>input_sequence_54961
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------------------------------ATGCCGCCACATTTTCCCAGCAATCCTGACCACGGACCGCACGTCACAGG
GCCATTCCACAGGCACAAGTCGATCCACCGGATCCTGGGGGGAGGGAAAGGTGCGCCATTCTTGTTCTGTTTGTAAGCAA
TTACCCTACACTATCTGCATCACCATAGTTTCTCCCCAAGCCGAC----GTAGTTATGGACACCGATGTTGGGCTTTGGT
TGCAGCTGCGGACGTTCTGCTGTGGAAGAACAGGAACGTGTCTGCTGGGGTTCTCGCTGGGGCCACGTTGACATGGTTCC
TGTTCGACGTGGTTGAATACAATGCAGTTCCGCTCCTTTGCCAGATCGCCATCTTCGCAATGCTTGCCATCTTCATTGCG
TCAAATGCTGCGCAGCTCTTCGACAGGCATGGCTTCCTTTCTTTCCACGGAGAGGAGATATCCCAGTGTTTATTTATTTT
TTGAGTAATTGTCCCAGTATTTAGCTTTAAAGAATTTCAAAAGGTCGGCTGACCAATTTCAAATCGCAGGGCCCCGCCAA
GGATACCACAAGTCGTCGTCTCCGAACACGCCTTCAGAGAAATGGCCTTGACCATTCACCACAAACTGGAATATGCTGCA
TCTCTTCTTTATGATATCGCATGTGGAAAGGATCTGAAGAAATTTCTCATGGTACGAAATTCTCTTATTTGCTATCTTAG
TCAAGAAAAGACAAACCATGTGACAAGTCTTGTTCCAGATCGACATTATGGATTAATACAGAAACACTTAAGAGATCTGA
ATCAACCAGATTAGACATGACATGCCACTCAAATCAACGTTTAGCCAATATAGTTCACAACGTTATTTTGCTATTGCTCT
TCAACTTAAACTTGTACTGACATTCAAATTGTTACTATTGTTATAAGGTGGTAGGATCCCTGCTGTTATTGTCAGTGATT
GGAGGTTCTTGCAGCTTCACAAGCCTACTCTACCTTGGTAAGTAGAACAGAAATAGTAACGTTCAAGAAAACCAAATACA
GAAGGTGGAACTAACTAGTAACTACAGAAAGGATGCTAGGAGAACACATAAACTAATGCAGTCTCACAGAAAAATGTAAA
ACTGAAATTTCTAAATAGTATAACAAGTAGTATGTGTTTCTTACTTTCACAGGATTCTTGTGTGCCCACACTTTGCCAGT
GTTGTACCAACATTACGAGACAGAAGTGGACCATCTCGTTGCAAGGGGTGGCCAAGACATCAAGAAGTTCTATGAGAAGG
TTGATTCCAATTTGCTCAACAAAATACCAAGAGGCCCTGTCAAGACGAAGTTCAGATAA---------------------
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>chr3A_1_TraesCS3A01G261500
GGGCGCACGGCCGCAGCGCCCATGGGTCGCACTCCGAGCGCGCTGCCATGGACGCCCCGCGCACC---GCGCCCGACGCG
GTGAGCACGGCTACGAGGAACAGCACCGTGCAGGGCTTCATGGCTTCTCAGTGAAGGATTACTCTGTCTGG----TGGTT
TTGGGAGCACAAGAGAGGGTTGGCATACTATTTGTAGCAAGAGAACAGCGCACCCGGCACCCGCGCCATGCTCTATCTGG
AACAGTGCCGCTAAAACTTCGT-AAAGCTTTTGCATTGCACGGTTGCGTAAACGGTGGAGCACGGGCATTCCAATG-AGT
GCTTGGGGCTCCGGCACTGCTTCAGAGCTCGGGTCGCGTGAAGCACGCTGCTGCTGCTGCTTAGCGAGACATGTCCAAGG
TTTGCTGTGCAGATTACGTTTGTTAATTGAAGTGGGGTGACCGTGGAGCACACCGATAAAAGTGCCT-------------
----------------------------TGTTGAACAGATTTTCCAACATTGAGCAATGGCGAAATGGCGATAGTTGTTT
CTGGAATAAGGAGGCTGCTGGGACGA------------------GAGCGCCGTCAGAAATGCGGAGTAAGAAAGACGGCA
TCTTCATCACCGGGTCACAAAAGCTCTCACACTTGAGTAGGAGACGGCGAGTGCAGAAACGCTGGGGTGCGTCGCAAGTT
CACATTGATGCGTGTCACGGTCAGAACCCCATTGATGTTCACAGAGCATCAAGGTGCAGTTCCGGCAAGCTTCTGGCATA
AACTACTGGCAAACAGCTAAACTTGCTTC-AGTCTGGGCTCTGACGAAGAAAACATCTGGTTGAAGGAAACCCTTGCCCT
GCACCCGTTT-ATTCCCCTCCCTCAATTGCTCATCCTCCTACAGGCCAAGCTATCCTTTCCTTGTCAACATAGGCTTACC
