>input_sequence_56832
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------------------------------------------------------------------------ATGATGGG
TAATTACCATCTTCTTCTT---------------CTAGTCAT------------------GGTGGTGGCAGTAGTACTCC
ATGCCCCTGCGG---------CAGTGCAGGCGGCGGCGGCGCAGAAGCAGCTGGTGCCGTGCATGTACATCTTCGGCGAC
TCGCTGGTGGACAACGGCAACAACAACAACATCCTCAGCCTCGCCAGGGCCAACTACCGCCCCTACGGCGTCGACTTCCC
CGACGGCGCCGCCCCGCCCGGCCGCTTCACCAACGGCCGCACCATGGTCGACCTGCTCGCCGGCCTCCTCGGCTTCCAGC
CGCCCTTCATCCCGGCCTACGCCATGGCGCAGCCCTCCGACTACGCGCGCGGGCTCAACTTCGCCTCGGGCGCCGCGGGC
GTCAGGCCGGAGACCGGCAACAACCTCGGCGGCCACTACCCTCTGTCGGAGCAGGTGAGCCACTTCCGGTCGGTGGTGGG
CCAGATAGCGCCGGCGGGGAGGGACAAGCGCCTGGGCCGGTGCATCTACTACGTGGGCATGGGCAGCAACGACTACCTCA
ACAACTACTTCATGCCCGACTACTACAACACCGCCCAGACCTACGACCCCGCCGCCTACGCCGCCGCCCTCCTCCAGGAG
TACGAGCGTCAGCTCACCGCCCTCTACGCCCTCGGCGCCAGGAAGTTCGTCGTCGCCGGCGTCGGCCAGATCGGCTGCAT
CCCCTACGAGCTGGCCAGGATCGACGACGACGGCGAT---GACCAAGGACGAGGACGCCCCCCTCCTACTTCCGGCATCG
GCCTTGCGACCCCT---GGCATCACCGTCAGCATCGGCGGCAGCGGCGGCAACCGGAGCACAGCGAACGGCGGCGCGAAA
AA---GAGCGGGTGCAACGACAAGATCAACAGCGCCATCGCCATCTACAACAAGGGGCTGCTGGCCATGGTGAAACGCCT
CAACCGCGGGCAGCAGACGCCGGGGGCAAACCTCGTCTTCCTCAATGCCGTCAACAGCGGCAAGGACCTGGCGGCCAACG
CGGCGGCGTACGGGTTCACGGTGCTCGACCGCGGGTGCTGCGGCGTGGGGAGGAACAACGGCCAGATCACGTGCCTGCCC
ATGCAACGGCCCTGCGACGACCGCACCAAGTACATCTTCTGGGACGCCTTCCACCCCACGGAGGCGGCCAACAGGATCAT
AGCCAACAAGGTCTTCAGCTCATCCTCCACCTCCGACGCCTACCCCATCAACGTCAGCCGCCTCGCCGCCATATGA----
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>chr3B_1_TraesCS3B01G103100
CCACAACCGTCGTGAAACGGGAGCCATGAGGATCCACTGTCGTAGCGAATCGGGAACCGAGAAGCCTCTGCTGCAAATCA
CCGTCGTAGACGCCACGGCGTGTCGATGCACTGTCCTCGCAGCCA-TTGTACCATGCCACCATCAAGGTGTCCCCAAGTC
TCTGCCATGGCG---AACCTCTGCCGACGCATGTGTCGTCTAGAGCTACTGCAACAATCCAGCTGCAACGGCTCCC----
-GCAAGAAGATGATCCCTACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTATTAGTTAGAAAGTTTACG
TAAGGTGGGAACGTAAGTGTACGTAGGTGTAGCATTTTTGGAGATGGGGCGGCACCTTGGATTTCACCCCTACCCCCAAC
CCCATCCCAAACCC--------------TCCATGAGAAGGAAAAGAAAAAGGGAAAAAGAAAAGAAAAAACTCATTAACG
ATTTAACGTAGCTCATGCATATGCATGATCGAGTAAACCACCGCCAGCCAACCAATCCTACTGGCTGGCACTTGATGTTT
CGTCCTCTCTCCGTTTCTACTTTCAGCTGGCCGCCGTATCTTTT-CTATTCTAGCCGTGAGAGAGGTCACGATCCATCCG
TCGTTACACAATTCACGAGCTGCATGCA--------GCTAGCTCTTGGCCGATCGGTCACGGGCAATGCCATGCATCGAT
CCAGATCCAACGGTTGATCCACTTGTCCAGTACGTACTCTTACTGTATGTATATATATATATACGAGAGATTAAGTGAAT
TCATGCATGAGTTGCAGAGCATCGATCGATCGAGAAGCATAACAAACATTGCAAGCTAAGCTAGTTCGATCGATGATGGG
TAATTACCATCTTCTTCTT---------------CTAGTCAT------------------GGTGGTGGCAGTAGTACTCC
ATGCCCCTGCGG---------CAGTGCAGGCGGCGGCGGCGCAGAAGCAGCTGGTGCCGTGCATGTACATCTTCGGCGAC
