>input_sequence_79588
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------------------------------CTATAAGACGAGGCCTCCCTCCCTGTCCCAAGCTCGATCGATTCCAAAGC
CAGCCAGCCACCGACCGAGCGACAAATAATGGAGGGGCTCATCCCGTTCGTCTACAAGGCCATCAAGGAGCGGCGCACCC
GGAGCTACTCCAGGTGCGGCTCGGCGCGCGGCGCCGCCGTCGCGGACGAGGAAGACGTCTGGGAGCAGCAGAAGCAGCAG
TGG---GCGGCGGCGGACGGCGCGGGGAGGGAGGCGGGGCACTGGCGGCACCGGTCGCTGGAGGAGCTGGCCGGCGAGGT
GGGCTCCGCGGCGCCCGAGTGGCCGGCCCGCGGGGCGATGCGCAGGGGCCGGAGCGCCAGGATCTTCTCCTGCATCGGCG
GCATGTAATCAA-----------------------CCTCGATCCCAGCGTGCGTGCGTGCGTCGGCCGTCGGGGTGTGTA
GTACGTATGAATGGTACGTGGAAGCCTACGCGCGTA--------------------------------------------
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>chr3B_1_TraesCS3B01G436300
TGTACTTGATTCGGTTTTCGTGTGATTGCTACTAGCTGCTGCAGCGTCAATGAGCGAGTGCAATTCTTAAACGGAACCAT
GCATGTGTTAGTTGTCCGTGTTGCCAATTAAGAAGTGCCTTCTGCCGCTGTCCATGCCGTGCTGTACAAGGATTAGCTGG
ATGATTGGT--------------------TTAACAAATCGATTCCCA-TTTATGCCAGGTATCAGCAATTACGTGTTTTT
GGAAC---TTAGTATTCTTTTTTCCGCCTCCTGATTCTACCGTTTTTGTATGGATTC-GGAATTTTATTGGAG-------
-----------ATCAAACAAATGATCATTGGCCTCGTGTTTTTGCTGAGAGATACAGGTCAAACTTGTCCAAAGAGA---
-------CGGAGTTTTCATTGGTTTGCGCCAATCCAGAGTACAGGCCTACCT----CAAATGTACCCGTATCTAGCTCTA
GAAAAACTATACCTATATGGGCAACATCGAGGTGACTTTCAGACGTTATCTCGTCTCGCCACGCATCAAAACCTTG----
----------------CAGTTT----------------------------------------------------------
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-----TATTCTGTCACATTAATTCCGACCCTTGCAGTTTTCTCCATGCTCTTATTTTTT--G------------------
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---------------------------------ACCCATCG--------CAACGGAAAGTAGTTTGCTTTTCCGAACAAG
ATCATGAGCGCCTGTTGCCTACAGGCTGCCTAATCTGGTCCGGCATATACCGGCAAGTACCT---------------ACG
GACGGCCTAACCACGAACTCGAAGAAGGC--AAAAGAACAGCCGTCCGACCAAAACCATCGGCTGGCCAGACAACTGCAG
TTGGCTAATGGCCGGTCACTGATTGATTAGCACGATCGGGTAGAAGCTAGACAAAGCCGTCAACATCGGAGGTTTTCTGG
CAGTCGGGCACAAGCAACCATAACCAAAGCCCAATTGCAACTCCACCACGCCACCACACGCGAGGGAAAATCCCGAGTCA
AATGGCTTTTCTTTA---ATCTGTCGACGAGCATGCCCGCTGAAACCTACAAGAAGC---CGTCGCCCGGAGCACGGGCG
TAGACAGAACTGCACCTGCACCC------CCTATAAGACGAGGCCTCCCTCCCTGTCCCAAGCTCGATCGATTCCAAAGC
CAGCCAGCCACCGACCGAGCGACAAATAATGGAGGGGCTCATCCCGTTCGTCTACAAGGCCATCAAGGAGCGGCGCACCC
GGAGCTACTCCAGGTGCGGCTCGGCGCGCGGCGCCGCCGTCGCGGACGAGGAAGACGTCTGGGAGCAGCAGAAGCAGCAG
TGG---GCGGCGGCGGACGGCGCGGGGAGGGAGGCGGGGCACTGGCGGCACCGGTCGCTGGAGGAGCTGGCCGGCGAGGT
GGGCTCCGCGGCGCCCGAGTGGCCGGCCCGCGGGGCGATGCGCAGGGGCCGGAGCGCCAGGATCTTCTCCTGCATCGGCG
GCATGTAATCAA-----------------------CCTCGATCCCAGCGTGCGTGCGTGCGTCGGCCGTCGGGGTGTGTA
