>input_sequence_75241
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----------------------------ATGAGCTACTGGGGTTCCTCGCCGGCGTGGGGGGCGGCCCGCCACGGGCCGT
CTCCGATGGTGCCCCTCATGGTGGTGCTGGCCCTGGGGTGGGTCATCTACAACGAGGCCCTGTTGGAGTGTTACGAGCGG
GTGACCGAGGTGCGGGACACGGTGGCCGACAATGCCATGGTCTTCATCCTCGCCGCCGGGCTCCTGCTGCTCGCCGTCGT
CCTCCTCAGCAACCAGATGGAGGTGGTCCTGGTGCCGATGGTGCTGGTGCTGGTCATGCTCTTGATCCAGAACATCGTTG
TTGCTGCGCTCCTGCTGCTGCTGGCGGTGTACCTGGCCGGGATATACTACTACCCGCCTCACCGGGGCTACGGC------
------GGCGGCGGCGGCGGCTTCGCCGGGGCCGGGGGTGACTGGACGGGCTGGGGCTGCGGGCTGGGGTTCTACATGCT
GCTGCTGCTCTGCCTGGTGCTGTGCGCCATGTTTTCGGAGGAGGGCGGCAGCTGGTGGATCCCAGGCGTGCTGCTGGCTG
CATGCCTGCTCTGCCTCAACCTCTTCTCAGGTGGCAAAGTCTTAGGCCAGGAGTACTTTTAA------------------
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>chr5B_1_TraesCS5B01G374500
GAATTGAACTTACCGAAGGATTGCTGTTAGCAACTGGGATTGAAATTGGTTGGTTTGGGATCTAATCATGGTGGGGTGTT
GAGCCTGGAGGGAATGCAGCGAGCAAGGTGACCAAGTGCTCTCCAGAA-GCAGCTTCTTTGGAGACG-AACTCTCGCCGG
CAGACAAGCTGGGGTTCACCAAGGCAGCCATCCAGGCAAAACCAGACTCTGTTCTCAGTCCCAAAATAAGTGTCGTTGA-
----------------------------CAGGTGTTCTCCTCGCCTTTTGTGTGCATAGTTAGTTTGCTCAGAGATCAGT
CTCAAGTCTGAATTTTAGGAAGTTAATTTCCCTGTAAGATGGAGTGGGTTCCCATTGATCCTTAGGTCTTTGCAAAATTC
TCATTTTGCATGATGAAGCGCCTGTGCTGCCGAAG----------------------AGGTCGGCGCCACCTCGGCTTGG
GCGAAAGTTGACTGATTCACTCACAGAAGGTAAGATCAAGATAGTACTGTTTGCTACTGAGTTTTCTTGCGGGCCTCATT
ATATTCGTCGATAACATGCCATGTTCAATCTTCCAGGCTAGATTGTGGATACATATGGGTACTTGCTACCCAAGCCTTTT
GAAGAACAGGTAAGATGAGACATGTTTTCCCTTAATTCCATCAGCAGGAATCAACTTTTCCACATGTGTAGTTTGCTTGA
--------TGACTCATGGCCGATTTTCTCATTCTTAGCCCGATGATTGAATGGTGTCGTAAATGCATGAAAATGACCTGA
CCTTTAAGCATCCTATTTATATGCCATATTTCTCTTGGATTTGTTCATCTACCAGATTAAAGTAGGCCCCCTGCCTCCAC
TATACTCCAGGACAGTAGACATCATCACACACAAG--CAGGTAGTTATAATTAGTTGCAACCAGAAGAAGCTGATGAAAC
TTGCAT--TATATTTATATTGTCATCTTCTACGGCTAGCCCACTAC---TACTTATTAGCTGCAAGATCAGAAGCGACAT
AGAGAGTAAGCTGAACGAAGAGGCTGCCATGAGCTACTGGGGTTCCTCGCCGGCGTGGGGGGCGGCCCGCCACGGGCCGT
CTCCGATGGTGCCCCTCATGGTGGTGCTGGCCCTGGGGTGGGTCATCTACAACGAGGCCCTGTTGGAGTGTTACGAGCGG
GTGACCGAGGTGCGGGACACGGTGGCCGACAATGCCATGGTCTTCATCCTCGCCGCCGGGCTCCTGCTGCTCGCCGTCGT
CCTCCTCAGCAACCAGATGGAGGTGGTCCTGGTGCCGATGGTGCTGGTGCTGGTCATGCTCTTGATCCAGAACATCGTTG
TTGCTGCGCTCCTGCTGCTGCTGGCGGTGTACCTGGCCGGGATATACTACTACCCGCCTCACCGGGGCTACGGC------
------GGCGGCGGCGGCGGCTTCGCCGGGGCCGGGGGTGACTGGACGGGCTGGGGCTGCGGGCTGGGGTTCTACATGCT
