>input_sequence_86032
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---------------------------ATGGAGGGCCTCATCCCGTTCATCTACAGGGCCGTGGCGCAGTACAGGAAGGA
GGGGCAGGTCTCCCTCGCCGACCTGCTCTTCGACGAGCAGCCGTCCTCGTCGCCCACGGCGGCCTCGGCCTACTTCCGTC
TCCCCGGGGACTCCGGCCGGCACCAGCGCTTCTCGGGCGACTCCGGTGCGGCCGGAGCCGCGCGGCGGTCTCCGGCGCAC
CGTCGGCGCAGCATGGAGCATGGATCGTGGTGA-----------------------------------------------
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>chr1D_1_TraesCS1D01G282000
AGCAGACGATACGATCCGGTACGAACCGCCGCTCATTCTCTTCTTCTTCTCGCAAAAAGAA-------------------
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----------GAA-GAAAAACAACGATCTGGTATGAACTGTTGCCCGATCAGCATCTCCAGTGCCATAAACAAACCCCAG
CACCGCACCAGTTTACGCCGGCGAGGTCAACCCTAGCAATCATGCCTCCACGTCAGCCGCACGGGCCGCCATCTTCCCCA
TTGTTTACTCACGCTCGCCACGCAACGGCTCGACAAGTGTATCGGGGAAGAAGTCAGCAGCCAGATGGATCGATCTTCTT
GTCCGGTTGTCCCGCCCCGCCCTGGCAGCATAGTCGGCCGGGGTGAGGTGAGATCACGCTGAACTTTCCTTCCCGCCATG
GCAGCGATTTTCCGGAGGCTTACGCCACCGGCAGGCCTGGAGTTGGATAAAAAGAACTCGACCAATCATGGTCCGGGCGG
AGGTTTGTGTTTGCTTATCTTTTGTGGCAGGTAAGCTGTAGGCTTCAATCAAGG------GTTTTTCAGCCGAGAAATTA
CAGCAACTGACTGAAAATAACGTCGCTG------------TCCACTTGGAAAACTCGCCTTGCAAGACTGACCATCCCTT
GCGTTCAAGCCTCCTTCCC-------CTCCCCTACTGGGATTCCATAGCCCCAATGATTAATTAA----CCCGGAATAAT
GTCCTAGCTAGCTAGCAGTTACCCTGATGAATTCCCTTGTAATAGTACCCCTGAGTCCCTGACACGACACATTTTGGTTG
ATTGATTTCGGAGCTAAGGTGAAGCTGTCAGGGAACAATTA--------TCCTTCCTAGGCGAGCGTCCCATTTGGTCTC
TGATCTCTATCCACCCGGAGGCCTCTTCTGTTTTGGCTCCCTTTTTAAGCCCATGTCCTCCTCCTGCCTCGCCATCATTC
ATCCCAACAAAGCGTGTCAAACCTCTCCCTCAAGTGTTGTCCCAATAACCACTACTACCTCTCTCCACCGTCTTCTTCAG
CTCTCTCGAGCGAAAGCAAAGGGTGTCATGGAGGGCCTCATCCCGTTCATCTACAGGGCCGTGGCGCAGTACAGGAAGGA
GGGGCAGGTCTCCCTCGCCGACCTGCTCTTCGACGAGCAGCCGTCCTCGTCGCCCACGGCGGCCTCGGCCTACTTCCGTC
TCCCCGGGGACTCCGGCCGGCACCAGCGCTTCTCGGGCGACTCCGGTGCGGCCGGAGCCGCGCGGCGGTCTCCGGCGCAC
CGTCGGCGCAGCATGGAGCATGGATCGTGGTGATTGATTGTGATTGAAGCGCAGAAAGGCCAAGAATA------AAGGAA
ACAGAGCGAAGCAGGTGAAGACTTGCCTAGGTACGTCGTCGAGTACATGCAGATACGATGTGGATTGGTGGAAACCTCAA
-GTATTGGCCTAGCTAAGCTAATACGAGCTGCAGACCTGCAGTTTGTGTGTGCTATACATGCATGTATTGG---TATTTC
AATTCAGCTTGTAA--------TGA-------------TTGTCAACTGTAAATATGGGATGCGTAAGCGCAGGACCTCCG
AAGGAGTCCTGTGAAGAA-ATGTATAGTGTCAGAGTCCATT------CATGGAGTGTAATATGGCAATAAAAGCTTCACC
ATGTACAAAAAGGTTGTGTACACGCACACATGA---CTTGCTGCAAGACTGCAAAAGAAGCGAGTGTCAAGCATCAAGGT
TGCTAATTGCATCCGCGTTCTTCAGTTCAGTCTTCCTTTTCAAAGAAGAAGAAGAA-AAATCTCGTTTTCAGTTCGAAAT
CACGATAAAAACAACCTTCTGGTTTCACACCCAGAGCAAGAACAACCATTTTTCTCT-------TGAAACTCAGAAGAAC
AAGAATAACTTTGGTTGAAAAGATGTACAGTAT-----------------------------------------------
---------------------------------------------------------------ATCGAATCGCAAGAAAC
