>input_sequence_85574
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--------------------------------------------------------ATGTCGCAGAGGCCGGGGAGGCAC
CAGAGGAGGGCGTCGCAGAGCGTGTTCTCGCTGCCGGAGAACTTCGCCAGCCTGGAGGACGTGCCGGCCGACGGCGTCGG
CGAGCAGCGGAAGCCCGCCGCGGCGGGGGCGGACGCCTCCGAGCAGCAGCCCGCGAGGGCGCCGGCGGGGCGCCACCGGC
GGGCAATGTCGATGGCCGTGCCCTCCAGGGACCTGGACATGATCGCGGAGGACATGGGAAGCTACAAGTACGGCGCCTGA
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>chr3D_1_TraesCS3D01G349600
GGTGGTACAGTACTGAATAAACCAATTTCTAATCGGTTAATTAACATGCACTTATTGGGCAGTGTAGGAGCATTATGCAT
TTATGCTCTATGCTGCTAGAACTAACGATATATGTCGTGCTGGAATTCAAGGGAATAATTACTAGGTTCTCCGTATAGAA
CCGTTAGCAAGGAACCCCCGATCCGTACCAGCTCATTTTT-GTGATAAAATAGACGT----TTAAGAAAATAAGTTCGAT
TAGTGATAACTGTGCATGATTTGCTTTTGTTATTGCATGCTTGATTCCCTCTTCGGTTTGCACGTGGCTCTCTGCTAAAT
ATATCAGGACGGCTCATGAGTGAAGCACTAACCCAATAAAAATGGCGAGCCCGGTCCTGAGATTCCTGTACATGCGCCTC
ATGAGTGCCATTTGTTTACGCTCGTAGGAAGCTTCCTAGCGACATCCGAAACGTACGGAGGGCATACAGTACTGAGCAGC
CAGCCATGTCAACCAAGGGAGCAGCAGCCAGAAGTACGTGCCAAGTTGGCTATACTTTGCAAAGATGAGAGCACCACATC
AGCGAAGACGAACGTTAATCTGGTAATCATCGAGATGCTCGTATGCTTAATTGATGGCCACGTCCACCAAGCAAGTCCTT
AACCAGACGCGCGGGGCGGGTAGGAGCCATGCGCATGCACATGCACATGCATGCCGCTCGGCGCGCCATGGATATGCAT-
---GCACAAAGTCAATGGCCTTTGGAGCCAGGAACTGCCAGATCGCTCACAAATTTAATCTCTACTCCATGTTACAATAA
TTGTACTGCTG---GTACTGGTGAACAGGCTCGT-AATAGTTGGAAAAACAAATGGCAGACGAGCGTGCGCTGGGCGGGC
CTATATATACATCGGTGGCGTCCTGTAATTCAATCAAGCAGGCGGTAGCATCAC---ATCGTAGTAGTAGCTAGAGCTAG
CTAGGTCTCCTCGACGGCTCGACCCCAGTCTCAGTAGTTTCTCTTCAAGAATCAAGATGTCGCAGAGGCCGGGGAGGCAC
CAGAGGAGGGCGTCGCAGAGCGTGTTCTCGCTGCCGGAGAACTTCGCCAGCCTGGAGGACGTGCCGGCCGACGGCGTCGG
CGAGCAGCGGAAGCCCGCCGCGGCGGGGGCGGACGCCTCCGAGCAGCAGCCCGCGAGGGCGCCGGCGGGGCGCCACCGGC
GGGCAATGTCGATGGCCGTGCCCTCCAGGGACCTGGACATGATCGCGGAGGACATGGGAAGCTACAAGTACGGCGCCTGA
TTAGTAGC-TGTGTAGTTCACGTTTGTGTGTACGTACGTACGAGTTCTTCCCTGGCTGTTGGGTAGTGTCCTGTTCTGTT
CGCCGTTTGGTAGTGTTGTTCTGTGCTTTGTTTTTCGTGCTTCTCTGAATGTGTACTCCTTCCTTAATTTGCTTGCCTGA
CCAGAGTAAAGAAATCCCGCTGTTG----CAAATTTGCGGTGTTTGTGGCAAAGGTAGAAATTTACATACGTGCCTAGGT
TAGAGTAATGCGGCAC--AGCTCTTCGGAAGCAGGATGATTTACTGATTTTTCATTACGAAAGTACGATACAGTATTACA
GATGTGTATGGAACTCCTACCGTCGCTAAGCCGAGAGCGGAGAACCGTCGCTAATCCGATGCCAGACGGAGAACGGCGAC
GCCACGGTGGTGCCGGCCGGTGGGCGGGGCCAGCAAGACGAGTCGATGGTAGCAGATCCGGTGAACGGTGATGGAGATCA
TGGAGGTGACGCGAATCTTGCGAGGCTAGGCCAACGAACGGCGAGGTGGATCCGGTAGGCAACCCGACCTGTCACCGTGA
