>input_sequence_67108
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------------------------------------------------------------------ATGGCGTTACGCCT
CTCCGTCTCCTCGCCGCAGAGCACGGCCTCCTCGCCGGCCATCTCCTCATGCCGCCCCGCCGCCTGCGGCCGCTTCCTGG
CCTGCGTGGCCGCTTCTCAGAAGAGGAGCCTGATGGTGGTGTCCGGCTCTGACGGGAGGGGAGTGGCTCCGGTGAAGTCG
GGCGGCTTGGAGACGGCCACGACGGGAGCCGACGAGGTGGAAGCGCCCACAGCGGCGGTGGCGGTGACCGGGCAGGTCAC
GGAGGTCTGCAAGGACACCTTCTGGCCAATTGTCAAGGCAGCAGGGGAGAAGCCCGTCGTCCTCGACATGTACACCCAAT
GGTACTGTGCAAGCCCCATACATTTCTTCGTTTCAGCTCTTCTTCACTGATGAACTACTGTCTCAATCCCACATCTTCCT
GCCATACAAGCTAGACCAGATTATTTAGAGATGCATGTATATTGTTATAATCCAGATCAGATGTCATCCCGCAGCACAGT
GATGAAATTTCCTTGTCTGCAGGTGCGGCCCTTGCAAAGTTATGGCACCAAAATTCCAGGAGATGTCTGAGAAGGACCAC
GACGTCGTATTCCTCAAGCTCGATTGCAATCAAGACAACAGGGTATGTTAGAAACTGGAACCATCTTGCTATCTCATGTG
TATCTTGTATTTTGTTTGAATATATCATGGTAAGCTTCTTGGTGCTTGTCTTGTCAATTGTAGCCTCTTGCAAAGGAGCT
TGGCATAAGGGTTGTACCAACATTCAAGATTTTCAAGGATGGGAAGGTTGCAAAGGAGGTCACTGGTGCGAAGATTGATG
AATTAGCACGTGCGATTGAGGAAGTGAAGTCAAGCTGA------------------------------------------
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>chr3D_1_TraesCS3D01G413900
GCCGCTGCCGGACCTATCAGTGAGGTAGCTGCTGCCAG----CCGCTACCGTCCGCGATGGATACGTGGTTTTCGACCT-
TGCGTCGCGATCGTAACCGCACGTTGCAGGATCTCTGGTGTCTCCCGGTAAAATATCTCCGGCCGGAACTTTCCATTGCT
TCTGTGAAGAAGCTAGCGGAGCCACAGACATTGCCATCCAAGCTAGATTGTGTGCAAGCTGTAGAGGTTTTCTGGCAAGA
CAGGCAGAATTCGCACAACGTGGCGCACGCGCACGGTACAATCACGATCTATACTTTCGGTAGAGAGAGAAGCCAGTGGT
TTCATCT-------CGGGTGATGCTGATTCGTTTGGAGATGCTGGTTACTTTGTTCACTGGAGAGTGCAGAGCTGCCCTG
AATTACGCTGCACCATGAAAGTATATTCTTTTTTGGAGGAAGCATC---ATGAAAGTAATTGAAGCCGAACGTACTAGAT
GAAGACAAAGCAGGCGCAGTAAATTTACTCGTTTCAGTCAGAAATGGAAGGAGAAGCATCTAAGATGCTGATTCCATGTA
CTCCTAATATCCATCCTGATACCTCAAGAGTCATCAACTAGTCACGGTACACACATGTGGCGACGACCTGTGGCCGTGTG
TGGGCTCATAAGGTCCGTAGCCCACCAGTCGCCGGTGCAAGTGCCATACACAGATGTCACGCAAGCTGTCCGTGGAACAG
ATGCAACAAGGGCACCGGGCAGGCCACCACACGATCCGATCTTCCGGTTACCCAAAACACCCTCGGTGCTCACAAGTACA
GGATCCAGCGTCACCACAAAACCGCAGGAACTTCCGAGGGCAGCCACGTCCATTCTCGGAAGAAACCATCTCTGCCGGAT
AGCCGATATATACCACCAAGCAACCGGGATTTCCCCTCAAGCCCACCCACTCATCTTAG-CAG----------GAAAACA
CCACTCTGTACACCACCAACTAACACCACCCGTTGGGGGCGTTACCTTCCAAAACTCCAGCATCCAATGGCGTTACGCCT
CTCCGTCTCCTCGCCGCAGAGCACGGCCTCCTCGCCGGCCATCTCCTCATGCCGCCCCGCCGCCTGCGGCCGCTTCCTGG
