCCCTTTCACATGGAGCTGCTCGCTTTCGCTTATCCCATCCGTTTCTGCTTGTTCCGATCCA
AGAATACATA---TATGACTGGACCACGTGGATGGATTTGGA--CAAAGTTCACTGTAACCCACACATATCTTAATACTA
-------ATGAAAGTAGTAAAAACGCAGCTAGTGACCGTACTTATACTCTTTATATACATACACTCGGAGATCCGATCAG
GTCGGAGACTTTTCAGCCTCCCGTTTACGTGGAGTGCTAATTAACCCCTCTGATCTGGTGGTGGATATATCCTCCAACAA
AAGTATCGATCA------------------------------AGCTCAGCCAGAACGCCAACCATTTTAAATTCAATCAA
AAGGAGAAAAGAAAGAACTCAGCAGGCAA---CAACAGCATCTCCATTTTCAAAACCAGCCGGAGGCCGGAGCGGCC---
----GTGCCTCAAGTGTTCTATCTATCCGGGAAGGGAACTCGCCGCTGGGTCGAGGTGGTCGTTAGCACGTCAAGTTG--
TTTTTTCTCTCGAGCTCTCGTTAGCACGTCACGTTGACGTGGACGCGCGAGCGTGAAATCCGTAGCTATCCGGGCGTCCG
CCTACAAAAGGGGCA-AAGCGGTGCC-------------------ATCATCTCCACTACTGCTCAGATTAGTCCTGACTC
CTGAGCGGCTGAGCCAATCATACAGTGCGGCGTGTGCGAGCAGAGCTTCTA--TCTAGCAGAGAAGGGAAGGAGCGGGCA
GGATGCTGGAAGGGAAGGCGACGGTGGAGGACACCGACATGCCGGCCAAGATGCAGCTGCAGGCCACCTCGGCGGCGTCC
AGGGCGCTCGACCGCTTCGACGTCCTCGACTGCCGGAGCATCGCGGCGCACATCAAGAAGGTGAGCAACCATCCCAATCC
CGCCGCCCAAATCTACACCTC-CTGAATCTGCAGGTAACAAGCTAG-GACAGTGCAAGCGCTGCCGAATGATTGGATCTG
ATTCGGACGGCTGCGCTGCAGGAGTTCGACACGATCCACGGCCCGGGGTGGCAGTGCGTGGTGGGCTGCAGCTTCGGCTG
CTACTTCACGCACAGCAAGGGGAGCTTCATATACTTCAAGCTCGAGTCGCTCCGGTTCCTCGTCTTCAAAGGCATGGCGG
AAGAGCAGCCGCTGCCGTGCTGATCTGCTGCGCCCTCTCCTGTTTTAACGGCCGTGTGGACTACTCGATGATTACGGGGC
GGCAGCTAGCTACTACTAGTATCAACTCC-------AAATGCGCCAA----------TGTAACTTATTTCAGCTTTGCAT
-CGCAGTTCGCGACTGCGGTCTGAAACTCTGAATGCGTTGGATT-TGTGGAATTGATTTTCTAGCATGATGTTCCACTTT
TGATTCAGATGAATACAGATAAATTATGCTTCAGTATTGGTGAAGAATTGCTGCGGAATCAGTTGGCTTTTGGCTAATC-
------------GTAACTCACCTGTAAAACATAAGGAGATAAACGCGCTCCCTTTTTAGCTGCAAGA-------------
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--------------------------------------------------------------------ATTGGTGAAGAA
TATATATAA-----------------------------------------------------------------------
-------------------------------ATAAAAAAATCAACAACAGAAATAGGATTTCCGACCTACCGGATTCGAA
CCAGTGACCTAAGGATTGATCTGCAAATACTACAGTCCTCCGCTCTACCAACTGAGCTAAGGTCGGATT-----------
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>SNPs
---------------S-----------S-----S--S------S---S---SS------S------SS-S--S-------
---S-S--SS----------S---------------------S------------S------------------------
------------------------------------------S-------------------------------------
----S----------------------------------------------------------------------S----
---------SS---------------------------SSSSSS-------------------------S----------
SSSSSSS-------------------S---S-------S-----------------------------------------
-----------------------------------------------------------------------S--------
-----------------S-----SSSS------------------S--------------------------------S-
-------------S--------------------S-------------------S-------------------------
-S----------S------------------------------------S-S----------------S-----------
------------------------------------------------------------------------S-------
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---------------------------------------------------------------S----------------
----------------------------------------------------------------S--S------------
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---------------S--SS-S----------------------------------------------------------
--------------------------------------------------------------S-----------------
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-------S-----------------S---S---S-----S-S----S------SSS---------SSS------------
---S-----------S----S------------S-----------------SSSSSSSSSS-SSSS--------------
----------------------S-------------------S--S------------------S----------S-S--
---------S---------------S------------------------------------------------------
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--------------------------S------------S---S-------S--------SS-SS-SS------SS----
---S---SS-SSS-------SSSSS--SS-S-S-SSSSSS-SSS------------------------------------
-----------------S-----S---------------------------------------------SSS--------
----------S--SS---------S-S---------------SS------------S---------S-------------
---S---------------------------------S-------SS--S------S-----S--------------S--
-------------------------------------S-------------S---------SSS----------------
--------------------SS-------------------------SS--------------------------S----
-------------------------S-------S-----------------------S--------S--S----S-----
----S------------S-------------S---S--S--------------S-------SSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSS
>forward_584
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----ATCGATCGAGCCAGCAGAAC--------------------------------------------------------
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>reverse_3078
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-------------------------------------CGGGACCAGTCTGATGGATG-----------------------
----------------------
