>input_sequence_65388
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----------------GAACCAAGC----------CTTGCTCTCTCA----CTCATATCATTAGTCATTACCCGCACTGA
AAACCTTAGTACTTCTAC---CTAGCTTCCCGTGTAGCTCGAGGAAGAGAGAATCCAACGAGT-GGGAGCAATGGCGAAG
CCGCAGCAGGAGGTGTACTTCGTGTTCATGAACTTCGACCCTGTCTACGAGCGCCTGAGGGCCGATCGGTCTGTATACCT
TGCACAAAAATATAATGGCTTGCATC-TTCGTGTGCAATATATGTGCGCGGTTTTGATGGATGGTTTGTTGGGTTGGGTG
CAGGACGAAGCAGGGGTCGGCGACGCTGGACGCGTACCTGAGCCAGAAGCACGACAAGCTCCTCGCCAAGCTCCTCCAGC
CCGACACCTACTGGAAGAAGTCCTCGCTCGCCATCGTCGACGGATTCGCCGTCGAGATCACCGACGCTCAGGTCACCGCC
CGACCTATAACCTCACATG---CATGGATGTACATGGATCCATCATATG---------TACTGTACATGAAACTTCTCTT
ACACCCCTGATGGCATATATGATCGGTTGAACTATATACTGATGCAGGCGAGCGTGCTGAGGTCGGCGAAGGAGGTGAGG
GTGGTGGAGAAGAACCAGGAGCTTGCTTGACCAGCCAAACATCCAGGC--AGTTATAAGCATGATCTTTTAGATGCTTTG
AGCATCTGCCATAGCCATGGAAGCTTGGTTTATTATAAGCTAAGTCCCGAGTACGTTGATCAGTTGCTACTAGTCAA--G
CTTTTGCGGCGTAAGTGTATCGATCGGTGTGTGTTTTTGTGTGATCTCCCATGGCTTTGTTGACTCTAATGTCAAGCTCA
AGCTTAGCTACTATCTTTATATACTAGTGCGTACTG----TACTACTTAATTAGCATTAGCTGCAGTGATATAGATATAT
AAAGTTCTTCATC----AATC-----------------------------------------------------------
--------------------------------------------------------------------------------
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-------------------------------------------
>chr3D_1_TraesCS3D01G153700
TACAAGACAAGCTTAGCATGCATGGTATAA--------------------------------------------------
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--------------------------------------------------------------------------------
-------------------------------------ATGTAGCCTGTCG----TGCATGCATGATCAGCGACTCGG-CA
CGTTTCTAGAGATCCAAACATA----CAAGTGTACAGCATTACCAAAAATGTGCATGCATGGCAGCTAGCTCGATCTCGG
CCCCTCGCCGAGATCCTTGCCGGCCAGTGCCGTCCTTGCGCCGGATCCGATCGGTCCGGGCCCTCTCCTCTCCTCTCGCT
CTGGCCATGCACGCAGCAGCCGGGCGGCAGCCAGCTCTGCGTCGCATGCATATGCATGCATGCACGCGCCCGTACGTACT
GCGAGC------------TGCGCGCTCTGCTCACACTCACACCCCATCCCATCCGGATCTGGTACTGACCAGCA------
-CCAGCTGCGACGACATGCATGCGTACAATCCGGCCAGTCTCCGGCCTACAGCGCCTCTCCCTCTGAGTCCCAGGTGCAG
CGCAGAGATCTCGAGTCCTTGACCTCTTCCAGCTCTGTGCGAGATTCCATGCTACGTACATATCCACTGCGCCTGCATGC
AGGCCTGCGTCACCATCCCATGCCCCCTCCTGTCTTCCCAACCATCAGAGACATTCTATTGGATATTACCCACGAATCAT
ACAAAAAAATGTGTATGTATATACTC-TATCTTCTCCAGCAATCCAACTGCAACCCACATAAAATATACATGCGCG----
----CCACAGTGCCTGCAGCAAGCTGGCTATATGGACAAGTAAGGGTTGGTTAACTAGTGGCTGGACGTACGCACATGCA
TGTGCGTGCGCTTTTTATAGGCGAGATTCCCTTGACCAAGTTCAAGCCGGCCTAAGCTCGCGCAGTTGGCTGCATGTTTG
TTAGTTGCGTCGCGCTTTCGCTAATTTGACTAACCACTCTAGATCTAGGCTAATCTGGACTCAGTAAGAAAGATGC----