ATGGAC--ACTCTGTGCTACTCTAGTCTCCAATCAGGAAAGGAGTATGCGCGAGAAGCATAACTAAAGCATGCACGAATA
CTACATCAACTACGATCAGTTCATCTTCCGC----------CCACACGGACTCACGGACATTGTCCGCCTG---------
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--------------------------------------------------AATTTCATCTTTGTTAAATTAAGTTCGATA
TCCCCGCAAAAACAGAAAAAAAAAATTGGTTTGATATCGAGAGCCAAGCCCACACAAGAAACCCTCTCATCCTTGACTTC
TCATGCAGATGTTCCATTCAGATGATCTAGAGGCGCAGAGAGTATAGTCAACATGGCGTTGATGAAATTCGTACACATTT
GTAATCTCAAATTGCCTGACTTCTTTAACGGTGTTCCAGGTAGAGTTACACAACAAAATCAGA
>chr1B_1
AGCAGATGATACGATCTGGTACGAACCTCCGCTCATTCTCTTCTTCTT---GCAAAAAGAA-------------------
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----------GAGGAAAAAACAACGATCTGGTATGAACTGTTGCCCGATCAGCATCTCCAGCGCCATAAACAAACCCCAA
CACCGCACTAGTTTAAGCCGGCGAGGTCAACCATGCCAATCATGCCTCCACGTCAGCCGCACGGGCCGCCATCTCCCCCA
TTGTTTAACCACGATCGCCACGCAACGGCTCGACAAGTGTATCGGGGAAGAAGTCAGCAGCCAGGTGGATCGATCTTC--
------TTGTCCCGCCCCGCCCTGGCAGCATAGTCGGCCGGGGTGAG-----ATCACGCTGAACT----TTCCTGCCATG
GCAGCGATTTTCCGAAGGCTTACGGCACCGGCAGGCCTGGGGTTGGATAAAAAGAACTCGACCAATCATGGTCC-GGCGG
AGGTTTGTC-TTGCTTATCTTTTGCGGCAGGTAAGCTGTAGGCTTCAATCAAAG------GTTTTTCAACCGAGAAATTA
CTGCAACTGAG---GAACTACGTCGTTGTCCACTACGTACTCCACTTGGAAAACTCGCCTTGTAAGACTGACCATCCCTT
GCGTTCAAGCCTCCTCCCCTA-------CCCCTGCTGGGGTTCCATAGCCCCAATGATTAATTAATTAACCGGGAATTCT
GTTAGTTACCGG------GGGAAATTCTCATGG------------------TGAGTGTCTGGCACGACACATTTCGATTG
ATTGATTTCAGAGCTAAGGTGAAGCTGTCAGGGAACAATTA--------TCCTTCCCGGGTTAGTGTCCCATTTGGTCTC
TAATCTCTATCCACTCAGAGGAATGTTCTGTTTTGGCTCCCTTTTTAAGCCCATGTCCTCCTG---CCTCGCCATCAC--
--CCCAACAAAGCGTGTCAAACCTCTCCCTCAAGTGTTGTCCCAATAACCACTA---CTTCTCTCCACCATCTTCTTCGG
CTCTCTCGAGCGAAAGCAAAAGGTCTCATGGAGGGCCTCATCCCGTTCATCTACAGGGCCGTGGCGCAGTACAGGAAGGA
GGGGCAGGTCTCCCTCGCCGACCTCCTCTTCGACGAGCAGCCGTCCTCGTCGCCCACGGCGGCCTCGGCCTACTTCCGTC
TCGCCGGGGACTCCGGCCGCCACCAGCTCTTCTCGGCCGACTCCGGTGCGGCCGGAGCGGCGCGGCGGTCTCCGCCGCAC
CGTCGGCGCACCATGGAGCATGGATCGTGGTGACTGACTGTGATTGAAGCGCAGAAAGTCATCCAAGGGATAATAAGAAA
ACAAAGCAAAGCAGGTGAAGACTTGCCTAGGTACGTCGTCCAGTACATGCAGATACGATGTCGATTGCTGAGCAGCTGCA
CGTATTGGCCTAGCTAAGCTAATACGAGCTGCAGACCTGCAGTTTATGTGTGCTATACATGCATATATTTGTACTATTTC
AATTCAGCTTGTAAAATGATCGGTCCGTGAGTTGGTGGGTGTCAAATGTAAATATGGGATGCACAAGCGCAGGACCTCCG
AAGGAGGCCTGTGAAGAAGATGTATAGTGTCAGGGTCCATT------CATGGAGTGTAATATGGCAATAAAAGCTTCACC
ATGTACAAAAAGGTTATGTACACGCACACATGACTGCTTGCTGCAAGACTGCAAAAGAAGCGAGTGTCAAGTATCAAGAT
TGCTAATTGCATCCGTGTTCTTCAGTTAAGTCTTCCTTTTCAAAGAAGAAGAAAAAGAAATCTCGTTTGCAGTTCGAAAT
CAGGATAAAAACAACCTTCTGGTTTCATACCCAGAGCAAGAACAACCATTTTTTTTTCTCTTGATGAAACTCAGAAGAAC
AAGAATAACTTTGGTTGAAAAGATGTATTCCTCCGTTCCAAAATAGATGAACCAACTTTGTACTAACTCTAGTACAAAGT