CCTGCGTGGCCGCTTCTCAGAAGAGGAGCCTGATGGTGGTGTCCGGCTCTGACGGGAGGGGAGTGGCTCCGGTGAAGTCG
GGCGGCTTGGAGACGGCCACGACGGGAGCCGACGAGGTGGAAGCGCCCACAGCGGCGGTGGCGGTGACCGGGCAGGTCAC
GGAGGTCTGCAAGGACACCTTCTGGCCAATTGTCAAGGCAGCAGGGGAGAAGCCCGTCGTCCTCGACATGTACACCCAAT
GGTACTGTGCAAGCCCCATACATTTCTTCGTTTCAGCTCTTCTTCACTGATGAACTACTGTCTCAATCCCACATCTTCCT
GCCATACAAGCTAGACCAGATTATTTAGAGATGCATGTATATTGTTATAATCCAGATCAGATGTCATCCCGCAGCACAGT
GATGAAATTTCCTTGTCTGCAGGTGCGGCCCTTGCAAAGTTATGGCACCAAAATTCCAGGAGATGTCTGAGAAGGACCAC
GACGTCGTATTCCTCAAGCTCGATTGCAATCAAGACAACAGGGTATGTTAGAAACTGGAACCATCTTGCTATCTCATGTG
TATCTTGTATTTTGTTTGAATATATCATGGTAAGCTTCTTGGTGCTTGTCTTGTCAATTGTAGCCTCTTGCAAAGGAGCT
TGGCATAAGGGTTGTACCAACATTCAAGATTTTCAAGGATGGGAAGGTTGCAAAGGAGGTCACTGGTGCGAAGATTGATG
AATTAGCACGTGCGATTGAGGAAGTGAAGTCAAGCTGAGCAATTCCCTGGAAAGAAATGCACCAGTTAGCATGCTATCAC
TAGTGTACACTATGGGATGAAAACAGCCTTTGTGGAAGTGGATAATCACCGTGGAGAAAAACAGTTATTATAGTTCTTCT
GCTTATGATGATTTACCAATCGTTCTGGACAATATACACCCATCCATGTGGAGTGTATGCTGTAAATAGTCATTTAAATC
TTTCTGAAAATACGGTTGCTTCCTGATCTCACTAATTTGCAGGCCTACCAAGCATGTTTTGCAAAACATATATAAAAAAA
TCTTGTTCTTACAGATGTAAGCATCGTGACATTGAACTAAGATTGCTTTACTTAATTCATTCCTATTATACCGTGTGAAC
CATAGCTTAAATATCTATATAGTGTCTTAATAACTTCAAATATTAGCCGTTGGATATGCTCTATCAAACGGTTGAGAGAT
GGCAATCCGAACATTATCATCTGTTGAATAAAGTTTTCAACTCATAAGATTTTGCACGTTGCCTTCTAACTGAACCCCAA
CTCTATCATTTGATGTGTTCTAGAAACATCTTTCCCCATGCTTATCTGATTCTCTAATAAGAGATAGAAC--------AT
CTGGATTCTAGAGGGGTAAGAACCAAGTTGGGATAGAGTTGGATCTTGCCAATATGATTCAAGGAAAGGAAATAAATATC
AGAGTGTATTTTTCCATGATGTTATATATCTAAATGGAGTGCAAAGCACGTACAATTTACTAGTTTCGTT--AAAAATAC
TTATCTAAGATGCAGAGCTTAAACTGCAATAGCAGTTTGTGTGGAGATTACAAACTTACTATGGAAAAGTAACTCTGAAT
ACCTACGCAAATCAATATAAATTAGCCATGGTGAGTTCCAGGTATAAAATGAGCTGTGAAGAAATGAAGGTACCTTGCTA
GCATCTCAACTTAGTTGCATTCTTGATAGTTCAATTAGCCATGTTTTCTGCCTATGTAGCCTGCACCGATTTAACATATA
CTCCCTCC
>chr3B_1
GCCGCTGCTCGACCTATCCGTGACAGTGAGGTTGCTGCCGCTCCGCTACCGTCCGCAGTGGCTACATGTTTTTCTACCT-
TGCGTCGCGATCGTAGCCGCACGTCGCAGGATCTCTGGCGTCTCCCGGTAAAATATCTCCGGCCGGAACTTTCCATTGCT
TCTCTGAAGAAGCTAGCGGAGCCACAGACATTGCCATCCAAGCTAGATTTTGTGCAAGCTGTATAGGTTTGCTGGCGAGA
CAGGTAGAATTCGCACAACGTGGCGCACGCGCGCGGTACAATCGCGATCTATACTTCTGCTAGAGAGAGAGGCCAGTGTT
TTTCTCTCGTCTGATA-------CTGATTCTTTTGGAGATGCTGGTTACTTTGTTCACTGGGGAGTGCAGAGCTGCCCTG
AATTACGCTGCATCATGAAAGTGCC-TTTTTTTTGGAGGAAGCATC----TGAAAGTAATTGAAGCAGAACGTACTAGAT
GAAGACAAAGCAGGCGTCGTAACTTTACTCGTTTCAGTCAGAAATTGAAGGAGAAGCATCTAAGATGCTGATTCCATGTA