TCGCTGGTGGACAACGGCAACAACAACAACATCCTCAGCCTCGCCAGGGCCAACTACCGCCCCTACGGCGTCGACTTCCC
CGACGGCGCCGCCCCGCCCGGCCGCTTCACCAACGGCCGCACCATGGTCGACCTGCTCGCCGGCCTCCTCGGCTTCCAGC
CGCCCTTCATCCCGGCCTACGCCATGGCGCAGCCCTCCGACTACGCGCGCGGGCTCAACTTCGCCTCGGGCGCCGCGGGC
GTCAGGCCGGAGACCGGCAACAACCTCGGCGGCCACTACCCTCTGTCGGAGCAGGTGAGCCACTTCCGGTCGGTGGTGGG
CCAGATAGCGCCGGCGGGGAGGGACAAGCGCCTGGGCCGGTGCATCTACTACGTGGGCATGGGCAGCAACGACTACCTCA
ACAACTACTTCATGCCCGACTACTACAACACCGCCCAGACCTACGACCCCGCCGCCTACGCCGCCGCCCTCCTCCAGGAG
TACGAGCGTCAGCTCACCGCCCTCTACGCCCTCGGCGCCAGGAAGTTCGTCGTCGCCGGCGTCGGCCAGATCGGCTGCAT
CCCCTACGAGCTGGCCAGGATCGACGACGACGGCGAT---GACCAAGGACGAGGACGCCCCCCTCCTACTTCCGGCATCG
GCCTTGCGACCCCT---GGCATCACCGTCAGCATCGGCGGCAGCGGCGGCAACCGGAGCACAGCGAACGGCGGCGCGAAA
AA---GAGCGGGTGCAACGACAAGATCAACAGCGCCATCGCCATCTACAACAAGGGGCTGCTGGCCATGGTGAAACGCCT
CAACCGCGGGCAGCAGACGCCGGGGGCAAACCTCGTCTTCCTCAATGCCGTCAACAGCGGCAAGGACCTGGCGGCCAACG
CGGCGGCGTACGGGTTCACGGTGCTCGACCGCGGGTGCTGCGGCGTGGGGAGGAACAACGGCCAGATCACGTGCCTGCCC
ATGCAACGGCCCTGCGACGACCGCACCAAGTACATCTTCTGGGACGCCTTCCACCCCACGGAGGCGGCCAACAGGATCAT
AGCCAACAAGGTCTTCAGCTCATCCTCCACCTCCGACGCCTACCCCATCAACGTCAGCCGCCTCGCCGCCATATGAAATC
---GATCCACTCCACCTGATGATC-TCTTTAAGTAGCTACTACATCG---------TTTTTCAGTACAATAAAATTGT--
--------------GGTAATGCTAGGCGTGCGTTGATCAGACGTGTGGAGATCCAGATCAGCTACGCCCTGCACAGTCGG
CACTCACACTTAAATTGGTTGATCTAGTGCCTCGAATTGTTGCAACAAATATCTCT---CACATGCAACACTATTTTTTT
ATGTCAACTAGTAAAAAGTCCTTGTGTTGCTACGGGGCATATCAAACAGTTTGTTCAATACCAATTGTGTCTAATGTATG
CGTTTTGAATCCTCGTGTATTTCTTCTTCTTCTCTCACCATATCACCCTCTTCTCCCCATCGTGCATTTCTAGCTTTGAG
ATACTAATAAAATATAGTTTTAGTTTAACATGTCACTTGTCTCTTATGTCTCCATTACTATGAAAATATCGATATAAGCT
GGTTACATGCTTATTCACATAAGATCGGTACATGCAAGTTTAGTTTTTGACCATAAACACCTCTCGCTTTTTCCATTCCT
TCATTTATAGTAACTGCCCTACGAGAAAGTATCTGGTGATATGACTGTCGGTGTCAAAACCGGCGGATCTCGGGTAGGGG
GTCCCGAACTGTGCGTCTAAGGCTAATGGTAACAAGAGGCAGGGGACACGATGTTTTACCCAGGTTCGGGCCCTTTCGGT
GGAGGTAATACCCTACTTCCTGCTTGATTAATCTTGATGATATGAGTATTACAAGAGTTGATCTACCACGAGATCGTAGA
GACTAAACCCTAGAAGCTAGCCTATGATTATGATTGTTCTTGTCCTACGGACTAAACCCTCCGGTTTATATAGACACCGG
AGGGGGCTAGGGTTACACAGAGTCAGTTACAGAGAAGGAAATCTACATATCCGAATTGCCAAGCTTGCCTTCCATGCAAA
GGAGAGTCTCATCCGGACATGGGACGAAGTCTTCAATCTTGTATCTTCATAGTCCAACAGTCCGGCCA
>chr3D_1
CCACAACCGTCGTGAAACGTGAACCATGAGGATCCACTGTCGCAGCGAATCGGGGACCGAGAAGCCTCTGCTGCAAATCA
CCGT-GTAGATGCCACGACGTATCACTGCAGTGTCCTCGCAGCCATTTGTTCCATGCCACCATCGAGGTGTCCCCGAGCC
TCTGCCCTGGCATCCAACCTCTGCCGACGCGTGTGCCGTCTAGAGCTACTGCAACTATCCAGCCACGACGGCTCCTGCAG
TGCAAGAAGATGATCTCTACTCTACGCCGCCATCCTAAGACAAAATTTCCCACGGGCTTCCTCCGGCTGCGGCAAGGAGA