GTACGTATGAATGGTACGTGGAAGCCTACGCGCGTAATTAAGTGCTTGATTTTGC---TGCTTTAGCTGCTTATAATTAG
TTTAGCCTGTAAGGC------AAGGTTCAGGGTGGTCTGAAGAGTAGAAGGGAGTTCATGCAGTGCGCGCGTGTTGTGTG
TACTCCAACCAAAGTGTATATACAGTGCTTGGATTTTATGAAGATGACGATGTAAATGGTGGTGCATGTTTGTCTCTCAA
TCTGTCCAACTGACCGTACCGCCTGAATGGGCTCGTTTGCAAGCTACGTGTGCTGAAAACAGTGGCAACGGCGTCTGCAA
GGCTCCGTGGTTTTCCTATTCGTTTAGGGCTTGGTGCCAGTGCGAACGCCGATGTGCCTTGCTCGATCCCTTGCCGCCTC
CGGCATGCGCTGCGCGGGGCGGAGTGGACGATTGGAACGGGATGAAGCAGATTATCTGACTTTCTGATGGACGGAGTATC
TATGGTGCTGAGAGGATTCCGTCTCAAATCAGTCGTCGTCACTGGACAGGCGCGGCAGTTATTGGAGTCCAGGTTGTCAG
AATCATGATTAGGAGCTCTGACGGTAGAAATGTAAATTGTAGAATCTTAACTATCAGGATCGTAAAAACGTAGATTCTAG
TAACCAAAATCATAGAATCAAAGTGATTTGTTTGGAACGTAAAGTCTTAGAATCTTACTACAATAGAGCGATTCTTGATT
GGAGTAACCTGGTCCTTTTTGAGAATACAGCATGGAGATGAATCACCTATTCTGATCGGTCTTGTGTTTCAAATGAAGTC
GTTAATGTGCATCGAGAATTCCTCACGAGTATTATATCCTATCAATTTTTAGAATTCACATTGTATACGATTGTAGGTTT
TAACACAGTACATATCTTGTACTTGTACCAACACATGTGCAATATATAAAGAGACGTATGCACTCCAAGGGGTATGCGAT
TCCCTCAATCCTTCTAAACCTACTTTTATTACTTTTACATGGTATCAGACTAGGTCGTCCTCATGTCTTCCGTCGCCCTG
CTGTC
>chr3A_1
TGTACTTGATTCGGTTTTCGCGTGATTGCTACTAGC---TGCAGCTTCAATGAGCGAGTGCAATTCTTAAACGGAACCAT
GCCTGTGTTAGTTGTCCGTGTTGCCAATTAAGAAGTGTCTTCTGCTGCTATCCATGCTGTGCTGTACAACGATTTTGTTT
TTTGAACATGTGATGTATACAACGATTAGTTAACAAATTGATTTCCA-TTGATGCCAGGTATCAGCAATTGCGTGTTTTT
CTAAATTATTAGTCTTCCTTTTTCCACCTCCTGGTTCTACCATTTTTGTATGGATTC-GGAATTTTATTGGAG-------
-----------ATCAAATAAATGCTCATTGGCCTCATGTTTTTGCTGAGAGATACAGGTCAAACTTGTCCAAAGATATAG
AGAGAGACGGAGTTTTCA-TGTCTAGCGCCAATCCGGAGTAGTACACGCCTACCTC------------------------
----AAATAAACCTATATGGGCAACGTCGAGCTGACTTTCAGACGTTATCTCGTCTCGCCACGCATCAAAACCGTCTCAA
CAAGTAATCAAGAGGACACAACAAAGGGTTCAAGTCCCGATGCTTGTATTATTTATTAATTTATTTCAGGATTTTTGGCA
ATGCGCTTTTAATGGAAGGAGACATTCCCGTCGACAACGAAACGTCTACGATGATTAAGATGATATGCCGGCTCAGTTTC
TTGAAGGTGCTCGTAGGGGTATGGATGTATGTGTGTGCGTTCATAAAGATGAGTATATGCGGGTATGTATGAGCGCTTGC
GTCTGTACTGTGTTAAATTTTTTTTGATCTTTGCAGTTGTC-CCATGCTCTTATTTTTTTTG------------------
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---------------------------------ACCCATCGCAACGGTCCAACGGAAAGTAGTTTGCTTTTCCGAACAAG
ATCACGAACCTATTGCCT------------AAATATGGTCCGGCATATACCAGCAAGTGCTTTGACATGAGCAACGAACG
GACTGCCTAACCACGAAACC-AAGAAGGC--AA---AACAGCCGTCCGACCAAAGCCGTCGGCTGGCCAGACAACCGCAG
TTGGCTAATGGCCGGTCACCGATTGATTAGCACGATCAGGTAGAAGCCAGACAAAGCCGTCAACATCGGAGGTTTTCTGG
CAGCCGGGCACAAGCAACCATAACCAAAGCCCAATTGCAACACCACCACGCCACCACACGCGAGGTAAAATCCCGAGTCA
AATGGCTTTTCTTTATTAATCTGTCGACGAGCATGACCGCTGAAACCTACAAGAAGC---CGTCGCCCGGAGCACGGGCG