TGGTTCATCTATTTTGAGTACAAAGTTGGTTCATCTATTTTGGAACGGAGGGAGTAATATCGAATCGCATCGCAAGAAAC
ATGGAC--GTTATGTGCTACTCTTGTCTCTAATCAGGAAAGGAGTATGCGCGAGAAGCATAACTAAAGCATGCACGAATA
CTACATCAACTACGATCAGTTCATCTTCCGC----------CCACGCGGACTCACGGACACTGTCCGCCTG---------
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--------------------------------------------------AATG-CATCTTTGTTAAATTCAGTTCGATA
TCCCCGCAAAAACAG-AAAAAAAAATTGGTTTCATATCGAGAGCCAAGCCCACACAAGAAACCCTCTCATCCTTGACCTC
TC------------------------------------------------------------------------------
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>chr1A_1
AGCAGATGATACAATTTGGTACGAACCGCCGCTCATTCTCTTCTTCTT---GAAAAAAAAGGAAAAAACAACTATCTAGT
ATGAACTGTTGCCCTATTAGAGTAAGGGTATGAAAAATAAAAATACCCATGGATTTCTAAATGAGAAAAAAATTATACCC
ATCGGGTAAGGTGGGTATGGGTACGGAAAGGAAATACCCATACCCACATACCCGCAAACCCGTATACTACTACTCGCACG
TAAGGGTTCTTCTGTTTCTAGAACTGCTGTTTGATTAAGATGCGTACCTGATGAGCTTAACCTGCTGTGTGAGCAGGATT
GTAATGTTCCTGCTTAAGTAATGGAAGTGTTTTATTTGCAAAAAAACGTCAAGTAGGTCTTATGTGTCATTGACTAGATT
AAAAAAAGACATAAGTTACCGGGCGCTAAGTACAACTTGTCAAGTAGATTTGTTATCGTCTCCATCCTTGCACCTCCAAC
CACCTTTAAAAGGGAAAATGCCAGGGGTCGTGGCGACTACAAAGTGGGATATGGTCGTGGTCGCAGCTGCCCGATGCAAC
GTCCGGCTACTCCTACGAGGAACCCTATGTGCTCTGTCAATAACAAGGGCGGAGCATGACAAGCATACAATTTGGTGATG
CTCCGCACTTGACACTTTTTTTTAATTCCTATGATGCACGAATGTGTTGATGACTGGTCTATTGACGAATGTGTATGATG
TATGAATGGATTATTTGAATGTCCTGACAAGTGTTTAGTCAACTTTAAACATGCTGACATATAAACCTGAGGTGCAGGTT
TGGGCGGAAAATATCAAGATGGGTGCATACATATGTATATAGACATATTTTAAAATGTAGATTCACCATTTAAAAAAATG
TGTAGATTCACTCATTTTGCTTCATATGTAGTCACTTGTTGAAATCTCTAGTCCTTAGAAAGATAGAAACAGAAATAGTA
TGTTTGAAAGGTTTTAAATTGAGATTGGCAGGGGCCACGCGGACGCGTACCCTCTCTATCACAAATTATGACGTCCATTC
TTCTATCAGAGGAGATGATGGACCAATGCTCCTCCCAAGTGCAATGGAGGCCACTAATCCAGGCCATGGGTCTTCTTGAT
CATCCATTGACCCCGTACAGGTAAGTGCTTTTCTCGGTAGCACCAGGTGCTTCATATATAGCCTCCCCTTGTATGTCTTG
CTCTGTTGACGAGCAGTATGGGACTAAAACGTCCAGCGAGATCGATTAGACGCGTTGCCACGTACAGTAGTATATCCTTC
ATAGCTGCAGGCCCACGGGCTGAAGGCCGTCCGGCACTTGGGCTTTTGGGCTTAATTAAGGGGATAGGATAGCGTCCAGT
CCAAGCAAACGCAGAAAATCAGAATCATATGAGTTAAAAAATAAACGCTAGAAAAAATATGATTTGAAAATAAAATTTTA
AAAATATTTTCCGTTCAAATATGTTATAGACTTTTTGGAAACAAAAACAAAAAAAAAACTGAGACGCATTTGACCGCTGT
AGAAAATCAATCGGATATTGAGGTGAAGAAGGAAGCGCAAGCTTGTGCGGTTTCCGCGCACCTCTGCTCTTCTTGACCCA
GCCGTACCCATGGTTAGTTGGGACAGACCCATCAGCACCCAATACAATAGCCTTAGCCAATTAGAGATCCAGCTATCGAA
GCAAAGTACTACAAATAAATCCGACCGCCGGCTCATAGCAGCAGATGATACAATCCGGTACGAACCTCCGCTCATTCTCT
TCCTCTTCTTGAA-AAAAAACAACGATCTGGTATGAACTGTTGCCCGATCAGCATCTCCAGCGCCATAAACAAACCCCAG
CACCGCACCAGTTTACGCCGGCGAGGTCAACCCTAGCAATCATGCCTCCACGTCAGCCGCACGGGCCGCCATCTACCCCA
TTGTTTAGCCACGATCGCCACGCAACTGCTCGACTGGTGTATCGGGGAAGAAGTCAGCAGCCAGACGGATCGATCTTCTT