GCGAGGAGGGGAGGAGATG-------------------------------------------------------------
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---------------------------------------------GGGCCGGCACCTAGGATTTCACCCCTGCCCCCCAC
CCCACAACCCCGTGGAGCAAATTGGGCGTCCATGAGAAAGAAAAGAAAAAGGGGAAAAGAAAAGAAAAAACTCATTAACG
ATTTAACGTAGCTCATGCATCTGCATGATCGAGTAAACCACCGCCAGCCAACCAATCCTACTGGCTGGCTCTTGATGTTT
CGTC--CTCTCCGTTTCTACTTTCAGCTGGCCGCCGTATCTTTTTCTATTCTAGCCGTGAGAGAGATCACGATAGATCCG
TCGTTACACAATTCACGAGCTGCATGCATGCATGCAGCTAGCTCTTGGCCGATCGGTCACGGGCAATGCCATGCATCGAT
CCAGATCCAACGGTTGATCCACTTGTCCAGTACGTACTCTTGATG--------TATATATATACGAGACATCAAGTGAAT
GCATGCATGAGTTGCAGTAGATCGATCGATCGAGAAGCATAACAG-CATTGCAAGCTAAGCCAGTTCGATCGGTGATGGG
AAATTACCACCATCTTCTTCTTCGACGGTGGATGCTAGTCAT------------------GGTGGTGGCAGTAGCACTCC
ATGCGCATGGTGGTCTACTGGCAGTGCAGGCGGCGGCG---CAGAAGCAGCTGGTGCCGTGCATGTACATCTTCGGCGAC
TCGCTGGTGGACAACGGCAACAACAACAACATCCTCAGCCTCGCCAGGGCCAACTACCGCCCCTACGGCGTCGACTTCCC
CGACGGCGCCGCGCCGCCCGGCCGCTTCACCAACGGCCGCACCATGGTCGACCTGCTCGCCGGCCTCCTCGGCTTCCAGC
CGCCCTTCATCCCGGCCTACGCCATGGCGCAGCCCTCCGACTACGCGCGCGGCCTCAACTTCGCCTCGGGCGCCGCCGGC
GTCAGGCCGGAGACCGGGAACAACCTCGGCGGCCACTACCCTCTGTCGGAGCAGGTGAGCCACTTCCGGTCGGTGGTGGG
CCAGATACCGCCGGCGGGGAGGGAGAAGCGGCTCGGCCGGTGCATCTACTACGTGGGCATGGGCAGCAACGACTACCTCA
ACAACTACTTCATGCCCGACTACTACAACACCGCGCAGGCCTACGACCCCGCCGCCTACGCCGCCGCCCTCCTCCAGGAG
TACGAACTTCAGCTCACCGCCCTCTACGCCCTCGGCGCCAGGAAGTTCGTCGTCGCCGGCGTCGGCCAGATCGGCTGCAT
CCCCTACGAGCTGGCCAGGATCGACGACGACGGCGACGACGACCAAGGACGAGGACGCCCCCCTCCCACTTCCGGCATCG
GCCTCTCGATCCCT---GGCATCACCGTCAGCATCGGCGGCAGCGGCGGCAACCGGAGCACAGCTAACGGCGGCGCGAAA
AA---GAGCGGGTGCAACGACAAGATCAACAGCGCCATCGCCATCTACAACAAGGGGCTGCTGGCCATGGTGAAACGCCT
CAACCGCGGGCAGCAGACGCCAGGGGCAAACCTCGTCTTCCTCAACGCCGTCAACAGCGGCAAGGACCTGGCGGCCAACG
CGGCGGCGTACGGGTTCACGGTGCTCGACCGCGGCTGCTGCGGCGTGGGGAGGAACAACGGCCAGATCACGTGCCTGCCC
ATGCAGCGGCCCTGCGACGACCGCACCAAGTACATCTTCTGGGACGCCTTCCACCCCACGGAGGCGGCCAATAGGATCAT
AGCCAACAAGGTCTTCAGCTCATCCTCCACCTCCGACGCCTACCCCATCAACGTCAGCCGCCTCGCCGCCATATGAAATC
AA-GATCCACTCCACCTGATGATC-TCTTTAAGTAGCTACTACATCA---------TTTTCCAGCACAATAAAATTGT--
--------------GGTAATGCTAGGCGTGCGTTGGTCATACGTGTGGAGATCCTGATCAGCTACGCCCTGCCTGGTCGG
TACTCACACTTAAATTGGTTGATCTAGTGCCTCGAATTGTTGCAACAAAAATCTCCCACCACATGCAACACTATATTTTT
ATATCAA-------------------------------------------------------------------------
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>chr3A_566
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----------------------------TCCATGAGAAAGAAAAGAAAAAGGGGAAAATAAAAGGAAAACCTCATTAACG
ATCCTAGG-------------TGCATGATCGAGTAAACCACCGCCAGCCAACCAATCCTACTGGCTGGCACTTGATGTTT
