>input_sequence_77113
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---------------------ATGACGAAGATTTTCAGGTACAGATCGATTGATCGATCGAAACAATCTTCCGCCCTTTC
CTTCCCCCGAAACAAACCAGATCAATCGAGTCATCCATGCATGAAGCTTCAAGCTTCAAAGGTTCGCCATC------GAT
CCAATCCAAGTTTT---TTCTTCTTTGCAGGTGCAGCTACTATCGGTCGAAGCAACCCGACGAGCCGCCCGAGGAGGACG
AAGAATCGGCGGCGGGGGAATACGAGTACGTGGATCTCGAGGACGGCCAAGGCAAGCAAGGAGGCGGCGACGAGAGGCCG
GAATCCGGCCGTCTCGTGGACCCTGA------------------CGTCGTCTTCACCATTCACATCGCCGCCTTGTGCGT
AATGTTGGGCTCCTTCATCCTGAGCTACTCCTACCTCGGCACCGGCGTGGTGGCCGCGTGGCCGGACGACGTCCTCCAGA
TCATCCCGGGCGCCTTGTTGCTCGCCCTCGGGGCCGCCGCTTTCGCCGGTCTCGCCTTGCGAGTCTGCACTTTCTCCACG
TGGTTTACGGTTTTTTGTTGA-----------------------------------------------------------
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------------------------------------------------------------------------
>chr3D_1_TraesCS3D01G528400
CATGTGTGAGTCGCCACCAAAGGCTCGGAACGGCGAAGGTTGTCGTCGCACATGCAACGAATATTGATGATAGAGGAAGG
TCACACCGCAAAAATCTCTGTTTTGGACACTCTAGCAGAGTGGCAGTACCACACAGTCCACATGCTCTGATGCCCTCGTT
TGTAACAGTAGAATTGGTTAGCAAAACATAATCGTCGTTGACGTCGGATCTGAACGTCCAAGACCCTATGGCCCATTGTG
ACAACCGCATAGCAGTGTGGAACCACGGCGCCATCCGCGTGCCTGAGCACGGGACCGCCATATTGGGATATAGAAGGTCG
CCGTTGTCGTCCATATAACTACATACGGGATGGCGGCAACCAATGCCTCGTCACCATGGGCTGCTGACCCTGCGGGAAAC
ACCACCGCCAAAGTTGCACAATGGTACCCTCTG-CCTTAAGTCATCATCCATAGGTCATAGCTCGCCTCGCTCGCTGAAG
ACTATCAGAG-----ATCTTTCTGCCATCACCTTTATCGACCAGTGTCGGGACTTAACCCCCTAGAGGGAATAGTGTGCA
TTTTTCGTTGGGGATTCCCTAGAATAAAACATCGCGTCTTCCTTCGATTCCTTATGCGGGATATTCAATCAATTAGAATT
CAGGTTACCACCTCTAGCAGCACCGAGGGAAAGAAAACGGGCCGTGGGAAGGGAGGCGGGGGCGGTTGTAGGGAGGCATA
TACATGAGTACCTGGCTATGTACGTGATGGGACA-------TATCTTTTCGGAAG-AAAAAAAACTTGATGGACAGATGC
ATGCATGCAT----------ATAGGGCGCCAGAACTCTAAACTGAAACGGATAACAACACAGGTCGGATA----ATGACC
AAACTCCTCTCTACGTATAGGTTGCGGAACGCAACAGGCTCCGGTCCCTATTTCTCTCGTGTTACTTAACACG------T
ACTACTACGTACGTACGCAACAACTTGA----TTAATTTGCATCTAGCCGTATCGCAAGATCTCAGCGA-----------
------------CCCGTTTCGATGACGAAGATTTTCAGGTACAGATCGATTGATCGATCGAAACAATCTTCCGCCCTTTC
CTTCCCCCGAAACAAACCAGATCAATCGAGTCATCCATGCATGAAGCTTCAAGCTTCAAAGGTTCGCCATC------GAT
CCAATCCAAGTTTT---TTCTTCTTTGCAGGTGCAGCTACTATCGGTCGAAGCAACCCGACGAGCCGCCCGAGGAGGACG
AAGAATCGGCGGCGGGGGAATACGAGTACGTGGATCTCGAGGACGGCCAAGGCAAGCAAGGAGGCGGCGACGAGAGGCCG
GAATCCGGCCGTCTCGTGGACCCTGA------------------CGTCGTCTTCACCATTCACATCGCCGCCTTGTGCGT
AATGTTGGGCTCCTTCATCCTGAGCTACTCCTACCTCGGCACCGGCGTGGTGGCCGCGTGGCCGGACGACGTCCTCCAGA
TCATCCCGGGCGCCTTGTTGCTCGCCCTCGGGGCCGCCGCTTTCGCCGGTCTCGCCTTGCGAGTCTGCACTTTCTCCACG