GTCCGGTTGTCCCGCCCTGGCA-GGCAGCATAGTCGGCCGGGGTGAGGCGAGGTCACGCTGAACT----TTCCCGCCATG
GCAGCGG-TTTCCGACGGATTACGCCACT------------GTCGGATAAAAAGAACCCGGCCAATCATGGTCC-GGCGG
AGGTTTGTGTTTGCTTATCTTTTGCGGCAGGTAAGCTGTAGGCTTCAATCAAAGGCTTTTGTTTTTCAGCCGAGAAATTA
CAGCGACTGAG---AAACCACGTCGCTGTGCACTACGTACTCCACTTGGAAAACTCGCCTTGTAAGACTGACCATCCCTT
GCGTTCAAGCCTCCTCCCCTCGGCCCCTCCCCTGCTGGGATTCCATAGCCCCAATGATTAAT-AA----CCTGGAATTCT
GCCCTAGCTAGTTACCCTGGGAAATTCTCATGG------------------TGAGTGTCTGGCACGACACACTTTGATTG
GTTGGTTTCGGAGCTAAGGTGAAGCTGTCAGGGAACGAGCAATTATCCTTCCTTCCTAGGCGAGTAGCCCATTTGGTCTC
TGATCTCTATCCGCTCAGAGGAATGGTCTATTTTGCCTCCCTTTTTAAGCCCATGTCCTCCTC---CCTCGCCATCATTC
ATCCCAACAAAGCGTGTCAAACCTCTCCCTCAAGTGTTGTCCCAATACCCACTACCTCTTCTCTCCACCGTCTTCTTCAG
CTCTCTCGAGCGGAAGGAAAAGGTCTCATGGAGGGCCTCATCCCGTTCATCTACAGGGCCGTGGCGCAGTACAGGAAGGA
GGGGCAGGTCTCCCTCGCCGACCTCCTCTTCGACGAGCAGCCGTCCTCGTCGCCCACGGCGGCCTCGGCCTACTTCCGCC
TCCCCGGGGACTCCGGCCGGCACCAGCGCGTCTCGGCCGACTCCGGTGCAGCA---------CGGCGGTCTCCGGCGCAC
CGTCGGCGCACCATGGAGCACGGATCGTGGTGACCGATTGTGGTTGAAGCGCAGAAAGGCCAATAATA------AAGGAA
ACAGAGCGAAGCAGGTGAAGACTTGCCTAGGTACGTCGTCGAGTACATGCAGATACGATGTCGATTGCTGA---------
-------GCCTAGCTAAGCTAACACGAGCTTCAGACCTGCAGTTTATGTGTGCTATACATGCATATATTTG---TATTTC
AGTTCAGCCTGTAACGAGTCGGTGA-------------GTGTCAACTGTAAATATGGGATGCACAAGCGCAGGACCTCCG
AAGGAGGACTGTGAAGAAGATGTATAGTGTCAGAGTCCATACAAATACATGGAGTGTAATATGGCAATAAAAGCTTCACC
ATGTACAAAAAGGTTGTGTACACGCACACATGACTGCTTGCTGCAAGACTGCAAAAGAAGTGACTGTCAAGCATCAAGAT
TGCTAGTTGCATCCGCGTTCTTCAGTTCAATCGTCCTTTTCAAGGAAGAAGAAGAA---------TTTTCAGTTCGAAAT
AAGGATAAAAACAACCTTCTGGTTTCACACCCAGAGCAAGAACTACCATTGTTCTCT-------TGAAACTCACAAGAAC
AAGAATAACTTTGGTTGAAAAGATGTATGCG-------------------------------------------------
------------------------------------------------------------------GAATCACAAGAACA
CATGGAAGGTTCTGTGCTACTCTGGTCTCCCATCAGGAAAGGAGTACGCACGAGAACCATAATTAAAGCGCACACGAATA
TTACAGCAACTAGGATTAGTTTGTTTTTCGTACGCACGGATCAATGCGGACTCGCGGACATCGTCCACATGGCCGAAGCC
TTAACACTTGGGCGCCGGGTGGACGCCGAAGGGAAAAACAGGGGTAGGAGCACGTAAATTGGAATTTAAGAAAATTCTAG
GCACCTGTGCCCGGACAGATCCATTTGAAATAAGCTTGGAGTACCAAACAAATTTCATCTTTGTTAAATTCAGTTCGATA
TCCCCGCAAAACCGG---AAAAAAATTGGTTTGATATCGAGAGCCAAGCCCACACAAGAAAACCTCTCATCCATGACCTC
TC------------------------------------------------------------------------------
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>SNPs
------S---------S-------------------------------SSS-----------------------------
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--------------S----------------------------------------------S------------------
--------------------------------------------------------------------------S-----