GCTGCTGCTCTGCCTGGTGCTGTGCGCCATGTTTTCGGAGGAGGGCGGCAGCTGGTGGATCCCAGGCGTGCTGCTGGCTG
CATGCCTGCTCTGCCTCAACCTCTTCTCAGGTGGCAAAGTCTTAGGCCAGGAGTACTTTTAACCCTTGTGTTCTTCGGGG
CAGAGCTTAGTTATTGTTGTCTCATGGCATTA----------------CCGCTCATGGCTCCCTCCTTAGATTTGTCTGC
TATCATCATAAGAATTTTAGCAGACGCGTGGTGACCGGTGACGCCCTGCTGCAAGGATTTGAAA-GTAAAATGGACCTTT
AACAGCGTCCCATGCATCCCATTTGGCCATGTTGAGCATGCTGGGTCGAGCTTCAGAAGATTAAAACAGAGGAAACGGCC
ATCATTAACACGAAACACATACATCAAAGAGAAATGC------------------------TAAGATGAGCCATTAATAG
CACGTTCGTATGTGGAGTTTCAGACATAGCACAACTGAACTACCACTCTCAAAATGATTCGGCAAGTCTATCTGCAGGTG
AAGTTTACTCACGCCCAAGGATAATCGATTTGGGCCGTCTTTGCACTTTGTGTAGGGTAAATAACTCTACCAAGTACTCC
GTCCGTAAACTAATATAAGGGCGTAAGTAGTGATCTAAACGCTCTTATATTAACTTACAGAGGG----------------
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---------AGTACATACTGTATCTAAGAGCATCTCTAGTCCTCTATCCTTTAATCCTCTAAACTTATCATTTAATCTCC
TAAAACTTGAATTTGCGGGCACCTAGCCTTTTCCCTAAACTTAATCCCCTCAAACAAACTCGACCCCACATGTAAGCCTT
TCTTCATCATCTTCTTCCTTCTTCCTCTTCTTGCTTTCATGTGGCCAGCAACAACTTCTCGCCAGTAGATGATGTCCATG
AGCTAGCATGGGCCTGGGATAGATGATCCTCAAAAATAATTTGATAGAGGCTCACCGAACACGAAGTACACATGCGAGGA
AGCAGAGGAAATTTGTCCTCCACGGGCTTTGGTTTGGGCAGTTCTTTGTCTGAATGGGTTCTTATCCTCTCC---CTTCT
CCTAGTGGCACGACAATGTTGTCCGAAACGGAACGATTTATCAGAATCTGCGATGGCAGCCGGCGGCCAGTGTGTTCTCC
TTTATGTGATG
>chr5A_1
GAATTGAACTTACAGAAGGATTGCAGCTAGGGAC-GGGATTAAAATTGGTTGGTTTGGGATGTAATCATGGTGGGGTGTG
GAGTCTGAAGGGAATGCAGCAA-----GTGACCAAGTGCTCTACACAA-GCAGCTTCTTTGGAGATGAAACTCTGGCCGG
CAGAGAAGCTGGGGTTCACCAAGACAACCATCCAGGCAAATCCAGACTCTGTTTACTTTGTAT-----------------
----------------------AGTAAGCAGGCGTTCTCCTCGCCTTTTGCGTGCATAGTTAGTTTGTTCAGAGATCAGT
CTCAAGTCTGAATTTTAGGAAAATTATTTCCCTGTAAGATGGGGTGGGTTTCCATTGATCCTGAGGTCTTTGTGAAATTC
TCATTTTGCATGATGAAATCAGGGGTGGTGGTGATA----------------------------------------TTGG
CCAAAAGTTGACTGGTTCACTCACAGAAGGTAAGATCAAGATAGT--------CTACTGAGTTCTCTTGTGGACCTC---
--------------------------AATCTTCCAGGCTAGGTTGTGGATACATACATGTACTTGC--------------
---------------TGAGACATGTTTTTCCTTAATTCAATTAGCAGGAATCAGCTTTTCCACATGTGTAGTTTGCCTGA
--------TGACTCATGGCCGATTTTCTCATTCTTAGCCTGATTATTGAATGGTGTTGTAAATGCATGAATATGACCTGA
CCTTTAAGCATCCTATTTATATGCCATGTTTCTCCAGGATTTGTTCATCTACCAGATTAAAGTAGGCTCACTGCCTCCAC
TATACTCCAGGACAGTAGACATCAGCATCCACAAGCACAGGTAGTTACAATTAGTTGCAACCAGAAGAAGCTGATGAAAC
CTGCATTATATATTTATATTGTCATCTTCTACGGCTAGCCCACTAC---TACTTATTAGCTGCAAGATCAGAAGCGACAT
