>input_sequence_86604
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----------------------------------------------------------------------------ATGA
CGAGGCGGTTCTTGCCTCTTTGCGCGCTCCTCCTCGTGCTGCTCTGCATGGCGGCGAGCCTCGCGGAGGGGAGGCGCGGC
GGGGGACGCCCCATCATCGGCGGCGGCAGCGGCGGGGCCAGAGGGAGGGGCTCCGGCAGCCCGCGCGGCCTCAGCGGCGG
CACCTGGGCGGCGTGCGTCGGCTCCTCGCTGCTGGTCGCGGCGGCCATGCTCTTCTAG----------------------
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>chr3D_1_TraesCS3D01G320800
CAGTCGAGTGACGTCTGTGTTTTTTTTTTTGCTACAAGTGGCATGGTTGGATGCTAGAAACGGTGATGAAAAATGTTGTG
ATGGTATTGCAGGCAAGAACAATAAATTCTACAACCGTTCTAACTAAAATGCTACAACCGTCAATGAAGGATATTGCAAC
CGTTGAGATGGCGTTCTACAACCAGCATGATGGATGTTGCAACCGGTAGGAAAAATGTTGCGGCACAAAATGCTGCAAAG
TCGACTGAGAGTCTGAAACTTGGTTAAATCTCAGTGTTTTAGCAGGCTTGTTTGTAAAATCATAATCGAAACTGGTCGGA
CGTGCCACATTTCTATTTGCCTCTAACATGGACGTCAATTTCTCTCCGGCAAAACAATCAGCTAACCCGTGTAAAA---C
TTGGAGACGTGTGGTATTCGAGAAAACTTGGAGACGTGTACCATCGTGCACGAACTTAGAGAAGTCGGCAAGTCATACCA
ACATGAGCAGCTAACGACGAACCGACCTGGCACGTGCGTGCACTACGGAGCTTCGCTGTCAAGAAACCTGGAGCATATCC
CAG----------ATTATCATATCGCAGTCCATCAGCCAGGATAACACGCATACGATCCGATCCTTTCATCAGCCAACAG
AGTTACAAATCGTCGTCGTCTTCAGCGCACCGAAAACCAATTAACATGAATACATTAATCGATAATGGCAGGCAAACCGC
GACAACTTCTCACCCATCACGTAGAATAGAAACGTA----------------------CTCAAATCACCTGCACACGCTT
T-CATCAGAGACAAGAAGAACACTTCCATCCACTAAGACGTGGACTCGTGGCGTATTACCAGTCAAAACCCGTTGCCAGG
TCAACTCTGTACCCTGCATAAATATACACCACGAGCGATGATGCTGCCCACGACATCGAGTTGGAGCAGCAGAGCAGAGC
AAATAATCACAGAAGAATCTGCTGCCCGTACGTGCTTGTTTGGAGCTTGGTGCTTGGAGGCGAGGCTAGGAAGAAGATGA
CGAGGCGGTTCTTGCCTCTTTGCGCGCTCCTCCTCGTGCTGCTCTGCATGGCGGCGAGCCTCGCGGAGGGGAGGCGCGGC
GGGGGACGCCCCATCATCGGCGGCGGCAGCGGCGGGGCCAGAGGGAGGGGCTCCGGCAGCCCGCGCGGCCTCAGCGGCGG
CACCTGGGCGGCGTGCGTCGGCTCCTCGCTGCTGGTCGCGGCGGCCATGCTCTTCTAGCTTGCAGCGGCGGGAAGAGCTC
AAGAAGGATGGTTGGGCAACGTAAATGTTCTGTGCATTCGTTGGTTCTTTGTTACTACTGTCGATTTGATTGTTGTTGTA
TATACATAC----------GTGAGCGGATTGGCTAATTCATTCGATA---------------------------------
-TGTTTATCTTGATTATTAAGTGGATGCAGCCGTTCATATTGAGACACTGTATATGAGGATGTGCATGATCTGTTCTCGT
CAAAGTATGGTAGAGACAGCTCATGTGATTGCGCAGTGTGTTTAGCATCAAATCATATACTACTACCACGCCAACA----
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--------------TAGTTTATTTTCATAACATTTCACAGAACTACATCCTAGAAA-----------------ATGTTAA
ATGCATATTCCCTCCGTAAAGAAAT-------------------------------------------------------
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------------------------------------------------------------------------------AT
ACTTTTATATTGAGGGAGTACATGTAAATATCTTAGCTTTAATATTGAAAGAGGGTAAATCTGCAGTCCATCATCTCGAA
AACTCGCAGGGGCACAAATGCATGCACCCACCCATTTGCTTCAAGATTGGTGCACTAGTTTATGTCATTAACCCTTAATT
GTTGCACT--GGGTCCATGCATGCCAGTTTTTGGCAGAGTTGCATGCGCCACCCACCCCTCCTCCAATGCTTTTTTTTTT
AATTTTATCTTCAAATTTGAATCTATTGTATCTTTCGAACCGAAAGTACAAATTAAGTTCCATTTT--------GCATAT
TCATGTTCGTTGCAATGTGTACTTTCGAATAAGACCAGTTTTGAATACATTCAACACC---TTTTTAAAGTTTACCAAGT