CTCCTAATATCCATCGTGATACCTCAGGAGTCATCAACTAGTCACGGTACACACATGTGGCGACGACCTGTGGCCGTGTG
TGGGCTCATAAGGTCCGTAGCCCACAAGTCGCCGGTGCAAGTGTCATATACAGATGTCACACACGCTGTCCGTGGAACAG
ATGGAACAAGGAAACCGAGCAGGGCACCACACGATCAGATCTTCCGGTTAGCCAAAACACCCTCGGTGCTCACAAGTACA
GGATCCAGCGTCACCACAAAACCGCAGGAACTTCCGAGGGCAGCCACGTCCATTCTCAGAAGAAACCATCTCTGCTCGAT
AGCCGATATATACCACCAAGCAACCGGGATTTCCCCTCAAGCTCACCCACTCATCTGCTGCCGCTGCTTCAGAGAAAACA
CCGCTCTGCACACCACCAATTCACACCACCCGTTGGGGGCGTTACCTTCCAAAACTCCTGCAGCCAATGGCGTTACGCCT
CTCCGTCTCCTCGCCGCAGAGCACGGCCTCCTCGCCGGCCATCTCCTCATGCCGCCCCGCCGCCTGCGGCCGCTTCCTGG
CCTGCGTGGCGGCTTCTCAGAAGAGGAGCCTGATGGCGGTGTCTGCCTCTGATGGGAGAGGAGTGGCTCCGGTGAAATCC
GGCGGCTTGGAGACAGCCACGACGGGAGCCGGCGAGGTGGAAGCGCCCACAGCGGCGGTGGCGGTGACCGGGCAGGTCAC
GGAGGTCTGCAAGGACACCTTCTGGCCAATTGTCAAGGCAGCAGGGGAGAAGCCCGTCGTCCTCGACATGTACACCCAAT
GGTACTGTGCAAGCCCCATGCATTTCTCCGTTTCAGCCCTTCTTCACTGATGAACTACTGTCTCAATCTCACATATTCCT
GACATACAAGCTAGGCCAGATTATTTAGAGATGCATGGGTATTGTTATAATCAAGACCAGATGTCATCCCGCAGCAGAGT
GATGAAACTTCCTTGTCTGCAGGTGCGGCCCTTGCAAAGTTATGGCACCAAAATTCCAGGAGATGTCTGAGAAGGACCAC
GACGTCGTGTTCCTCAAGCTTGATTGCAATCAAGACAACAGGGTATGTTAGAAACTGGAACCATCTTGCTGTCTCATGTG
TATCTTGTATTTTGTTTGAATATATCATGGTAAGCTTCTTGGTG-----CTTGTCAATTGTAGCCTCTTGCAAAGGAGCT
TGGCATAAGGGTTGTACCAACATTCAAGATTTTCAAGGATGGGAAGGTTGCAAAGGAGGTCACTGGTGCGAAGATTGATG
AATTAGCGCGTGCGATTGAGGAAGTGAAGTCAAGCTGAGCAATTCCCTGGAAAGAAATGCAGCAGTTAGCATGCTATCAC
TAGTGTACACTATGGGATGAAAACAGCCTTTGTGGAAGTGGATAATCACCGTGGAGAAAAACAGTTATTATAGTTCTTCT
GCTTATGATGATTTACCAATCGTTCTGGACAATATACACCCATCCATGTGGAGTTTATGCTGTAAATAGTCATTTCAATC
TTTCTGAAAATACGGTTGCTTCCTGATCTCACTAATTTGCAGGCATACCAAGCATGTTTTGCAAATCATAT-TAAAAAAA
TCTTGTTCTTACAGATGTAGGCATCGTGACACTGAGCTAAGATTGCTTTACTCAATTCATTCCTATTATACCATGT-AAC
CATAGCTTAAATATCTATAAAGTGTCTC-ATAACTTCAAATATTAGCCATTGGATATGCTCTATCAAACGGTT--GAGAT
GGCAATCCGAACATTATCATCTGTTGAATAAAGTTTTCAACTCATAAGATTTTGCACGTTGCCTTCTAACTGAACCCCAA
CTCTATCATCTGATGTGTTCTAGAAACATCTTTCGCCATGCTTATCTGATTCTCTAATAAAATAAGAGACTAAGAACAAT
CTGGATTCTAGAGGGGTAAGAACCAAGTTGGGATAGAGTTGGATCTTGCCAATATGATTCCAGGAAAGGAAATAAATGTC
AGAGTGTATTTTTCCATGCTGTTATATATCTAAATGGAGTGCAAAGCAGGTACATTTTACTAGTTTTGTTAAAAAAATAC
ATATCTAAGATGCAGAGCTTAAACTGCT-----------TGTGGAGGTTACAAACTTATTATAGAAAAGTAACTCTGAAT
ACCTACGCAAATCAATATAAATTAACCATGGTGAGTTCCAAGTATAAAATGAGCTGTGAAGAAATGAAGGTACCTTGCTA