TGGTTTACGGTTTTTTGTTGAGATATATTCATCATTTAGCTACTTTA---TTATTGTCTCCAC----TGCATCCAGTATG
AATTTATCTGTTATT----ATTATCTTTGTAGCTAATTGTGCTAGCTACAGGCCGTTTCATATAATTTTGTCTGAAGTCA
AAGGACATTGGATTTCACCAAACTTATATAAAAGTGTATCAACATTGGCAATACCAAATCAATATCATTATGGAATGTAG
TTTCATATTATATATATTTGGTATTGTAGATGTTTCTATTTCTTAGGGGGGCTGTCTAGGCACATCTAGACGTGCCCTAG
TTACTGCACATCTAATTGACTCAATCAAATATAAAAGTGAAAGCAAAAAAAGGAAATATTTGCATGAATTATCTCCACGT
AAAATCAGTGAAACATAACTTATATGTTAAAATAGTGTGGAGGTGTTTGTTTTGATAAATATTATGCGTCATACGATTAC
AGCGTCAATTGATACCCTTATTTAGTGTTTGGTTAGCTCAGCTCCTTAACGCATACAACGTAAACAGTTTACAGGCCAAG
TCAAATTTGATTCGGCAGTAAATGAGTCACGTTTCCGGACGACCAGCGACTTCCATCTTCTCTTAGGCTATGTTTGGTTG
CCTGGGTGAGAAATTCCAGGGCAGAAACAGCACGGGAGTAATTTTCTTGACAACTTGAAATCCACGGGCTATTCTTCCAC
CACCATTTGGCACTTCGGGACGAGGTTTTCTGGCCTCCATGAAGAAAAGAGAGAAAAGCAGGAGAGAAAAAAAATGAGGC
TCTCCTCTTGAAGCTGGGTGCCGCATCACCGAGCAAGCGAGACCCATCTTCAACCTCGGATTAACCATGCAAATCAGCAT
AGCCAGCCGCCGGCTGCAAGGAAGGCCGACAAAGCAGCCGGCGATGTAGTAGATTCCTTTACAGGCATGAACCAAACAAA
ACAGAGATTTATATATCCATTACATCCCCGTTCCGGGCGTGATCTAATTCCCTTACCATTTACGTTGCCGCT
>chr3A_1
CATGTGTGAGTCGCCACCAAAGGCTCGGAACGACGAAGGTTGTCGTCGCACATGCAACGAATATTGATGAGAGAGGAAGG
TCACACCGCTAAAATCTCTGTTTTGGACACTCTGGCAGAGTGGCAGTACCACACAGTCCACATGCTCTGATGCCCTCGTT
TGTAACGGCAGAATTGGTTAGCAAAACAAAATCGTCGTTGACGTCAGATCTAAAGGTCCAAGACCCTACGGCCCATTGTG
ACAACCGCATAGCAGTGTG-----------CCATCCGTGCGCCTGAGCGCAGGACCGCCATATTGGCACATAGAAGGTCG
CCGATGTCGTCCATATAACTACATATGGGATGGAGGGAACCCAGCGA----------------------------GAAAC
ACCAGCGCCAAAGTTGCACAACGATACCCTCTGCCCTTAAGTCATCATCTGGAGGTCACGTCTCGCCTCACCCGCTAAAG
ACTATCAGAGCAGAGATCTTTCTGCCATCGCCTTCATCGACCAGTGTCGAGACTTAACCCCC------------------
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-----TACCACCTCTAGCAGCACCGAGGGAAAGAAAACGGGCCGTGGGAAGGGGGGC--------------GGAGGCATG
T--ATGAGTACCTGGCTATGTACGTGATGGGACA-------T--CTTTTCGGAAG-AAGAAAAACTTGATGGACAGATGC
ATGCATGCATGCAT----ATA--GGGCGCCATAACTCTAAACTGAAACGGATAACAACACAAGTCGGATA----ATGACC
AAACTCCTCTCTACGTATAGGTTGCGGAACGCAACAGGCTCCGGTCCCTATTTCTCTCGTGTTACTTAACACG------T
AC------GTACGTACGCAACAACTTGA----TTAATTTGCGTCTTGCCGCATCGCAAGATCTCAGCGA-----------
------------CCCGTTTCGATGACGAAGATTTTCAGGTACAGATCGATTGATCGATCGAAACAATCTTCCGCCCTTTT
CTTCCCCCGGAAAAGACCC---CAATCGAGTCATC----CATGAAGCTT--AGCTTCAAAGCTTCGCCATG------GAT
CCAATCCAAGCTTTTTCTTCTTCTTTGCAGGTGCAGCTACTATCGGTCGAAGCAACC------------CGAGGAGGACG
AAGAATCGGCGGCGGGGGAGTACGAGGACGTGGATCTCGAGGACGGCCAAGGCCAGCATGGAGGCAGCGGCGAGAAGCCG
GAATCCGGCGGCAGCGTGGACTCTGATGGGCCGCTCACAATCGACGTCGTCGGTACCATTCTCATCGGCATCTCCTTCAT