TTCAAATATTAAAACTTGCTAGTCATAATATTATGTTTTAC----------AAAC---TTACCATTCATTCTATCAAGTT
ATAGTAGTTGAAACACTTTT--------AAAACTCGTCAAAATGTTAGAGCCCCCACATGGTTTTAAGTTTCACTT-TTG
AACTTATTCATTT------------CTATTGAGT----TTCAGCAGTTGAAACATAGCAAAATTTTAAATGC--GTCAAA
ACGTATA-CAAATTGGTCTTGTTTCAAAAGATATAATAGATTAA
>chr3B_285
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--------------------------------------------GGCTTGTTCGTAAAATCATAATCGAAACTGGTCGGA
CGTACTATTTGT--------CTCTAACAAGGACGTCACTTTCTCTCCGGCAAAACAATGTGC--ACCCGTGTAAAAAAAC
TTGGAGACGTGTCGTACTCGAGAAAACTAGGAGACGTGTGCCATCGTGCACGAACTTACAGAAGTCGGCAAGTCGTACCA
ACATG---AGCTAACGACGAACCGACCTGGCACGTGCATGCACTACCGAGCTTCGCTGTCAAGAAACCTGGAGCATATCT
CATCCCAGATTAAATTATCATATCGCAGTCCATCAGACAGGGTAACACGCATA-----CGATCCTCTCATCAGCCAGCAG
TCACAAA-----TCGTCGTCTTCAGCGCATCGAAAACCATTTACCATCAATACATTAATCGACAATGGCAGGCAAACCAC
GACAGCTTCTCACCCATCACGTAGAAGAGAAACGTAGCTACTCTTACTACTTCTCGACCTCAAATCACCTGCACACGCTT
T-CAGATATAAGAAGAGGAACATTTCCATCCACTAAGATGTGGACTCGTGGCGTAT-ACCAGTCAAAACCCACTGCCAGG
TCAACTCTGGATCCTGCATAAATATACACCACGAGCGATGATGCTGCCCACGACATGGAGTTGGAGCAGCAGAGCGGAGG
AAATAATCACAGGAGAATCTGCTGTCCGTGCGTGCTTGTTTGTTTGGA---GCTTGGAGGCGAGACTAGGAAGAAGATGA
CGTGGCGGTTCTTGCCTCTTTGCGCGCTCCTCCTCGTGCTGCTCTGCATGGCGGCGAGCCTCGCGGAGGGGAGGCGCGGC
GGGGGACGCCCCGTCATCGGCGGCGGCAGCGGCGGGGCCAGAGGGAGAGGGTCCGGCAGCCCGCGCGGCCTCAGCGGCGG
CACCTGGGCGGCGTGCGGCGGCTCCTCGCTGCTGGTCGCGGCGGCCATGCTCCTCTAGCTTGGAGCGGCAGGAAGAGCTC
GAGAAGGATGGTTGGGCAATGTAAATGTTCCGTGGATTCGTTGGTA-------ACTACTATTGATTTGATTGTTGTTGTA
TATACATAC--ATACATTCGTGAGCGGATTGATGAATTCATTTCATA---------------------------------
-T------------------------------GTTCATATTGATACACTGTATATGTGGATGTGCATGATCTGTTCTCGT
CAAAGTATCGTAGAG--------TGTGATTACGCAATGTGTTTAGCATCAAATTAAATACTACTCCCTCCGTTCGGAATT
ACTTGTCACAAAAATGGATAAAAATGGATGTATCTACAACTGAAATACATCTAGATACATTCATTTTTTGACGAGTAATT
CTGAATGGAGGGAGTACCACAGAGACATACTCCCTCCGTCCCATAATGTAAGACGTTTTTTGACACTAGTAAGACGTTTT
TTGACACTAGTAAGACGTTTAACATCTTACATTATAGTGTCAAAAAACGTCTTACTAGTGTCAAAAAACGTCTTACATTA
TGGGACGGAGGGAGTAGTTTATTTTCATAACATTTCACAGAACCACATCGTAGAAACATAATGTGGTTATGTTATGTCAA
ATACATACTCCCTCTGTAAAGAAATGTGATTATGTTATGCCAAATACTCTCTCCGTTGCTAAATATTTGTCTTTTTAGAG
ATTTTAAATGGACTAACACATACGAATGTATATAAACATATTTTAAATTGTAGATTTACTTATTTTGTTTCGTATGTAGT
CACTTGTTGAAATCTTTAGAAAGACAAATATTTAGGAACGAAGGAAGTACATAACATTTCACTGATCTAAATGCTCTTAT
ACTTCTTTTCGGAGAGAGTACATGTAAATATCTTAG----------------------ATCTGCAGTCCATCATCTCGAG
AACTCACAGGGGCACAAATGCATGCAACCACCCATTTGCTTCAAGATTGATGCACTAGTTTATGGCATTAACCCTTAATT
GCTACACTTGGGATCCATGCATGCCAGCTTTTAGCAGAGTTGCATGCGTCACCCACCCCACCTCCCATGTTTTTTTTAT-
-ATTCTACCTTCAAATTTGAATTTCTTGTATCTTTTGAACCGAAAGTACAAATTAAGTTTCA-TTT--------GCATAT
TCATGTTCGTTGCAATGTGTACTTTTGAACAAGACCAGTTTTGAATACATTCAACACC---TTTTTAAAGTTTACCAAGT
TTCGAATATTAAAACTTGCCAGTCATAATATTATGTTTTAC----------AAAC---TTA---TTCATTCTATCAAGTT
ATACTAGTTGAAAAGCTTTT--------AAAACTTGTCAAAACTTTAGAGCCCCCACACGGTTTTAAGTTTCACTT-TTG