AAAAACAAAT-AGAAAGTGACATGGGCACAGCGCTCGTGCTATCGTGCGCATGACCTCACCCGGCCGGGCTGCTCGAAG-
-------------CCCCATCGCGCGCGCTCACAGCCTCCAGTTAGTGGGCCCGCCCAGGAATGCGTCC-TTTTTTTTGCA
CCTAGTTTTTTCGAAGGTCGTTTTA---------------------------ATATGGATTCAAAAAAGAATGTAAATTC
AAAATATGTTCACGAATTAAAAAATATCACGGA-TTGAAAATATGTTCACAAATTCGTAAAGTGCTCATGAATTCAAAGA
AAGTTCACAAATTCAAAAATAATTCGTGGATTCAAAAATGTTGACGAATTCAAAATTTGTTCGTGACACAATAAAAATGT
CCACACATTCAAACATTGCTCGAGGATTTGAAATAGTGTTCAGGAACTCAGAAACAGTTAACGAGCTTGAAATATTATTC
GTGAATTCAAA---------------------------------------------------------------------
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>chr3A_3
--TGGTACAGTACTGAATAAACCAGTTTCTAATCGGTTAATTAACAAGCACTTATTAGACAGTGTAGGAGCATTATGCTA
TATGAGTATATGGTGCTAGAACTGACGATATATGTCGTGCTGGAATTAAAGGGAGTAATTACTAGGATCTCCGTATAGAA
CCGTTAGCAAGGAAC-CCCGATCAGTACCAGCTCATTTTT-GTGATAACCTAGACGT----TTAAGAAAATAAGTTGGAT
TTGTGATAACTGTGCATGATTTGGTTTTGTTATTGCATGGTTGATTCCCTCTTTGGTTTGCACGTGGCTCTCTGCTAATC
ATGTCAGGACGGCTCATGAGTGAAGCACTAACCCAATAAAAATGGCGAGCCTGGTCCTGAGATTCCTGTACATGCGCCTC
ATGAGTGCCGTTTGTTTAAGCTCGTAGGAAGCTTCCTAGCGACATCCGAAACGTACGGAGGACATACAGTACTGAGCAGC
CAGCCATGTCAACCAAGAGAGCAGCAGCCAGTAGTGCGTGCCAAGTTGGCTATACTTTGCAAAGATAAGAGCACCACATC
AGCAAAGACGAACGTTAATCCGGTAATCAACAAGATGCTCATATGCTTAATTGATCGCCACGTTCAGACCAA--------
-------------------GTAGGAGCCATGCGCATGCGCATGCACATGCATGCAGCTCCGCGCGCCATGGATATGCAT-
---GCACAAAGTCAATGCCCTTTGGAGCCATGGACTGCCAGATCGCTCACAAATTTAATCACTACTCCATGTTACAATAA
TTGTACTGCTGTTAGTACTGGTGAACAGGCTCGT-AATAATTGGGAAAACAAATTGCAGACGAGCGTGCGCTGGGCAGGC
CTATATATACATCGGTGGTGCCCTGTAGTTCACTCAAGCAAGCGGTAGCATCATCATATCGTAGTAGTAGCTAGAGCTAG
CTAGGTCTCCTCGAC--------CCCAGTCTCAGTAGTTTCTCTTCAAG-------ATGTCGCAGAGGCCGGGGAGGCAC
CAGAGGAGGGCGTCGCAGAGCGTGTTCTCGCTGCCGGAGAACTTCGCCAGCCTGGAGGACGTGCCGGCGGACGGCGTCGG
CGAGCAGCGGAAGCCCGCCGCGGCGGGGGCGGACGCCTCCGAGCAGCAGCCCGCGAGGCCGGCGGCGGGGCGCCACCGGC
GGGCAATGTCCATGGCCGTGCCCTCCAGGGACCTGGACATGATCGCGGAGGACATGGGAAGCTACAAGTACGGCGCCTGA
TTAGCGGGACGTGTAGTTCACGCTGGTGTGTACGTACGTACGAGTTCTTCCCTGGCTGTTGGGTAGTGTCCTGTTCTGTT
TGCCGTTTGGTAGTGTTGTTCTGTGCTGTGTTTTTCGTGGTTCGCTGAATGTGTACTCCTTC----ATTTGCTTGCCTGA
CCTGAGTAAAGAAATCCCGCTGTTACAAA-----TTTCAGTGTTTGTGGCAAAGGTAAAAACTTACAAACGTTCCTAGGT
TACCATAATGCGGCAC--AGCTCTTGGGAAGCAGGGTGATTTACTGATTTATCATTACGAAAGGATGATACAGT------