AATGGTAGGCTGCTTCTTCCTGGGTGGCTCCTACCTCCAGGCCGGC---CTGA---CGGGGGCGGACGTCGCCCTCCTGG
TCATCACCGGTGCCTTGTTGCTCGCCGTCGGGGCCGCCGGTTTGGCCGGTCTCGCCTTGCGAGGCTACACTGTCTCCTCG
TGGTTTAGGGTTTCTGATTGAGATATATTTTCATCCTGTGCTTACTTTATTTATTGTCTCCAA----TGGATCCAGAGTG
GATCGATCTGTTATTATAGATCATCTTTGTAGTTAATTGTGTTAGCTACCGGCTGTTT----------------------
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>chr3B_640
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-----TACCACCTCTAGCAGCACTGAGGGAAAGAAGACGAGCCGTGGGAAGGGAGGCGGGGTCGGTTGCAGGGAGGCATG
T--ATGAGTACCTGGCTGTGTACGTGATGGGACATTACTCCTATCTTTTCGGAAGA--AAAAAACTTGATGGACAGATGC
ATGCATGCATGCAT----ATATAGGGCGCCAGAACTCTAAACTGAAACGGATAACAACACAAGTCGGATATATAATGACC
AAACTCCTCTCTACGTATAGGTTGCGGAACGCAACAGGCTCCGATCCCTATTTCTCTCGTGTTACTTAACACGGAGTACT
AC------GTACGTACGCAACAACTTGA----TTAATTTGCGTCTAGCCGTATCGCAAGATCTCAGCGA-----------
------------CCCTTTTCGATGACGAAGATTTTCAGGTACAGATCGATTGATCCATCGAAACAATCTTCCGCCCCAGA
AA-------AAAAAAAACAGATCAATCGAGTCATC----CATGAAGCTTCAAGCTTCAAAGCTTCGCCATGCATATGGAT
CCAATCCAAGCTTTTTCTTCTTCTTTGCAGGTGCAGCTACTATCGGTCGAAGCAACC------------CGAGGAGGTCG
AAGAATCGGCGGCGGGGGAGTACGAGTACGTGGATCTCGAGGACGGCCAAGGCAAGCGTGGAGGCCGCGGCGAGAAGCCG
GAATCCGGCGGCGGCGTGGACTCTGATGGGCCGCTCACGATCGACGTCGTTGGCACCATTCTCATCGGCATCTCGTGCAT
AATGGTAGGCTGCTTCTTCCTGGGTGGCTCCTACCTCCAGGCCGGCGGCCTG---GCGGGGCAAGACGTCGCCCTCCTGG
TCATCACCGGCGCCTTGCTGCTCGCTGTCGGGGCCGCCGCTTTGGCCGGTCTGGCCTTGCGAGGCTACACTGTCTCCTCG
TGGTTTAGGGTTTCTAATTGAGGTGTATTTTCATCCATCCTTTGCTTACTTTATTGTCCCCATTAGTTGGATCCAGTGTG
AATTGATCTGTTATT----ATCATCTTTGTAGTTAATTGTATTAGCTACCGGCCGATTT---------------------
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>chr3D_738
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-----------------------GTGATGGGACA-------TATCTTTTCGGAAGAAAAAAAAACTTGATGGACAGATGC
ATGCATGCATGCATGCATATA--GGGCGCCAGAACTCTAAACTGGAACGGATAACAACACAAGTCGGATT----ATAACC
AAACTCCTCTCTACGTATAGGTA-CGCAACGCAACAGGCCCCAGTCCCTATTTCTCTCGTGTTACTTAACACG------T
AC------GTACGTGCTCAACAACTTGACTAATTAATTTGCATCTAGTCGTATCGCGAGATCTCAGGAGCGACCCTTTTC
CACGATTTCTGTCCTGTTTCGATGACGAAGATTTTCAGGTACACATCGATTGATCGATCGAAACAATCTTCCGCCCTTTT
CTTCCCCCGGAAAAGACCC---CAATCGAGTCATC----CATGAAGCTTCAAGCTTCAAAGCTTCACCATG------GAT
CCAATCTAAGCTTTTTCTTCTTCTTTGCAGGTGCAGCTACTATCGGTCGAAGCAACCT---GAGCCGCCTGAGGAGGACG
AAGAATCGGCGGCGGGGGAGTACGAGTACGTGGATCTCGAGGACGGCCAAGGCAAGCGTGGAGGCAGCGGCGAGAAGCCG
GAATCCGGCGGCGGCGTGGACTCTGATGGGCCGCTCACGATCGACGTCGTTGGCACCATTCTCATCGGCATCTCGTGCAT
AATGGTAGGCTGCTTCTTCCTGGGTGGCTCCTACCTCCAGGCCGGC---CTG---GCGGGGCCAGACGTCGCCCTCCTGG
