>input_sequence_83075
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-----ATGGCGCCGCCGATGCCGAGCCGCGC---------GCTCATCGTCGCCGTTGCCGCGCTCCTCGTCCTCGTCGTC
GCAGCCGAGCTAGATGCGGGAAGCAGCGGGTGGCCAGCGGAGGATTACGGCGGCGGCGCCG------CCATGCAGGCGGC
GTGCAGGGTGGAGGACGAGGAGGGGTGCGGCGGAGAGGCGACGCCGCGGAGGCATCTGGGCGGAGGCGGCTACATCGGCT
ACGACGCGCTGCGGCGCAACGCCGTGCCGTGCTCGGTCCGCGGCGCGTCCTACTACAACTGCCGCCCCGGCGGGCAGGCC
AACCCCTACTCCCGTGGCTGCTCCTCCATCACCCGCTGCAGAGGATAG--------------------------------
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>chr3D_1_TraesCS3D01G444500
TCCAAATAATGCTGTATACATCTAGAAGCCCAGATATATTGAATCTGCCCATCATGCAAATGTCAGAGCGAGCGAGGCCT
GTCTGTGTATGTCGCCCAGATC-G-ATTTCTTAAAACTAGCTGTGTTTCAGCTGGATGTATGCAGCTGCAGATACAGCCA
AGATATGCTTAAGAAATGGTTGCCCCTCACGTGCCCGCGGCGCCCGCGGACAAAACCT-CCCCGTATCCTATTGCCGCGC
CATGTTACCATGTTGTTGTCAAGGGTCAA----GATCGTCGTCGTTAGCCGCTGCCGCCCGGG--------CACTGTAAA
CAAGTGCAGTTAAAGATATCGCCAGAATCCACACACAGGTTTTGTAGTACATCGGGCACAGTAACTTAA-CAAGCCACTG
CGTAGAAACTAGCAAGTGAGGATAGGGTTCTTGCTT-GGAGGTTTGATCGAGGCAAAGAAAAGTCAGTGTGTCCTAGA--
---------GCATGTGGATCGTGTATTAACAATCCCAACGAAGTACACACATC---TTGTACTGCCATCTGTTCTTAAAT
TTGGCATGTTCTTCCAGCCGGCCGGACGCCCTAATTAACACAGCATGGATCTGGCCAACCGTTTGCTTCGCTTACCAAAT
ATCCAAAAGACATCAGTCCTCTTCGTGTCAGCAAAA--------------------------------------------
--------------------------------------------------------------------------------
------------------------------TGAGGGTTTGCTTGTTTTCATATTTTTTAATTTCAAATTACAAAATGTTA
CCAGTACAAA--TGTGTAGTAGTGCAAGGATTTGAGGTTGGAAAGTCAGTCATTGCCGCGTAC--TGAGTGATTCACACT
CCCTCTCCGCATTTAGAACTCTGCTGATTTCTTTAAGCGACCGTCCTGATGGGATCTTAACCACACTGCACCC-------
-CGGCCAGTCCACTACCCCACACGTC----GACACACAAGCACAAGAGCGAAGGCAGCAGCACTACAGCTTTACACTAGT
GTCATAGCTCGATCGGCGCAGGCTAGT----TAGTAACGTCGACCCCCGCCCTCCCGGAGCGCAGCATCTGGCAGGGTGC
ACGAGATGGCGCCGCCGATGCCGAGCCGCGC---------GCTCATCGTCGCCGTTGCCGCGCTCCTCGTCCTCGTCGTC
GCAGCCGAGCTAGATGCGGGAAGCAGCGGGTGGCCAGCGGAGGATTACGGCGGCGGCGCCG------CCATGCAGGCGGC
GTGCAGGGTGGAGGACGAGGAGGGGTGCGGCGGAGAGGCGACGCCGCGGAGGCATCTGGGCGGAGGCGGCTACATCGGCT
ACGACGCGCTGCGGCGCAACGCCGTGCCGTGCTCGGTCCGCGGCGCGTCCTACTACAACTGCCGCCCCGGCGGGCAGGCC
AACCCCTACTCCCGTGGCTGCTCCTCCATCACCCGCTGCAGAGGATAGAG--ACCCACGGCGTACAGCTTCCTCCTACCT
CGCCGTCGCCGCCGGCCGC-----------CGTCCGGTGGTTCTTGTAGGATCTTGTAAGTTGTAAGACATGTTCGATTG
ATTTTC-T-CTTCTTCTTCCTTCCGTCGGCGGTTCTTGTTT-GGGGTTTCAGTATACGGGATTCAGTCCGAGAATGATTC
GTTGAGCAAATCATCCATGGCAACTTT-TGTACTTGGAGGCAATGTACCGATGCATCGATCGTGAAATCAATGTTACTGA
TTCGTTTGAACTGTACTGTGCGATTGGTAAATAGTACCG-----------------------------------------
-------------------AGTATTACTGCCACGGTGTTTTAATCGAGTTCATAGTTTTCAGACTGTCTGTAGCGTGCGT
GCGTACGTACATGATCGGTAAATAAATCCGTGGTCCTGTCCCGGAGGCAACGAATCGCACTACTCCTGGACGGATGGATC
GATCGATCGCGTTGGTGCTGCCACTTGCCAGTATAATTTATTATTGCGATACGGGCGATGCATTGCACATGAAGCGTGCG
AGCTGCGTAGGAACTGGCGCACCGACAGCCTCTGGAGAGCACGAGACTTTAGTGTTTTGTTTGAGCCCAGATCGGAAGTG