AACTTACTGATTTTCTCGTTCATTT----TTATCAAGGTTCAGCAGTTGAAACTTAGCGAAATTTTAAATGC--GTCAAA
ATGTATA-CAAATTGGTCTTGTTTCAAAATATATAATAGATTAA
>chr3A_694
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------------------------------------------------------------------GGCAGGCAAACCGC
GACAGCTTCTCACCCATCAAGTAGAGTAGAAACGTA----------------------CTCAAATCACCTGCACACGCTT
TTCATCAGAGACAAGAAGAACATTTCCATCCACTAAGACGTGGACTCGTGGCGTGT-GCCAGTCAAAACCCGTTGCCGGG
TCAACTCTGGATCCTGCATAAATATACACCACCCGGGATGTTGCTGCCCACGACATCGAGTTGGAGCAGCCGAGCAGAGG
TAGTAATCACAGAAGAATCTGCTGCCCCTGCGTGCTTGTTTGGAGCTTGGTGCCTGGAGGCGAGGCTAGGAAGAAGATGA
CGAGGCGGTTCTTGCCTCTTTGCGCGCTCCTCATCGTGCTGCTCTGCATGGCGGCGAGCCTCGCGGAGGGGAGGCGCAGC
GGGGGGCGCCCCATCATCGGCGGCGGCAGCGGCGGGGCCAGAGGGAGAGGGTCAGGCAGCCCGCGCGGCCTCAGCGGCGG
CACCTGGGCGGCGTGCGTCGGCTCCTCGCTGCTGGTCGCGGTGGCCATGCTCTTCTAGCTTGCAGCGGCGAGAAGAACTC
AAGAAGGATGGTTGGGCAATGTAAATGTTCTGTGGATTCGTTGGTTCTTTACTACTACTGTCGATTTGATTGTTGTTGTA
TATACGTACAGATACATTCGTGAGCGGATTGATGAATTCATTTGACATGTTCTATCTTGATTAAGTGGATTATGGGCAGT
TT------------------------------GTTCATATTGAGACACCGTATATGTGGATGTGCATGATCTCTCCTCGT
CAAAGTATCGTAGAGACAGCCCATGTGATTTCGCAGTGTGTTTAGCATCAAATCAAATACTACCACACA---AACA----
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--------------TAGTTTATTTTCATAACATTTCACAGAACCACATCGTAGAAACATAATGTGGTTATGTTATGTCAA
ATACATACTCCCTCGGTAAAGAAATGTGATTATGTTATGTCAAATAC---------------------------------
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--------------------------------------------------ATAACATTTCACTGGACTAAATACTCTTAT
ATTTTTTTAGGGAGAGAGTACATGTAAATATCTTAG----------------------ATCTGTAGTCCATCATCTCGAA
AACTCACAGGGGCACAAATGCATGCAACCACCCATTTGCTTCAAGATTGATGCATTAGTTTATGTCATTAACCCTTAATT
GCTACACTTGGGGTCCATGCATGCTATCTTTTAGCAGAGTTGCATGCGTCACCCACCCCACCTCTCATG-TTTTTTTAT-
-ATTTTATCTTCAAATTTGAATCTATTGTATCTTTCAAACCAAAAGTACAAATTAAGTTTCA-TTT--------GCATAT
TCATGTTCGTTGCAATGTGTGCTTTCGAATAAGACTAGTTTTGGATACATTCAACACC---TTTTTAAAGTTTACCAAGT
TTCAAATATTAAAACTTGCTAGTCATAATATTATGTTTTAC----------AAACTTATTA---TTTATTCTATCAAGTT
ATACTAGTTGAAACGCTTTT--------AGAACTTGTCAAAATGCTAGAGCCCTCACATGGTTTTAAGTTTCACTT-TTG
AACGTACTGATTTTATTGTTCATTT----TAAGT----TTCAGCAGTTGAAACTTAGCAAAATTTTAAATGC--GTCAAA
ATGTATA-AAAATTGGTCTTGTTTCAAAAGATATAATAGAATAA
>chr3A_1669
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----------------------------------------------------------------------------CGAA
AACTCGCACGAGCACGCATGCATGTGGCCACCCATTTGCTTCAAGATTGGTGCACTAGTTTATGCCATTAACCCTTAGTC
ACTGCACT--GGGTCCACTCATGCTAGCTTTTGCTCGAGTTGCATGCGTCACACACCCCGCCTCATA-----------TT
CATTTTATCTTAAAATTTAAATCTATTGTATCTTTTGAACCGAAAGTTCAAATTAAGTTTCA-TTGGAAACTTGGCATAT
TCCCATTCATTGCAATGAATACTTTTGACTAAGACCAATTTC-AATACATTTAGACATCTTTTTTCAATTTTTACCAGGT
TTCTT--------------TAATCATAATATTAAGTTTTACCAAGTTGTACAAACTTATCA---TTCGTTCTATCAAGTT
TTAGTAGTTGAAACTTATTGAAGTTTGAAAAACTTGTCAAATCACTGGAGCCCCCATA-GGTTTTAAGTTTCAGTTCTTA