--------AGCTAGCTCCCTCCCGGCCGGTGACATGATCAGCATGTGACCACCTCCTCTCCCCCGGCTATAAATAGCGGC
CCATAGCAATGATATGGAACCAAGC----------CTTGCTCTCTCA----CTCATATCATTAGTCATTACCCGCACTGA
AAACCTTAGTACTTCTAC---CTAGCTTCCCGTGTAGCTCGAGGAAGAGAGAATCCAACGAGT-GGGAGCAATGGCGAAG
CCGCAGCAGGAGGTGTACTTCGTGTTCATGAACTTCGACCCTGTCTACGAGCGCCTGAGGGCCGATCGGTCTGTATACCT
TGCACAAAAATATAATGGCTTGCATC-TTCGTGTGCAATATATGTGCGCGGTTTTGATGGATGGTTTGTTGGGTTGGGTG
CAGGACGAAGCAGGGGTCGGCGACGCTGGACGCGTACCTGAGCCAGAAGCACGACAAGCTCCTCGCCAAGCTCCTCCAGC
CCGACACCTACTGGAAGAAGTCCTCGCTCGCCATCGTCGACGGATTCGCCGTCGAGATCACCGACGCTCAGGTCACCGCC
CGACCTATAACCTCACATG---CATGGATGTACATGGATCCATCATATG---------TACTGTACATGAAACTTCTCTT
ACACCCCTGATGGCATATATGATCGGTTGAACTATATACTGATGCAGGCGAGCGTGCTGAGGTCGGCGAAGGAGGTGAGG
GTGGTGGAGAAGAACCAGGAGCTTGCTTGACCAGCCAAACATCCAGGC--AGTTATAAGCATGATCTTTTAGATGCTTTG
AGCATCTGCCATAGCCATGGAAGCTTGGTTTATTATAAGCTAAGTCCCGAGTACGTTGATCAGTTGCTACTAGTCAA--G
CTTTTGCGGCGTAAGTGTATCGATCGGTGTGTGTTTTTGTGTGATCTCCCATGGCTTTGTTGACTCTAATGTCAAGCTCA
AGCTTAGCTACTATCTTTATATACTAGTGCGTACTG----TACTACTTAATTAGCATTAGCTGCAGTGATATAGATATAT
AAAGTTCTTCATC----AATCTTACTAGCTAGGGT---CTACTGATATTCAGAGGATGACTTTGAAGA-TCGAACCCTGC
AATGTAATGGTGATTATAGATGAATGAGCAATTAGTC----AAAAAAGTATCTGTGTAGCAGTAGTATTTTATAATCTCA
TGCATGTACTCTCTTTCGGTGTCCAACATGCATGGCAGTGTGTGTCTGACTTTTGGGTCTTGTTTCTGTATGCAATATGT
GTAATGCATGGGTAGATGCATGCTTTGGGTGCCTAATGTGAGTGGTTTAAGGTCTTGGGTTGACTTGTGAAAACTACAAG
ACA---------AGGAGGTTTTGTTGATGAGTGGACTCGGCCTCTCGAACCGCTGATCATGATATGATTCCTACACTTGC
GAGTTTCCGAGATGAGGAAACCTCTCGTGGAAACCTGCAATGATAACACAAATAATTGCACTGATTTGTGCGTGAGCGTA
CGTGGTTCCGTGCGTGCCGGGAGAGATGATCGATGCAGTGCGTGTGGAAGCACTTTGATTCCAGTTTTCAGGCCTAGAGA
ACCGTAGGCAGAACAGCAGCATGCACGCTTGTTCGACTGTACGTGTGCCTATCATTTTCCGACACGTATCGCTCTGCCTG
ACAAAGCTGCCACCCGGCGGTGCACCGTGGGATCCGCGCGAATAG-GAAAACATATAAAATGAAAAAGGATGTATCTAGA
GCTCATCTAAACATAAATATTTATGTCACATCTAATTTCTGGTTTTAAC------------TTTTTATACGTTCTTGTGT
TTC--------------------------------TGGTTGCTGCAGCGCCGGTCGTTTTCCTGTACCCTCTTCTCGACC
GTAGTGGAGTGGAGGAGCACACAATCCCGTAGCATAGTATTACTAACTACAGAACCAGAAAAAGAAAAAGAACAGGTTTT
TGGTCTCAGGATGTATCGAGTACTGAACACCCATATTTTCCGCAATTTGAGCTCAAAGTATTTACTAGTTGGGCTATAAG
GGCATCTTCAATGCCGACCCACAAACCTACCGCTACTGTTCGG
>chr3B_1
TACAAGACAAGCTTAGCATGCATGGTATAA--------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-------------------------------------ATGTAACCTGTCGTGCATGCATGCATGATCAGCGACTCGGTCA
CGTTTCTGGAGATGCAAACATACAAACAAGTGTACAGCATTACCAAAAATGTGCATGCATGGCAGCTAGCTCGATCTCGG
CCCCTCGCCGAGATCCTTGCCGGCCATTGCCGTCCTTGGGCAGGATCCGATCCGTCCGGGCCCTCTCCTCTCCTCTCGCT