CAGGCCGAG------CTGCACCC------CCTATAAGACTAGGCCTCTCTCCCTGTCCCAAGCTCGATAGATTCCAAAGC
CAGCCAACCACCGACCGATCG----ATAATGGAGGGGCTCATCCCGTTCGTCTACAAGGCCATCAAGGAGCGGCGCACCC
GGAGCTACTCCAGGTGCGGC------------GCCGCCGTGGCGGACGAGGACGACGACTGGGAGCAGCAGAAGCAGCAG
CGGGCCGCGGCGGCGGACGGCGCGGGGAGGGAGGCGGGGCACCGGCGGCACCGGTCGCTGGAGGAGCTGGCCGGCGAGGT
GGGCTCCGCGGCGCCGGAGTGGCCGGCCAGCGGGGCCATGCGCAGGGGCAGGAGCGCCAGGATCTTCTCCTGCATCGGCG
GCATGTAATCAAATCAACCTCGCCGCGACGACGTCCGTCGATCCGACCGAGCGTGCGTTGGTGTGTGTAGTAAGTAC--A
GTACATACGAATGATACGTGCAAGCCTACGCG-GTTACGAAGTGCTTAGCTTTGCTTGTGCTTTAGCTGCTTG--ATTAG
TCGTGCCTGTAAGCTTGGTATAAGGTTGAGGGTGATCTCAAGAGTAGAAGGGAGCTCGTCTAGTGCGCGCGTGTTGTGTG
TACTCCAACCAAAATGTATATACA--------------------------------------------------------
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>chr3D_40
---------------------------------------TGCAGCGTCAATGAGGGAGTGCAGTTCTTAAACGGAACCAT
GCATGTGTTAGTTGTCCGTGTTGCCAATTAAGAAGTGTCTTCTGCTGCTGTCCAAGCTGTGCTGTACAACGATTAGCTGG
---------------------ACGAGTAGTTAACAAATCGATGCCCATTTGATGCCAGGTATCAGCAATTCCGTGTTTTT
TCAA---ATTAGTCTTCTTTTTTCCACCTCATGATTCTACCATTTTCTGTACCGCCTTGGAATTTTATTGGAGATACGTA
CAGGTGAAATGATCAAACAAATGATCATTGGCCTCGTGTTTCTGCTGAGAGATACAGGTCAAACTTGTCCAAAGAGATGG
AGAGAAGCGGAGTTTTTGTTGTCTAGCGCCAATCCGGAGTAGTACACGCCTACCTCCAAATGTACCCGTATCCAGCTCTA
GAAAAACTAAACCTATATGGGCAACATCGAGCTGACTTTCAGACGTTATCTCGTCTCACCACGCATCAAAACCGACTCGA
CAAGCAATCAAGAGGACAGATT----------------------------------------------------------
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-----TTGTCCGTCACAATAATTCTAACCCTTGAAGTTCTCCTCATGCTTTTATTTTTTATCCATGTTGACATATAATAT
GCTGCCTAGTCTCTTCCATCAGACCAGTCTTTTGTTTGCATTGGCCAGGGCATGTATTTCTACATGGTATCAGAGTCAAG
AGGTCTTGAGTTCAAAACCTAGCTGGCGCAATTAAATTGCAGCCCACTTTCGATGTTGACGTATAATGTAGATCGATTTT
TTGGTTGCATTGGCTAGAACATGAACTTCTATAACCCATGG--------CAACGGAAAGCTGTTTGCTTTTCCGAACAAG
ATCACGAGCCTATTGCCAAACAGGCTGCCCAAATACGGTCCGGCATATACCAGCATGTGCCTTGACA-------------
---TGCCTAACCACGAAACC-AAAGAAGGCAAA---AACAGCCGTCCGACCAAAACCATCGGCTGGCCAGACAACTGCAG
TTGGCTAATGGCCGGTCACTGATTGATTAGCACGATCGGGTAGAAGCCAGACAAAGCCGTCAACATCGGAGGTTTTCTGG
CAGTCGGGCACAAGCAACCGTAACCAAAGCCCAATTGCAA---CACCACGCCACCACACGCGAGGTAGCATCCCGAGTCA
AATGGCTTTTCTTTTAA------TCCACGAGCATGCCCGCTGAAACCTGCAAGAAGCCGTCGTCGCCCGGAGCACGGGCG
CAGGCGGAG------CTGCACCCGCACCCCCTATAAGAGGTCGCCTCCCTCTCTGTCCCAAGCTCCATAGATTCCAAAGC
CAGCCAACCATCTAATCAG-------TAATGGAGGGGCTCATCCCGTTCGTCTACAAGGCCATCAAGGAGCGGCGCACCC
GGAGCTACTCCAGGTGCGGCTCGGCGCGCGGCGCCGCCGTCGCGGACGAGGACGACGTCTGGGAGCAGCAGAAGCAGCAG
TGG---GCGGCGGCGGACGGCGCGGGGAGGGAGGCGGGGCACCGGCGGCACCGGTCGCTGGAGGAGCTGGCCGGCGAGGT