AGGGAGCAAGCTGAACGAAGAGGCTGCCATGAGCTACTGGGGCACCTCGCCATCGTGGGGGGCGGCCCGCCACGGGCCAT
CTCCGATGGTGCCCCTCATGGTGGTGCTGGCCCTGGGGTGGGTCATCTACAACGAGACCCTGCTTGAGTGTTATGAGCGG
GTGACTGAGGTGCGGGACACCGTGGCCGACAATGCCATGGTCTTCATCCTCGCCGCCGGGTTCCTGCTGCTCGCCGTCGT
CCTCCTCAGCAACCAGATGGAGGTGGTCCTGGTGCCGGCGGTGCTGGTGCTGGTCATGCTCCTGATCCAGAACATCGTTC
TTGCCGCGCTCCTGCTGCTGCTGGCGGTGTACCTGGCTGGGATATACTACTACCCGCCTCACCGGGGCTACGGCTACGGC
GGCGGCGGCGGCGGCGGCGGCTTCAGCGGGGCCGGGGGTGACTGGACGGGCTGGGGCTGCGGGCTGGGGTTCTACATGCT
GCTGCTGCTCTGCCTGGTGCTGTGCGCCATGTTTTCGGAGGAGGGCGGCAGCTGGTGGATCCCGGGCGTGCTGCTGGCTG
CGTGCCTGCTCTGCCTCAACCTCTTCTCAGGTGGCAAAGTCTTGGGCCAGGAGTACTTTTAACCCTTGTGTTCTTCGGGA
CAGAGCTTAGTTATTGTTGTCTCGTGGCATTACCAGATGGTGATGTAGCCGCTCATGGCTCCCTCCTTAGATTTGTCTGC
TACCATCATAAGAATTTTAGCAGACGCGTGGTGACCGGTGACGCTCTGCTGCAAGGATTTGGAAAGTAAAATGGACCTTT
AACAGCGTCCCATGCATCCCATTTGGTCATGTTGAGCATGCCGGGTCGAGCTTCAGATGATTAAAACAACGGGAAAAGGC
ATACAACTGAACTAGCACTCTCAACATGAGCTTCAGATGATTAAAACAACGGGAAATGTTGTAAGATGGGCCACTAATAG
CACCTTCATATGTGGAGTTTCAGGCAT---ACAACTGAACTAGCACTCTCAACATGATTCGGCAAGTCTATCTGCAGGTG
AAGTTTGCTCGCGCCCAAGGGTAATCGATTTGGGATGTCGTTGCACTTC--GTAAGGTAAATAACTCTTATCAAGTACAT
GCAGACTAAGGCATAGCCTAGTGTTAGAAAGGGGCTCATGCCTTCCCACCCACCCTCATGTTCTATTACTTACAATTTAA
ATTTGTTGCATCAATTATACTGTAGGACAATAAGAGCAACTCCAACGGCCGCGCCAAAAGACGCGCGCGCGGTAAACCCA
GCTTTTAGTGCGCGCGGGACGTTTTGCCGCGCTCCAGCGGTGGCGGGAAACTCACACGCGCGGGAACCGTTTGCGCGCAC
GCACGAAAAGGCGCTAGCTCGCGTGCCATTTTTTGCGCACCGCTTTCGGCGCGCGCCACGTGCCTTTTCCACGCCTCCTC
TTCTCCTCTTCCTCTCCCTGTCTGCCACGCGCCGCTCCAGCGCCCCGCCACCGACGTGCCTCCACCGCTCCAGCGCCCCG
CCACCGCCGCGCCGCCGTGCCGCCGAGGAGCGTCCGGCTACCGCAGCGTCCGCCTACGCCCTAACGGCGGCTACTACTTG
GAGATACGCTCCGGCGATCTTCGGCTTGGCCTCGGCACCTACAGGACTGCGCGCGAGGCCGCCTGCACGTACGACGCGGC
GGCGTGGCGCCTAGGCCGGCCGCGCGGGCAGATGAACTTCCAAGATGTGTACACGCTCCAGCAGGCGCTCGACGTCGCCC
CGCCGCCTCGTCTGAACACGGCACAAGACCGTACGGAGCACGCCGAGCGGCAGCGCCACCTCCTCGTCGCCCAGGAGGAC
GAGCGGGTCATGGCGGAGTGGGGCCGGCGCCACCCGGAGGACGTCGCCTACGAGCCTACTGGGCAAGGCGTCGCGAGGAG
GATACGCGAAGGCGCCGCGAGGAGCGGTTGGACAGGTGTCGGCAGAAGGCATTGGCGAATGCGCAGCCCGATCTCGTTGC
AGCAGGTGGGAGGTCGTTTTTCACGAAAGACGATGATCGTTGGTTGGACATATGGCTAGATATCTCGGACGACATCGCCG
AGGATGATAATGATGATAGCGACTTAGAGTAGTTTTCTATGCAATCTATCTAGGCCTCCTTTGGTTTAGAGGAATTTCAT
AGGAATTCTAGAGGATAGGATTCTTATAGGATTTTTTTCCTTTAGAGCCCTTTGGTTCATAGGAATGGATTCCTATTCTT
ACATAGGATTGGTTCCTATCCTCCACATTTCATAGGAAAATAAAAAAGAGCCTAGACTCAATGGAAAAATTCCTTTGGTG