CTTTAGAGCTCATACTAGCATTTAGGTGCCTATAAAGACGCAATTTCTGCAACTAAACAGATCAGACATCTAACAAATCA
ATCAGGTGAACATCCCAAACGCGTGAAGTCATGCCGCCACATTTTCCCAGCAATCCTGACCACGGACCGCACGTCACAGG
GCCATTCCACAGGCACAAGTCGATCCACCGGATCCTGGGGGGAGGGAAAGGTGCGCCATTCTTGTTCTGTTTGTAAGCAA
TTACCCTACACTATCTGCATCACCATAGTTTCTCCCCAAGCCGAC----GTAGTTATGGACACCGATGTTGGGCTTTGGT
TGCAGCTGCGGACGTTCTGCTGTGGAAGAACAGGAACGTGTCTGCTGGGGTTCTCGCTGGGGCCACGTTGACATGGTTCC
TGTTCGACGTGGTTGAATACAATGCAGTTCCGCTCCTTTGCCAGATCGCCATCTTCGCAATGCTTGCCATCTTCATTGCG
TCAAATGCTGCGCAGCTCTTCGACAGGCATGGCTTCCTTTCTTTCCACGGAGAGGAGATATCCCAGTGTTTATTTATTTT
TTGAGTAATTGTCCCAGTATTTAGCTTTAAAGAATTTCAAAAGGTCGGCTGACCAATTTCAAATCGCAGGGCCCCGCCAA
GGATACCACAAGTCGTCGTCTCCGAACACGCCTTCAGAGAAATGGCCTTGACCATTCACCACAAACTGGAATATGCTGCA
TCTCTTCTTTATGATATCGCATGTGGAAAGGATCTGAAGAAATTTCTCATGGTACGAAATTCTCTTATTTGCTATCTTAG
TCAAGAAAAGACAAACCATGTGACAAGTCTTGTTCCAGATCGACATTATGGATTAATACAGAAACACTTAAGAGATCTGA
ATCAACCAGATTAGACATGACATGCCACTCAAATCAACGTTTAGCCAATATAGTTCACAACGTTATTTTGCTATTGCTCT
TCAACTTAAACTTGTACTGACATTCAAATTGTTACTATTGTTATAAGGTGGTAGGATCCCTGCTGTTATTGTCAGTGATT
GGAGGTTCTTGCAGCTTCACAAGCCTACTCTACCTTGGTAAGTAGAACAGAAATAGTAACGTTCAAGAAAACCAAATACA
GAAGGTGGAACTAACTAGTAACTACAGAAAGGATGCTAGGAGAACACATAAACTAATGCAGTCTCACAGAAAAATGTAAA
ACTGAAATTTCTAAATAGTATAACAAGTAGTATGTGTTTCTTACTTTCACAGGATTCTTGTGTGCCCACACTTTGCCAGT
GTTGTACCAACATTACGAGACAGAAGTGGACCATCTCGTTGCAAGGGGTGGCCAAGACATCAAGAAGTTCTATGAGAAGG
TTGATTCCAATTTGCTCAACAAAATACCAAGAGGCCCTGTCAAGACGAAGTTCAGATAAAATAAACTCCATGAAGCTGTC
AGGACATAATAATAATTCCAACCAAGATCCTGGAGTAGATTTCAAGAAAAATGAACCTGCTATAAGAAAATATGATTGCA
CGAACCAAGTCCCAGATAGGCGAAGTTGATGAAACACCAGTTGAGTTCAGACCTGACTGCTAGCATCCAGATGTACGGTA
CCTATTAATGTATACAAGCATACTCCATCAGCGAAGCAATCTATGTGAGAATACCTCTGATGCTATAATCTCAAAAACAG
TATCCACTGTGACACCGATGAGTCTGTACATGTATGACACATGAAAAGTGTCCAATAACAGCATACCCAAAAAGACAAAC
AGAAAG-ATTACATGGCTTTCAAGAAAAAAATAACAGGGCCACCATCGCCTTCTGACATCTGTAGTACTAATGGAATGTG
TTTTTGCCTTTACTAATACAAACATAACAGTTATTATTTGCATGGCAAAACTACGAAATCAAACACTGCCATGACTATTT
GCAAAGCTTCGCCCAAGAGAAAAACATCTTGAATCTGGTGTAGGATAGGACCAAGTGTTCGAGACATCAGAGCCCTTGTT
TTTTTCTTAATTCAGTAGATGAAATGTCTATGCGGAACTTCTCCTCTGGTATAGAGATAAACATGTCCTTCAACTCTGTT
GGAATATTTAATTCTTCAAGGACCTTCAAAACAAATAGTGAAGTACATGAGCAGACAAAGAATTTCAGTGCATGTAAAAC
AAAACATCAAGGCCATTTCATACCTTGAATACTCCTTCAATCTCTCGACCACCAACCAGAAATGTTGTGCCAGTGCTTTT
ACATTCAAGAAGAATCTCCAGCATTCTGTTGTAGTCACCTCCATAATACTTAGGCTGCCATGAGTAAACTTCATTTAGTT
TGAAAAATAAAACACTCAATTGTCGAACATCCATTCTAAGATAGCATTCAATAACTGAATTCGAGAATTATATGATTCAG
CCAAATATATCCTGAATAAC
>chr3B_1
GGGCGCACGGCCGCAGCGCCCATGGGTCGCACTCCGAGCGCGCTGCCATGGACGCCCCGCGCACCACCGCACCGGACGCG