--TGCGTATGGCACTCATACCGTCGCTAAGCCGACAGCCGAGAACCGTCGCTAATCCGATGCCAGACGGAGAACGGCAAC
GCCACGGTGGTGCCGGCCGGTGGGCGGGGGCAGCCAGAGGAATCGATGGTGGCAGATCCGGTGAACGGTGATGGAGATCA
TGGAGATGACGCGAATCTTGCGAGGCTAGGCTAACGAGCGGCGAGGTGGATCCGGTAGGCAACCCGACCTGTCACCGTGA
AAAGA-AAAT-AGAAAGTGACGTCGGCACAGCGCTCGTGCTATCGTGCGCATGACCTCGCCCGGGCGTGCTGCTGGAAG-
-------------CCCCATCGCGCTCGCTCACAGCCTCCCGTTAGTAGGCCCGCCTATGAATGCGTCTTTTTTTTCTGCA
CCTGGTTTTTTCAAAGGTAGCTTTTTTTACCTAGGTCGGTTGCTAATTAAAGATATGAATTAAAAAAAATC-ATAAATTC
AAAAAATGTTGACGAATTCAAAAAAATCACGGGTTTGAAAAAACGTTCGCGAATTCATAAAGTGCTCATGATTTCAAAGA
AAGTTCA-------------------TGGGTTCAAAAATGTTGAGGAATTCAAAAGTTGTTCATGACGTCA-AAAAATGT
CCACAAATTA--------CTCGAGGATTTGAACTAGTGTTCACGAATTCA-AAAAAGTTCGCAATCTTGAAATATTATTC
ATGAATTCAAAAAATGTTGATGGATTTGAAAATAATGTTCATGAATGGATAAAATGCTTGCAGATTTGAAAAATGTTAGT
GATTTCAAAAAATATTCATAAGTTCAAAAAACATCATGAATTTGAAAATTGATTGGGAAGCTACAAGTACGGCGCCTGAT
TAGTAAGATGTGTATTTCACGCTGGTGTGTACGTACGTACGAGTTCTTCCGTGGCTGTTGGGTAGTGTCCTGTTCTGTTC
GCCGTTTGGTAGTGTTGGTCTCTGTGCTGTGTTTTTCGTGCTTCTCTGAATGTGTACTCCTTCATTTGCTTGCCTGGCCT
CAGTAAAGAAATCCCGCTGTTGCAAATTTGCAGTGCTTGTGGCAAAGGTTAAAATTTAAATACGTGCCCAGGTTACAGTA
ATGCGGCACAGCTCTTCGAAAGCAGGATGATTTGCTGATTTTTCATTACCAAAGGATGATACAGTTGTGTATGGCACTCA
TACCGTCGCTAAGCCGAGAGCCGAGAACCGTCGCTAATCCGATGCCAGACGGAGAACGGCGATGCCACGTTGGTGCCGGC
GGGTGGGCGGGGCCAGCGGGACGAGTCGATGGCAGCAGATCCGCTGAACGGTGACGAGAATCTTCCGAGGGTAGGCCAAC
GGGCGGCGAGGTGGATCCGGTAGGCAACCCGACCTGTTACCGTGAAAGAAAATAGAAAGTGACGTCGGCACAGCGCTCGT
GCTATCGTGCGCATGACCTCGCCCGGGCGTGCTGCTCGAAGCCCCATCGCGCGCGCTCACAGCCTCGCGTTAGTAGGCCC
GCCCATGAAAGC
>chr3B_38
-------------------------------------TAATTAACAAGCACTTATTAGACAGTGTAGGAGCATTATG---
-----CTATATGGTGCTAGAACTGACGATATATGTCGTGCTGGAATTCAAGGGAATAATTACTAGTATCTCCGTATAGAA
CCGTTAGCAAGGAACCCCCGATCCGTACCAGCTCATTTTTTGTGATAACTTAGACGTTTAATTAAGAAAATAAGTTCGAT
TTGTGATAACTGTGCATGATTTGGTTTTGTTATTGCATGGTTGATTCCCTCTTCGGTTTGCACGTGGCTCTCTGCTAATC
ATGTCAGGGCGGCTCATGAGTGAAGCACTAAGCCAATAAAAATGGCGAGCCCGGTCCTGAGATTCCTGTACATGCGCCTC
ATGAGTGTCATTTGTTTACGCTCGTAGGAAGCTTCCTAGCGACATCCGAAACGTACGGAGGACATACAGTACTGAGCAGC
CAGCCATGTCAATCAAGGGAGCAGCAGCCAGCAGTACGTGCCAAGTTGACTATACTTTGCAAAGATGAGAGCACCACATC
AGCAAAGACGAACGTTAATCTGGTAATCATCAAGATGCTCGCATGCTTAATTGATGGCCACGTCCAACAAGCAAGTCCTT
AACCAGACGCGCGGGGCGGGTAGGAGCCATGCGCATGCACATGCACATGCATGCAGCTCCGCGCGCCATGGATATGCACG
TACGCACAAAGTCAATGCCCTTTGGAGCCAGGAACTGCCAGATCGCTCACAAATTTAATCACTACTCCATGTTACAATAA