GCATCCCAACTTAGTTGCAGTCTTGATAGTTCAATTAGCCATGTTTTCTGCCTC---AGCCTGCACCGATTTAACATATA
--------
>chr3A_27
A-----------------------------GTTGCTGCCGCTCCCCTACCGTCCGCGATGGTTACGTGTTTTTCTACTTC
TGCGTCGCGATCGTAGCCGCACGTCGCAGGATCTCTGGCGTCTCCCGGTAAAATATCTCCGGCCAGAACTTTCCATTGCT
TCTCTGAAGAAGTTAGCGGAGCCACAGACTTTGCCATCCAAGCTAGATTTCGTGCAAGCTGTGGAGGTTTTCTGGCAAGA
CAGGCAGAATCCGCACAACGTGGGGCACGCGAGCGGTACAATCGCGATCTATACTTCTGCTAGAGAGAAAAGCCAGTGGT
TTCATCTCGGCTCTCGGGTGATGCTGATTCGTTTGGAGATGCTGGTTACTTTGTCCACTGGAGAATGTAGAGCTGCCCTG
AATTACGCTGCATCACGAAAGCACGTTTTTTTTTGGAGGAAGCATCATCATGAAAGTAATTGAAGCAGAACA---TAGAT
GAACACAAAGTAGGCGAGGTAACTTTACTCGTTTCAGTCAGAAATGGAAGGAGAAGCATCTAAGATGCTGATTCCATGTA
CTCCTAATACCCATCGTGATACCTCAGGAGTCATCAACTAGTCACGATACACACATGTGGCGACGACCTGTGGCCGTGTG
TGGGCTCATAAGGTCCGTAGCCCACAAGTCGCCGGTGCAAGTGTCACATACAGATGTCACACACGCTGTCCGTGGAACAG
ATGGAACAAGGGAACCGAGCAGGGCACCACACGATCAGATCTTCCGGTTACCCAAAACACCCTCAGCGGTGACAAGTACA
GGATCCAGCGTCACCACAAAACCGCAGGAACTTCCGAGGGCAGCCACGTCCATTCTCAGAAGAAACCATCTCTGCCTGAT
AGCCGACATATACCACCAAGCAACCGGGATTTCCCCTCAAGCTCACCCACTCATCTGCTCCAG----------GGAAACA
CCACTCTGTAGACCACCAACTCACACCACCCGTTGAGGGCGTTACCTTCCAAAACTCCTGCATCCAATGGCGTTACGCCT
CTCCGTCTCCTCGCCGCAGAGCACGGCCTCGTCGCCGGCCATCTCCTCATGCCGCCCCGCCGCCTGCGGCCGCTTCCTGG
CCTGCGTGGCGGCTTCTCAGAAGAGGAGCCTGATGGTGGTGTCTGGCGCTGACGCGAGGGCAGTGGCTCCGGTGAAGTCG
GGCGGCTTGGAGACGGCCACGACGGGAGCTGACGAGGTGGAAGCGCCCACAGCGGCGGTGGCGGTGACCGGGCAGGTCAC
CGAGGTCTGCAAGGACACCTTCTGGCCAATTGTCAAGGCAGCAGGGGAGAAGCCCGTCGTCCTCGACATGTACACCCAAT
GGTACTGTGCAAGCCCCATACATTTCTCCGTTTCAGCTCTTCTTCACTGATGAACTACTGTCTCAGTCTCCCATATTCCT
GACATACAAGCTAGGCCAGATTATTTAGAGATGCATGGGTATTGTTATAATCAAGACCAGATGTCATCCCACAGCAGAGT
GATGAAACTTCCCTGTCTGCAGGTGCGGCCCTTGCAAAGTTATGGCACCAAAATTCCAGGAGATGTCTGAGAAGGACCAC
GACGTCGTATTCCTCAAGCTCGATTGCAATCAAGACAACAGGGTATGTTAGAAACTGGAACCATCTTGCTGTCTCATGTG
CGTTTTGTATTTTGTCTGAATATATCATGGTAAGCTTCTTGGTG-----CTTGTCAATTGTAGCCACTTGCAAAGGAGCT
TGGTATAAGGGTTGTACCAACATTCAAGATTTTCAAGGATGGGAAGGTTGCAAAGGAGGTCACTGGTGCGAAGATTGATG
AATTAGCGCGTGCCATTGAGGAAGTGAAGTCAAGCTGAGCAATTCCCTGGAAAGAAATGCAGCAATTAGCATGCTATCAC
TAGTGTACACTATGGGATGAAAACAGCCTTTGTGGAAGTGGATAATCACCGTGGAGAAAAACAGTTATTATAGTTCTTCT
GCTTATGATGATTTACCAATCGTTCTGGACAATATACACCCATCCATGTGGAGTGTATGCTGTAAATAGTCATTTAAATC
TTTCTGAGAATACGGTTGCTTCCTGATCTCACTAATTTGCAGGCATACCAAGCATGTTTTGCAAAACATATTT-AAAAAA