GCGAGCATGGCTACGAGGAACAGCACCGCGCAGGGCTTCATGGCTTCT----------TTGCAGTGGACTCTGTCTGGTT
TTGGGAGCACAAGAGAGGGTTGGCATACTATTTGTAGCAAGAGAACAGCTCACCCGGCACCCGCGCCATGCTCTATCTGG
AACCGTGCTGCTAAAACTTACTAAAAGCTTTTGCATTGCACGGTTGCGTAAACGGTAGAGCACGGGCATTCCCATG-AGT
GCTTGGGACTCCGGCACTGCTCCGGAGCTCGGGTAGCGCGAAGCACGCTGCTGCTGCTGCGTAGCAAGACATGTCCAAGG
TTTGCTGTGCAGATTACGTTTGCTAATTGAAGTGGGGTGACCGCGGAGCACACCGATAAAAGTGTCTGGTCTATAAACAC
TCAACCAAGCGTTGATAAC----ACAGGTGTTGAACAGATTTTCCGACGTTGAGCAATGGCGAAATGGCGATAGTTGTTT
CTGGGGTAAGGAGGCTAAGAAGCAACACGGCTGCCGGCTGGGACGAGCACCGTGAGAAATGCGGAGTAAGAAAGACGGCA
TCTTCATCACCGGGTCACAAAAGCTCTC-CACTTGAGTAGGAGACAGCGAGTGCAGTCGCGAGTTCA-------------
-----------------------------CATTGATGTTGACAGAATATCAAGATGCAGTTCCGGCAAGCTTCTGGCATA
AACTACTGGCAAACAGCTAAACTTGCTTCTAGTCTGGGCTCTGACGAAGAAAACATCTGGTTCAAGGAAACCCTTGCCCT
GCATCCGTTT-ATTCCCCTCCCTCAATGGCTCATCCTCCTATAGGCCAAGCTATCCTTTCCTTGTCAACATGGGCTTACC
CTTTAGAGCTCATACTAGCATTTAGGTGCCTATAAAGACGCAATTTATGCAA-------GATCAGACA--TAACAAATCA
ATCAGGTGGACATCCCAAACGCGTGAAGCCATGCCGCCACATTTTCCCAGCAATCCTGACCACGGGCCACACGTCGTGAG
GCCGTTCCACAGGCACAAATCGATCCACCGGATCCTGGGCGGAGGGAAAGGTACGCCGTTCTTGTTCTGTTTCTAGGCAA
TTAC---------TCTGCATTACCATAGTTTTCTCTCCAAGTCGTGGGAGTAGTTACGAACACCGGTGTTGGGCTTTGAT
TGCAGCTGCGGACATTCTGCTGTGGAAGAACAGGAAAGTGTCTGCTGGGGTTCTCGCTGGGGCCACGTTGACATGGTTCC
TGTTCGACGTGGTTGAATACAATGCAGTTCCGCTCCTTTGCCAGATCGCCATCTTCGCTATGCTTGCCATCTTCATTGCC
TCAAATGCTGCGCCGCTCTTCGACAGGCATGGCTTCTTTTCTTTCCACAGAGAGGAGATATCCCAGTATTTATTTTTC--
--GAGTAATTGCCCCAGTATTTAGCTTTAAAGAATTTCAAAAGGTCGGCTGACCAATTTAAAATCGCAGGGCCCCGCCAA
AGATACCACAAGTCGTCGTCTCTGAACACGCCTTCAGAGAAATGGCCATGACCATTCACCACAAACTGGAATATGCTGCA
TCTCTTCTTTATGATATCGCATGTGGAAAGGATCTGAAGAAATTTCTCATGGTACGAAATTCTCTTATTTGCTATCTTCG
TCAAGAAAAGACAAACCATGTGACAAGTCTTGTTCCAGACCGATATTATGGATTAATACAGAAACACTTAAGAGATCTGA
ATCAACCAGATTAGACATGACACGACACTCAAAACAACGTTTAGCCAATATAATTCACAACGTTATTTTGCTATTGCT--
-CAACTTAAACTTGTACTGACATTCAAATTGTTTCTATTGTTATAAGGTGGTAGGATCCCTGCTGTTATTGTCAGTGATT
GGAGGTTCTTGCAGCTTCACAAGCCTACTCTACCTTGGTAAGTAGAACAGAAATAGTAACGTTCAACAAAACCAAATACA
GAAGGTAGAACTAACTAGTAACTACAGAAAGGATGCTAGGAGAACACATAAACTAATGCAGTCTCACAGAAAAATGTAAA
ACTGAAATTTCTAAATAGTATAACAAGTAGTATGTGTTTCTTACTTTCACAGGATTCTTGTGTGCCCACACTTTGCCAGT
GTTGTACCAACATTACGAGACAGAAGTGGACCATCTCGTTGCAAGGGGTGGCCAAGACATCAAGAAGTTCTATGAGAAGG
TTGATTCCAATTTGCTCAACAAAATACCAAGAGGCCCTGTCAAGACGAAATTCAGATAAAATAAACTCCATGAAGCTGTC
AGGACATAATAATAATTCCTACCAAGATACTGGAGTAGATTTCAAGAAAAATGAACCTGCTATAAGAAAATATGATTGCA
CAAACCAAGTCCCAGATAAGCGAAGTTGATGAAACACCAGTTGAGTTCAGACCTGACTGCTAGCATCCAGATGTACGGTA