CTGGCCATGCACGCAGCAGCCGGGCGGCAGCCAGCTCTGCGTCGCATGCATATGCATGCATGCACGCGGACGTACGTACT
GCGAGCCAGTCTGCGAGCTGCCCGCTCTG------CTCACACCCCATCCCATCCGGATCTGGTACTGACCAGCA------
-CCGGCTGCGACGACATGCATGCGTACAATCCGGCCAGTCTCCAGCCCCCCCCT-CTCTCTCTCTGAGTCCCAGGTGCAG
CGCAGAGATCTCGAGCCCTTGACCTCTTCCAGCTCTGTGCGAGATTCCATGCTACGTACACATCCACTGCGCCTGCATGC
AGGCCTGCGTCACCATCGCATGCGCCCTCCCGTCTGCCCAACCATCAAAGACATTCTATTGGATATTGCTCACGAACCAT
AC--AAAAATGTGTATGTATATACTC-TATCTTCTCCAGCAATCCAACTGCAACCCACATATAATATACATGCTCACGCA
CCCTCCACAGTACCTGCAGCAAGCTGGCTATATGGACAAGTAAGGGTTGGTTAACTAGTGGCTGGACGTACGCATATGCA
TGTGCCTGCGCTTTTTATAGGTGAGATTCCCTTGACCAAGTTCAAGCCGGCCTAAGCTCGCGCAGTTGGCTGCATGTTTG
TTAGTTGCGTCGCGCTTTCGCTAATTTGACTAATCACTCTAGATCTAGGCTAATCTGGACACAGTAAGAAAGCTTGCAGG
TACAAGCTAGCTAGCTCCCTCCCGGCCGGTGACATGATCGGCATGTGACCACCTCCTCTCCCCCGGCTATAAATAGCGGC
CCATAGCAATGATATGGAGCCAAGCCAAGCAAGCACTTGCTCTCTCTCTCTCTCATATCATTAGTCATTACCCGCACTGA
AAACCTTAGTACTGCTAGCTACTAGCTTCCTGTGTAGCTCGAGGAAGAGAGAATCCGACTGAGTGCGAGCAATGGCGAAG
CCGCAGCAGGAGGTGTACTTCGTGTTCATGAACTTCGACCCTGTCTACGAGCGCCTGAGGGCCGATCGGTCTGTATACCT
CGCACATAAATATAATGGCTTGCATCTTTGTA-TGCAATATATGTGCGCGGTTTTGATGGATGGTTTGTTGGG-----TG
CAGGACGAAGCAGGGGTCAGCGACGCTGGACGCGTACCTGAGCCAGAAGCACGACAAGCTCCTCGCCAAGCTCCTCCAGC
CCGACACCTATTGGAAGAAGTCCTCGCTGGCCATCGTCGACGGATTTGCCGTCGAGATCACCGACGCTCAGGTCACCGCC
CGGCCTATAACCTCACATG---CATGGATGTACATGGATCCATCATATG---------TACTGTACATGAAACTTCTCTT
ACACCCCTGATGGCATATATGATCGGTTGAACTATGTACTGATGCAGGCGAGCGTGCTGAGGTCGGCCAAGGAGGTGAGG
GTGGTGGAGAAGAACCAGGAGCTTGATTGACCAGCCAAACATCCAGGC--AGTCATAAGCATAATCATTTAGATGCTTTT
GGCATCTGCCATAGCTATGGAAGCTTGGTTTAGTATAAGCCAAGGCTGGAGAACGTTGATCAGTTGCTATTAGTCAATTG
CTTTTGCGGCGTAAGTGTATCGATCGGTGTGTGTTTTTGTGTGATCTCCCATGGCTTTGTTGACTCTAATGTCAAGATCA
AGCTTAGCTGCTATCGTTATATACTAGTACGTACTACTACTACTATTTAATTAGCACTAGCTGCAGTAATATAGATATAT
AAAGTTCATCATC----GATCTTACTAGCAAGGGTCTACTACTGATATTCAGAGCAAGACTTTGAAGATTTGAACCCTGC
AATGTAATGGTGATTATAAACGAATGATCAATTAGTTAAAAAAAAAACTATCTGTGTAGCGGTAGTATTTTATAAGCTCA
TGCATGTACTCTCTTCCGGTGTCCAACATGCATGGCAGTGTGTGTATGACTTTTGGTTCTTGTTTCTATATGCAATATGT
--AATGCATGGGTAGATGCATGCTTTGGGTGCCTAATGTGAGTGGTTTAAGGTCTTGGGTTGACTTGTGAAAACTACAAG
ACAAGGATGAGGAGGAGGTTTTGTTGATGAGTGGACTCGGCCTCTCGAACCGCTGATCATGATATGATTCCTATACCAGC
GAGTTTCCGAGATGAGGAAACCTCTCGTGGAAACCTGCAATGATAACACAAATAATTGCACTGATTTGTGCGTGAGCG--
--TGGTTCTGTGCGTGCCCGGAGAGATGATCGATGCAGTGCGTGTGGAAGCACTTTGATTCCAGTTTTCAGGCCTAGAGA
ACCGTAGGCAGAACAGCAGCATGCACGCTTGTTCGACTGTACGTGTGCCTATCATTTCCCGACACGTATCGCTCTGCCTG
ACAAAGCTGCCACCTGGCGGTGCACTGTAGGATCCCCGCGAAAAGCGAAAACATATAAACT-AAAAAGTGCGTGTCTAGT
GCTAATCTAGATGTGACATATTATGTCACATCTAATTTCTGTTT------------------------------------