TCAACCAAATGACATCTTGTTTCCTATTCCTATTTATAGGATTTGAGATACATGTCATCTCATTTCCTACAAGATTCCTA
TTCCTATGATAATCCTATCCTATGAACCAAAAGAGATACAATCTATGTTTTCAATGTAAAATACCTTTATATTGTTTTAA
AAATATATATGCAATCTATCTAGTTTCTATGCTTCCGATGCATACATCTAGTTTGTAGAATGAGCGCGCGTTGCTGGAGT
GGCGCGCGCGCTGCATTTTAGCGCGGCTGCTGGAGCGGGCGCTGCGCGCCGCGCCAAACCAGACAATGGGCGCATGCTAA
AGCTGTTTTTTGTGCGCGGCGCGTTCGGCGCCTGTTGGAGATGCTCTAATGCTAAACGTATAAAGAGTTACACTTAATTA
CATGCTGACTAGGATTCTTTCTTTCTAACTACCCCCCTCCCCCCCACACACAAATATCCAATCAAAACTCACGAGCGTGT
AAATCCCCCATAACTCTTTGTATGTCTAGCATTACTCTACTGGAGGGGCCTCCTTTACAGTCCTTCTGTCAAAAAAGAAA
AACCTACCAAGAACATATTGTATTTAAGAGCATCTCTAGTCCTTCTCCC-----------------ATCCTTCAATTTTC
TAAAATTTGAATTTATTTCCACCTAATCTTTTCCCTAAACTTAATCCC-TCAAATGATCTCAACCCTACATGTAAGCCTC
ACT---TCATCTTCTTCCTTCTTCCTCTCCTTCCTTCCAAGCGACCAACAACTACTTCTGGCCAGTAGACGGTGTCCATG
GGCTAGCATGGGCCTGGGATAGATGATCCTCAAAAATAATTTTATAAAGGCTCACCGAACACGAAGTACGAATGCGAGAA
AGTAGAGGAATTTTGTCCTCCATGGGCCTTGGTTTGGGCAGTTCTTCGTTTGAATGCTTTCTTATCCTCTTCCTTCTTCT
CCTAGTGGCATGACCATGTTGTCCAAAATAGAACGATTCATCAGAATCTGCAATGGCAGCCGTTGGCCAATGTGTTCTTC
TTTATGTGATG
>chr5D_1
GAATTGAACTTACCGAAGGATTGCAGTTAGCAGCTGCGATTAAAATTGGTTGGTTTGGGATCTAATCATGGTGGGGGGTG
GAGTCTGGAGGGAATGCAGCAAGTCAGGTGACCAAGTGCTCTACACAAAGCAGCTTCTTTGGAGGTG-AACTCTCGCCGG
CAGACAAGCTGGGGTTCACCAAGACGGTCATCCAGGCAAAGCCAGACTCTGTTTACTCTGCAGTAAGCAAGTCCAGGCAA
AGCCAGACTCTGTTTACTCTGCAGCAAGCAGGCGTT---CTCGCCTTCTGCATGCATAGTTGGTTTGTTCGGAGATCAAT
CTCAGGTCTGAATTTCAGGAAAATAATTTCCCTGTAAGATGGAGTGGGTTCCCATTGATCCTTAGGTCTTTGCAAAATTC
TCATTTTGCATGATGCAATCAGGGGTGGTGGGAATGTTGATGTGAAGCGCCTGTCGAAGGCCGGCGCCGCCTCGGCTTGG
CCGAAAGTTGACTGATTC--------------------------------------------------------------
-----------------------------------------------------------------CTACCCAAGCCTTTT
GAAGAACAGGTAAGATGAGACATGGTTTCCCTTAGTTCCATTAGCAGGAATCAGCTTTTCCACATGTGTAGTTGCCTGAT
AACTTATGTGTCTTATGACTGATTATCTCATTCTTAGCATGATGATTAAATAGTGTCATAAATGCATGAAAATGGCCTGA
CCTTTAAGCATCCTATTTATATGCCATGTTTCTCCAGGATTTGTTCATCTACCAGATTAAAGTAGGCCCACTGCCTCCAC
TATACTCCAGGACAGTAGACATCAGCATCCACAAGCACAGGTAGTTACAATTAGTTGCAACCAGAAGAAGCTGATGAAAC
CTGCATTAC--------ATTGTCATCTTCTACAGCTTGCCCACTACTAGTACTTATTAGCTGCAAGATCAGAAGCGACAT
AGAGAGCAAGCTGAACGAAGAGGCTGCCATGAGCTACTGGGGTTCCTCGCCGGCGTGGGGGGCGGCCCGCCACGGGCCGT
CTCCGATGGTGCCCCTCATGGTGGTGCTGGCCCTGGGGTGGGTCATCTACAACGAGGCCCTGCTGGAGTGTTACGAGCGG