TCTTGTTCTTACAGATGCAGGCATCATGACACTAAGCTAAGATTGCTTTACTCAATTCATTCCTATTATACCATGTGAAC
CATAGCTTAAATATCTATAAAGTGTGTCAATAACTTCAAATATTAGCCGTCGGATATGCTCTATCAAACAGTTGAGAGAT
CGCAATCCGAACGTTATCATCTGTTGAATAAAGTTTTCAACTCATAAGATTTTGCACATTGCCTTCTAACTGAACCCCAA
CTCTGTCATCTGATGTGTTCTAGAAACATCTTTCCCCATGCTTATCTGATTCTCTAATAAAATAAGAGACTGAGAACAAT
CTGGATTCTAGAGGGGTAAGAACCAAGTTGGGATAGAGTTGGATCTTGCCAATATGATTCCAGGAAAGGAAATAAATATC
AGTGTGTATTTTTCCATGCTGTTATATATCTAAATGGAGTGCAAAGCACGTACAATTTACTGGTTTTGTT--AAAAATAC
TTATCTAAGATACAGAGCTTAAACTGCAATAGCAGTTTGTGTGGAGATTACAAACTTATTATGGAAAAGTAACTCTGAAT
ACCCACGCAAATCAATATAAATTAACCATGGTGAGTTCCAAGTATAAAGTGAGCTGTGAAGAGATGAAGGTACCTTGCTA
GCATCCCAACTTAGTTGCATTCTTGATAGTTCAATTAGCCATGTTTTCTGCCTC---AGCCTGCACCGATTTAACATATA
--------
>SNPs
--------SS--------S----SSSS-SS-S---SSS-----------------------S------S-----S-----
---------------S--------S-------------S-----------------------------------------
---S---------------------------------------------S------------------------------
--------------------------------S----------S------------SS-S--------------------
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------------S----------SS--S--------------------------------------S-------------
----------------SS----S---------------------------------------------------------
---------------S----------S-----------------------------------------------------
-------------------------S-----------------S----S-----------S--S----------------
---S--------S----S-----S------------S-------------------------------------------
---------------------------------------------------------S------------------S---
------------------------------------------S-------------SSS---------------------
---------------------S------------------------------------S---------------------
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----------S--------------------------------S------------------------------------
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---------------------------S----------------------------------------S-----S-----
-S------------S----------------------SS-------------S---S-------------------S---
-------S------------------------------------------------------------------------
----------------------------------------------------------------------S---------
--------------------------------------------SSSSS-------------------------------
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-------S-----------------------------------------------------S------------------
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--------------------------------------------S--------------------------S--------
-------------------S-----------S---S----------------S-------------------S-------
-------------------S-------S----------------------------------------------------
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---------S--------------------------------------------------S-S-SSSS------------
------------------------------------------------------------S-------------------
------------------S-----------------------------------------------S-------------
----------------------------------------------------------S---------------------
------------------------S---------------S---------------------------------------
-----S-----------------------------------------------SSSS-----------------------
SSSSSSSS
>forward_119
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-------------------CACGTTGCAGGATCTCTGGT-----------------------------------------
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>reverse_1131
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----------CGCTTCTCAGAAGAGGAGCC--------------------------------------------------
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>forward_937
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-------------------------------------CAAGCCCACCCACTCATCTT-----------------------
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>reverse_1848
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-------ACGTGCGATTGAGGAAGTGA-----------------------------------------------------
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>forward_1528
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--------------------------------------------------------------------CCGCAGCACAGT
GATGAAAT------------------------------------------------------------------------
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>reverse_2745
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------------------------GCCATGGTGAGTTCCAGGTA------------------------------------
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