TTGTACCGCTGTTAGTACTGGTGAACAGGCTCGTAAATAATTGGAAAAACAAATTGCAAACGAGCGTGCGCTGGGCAGGC
CTATATATACATCGGTGGTGCCGTGTAATTCAATCAAGCAGGCGGTAGCTTCAC---ATCGTAGTAGTAGCTAGAGCTAG
CGAGGTCTCCTCGAC--------CCCAGTCTCAGTAGTTTCTCTTCAAG-------ATGTCGCAGAGGCCGGGGAGGCAC
CAGAGGAGGGCGTCGCAGAGTGTGTTCTCGCTGCCGGAGAACTTCGCCAGCCTGGAGGACGTGCCGGCGGACGGCGTCGG
CGAGCAGCGGAAGCCCGCCGCGGCTGGGGCGGACGCCTCCGAGCAGCAGCCCGCGAGGCCGGCGG---GGCGCCACCGCC
GGGCAATGTCGATGGCCGTGCCCTCCAGGGACCTGGACATGATCGTGGAGGACATGGGAAGCTATAAGTACGGCGCCTGA
TTAGCAAGATGTGTAGTTCACGCTGGTGT----GTACGTACGAGTTCTTCAGTGGCTGTTGGGTAGTGTCA-GTTCTGTA
CGCCGTTTGGTTGTTTTGTTCTGTGCTGTGTTTTCACTGTTTCCCCGAATGTGTACTCCTCC-----TTTGCTTACCTGA
CCAGAGTAAAGAAATCCCGCTGTCTGTTTCAAATTTGCAGTGTTTCTGGCACAGGTAAAAATTTACATACGTGCTTAGGT
TACAGTATAATGCGACAGAGCTCTTCGGAAGCAGGATAATTTACTGATTTTTCATTCC-AAAGGATGATACAGTTG----
--TGTATATGGAACTCCTACCGTCGCTAAGCCGAGAGCCGAGAATCGTCGCTAATCCGATCCCAGACGGAGAACGACGAT
GCCACAGTGGTGCCGGCCGGTAGGCGGGGCCAGCGAGACGAGTCGATGGTAGCAGATCCGGTGAACGGTGATGGAGATCA
TGGAGGTGACGCGAATCTTGCGAGGCTAGGCCAACGAGCGGCGAGGCGGATCCGGTAGA-----CGACCTGTCACCGTGA
TTTTTTTTTTAAGAAACTGACATCGGCACAGCGCTCGTGCTATCGTGCGCATGACCTCATCCGGCCGTGCTTTTTGTTTG
TGCTGCTCGAATCCCCCATCGCGCGCGCTCACAGCCTCCTGTTAGTGGGCCCGCCCAGGAATGCGTCTTTTTTTTCTGCA
CCTGGTTTTTTCGAAGGTCG-TTTTTTTACCTAGGTCGGTTTCTAATTAAAAATATGTGAATTAAAAAATC-GTAAATTC
AGAAAATGTTGACGAATTCAAAAAATTCACGGATCTGAAAAAAAGTTCACAC--------AGTGCTCATGATTTCAAAGA
AAGTTCA-------------------CGGATTCAAAAATGTTGACAAAATAAAAATTTGTTCGTGGCGTCA-AAAAATGT
CCACAAATTA--------CTCGAGGATTTGAAATAGTGTTCACGAATTAA-AAAAAGTTCAGAATATTGAAATATTATTC
ATCAAT--------------------------------------------------------------------------
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>SNPs
SS----------------------S---------------------S---------S-S-------------------SS
-SSSS--S----S----------S------------------------------------------S-------------
------------------------------------------------SS------------------------------
-S---------------------S---------------S--------------------------------------SS
--S-----------------------------------------------------------------------------
-------------------------------------------------------------S------------------
-------------------------------S------------------------------------------------
---S---------------------------S----------------------------------S-------------