CCTATTAATGTATACAAGCATACTCCATCAGCGAAGCAATCTATGTGAGAATACCTCTGATGCTATAATCTCAAAAACAG
TATCCACTGTGACACCGATGAGTCTGTACATGTATGACACATG--AAGTGTCCAATAACAGCATACCCAAAAAGACAAAC
AGAAAG-ATTACATGGCTTTCAAGAAAAAAA-AACTGGGCTATCATCGCCTTCTGACATCTGTAGTACTAATGGAATGTG
TTTTTGCTTTTACTAATACAAACATAACAGTTATTATTTGCATGGCAAAACTATGAAATCAAACACTGCCATGACTATTT
GCAAAGCTTCGCCCGAGAGACAAACATCTTGAATCTGGTGTAGGATAGGACCAAGTGTTCGAGACGTCAGAGCCCTTGTT
TTTTTCTTAATTCAGTAGATGAAATGTCTATGCGGAACTTCTCCTCTGGTATAGAGATAAACATGTCCTTCAACTCTGTT
GGAATATTTAATTCTTCAAGGACCTTCAAAACAAATAGTGAAGTACGTGAGCAGACAAAGAATTTCAGTGCATGTAAAAC
AAAACATCAAGGCCATTTCATACCTTGAATACTCCTTCAATCTCTCGACCACCAACCAGAAATGTTGTGCCAGTGCTTTT
ACATTCAAGAAGAATCTCCAGCATTCTGTTGTAGTCACCTCCATAATACTTAGGCTGCCATGAGTAAACTTCATTTAGTT
TGAAAAATAAAACACTCAATTGTCGAACATCCATTCTAAGATAGCATTCAATAACTGAATTCGAGAATTATATGACTCAG
CCAAATATATCCTGAATAAC
>chr3D_1
GGGCGCACGGCCGCAGCGCCCACGGGTCGCACTCCGAGCGCGCTGCCATGGATGCCCCGCGCACC---GCGCTGGACGTG
GTGAGCACGGCTACGAGGAACAGCACCGCGCAGGGCTTCATGGCTTCTCAGTCACGGATTGCAGTGGACTCTGTTTGGTT
TTGGGAGCACAAGTGAGGCTTGGTGTACTATTTGTAGCAAGAGAAG-------CCGTCACCCGTGCCATGCTG--TCTGA
AATTGTGCCGCTAAAATTTT---AAGGCTTTTGAATTACACGGTTGCGTAAACGGTGGAGCATGGGCATTCCCATGGAGT
GCTTGGGACTCCGGCACTGCTTCGGAGCTCGGGTAGCGTGAA----GCTGCTGCTGCCGCCTAGCAA-------------
----------AGATTATGTTTGTTATTAATAATGTGCT---------GCACACCGATAAAAGTGTCTGGTCTGTAAACAC
TCAACCTAGTGTCGAGCCTAGTGACCGGTGTTGAACAGATTTTCAAATGTTGAGCAATGGCGA---------AGTAGTTT
CTGCAATATGGAGGCTAAGAGGCAACACCGTCGGAGAGTTCGTGT-----------------------------------
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------------------------------------------------------------------AAGCTTCTGGCATA
AACTACTGGCAAACAGCTAAACTTGCTTCTAGTCTAGGCTCTGACCAAGAAAACATCTGGTTGAAGGAAACCCTTGCCCT
GCATCCGTTTTATTCCCCTCCCTCAATTGCTCGTCCTCCTATAGGCCAAGCTATCCTTTCCTTGTCAACATAGGCTTACC
CTTTAGAGCTCATACTAGCATTTAGGTGCCTATAAAGACGCAATTTCGGCAACTAAACAGATCAGACATCTAACAAATCA
ATCAGGTGAACATTCCAAACGCGTGAAGTCATGCCGCCTCATTTCCCCAGCAATCTTGACCACAGACTGCACGCCGCAGG
GCCA----------------------------------------------------------------------------
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--------TTCCAAATAGTATAACAAGTAGTGTGTG--------------------------------------------
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----------------------------------------------------------------AGGAAATATGATTGCA
CGAACCAAGTCCCAGATAAGCGAAATTGATGAAACACCAGTTGAGTTCAGACCTGACTGCTAGCATCCAGATGTACGATA
CCTGTTAATGCATACAAGCATACTCCATAAGCGAAGCAATCTATATGAGAATACCTCTGATGCTATAATCTCAAAAAAAG
TATCCACTGTGACACCAATGAGTCTGTACATGCATGACACATGAAAAGTGTCCAATAACAGCATACCCAAAAAGGCAAAC