--------------------------------------------------------------------------------
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--------------------------------------------------------------------------------
-------------------------------------------
>chr3A_1
TACAAGACAAGCTTAGCATGCATGGTATAGTTGATACTACCTCCATTTCAAAATATAGTGCGCCCGCGCTTTCTGAGGTT
CAACTTTGATCATAAATTTAACCAACGAGACCAACTACGACGGGAGAAAAAAATTATATAATTGAAAACTTCTTTCGAAT
ACTAATTCACTGATATAATTTTTGCTCCCGCCGTAATCGGTATTGCTAATTAAATTTACGATCAAAGTTAAAGCACGTGA
ATAAAGGAAGCACTACATTGTGGAATGGAGGAAGTATATGTAACCTGTCGTGCATGCATGCATGATCAGCGACTCGGTCA
CGTTTCTAGAGATGCAAACATA----CAAGTGTACAGCATTACCAAAAATGTGCATGCATGGCAGCTAGCCCGATCTCGG
CCCCTCGCCGAGATCCTTGCCGGCCAGTGCCGTCCTTGCGCCGGATCCGATCGGTCCGGGCCCTCTCCTCTCCTCTCGCT
CTGGCCATGCACGCAGCAGCCGGGCGGCAGCCAGCTCTGCGTCGCATGCAT------GCATGCTCGCGGCCGTACGTACT
GCGAGC------------TGCCCGCTCTG------CTCACACCCCATCCCATCCGGATCTGGTACTGACCACTGACCAGC
GCCAGCTGCGACGACATGCATGCGTACAATCCGGCCAGTCTCCAGCCTACAGCGCCTCTCCCTCTGAGTCCCAGGTGCAG
CGCAGAGATCTCGAGCCCTTGACCTCTTCCAGCTCTGCGCGAGATTCCATGCTACGTACATATCCACTGCGCCTGCATGC
AGGCCTGTGTCACCATCGCATGCCCCCTCCCCTCTGCCCAACCATCAGAGACATTCTATTGGATATTGCTCACGAACCAT
AC--AAAAATGTGTATGTATATACTCTTATCTTCTCCAGCAATGCAACTGCAACCCACATAAAATATACATGCGCG----
----TCACAGTGCCTGCAGCAAGCTTGCTACATGGACAAGCAAGGGTTGGTTAACTAGTGGCTGGACGTACGCACATGCA
TGTGCGTGCGCGTTTTATAGGCGAGATTCCCTTGACCAAGTTCAAGCCGGCCTAAGCTCGCGCAGTTGGCTGCATGTTTG
TTAGTTGCGTCGCGCTTTCCCTAATTTGACTAATCACTCTAGATCTAGGCTAATCTGGACACAGTAAGAAAGATGCA---
--------AGCTAGCTCCCTCCCGGCCGGTGACAAGATCGGCATGTGACCACCTCCTCTCCCCCGGCTATAAATACCGGC
CCATAGCAATGATATGGAACCAAGCCAAGCTAGCACTTGCTCTCTCA----CTCATATCATTAGTCATTACCCGCACTGA
AAACCTTAGTGCTGCTAC---CTAGCTTCCTGTGTAGCTCGAGGGAGAGAGAATCCAACGAGC-GCGAGCAATGGCGAAG
CCGCAGCAGGAGGTCTACTTCGTCTTCATGAACTTCGACCCTGTCTACGAGCGCCTAAGGGCCGATCGGTCTGTATACCT
TGCACATAACTATAATGGCTTGCATC-TTCTA-TCCAATATATGTGCGCAGTTTTGATGGATGGTTTGTTGGCTTGGGTG
CAGGACGAAGCAGGGGTCGGCGACGCTGGACGCGTACCTGAGCCAGAAGCACGATAAGCTCCTCGCCAAGCTCCTCCAGC
CCGACACCTACTGGAAGAAGTCCTCGCTGGCCATCGTCGACGGATTCGCCGTCGAGATCACCGACGCTCAGGTCACCGCC
CCGCCTATAACCTCACATGCATCATGGATGTACATGGATCCTCATACATGCTCACCTCTACTGTACATGAATCTTCTCTT
ACACCC-TGATTGCACACATGAGCGACTTAACTATATACTGATGCAGGCCAGCGTGCTGAGGTCGGCCAAGGAGGTGAGG
GTGGTGGAGAAGAACCAGGAGCTTGCTTGACCAGCCAA-CATCCAGGCGAAGTTATAAGCATAATCATTTAGATGCTTTG
AGCATCTGCCATAGCTATGGAAGCTTGGTTTATTATAAGCTAAGGCCGGAGTACGTTGATCAGTTGCTACTAGTCAATTG
CTTTTGCGGCGTAAGTGTATCGATCGGTGTGTGTTTTTGTGTGATCTCCCATGGCTTTGTTGACTCTAGTGTC-AGCTCA