GGCAGATGCAGCCAGAGTAGCATAACCGCACGACAGTGCCGGCTAGTTGATGATGGATTACTGATTTTACTGTTCCATTT
CACAAGTTGTCATGCCGCCGCCTCAGAACATCTGCAACCGCACCCCATTTTCCCCTGGACGCTCACACGGACAGCTTGAA
CATCGTCTGAATCCAAAAACATCATCCAACAGCCCATACGTGGGGTGGATATGTGGCCGCTTGGACTCACCCGGGCAC--
TCGCCATGTTGGACAGACCCATCTCGACCTCACACACTAGTAGAAAAAGGCCCATCTGTCCCGGTATATAAGACCCATCT
GTCCCGGTTGGGGAACCGGGACTAAAGGGTCGTTACTAATGCCTAGGCCTGTAGTCCCGGTTCTTATACTAACCGGGACA
GATGGGC
>chr3B_1
TCCAAATAATGCTGTATACATCTAGAAGCCCAGATTTATTGAATCTGCCCATCATGCAAATGTCAGAGCGAGCGAGGCCT
GTCTGTGTATGTCGCCCAGATC-GGATTTCTTATAACTAGCTGTGTTTCAGCTGGATGTATGCAGCTGCAGATACAGCCA
AGATATGCTTAAGAAATGGTTGCCCCTCACGTGCCCGCGGCGCCCGCGGACAAAACCTCCCCCGTATCCTATTGCCGCGC
CATGTTACCATGTTGTTGTTAACGGTCAAGATCGATCGTCGTCGTTAGCCGCTGCCGCCCGGG--------CACTGTAAA
CAAGTGCAGTTAAAGATATCGCCAGAATCCACACACAGGTTTTGTAGTACATTGGGCACAGTAACTTAAGCAAGCCACTC
CG-------TAGCAAGTGAGGATAGGGTTCTTGCTTTGGAGGTTTGATCGAGGC-AAGAAAAGTCAG--TGTCCTAGATC
GAGCGAGGCGCATGTGGATCGTGTATTAACAATCACAACGAAGTACACACATTTTGTTGTACTGCCATTTGATCTTAAAT
TTGGCATGTTCTTCCGGCCGGCCAGACGCCCTAATTAACACCGCACGGATCTGGCCAGCCGTTTGCCTTGATTACCAGGA
G-GCAAAAGACATCAGTCCTCTTCGTGCCAGAAA----------------------------------------------
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------------------------------TGAGGATTTTCTTGTTTTTATTTTTAAAAATTTCAAATTACGAAATTAC-
----------------------------------AGGTTGAAAAGTCAGTCATTGCCGCGTATATTGATTGATTCTCACT
CCCTCTCCGCATTTAGAACTCTGCTGATTTCTTTAAGCGACCGTCCTGATGGGATCTTAACTACACTGCACGTCTGCATC
ACGG-----CCACTACCCCACACGTC----GACACACAAGCACAAGAGCAAAGGCAGCAGCACTGCAGCATTGCGCTAGT
GTCATAGCTCGATCGGCGCAGGCTAGCTAGCTAGTAGCGTCGACCCCCGCCCTCCCGGAGCGCAGGATCTGGCAGGGTGC
GCGAGATGGCGCCGCCGCTGCCGAGCCGCGC---------GCTCATTGTCGCCATTACCGCGCTCCTCGTCCTCGTCGTC
GCAGCCGAGCTCGATGCGGGCAGCAGCGGGTGGGCAGGGGAGGATTACGGTGGCGGCGCCGCCAC------GCAGACGGC
GTGCAGGGTGGAGGACGAGGAGGGGTGCGGCCGGGAGGCGACGCCGCGGAGGCATCTGGGCGGCGGCGGCTACATCGGCT
ACGACGCGCTGCGGCGCAACGCCGTGCCGTGCTCGGTGCGCGGCGCGTCCTACTACAACTGCCGCCCCGGCGGGCAGGCC
AACCCCTACTCCCGCGGCTGCTCCTCCATCACCCGCTGCAGAGGCTAGAGGCACACACGACGTACAGCTTCCTCCTACCT
CACCGTCGCCGTTTGTCGTCGTCGAGTGCTCGTCCGGTT----TTGTAGGATCTTGTAAGTTGTAAGACATGTTCAATTG
ATTTTCTT-CTTCTTCTTCCTCCCGTCGGCGGTTCTTGTTTTGGGGTTTCATTATACCGGATTCAGTCCGAGAATGATCC
GTTGAGCAAATCATCCATGACTAG-TT-TGTAATTGGAGGCAATGTACCGATGGATCGATCGTAAAATTAAAGTTACTGA
TTCGTTTGAACTCTACTGTGCGATTAGTAATGCTCGATTGCTCATACGTGTATAACTCCCGCCCCGATTGATTGTTCTGC
CGTCTGTCTGCCACGAAATAGTATTACTGCCACGCCACGGT------GTTCAAAGTTTTCAGAGTGTCTATAGCGTGCGT
ACGTACG----TGATCGGTAAATAAATCCGTGGTCCTGTCCTGGAGGCAACGAATCGCACTACTCCTGGACGAATCCATC
GATCGATCGCGTTGATGCTGCCACTTGCCAGTATAATTTATTAGTGCGATACGGGCGATGCATTGCACATGAAGCGTTCG
AGCTGCAGAGGAACTCGCGCACCGACAGCCTCTGGAGAGCACGAGACTTTAGTGTTTTTTTT------------------
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>chr3A_39