TCATCGCTGGCGCCTTGTTGCTCGCCCTCGGGGCCGCCGCTTTGGCCGGTCTCGCCTTGCGAGGCTACACTGTCTCCTCG
TGGTTTCGGGGTTCTGATTGAGATATATTTTCATCCATCATTTGCTTACTTTATTGTCTCCATTAATTGGATCCGGTGTG
AATTGATCTATTATT----AT-----------------------------------------------------------
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>SNPs
--------------------------------S-------------------------------------S---------
---------S-----------------------S----------------------------------------------
------S-S-------------------S----------------S-----S--S-------------S-----------
-------------------SSSSSSSSSSS-------S-S--------S-S---------------S-S-----------
---S---------------------S-------S--S----S-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----
----S----------------S-S-------------------------SSS------SSS--------S-S----S---
-----------------------------S----S--------------S------------SSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSS--------------------------------------------------------S------S----------S
-SS-----------------------------------------------------------------------------
-------------------------------------------------------------S------------------
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--SSSSSS------------------------------------------------------------------------
-------------------------------------------------------------------------------S
------------S----------------------SSSS----------------------S--------S---------
----------S----------------------------------------------SSSS-------------------
-------------------S--------------------------------------S------S---S-----S----
---------S-SSS-------S-----------------------------SS--------S-----S-SS--S----S-
----S-S----S----S-----S-SSS----------SSSS------SSS--SSS---S---------S--S-----S-S
-----S-S-----------------------------------S-------------------S--S----S-----S--
-------S-----S-SS------------SSSSSSS-SS--SSSS-S---------------S------S-------S--
----S----------------S----------S--------S-------S--------SSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_377
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-------------------------------------AACCAATGCCTCGTCACCAT-----------------------
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>reverse_2469
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--------------------------------------------------------------------GCAAATCAGCAT
AGCCAGCC------------------------------------------------------------------------
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