GGGCTCCGCGGCGCCCGAGTGGCCGGCCCGCGGGGCGATGCGCCGGGGCCGGAGCGCCAGGATCTTCTCCTGCATCGGCG
GCATGTGATCAA--------------------------------------------------------------------
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>SNPs
--------------------S---------------SSS-----------------------------------------
-------------------------------------S-------S-----------S-----------S----------
S-SSSSSS------------------------------------------S-------------------S---------
SS--S--------S-----------S---------------S--------------------------------------
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---------------------SS-S----------S-----SSSSS-SS-SS--------------------S-------
---------S---------------------S-----------------------------------------S-S----
-------------------S------------------------------------------------------------
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-------S----------------S-------------S--S--------------------------------------
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----S----SSS-SSSSSSSSSS-SSSS--S---S----------------S------S---------------------
---S-------------SS-S------------SSS--------------------------------------------
-----------------------------------------------S--------------------------------
-----------------------------------------S-----------------------S--------------
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S--S-S--SSSSSSS-----------------------------------------------------S-----------
------S--------------SSSS-------------------------------------------------------
----------------------------------------------------S---------------------------
------------------------------------------S-------------------------------------
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------------------------------------S-------S-S--S--------SS--SS-SSSSSSSS--SSSS-
----S--S-----S------S-----------S--S-SS--------SSS----------------------SSS-----
-SSS---------SS------------S------S---S---------------S--S-SS-------------------
-------------S----------SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSS
>forward_444
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------------------------TGCGCCAATCCAGAGTACAG------------------------------------
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>reverse_2938
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---------------------------------------------------------ATGCACTCCAAGGGGTATGC---
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