AGCTTAGCTACTATCTTTATATACCACGTAC---------TACTACTTAATTAGCACTAGCCGCAGTAATATAGATATAT
AAAGTTCTTCATCGATCGATCTTACTAGCTAGGGT---CTACTGATATTCAGAGGACGACTTTGAAGA-TTGAACCCTGC
AATGTAATGGTGATTATAAATGAATGAGCAATTAGTC----AAAAAAGAATCTGTGTAGCGGTAGTATTTTATAAGCTCA
TGCGTGTACTCTCTTTCGCTGTCCAACATGCATGGCAGTGTGTGTCTGACTTTTGGGTCATGTTTCTATATGCATGGGTA
G------ATGGCTAGACGCATGCTTTGGGTGCCTAATGTGAGTGGTTTAAGGTCTTGGGTTGACTTGTGAAATCTACAAG
ACAAGGAAGAGGAGGAGGTTTTGTTGATGAGTGGAGTCGGCCTCTCGAACCGCTGATCATGATATGATTCCTACACTTGC
GAGTTTCCGAGATGAGTAAACCTCTCATGGAAACCTGCAATGATAAGACAAATAATTGCACTGATTTGTGCGTGAGCG--
--TGGTTCTGTGCGTGCCGGGAGAGATGATCGATGCAGTGCGTGTGGGAGCACTTTGATTCGAGTTTTCAGGCCTAGAGA
ACCGTAGGCAGAACAGCAGCATGCACGCTTGTTCGACTGTACGTGTGCCTATCATTTCCCGACACGTATCGCTCTGTCTG
ACAAAGCTGCCACCGGGCGGTGCACTGTAGGATCCCCGCCAATAGCGAAAACATATAAACT-AAAAAGTGCGTGTCTAGT
GCTTATCTAGATGTGACATAATATGTCACATCTAATTTCTATTTAGTGACCCCATTGTTTGTTTGTATACGTTGTTGTGT
TTATTCATGTACTATACTTTGCTTGCGAGATGTGTTGGTTGCTGCAGCGTCC-TCGTTTTCCTATACCCACTTCTCACT-
GTAGTGGAGTGGAGGAGCACACAATCCCGTAGCATAGTATTACTAATTACAGAACCAGAAAAAAAAAAG-----------
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-------------------------------------------
>SNPs
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------------------------------------------S-------------------------------------
-------------S------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------S-----------
---------------------S-------SSSSSS---------------------------------------------
-------------------------------------------S------------------------------------
---------------S----------------------------------------------------------------
-----------------S------------S----S-------------------------------S-S------S---
--SS----------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
---------------------------------S--------------------------S-------------------
---------------------------------------S----------------------------------------
--------------------------------------------------------------------------------
-------------S----------------S-------------------------------S--S--------------
--------------------------------------------------------------------------------
------S-----------------------SSS-----------------------------------------------
--------------------------------------------------------------------------------
----------------------------S---------------------------------------------------
--S-----------------------------------------------------------------------------
-------------------------------------------------------------------S------------