CGTCCTCTCTCCGTTTCTACTTTCAGCTGGCCGCCGTATCTTTT-CTATTCTAGCCGTGAGAGA--TCACGGTCGATCCG
TCGTTACACAATTCACGAGCTGCATGCATGCATGCAGCTAGCTCTTGGCCGATCGATCACGGGCAATGCCATGCATC---
---GATCCAACGGTTGATCCAGTTGTCCAGTACGTACTCTTACTG--------TATATATATACGAGAGTTTAAGTGAAT
GCATGCATGAGTTGAAGTGGAACGATCGGTCGAGAAGCATAACA-ACATTGCAAGCTAAGCTAGTTCGATCGGTGATGGG
TAATTACCATCATCTTCTT---------------CTTCGACGGTGGGTGCTAATTGTGGCGGCGGTGGCCGTAGTACTGC
ATGCCCATGGGGATCTACAT---GTCCAGGCGGCGCAG---AAGCAGCAGCTGGTGCCGTGCATGTACATCTTCGGCGAC
TCGCTGGTGGACAACGGCAACAACAACAACATCCTCAGCCTCGCCAGGGCCAACTACCGCCCCTACGGCGTCGACTTCCC
CGACGGCGCCGCGCCGCCCGGCCGCTTCACCAACGGCCGCACCATGGTCGACCTGCTCGCGGACCATCTCGGCTTCCAGC
CGCCCTTCATCCCGGCCTACGCCATGGCGCAGCCCTCCGACTACGCGCGCGGCCTCAACTTCGCCTCGGGCGCCGCCGGC
GTCAGGCCGGAGACCGGCAACAACCTCGGCGGCCACTACCCTCTGTCGGAGCAGGTGAGCCACTTCCGGTCGGTGGTGGG
CCAGATAGCGCCGGCGGGGAGGGACAAGCGGCTGGGCCGGTGCATCTACTACGTGGGCATGGGCAGCAACGACTACCTCA
ACAACTACTTCATGCCCGACTACTACAACACCGCCCAGGCCTACGACCCCGCCGCCTACGCCGCCGCCCTCCTCCAGGAG
TACGAGCGCCAGCTCACCGCCCTCTACGCCCTCGGCGCCAGGAAGTTCGTCGTCGCCGGCGTCGGCCAGATCGGCTGCAT
CCCCTACGAGCTCGCCAGGATCGACGACGACGCCGAT---GACCAAGGACGAGGACGCCCCCCTCCCACTTCCGGCATCG
GCCTTACGATCCCTGGCGGCATCACCGTCGGCATCGGCGGCAGCGGCGGCAACCGGAGCGCAGCTAACGGCAGCACGAAA
AGTAGGAGCGGGTGCAACGACAAGATCAACAGCGCCATCGCCATCTACAACAAGGGGCTGCTGGCCATGGTGAAACGCCT
CAACCGCGGCCAGCAGACGCCGGGGGCAAACCTCGTCTTCCTCAACGCCGTCAACAGCGGCAAGGACCTCGCGGCCAACG
CGGCGGCGTACGGGTTCACGGTGCTCGACCGCGGCTGCTGCGGCGTCGGGAGGAACAACGGCCAGATCACGTGCCTGCCC
ATGCAGCGCCCCTGCGACGACCGCACCAAGTACATCTTCTGGGACGCCTTCCACCCCACCGAGGCCGCCAACAGGATCAT
AGCCAACAAGGTCTTCAGCTCATCCTCCACCACCGACGCCTACCCCATCAACGTCAGCCGCCTCGCCGCCATATGAAATG
CGGGATCCACTCCACTTGATCTCTTTATTGAAGTAGCTACTACTACTTCATCGTATTTCTTCACTACAATAAAATTGTGA
AAATCAAGGGACTGGGTACTGCTAGGCGTGCGTTGGTCAGACGTGTGGAGATCCTGATCAGCTACGCCCTGCATGGTCGG
TACTCACACTTAAATTGGTTGATCTATA-CCTCAAATTGTTGCAACAAATATCTCCCACTACATGCAACACTATTTTTTT
TATATCAA------------------------------------------------------------------------
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>SNPs
-------------------S--S-------------------S-----------S-------------------------
----S-----S------S---S--SS----S-------------------S-------------S----------S--S-
------S----S------------------S----S-------------------S-------SS-S--------S----
---------------S----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS---S--------S-------------S-----S--
----SSS-SSSSSS------------------------S--------------S--------------------------
--------------------S-----------------------------------------------------------
-----------------------------------------------------------------S--------S-----
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---------------------------------------------SSSSSSSS---------------------------
S----------------S-S------------------------S---------------------------S-------
-----------S--------------------------------------------------------------------
------S--S----------------------------SSS---------------------------------------
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------------S-------------------------------------------------------------------
----------------------------------------------------S-----------------------S---
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------------------------------S-------------------------------------------------
--------------------------------------S-----------------------------------------
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------------------------------------------------------------------S-------------
-----S---S------------------------------------------------------S---------------
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---------------------------------------------S----------------------------------
----------------------------------S---------------------------------------------
-----S--------------------------------------------------------------------------
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----------------------------------------------S---------------------------------
-----------------------------------S------------------S------------------SS-----
S------------------------------------------------------S------------------------
--S----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_131
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-------------------------------CTGTCCTCGCAGCCATTGTA-----------------------------
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>reverse_1413
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----------------------------------------------------GCTCAACTTCGCCTCGGG----------
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>forward_1127
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-------------------------------------------------------------------GCAGTAGTACTCC
ATGCCCC-------------------------------------------------------------------------
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>reverse_2577
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----------------AGTCCTTGTGTTGCTACGGG--------------------------------------------
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