GTGACCGAGGCGCGGGACACCGTGGCCGACAATGCCATGGTCTTCATCCTCGCCGCCGGGCTCCTGCTGCTCGCCGTCCT
CCTCCTCAGCAACCAGATGGAGGTGGTCCTGGTGCCGGCGGTGCTGGTGCTGGTCATGCTCTTGATCCAGAACATCGTCG
TCGCGGCGCTCCTGCTGCTGCTGGCGGTGTACCTGGCCGGGATATACTACTACCCGCCTCACCGGGGCTACGGC------
------GGCGGC---------TTCGCCGGAGCCGGGGGTGACTGGACGGGCTGGGGCTGCGGGCTGGGGTTCTACATGCT
GCTGCTGCTCTGCCTGGTGCTGTGCGCCATGTTTTCGGAGGAGGGCGGCAGCTGGTGGATCCCGGGCGTGCTGCTGGTTG
CATGCCTGCTCTGCCTCAACCTCTTCTCAGGTGGCAAAGTCTTAGGCCAGGAGTACTTTTGACTCTTGTGTTCTTCGGGA
CAGAGCTTAGTTATTGCTGTCTCGTGGTATTACCG---------------------------------------------
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>chr7D_1037
GCCTCGCCAGT---------------------------------------------------------------------
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---------------------------------------------------------------------------GCCGT
CTCCGATGGTACCTCTCATGGTGGTCCTGGCCTTTGGGTGGGTCATCTGCAATGAGACCCTGATGGAGTGGTATGTGCAG
GTGACTGACGTGCAGGAGACGGTGACCGACAATACCCTCATCTTCATCCTCGCCTCT-GGTTCCTGCTGCTCGCGGTCGT
CCTCCCTAGCAGCCGGATGGAAGTGGTCCTGGTGCCGACGGTGCTGGTGCTGGTCATGCTCTTGATCCAGAACATCGTTG
TTGCCGCGTTCCTGCTGCTGTTGGCGGTGTATTTCGCCGGAATATACTACTACCCACCTCATCGGGGCTACGGT------
------GGCAGCGGCAATCTCACCAACC---CCGACGATGACTGGACAGGCTCT------GGGCTGGGGTTCTACCTGCT
GCTGCTACTTTGCCTGGTGTTGTGCCCCATGTTTTCAGAGGAGGGGGGCAGCTGGTGGATCCCAGG-GTGCTGTTGGCTG
CATGCCTGCTCTGCCTCAACCTCTTCGCAGGTGGCAAAGTCTTAGGCTATGAATACATTT--------------------
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>SNPs
------------------------S----------------S-------------------------------------S
---S----------------S--SS-----------------S--S-------------------S--------------
-----------------------S----------------S------------SS-SS-S-SSS--SS-SSSS-SSSS--
--------------------------------S-----------------S----------------S------------
---------------------SS---------------------------------------------------------
-----------------SSSSSS-SSSSSSS---S-------------------------S-------S-----------
S--------------------------------------------SSSSSSSS----------S-----S--S----SSS
SSSSSSSSSSSSSSSSSSSSSSSSSS---------------S-------------SSS----------------------
-----------------------------------------S-----------S--------------------------
---------------------------------------S----------------------------------------
---------------------------S------SS---------------------------------S----------