--------------------------------------------------------------S---S-------------
---------------S----------------------------S--S--------------------------------
--------------------------------------------------------------------------------
----------------------------S------S--------------------S----------S------------
-----------------S--------------------------------------S-------------S---------
------------------S-----------------------------------------S--------------S----
-------------------------------------------------------------------S------------
-S------------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------------------------------SS
SS------S-----------------------------------------------------------------------
---------------------------------------------------------S----------------------
--------------S----------S--S------S-----------------------S-S------SSS--S-----S
---S-----S-SS-S-SSSS---------------------S--SSSSS---------------S--------S------
--S----------------------------------------------S-SS----------S-----S------SSSS
----------------------------------------------S----------------S----SSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_684
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------------------------TACAATCCGGCCAGTCTCCG------------------------------------
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>reverse_1552
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-------------------------------TGTGCAATATATGTGCGCGG-----------------------------
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>forward_736
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-----------------------------------------------------------------------------CAG
CGCAGAGATCTCGAGT----------------------------------------------------------------
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>reverse_1908
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-------------------------------------------------------------------GAAGGAGGTGAGG
GTGGTG--------------------------------------------------------------------------
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-------------------------------------------
>forward_1240
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----------------------CGGCCGGTGACATGATCA----------------------------------------
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>reverse_3285
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----TCTTCAATGCCGACCCACAA-------------------