AACGTACTGATTTTATTCTTCATTTCTATTAAAC----TTCAACAGTTGAAACTTAGCAGCATTTTAAAGACATGTCAAA
ACATATTCAAAGTTTGTCTTATTTCAAA----------------
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS--------S---------------------------
---S-S-SS-S-SSSSSSSS--------S--------S--------------------SS--SS----------------
------------S---S-----------S----------S------------------S---------------S-----
-----SSS-----------------------------S--------S--------------------------------S
--S---------------------------------S----S-----------SSSSS-------S----------S---
SSSS-S-SSSSS-----------------S---------S---S---S--------------S-----------------
----S---------------------------------------------------------------------------
----------------------S---------------------------------S-----------------------
---------S-S-------------------------------------------------------------------S
-----------------------------S--------------------------------------------------
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-----------------------------------------------S--S-----------------------------
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-------------------S--------------S---------------SS----------------------------
-------------------------------SSS--------S-------------------------------------
--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSS------------------------S-----------------------
--------S-----------S---------S------------------------S-----------S-SSS--------
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-------------------------------------------S-----S---------------------------S--
--S----S------S-----------------------------------------------------------------
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------S--SS---S---------------------SSSSSSSSSSSSSSSSSSSSSS----------------------
--------------------------S-----------------------------------------------------
-S-------------------------S--------------------S----------S-----S---S-------S--
S----------------------------------------------------------S--S-----------------
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-------------------------------------------------------------SSS----------------
--------------S-------------------S---------------------------------------------
------S-S---------------------S----------------------S--------------------------
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>forward_177
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-----------------------------------------------------------------------------AAC
CGTTGAGATGGCGTTCT---------------------------------------------------------------
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>reverse_1459
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------------------AAGTGGATGCAGCCGTTCAT------------------------------------------
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