------------------------------------------------------S----S--------------------
-----------------S------------------------------------------S-------------------
---------------------------------------S--------------S---------------------S---
------------------S-S-----------------------------------------------------------
---------------SSSSSSSS--------------------------SSSSSSS------------------------
--------------------------------------------------------------------S-----------
----------------------------------------------------------S--S------------------
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----S--S--------------S-S-------------------------------------------------------
---------------------------S-----------S---S------------------SSSS--------------
------------------------S-------------S------------------S----------------------
--S------------------------------------------------------------S-S--------SSSSSS
SS------------------------------------S-----------------------------------------
----------------------------------S---------------------------------------------
-------------------------------------S------------------------------------------
---S-S-----------------S-------------------------------------------S------S-----
---------------------------------------S---------------------------S-------S----
---S----------------S---S--------------------------------S---S------SSSS--------
----S-----S-------S-----S----------------S-S------------S--------------S--------
-------SSSSSSSSSSSSSSSSSSS-----------------------------------------SSS-S--------
-----S---SSSSSSSSS------------------------S---S---S---S----S--S-S---------------
S-------------------------------------------------------------------------------
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>forward_977
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-----------------------------------------------------------------------------TAG
CTAGGTCTCCTCGACGG---------------------------------------------------------------
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>reverse_2283
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------------------------------------------GGAACTCAGAAACAGTTAACGAGC--------------
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