--------------------------------------TTGAATCTGCCCATCATGCAGATGTCAGAGCGAGCGAGGCCT
GTGTGTGCATGTCGCGCAGATCAG-ATTTCTTAGAACTAGCTGTGTTTCAGCTGGATGTATGCAGCTGCAGATACAGCCA
AGATATGCTTAAGAAATGGTTGCCTCTCACGTGCCCGCGGCGCCCGCGGACAAAACCTCCCCCGTATCCTATTGCCGCGC
CATGTTACCATGTTGTTGTTAAGGGTCAAGATCGATCGTCGTCGTTGGCCGCTGCCGCCCTGGCTGCTAATCACTGTAAA
CAAGTGCGGTTAAAGATATCGCCAGAATCCACACACAGGTTTTGTAGTACATTAGGCACAGTAACTTAGGCAAGCCGCTC
CG-------TAGCAAGTGAGGATAGGGTT-TTGCTC-GGAGGTTCGATCGAGGCAAAGAAAAGTCAG--TGTCCTAAA--
---------GCATGTGGATCGTGTATTAACAATCCCAACGGAGTACACACATC---TTGTACTGCCATTTGATCTTAAAT
TTGGCATGTTCTTCCAGCCGTCCGGCCGCCCTAATTAACACCGCATGGATCTCGCCAACCATTTGCTTCGCTTACCAGGT
G-CCAAAAGACATTAGTCTTCTTCATGTCAGTGAGACGGAGCTACCTTTGTTAGCACGGGGTCAATTGACCCCCAATGAA
ATTAGCAAGATCTTCACTAACTAATTACTAATCGATATACATTTATAGAACATGACCCCACTGTCATAGAACATGACCCC
ACTAAGCTATTTTTTAGCTTTGTCTGTGAGTGAGGGTTTGCTTGTTCTTATTTTTCAAAATTTCAAATTACAAAATGTTA
CCAGTACAATTGTGTGTAGTAGTGCAAGGATTTCGGGTTGAAAAGTCAGTCATTGCCGCGTAT--TGATTGATTCTCACT
CCCTCTCCGCATTTAGAACTCTGCTGATTTCTTTAAGCGACCGTCCTGATGCGATCTTAACTACACTGCAGCC-------
-CGG-----TCACTACCCCACACGTCGACGGACACACAAGCACAAGAGCAAAGGCAGCAGCACTGCAGCATTGCGCTAGT
GTCATAGCTCGATCGGCGCAGGCTATCTAGCTAGTAGCGTCGACCCCCGCCCTCCCGGAGCGCAGCGTCTGGCAGGGTGC
GCGAGATGGCGCCGCCGCTGCCGAGCCGCGCCGCACTTGCGCTCATCGTCGCCGTTGCCGCGCTCCTCGTCCTCGTCGTC
GCAGCCGAGCTAGACGCGGGCAGCAGCACGTGGGCAGCGGAGGATTACGGCGGCGGCGCCGTCACCGCCATGCGGGCGGC
GTGCAGGGTGGAGGACGAGGAGGGGTGCGGCGGGGAGGCGACGCTGCGGAGGCATCTGGGAGGGGGCGGCTACATCGGCT
ACGACGCGCTGCGGCGCAACGCCGTGCCGTGCTCGGTCCGCGGCGCGTCCTACTACAACTGCCGCCCCGGCGGGCAGGCC
AACCCCTACTCCCGCGGCTGCTCCTCCATCACCCGCTGCAGAGGCTAGCTATCCACG----------------CGTACCT
CGCCGTCGCCGCCGTCG---GTCGACTGCTCGCCCGGTGGTTCTTGTAGGATCTTGTAAGTTGTAAGACATGTTCGATTG
ATTTTC-TTCTTCTTCTTCTTCCAGTCGGTGATCCTTG-TTTGGGGTTTCATTATACCGGATTCAGTCCGAGAATGATTC
GTTGAGCAAATCATCCATGGCTAC-TTCTGTAATTGGAGGCAATGTATCGATGGATCGATCGTGAAATTCATGTTACTGA
TTCGTTTGAGCTGTACTGTGCGATCGGTAAATAG----G-----------------------------------------
-------------------AGTATTACTGCTACGGTGTTTTAATCGAGTTCAGAGTTCTCAGACTGTCTGTAGCGTGCGT
ACGTACG----TGATCGGTAAATAAATCCGTGGTCCTGTCCTGGAGGCAACGAATCGCACTACTCCTGGACGGATCCATC
GATCGATCGCGTTGATGCTGCCACTTGCCAGTATAATTTATTAGTGCGATACGGGCGATGCATTGCACATGAAGCGTTCG
AGCTGCGTAGGAACTGGCGCACCGACAGCCTCTGGAGAGCACGGGACTTTAGTGTTTTGTTTGAGCCCAGATCGGAAGTG
GGCAGATGCAGCCAGAGTAGCATGACCGCACGACAGTGCCGGCTAGTTGATGATGGATCACTGATTTTACTGTTCCATTT
CACAAGTTGTCATGCCGCCTCG---GAGCATCTGCAACTGCACCCCACTTCCCCCTAGACGCTCGG-------------A
CATCGTCTGAATCCAAAAACATCACCCAACAGCCTATACGTGGGGTGGATATGTGGCCGCTTGGACACACGCGGACATGT
TCGTCATGCTGGACAGACCCATCTCGACCTCACACA--------------------------------------------
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>SNPs
-----------------------------------S--------------------------------------------
---------------------------------S----------------------------------------------