AGAAATAATTACATTGCTTTCCAAG--AAAATAACAGGGCTACCATTGCCTTCTGACATCTGTAGTACTAATGGAATGTG
TTTTTTCGTTTACTAATACAAACATAACAGTTATTATTTGCATGGCAAAACTATGAAATCAAACACTGTCATGACTATTT
GCAAAGCTTCGCCCAAGAGACAAACATCTTGAATCTGGTGTAGAATAGGACCAAGTGTTCATGACATCAGAGCCTTTGAC
TTTTTCTTAATTCAGTAGATGAAATATCTATGCGGAACTTCTCCTCTGGTATAGAGATAAACATGTCCTTCAACTCTGTT
GGAATATTTAAATCTTCAAGGACCTTCAAAACAAATAGTGAAGTACGTGAGCAGACGAAAAATTTCAGTGCATGTAAAAC
AAAACATGAAGGCCATTTCATACCTTGAATACTCCTTCAATCTCTCGACCACCAACCAGAAATGTTGTGCCAGTGCTTTT
ACATTCAAGAAGAATCTCCAGCATTCTGTTGTAGTCACCTCCATAATACTTAGGCTGCCATGAGTAAACTTCATTTAGTT
TGAAAAATAAACCACTCAATTGTCGAACATCCATTCTAA-ATAGCATTCAATAACTGAATTTGAGAATTATATGACTCAG
CAAAATATATCCTGAATAAC
>SNPs
-------------------------------------------------------------------------S------
----------------------------S-----------------------S-S-----S-SS--SSSSS---------
-------------------------------------------------S------------------------------
---S---------------SS---------------------------------------------------S-------
-------S---------------S----------S-------------------------S----S--------------
-------------------------------------------S--------------------S---------------
------------------------------------------------S-------------------------------
----------------SSSS--SSSS----------------------S----S--------------------------
----------------------------S----------------S----------SSS--SSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSS----------S-----SS------S--------------------------
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---S-------------------------------------S--------------------------------------
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---------------------------------------------------------------------------S----
------------------S--------------------S------------S----S--------------S--S----
----SSSSSSSSS-------S----------SSS-S-S-SSSSSS-----------S-S------S------------S-
-------------S----------------------S-------------------------------------------
----------------------------------------------------------S--------------------S
-------------S----------------------S-----------S------------------S-------S-SSS
SS---------S-----------------------------------------------S--------------------
S---------------------S------------------------S--------------------------------
------------------------------------------------------------------------------S-
---------------------------------------S---S------------------------------------
----------------------S-S--------S------------------S-------------------------SS
S--------------------------------S----------------------------------------------
------------------------------------------------------------------S-------------
------S-------------------------------------------------------------------------
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-------------------------------------------------S------------------------------
-------------------S--------S---------------------------------------------------
------------------S-------------------------------------------------------------
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----------------------------------------S---------------------------------------
-------S---------------------------------------------S--------------------------
--------------------S-----------------------------------------------------------
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----------------------------------------------S---------------------------------
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---------------------------------------------------------------------------S----
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>forward_726
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------------------------------------------------------------------GTGCGTCGCAAGTT
CACATT--------------------------------------------------------------------------
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>reverse_1601
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GGATACCACAAGTCGTCGTCT-----------------------------------------------------------
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>forward_727
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-------------------------------------------------------------------TGCGTCGCAAGTT
CACATTG-------------------------------------------------------------------------
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>reverse_1623
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----------------------CGAACACGCCTTCAGAGAAA--------------------------------------
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>forward_742
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--CATTGATGCGTGTCACGGTC----------------------------------------------------------
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>reverse_2499
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------------------GGCGAAGTTGATGAAACACCA-----------------------------------------
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