-------SS----S------------------------------------------------------------------
------------------------------------------------S----------------SSSS-----------
--------------S-------------------------S---------------------------------S-----
------------------------S---------------------------S---------------------------
----------SSSS---SS-------------------------------------------S-----------------
---------------S-----------------S-------------------------------------S-----SS-
-----------S--S-SSSSSSSS-SS-S-SSSSSSSSSSSSSSSSSSSSS-----SS---S--------------S---
----------------------------------------------------------------S---------------
--------------S-S----SS-S--------------------------------------SSS--------------
-------------------------------------------------------SS-S---------------------
--------------------S---S-------------------------------------------------------
------------------------S-------------------------------------------------------
------------------------------------S---------------------S---------------------
----------S----------------------S-----------------------------S----------------
-------------------------------------------------------------S-----S--SSS-S--SS-
---------------------------------------------S------------------S----S----------
--------------------------------------S-----------------------SS----------------
------S-------------------------------------------------------------------------
------------------------------------------------------------------------------S-
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--S-----------------------------------------------------------------------------
---------------------------SSSSSS-----------------------------------------------
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--------SS-------------S--------------------------------------------------------
---------------------------------------------S----------------------------------
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----------------------------------------------------------------------S---------
---------------S-------------------------------------------------------------S--
--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_2625
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---------------------------------------------TAAGCCCATGTCCTCCTCCT---------------
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>reverse_3886
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---------------------------------------------ACGGACTCACGGACATTGTC---------------
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