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-------------------S------------------------------------------------------------
----------------------------------------------------S--------------------------S
--SSSSSSS----------------------------------------------------------SS-----------
--------------------------------------------------------------------S--S--------
-----------------------------------------S-----------------------------------SS-
SS-----------------------------S--S---------------------------------------------
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------------------------------------------------S--S---SSS----------------------
---------S-----------------------S------S---------------------S-----S------S----
-------------------------------------------------------------S------------------
----SSSSS----------------------------------------S--------------S----S--S-S-----
--------------------------S---------S-------------------------------------------
S----------------S--------------------------------------------------------------
--------------------S------------S----------------------------------------------
---------------------------------S-----------------------------S----------------
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--------------S-----------------------------S---------S----S--------------------
------------------S-------------------------------------------------------------
---------------------S-----------------------------S-----S----------------------
---------------------S--S-------S--------------------S--------------S-----------
----------------------------------SSSS------------------------------------------
----------------------------------------------------S---------------------------
S------SSSS------------------------------S---------------------------------SS---
--------------S----------------------------S---------------------------------S--
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-----------------------S----------------------------------S---------------------
-------------------S-SSSS--S----------S--------S--S-----S-------SSSSSSSSSSSSSSS-
------------------------S---------S-------------------------------S---S---S--S--
---S----S---------------------------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSS
>forward_1090
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------------------------------GACACACAAGCACAAGAGCG------------------------------
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>reverse_2387
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------------------------------------------------------------------ACGGACAGCTTGAA
CATCGT--------------------------------------------------------------------------
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