------------------------S--SS------------------S--------------------------------
S-------------------------------------------------------------------------------
------S-------------------------------------------------------------------------
--------------------------------------------------------------S-----------------
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--------------------------------------S-----------------------------------------
----S---------------------------------------------------------------------------
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-------------------------------------------------------------------------------S
-----------------------S--------------------------------------------------------
--S-----------------------------------------S----------------S------------------
--------------------------S--------------S---------------S----------SS--S--SS-S-
--SSSSSSS-SSS-S---SSS--S--SSSSSSSSS-S-------------------------------S----S------
---S---S---------------S---SSS------------S---------S---------------------------
------S---S---------S-------------SS---S--------SSS---S-------------SSSS-SSSSSSS
-SSSSSS--SSS---SSSSS-S--S--S-SS-SS--S-SSS--SSSSSSSS-S-S-SSS-SSSS----------------
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-----------S-----S-----S-------------------SSSS--SSSSSSSSSSSSSSSSS---S--S---S-S-
-----S--------SSSSS------SS---------------------S-----SS-S---S----S------------S
S--SSS----------------------S---S---S--S-S-S---S----S------S---------S-S--------
S-----------------------------------------S---S----------------------SS-------S-
--S-------S-----------S----S------------------S--S------SS------------S---------
----------S---S---------S---SS--------S------------S----------SS-----S--------S-
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>forward_559
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-----------------------------------------------------------AGTTTTCTTGCGGGCCTCAT-
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>reverse_4231
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----------------------------------------------------------------------CATGCGAGGA
AGCAGAGGAA----------------------------------------------------------------------
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