>input_sequence_69869
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----------------------------------------------------------ATGGCGACCATGGCCGGGCGCT
ACTGGTGCAGCTAC---AGCTCGCCT------TCTGCGCCGCCGCCCCAGCGGCAGCGCGGGCCTCCGCTGCAGCCGCGA
CACACGGGAGGACGGGGAAGGGGACTCCGGCGACCGAGCCTACGGGCGGCCGCGTCGGCGGCGGGGGAGCCCGTGAAGGC
GGCCACGGACGCCGAGTTCTTCCAGCCCGCCGACTCGAGGCCCATCATGCTCTTCGACGGCGTGTGCAACCTCTGCAACG
GCGGCGTCCGGTTCGTGCGGGAGCGCGACCCTGGCCGGAGCATCAGGTACATCCCCCTCCAGAGCGACTCCGGGAGGAAG
CTCCTGCGCCGGTCCGGCAGAAGCCCCGACGACATCTCCAGCGTCGTCCTCGTCGAGAAGGACAGGTAACCATCGCC---
----TCTAGCTGCTCTGCTATTGTTAATGGACATCAGCCATGGACCAAGT--ATCAGAAATGTTGTTGCT--GTGCAGGT
CCTACATCAAGTCTGAAGCTGTGCTGAGGATAATGGAGTACCTCAACCTGCCGTTCCCGCAGCTCGCCGCGTTCCTCAAA
ATTGCCCCTCTGTAAGCTCAATTCACACACACACG--GCATGCTTTCAATTGAACCACTGCAATTGCA-----AACTACT
AATTCTTGGCGGTGCCATGGCTAGGTTTGTGAGGGACTTCGCCTACGACAACGTCGCGAACAACCGGTATGTGGTGTTCG
GCCGGTCAGAGACAGAATCATGCGAGATACTCTGA---------------------------------------------
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>chr3A_1_TraesCS3A01G129300
TTCTAAAGAACAACGGCCTCGCTGTTGAGAAGAGTAAGAATCTTCTTCTTTCCCTGTAATGTAGACTATGTCTGATCAAA
TGGTGTTGTTATGCGAAAATTGCTACGTGTGATCATGATCAAACGGCTGTGCGGGCGTTCGCTGGGGCCTCCCTCCCAGG
GAACGTCAGCCAGTTAACATTACCGTTTATCATTATGTGCTCTGAACTTTCCTCTTTTAACCTTGATGTGTGTAGAGATT
AGGACATCCACAGTGGAAATAAATGACGAATCTAGAGGCCGCCCATTCCAAAAGGCCAAGGTCAGAGAA-----------
------GAACAACAGTTTGGCTTGTCTCTTTGGTTGCCAGTG--TGTCATTTCTCTGATGTATGAAATTCGACTTA---A
CAACTAAAACTGACATGGATATATGTTCACGCAGATTGAGATAGAGTTGGGGAAGAGCGAGAAATTCGACGAGTTGATGG
CCTCTGCTGCGGCAGACGCCGAAGAAGGCGAGGAGGAGGCCTGAAGAACCAAACAAAGCCGTAGCGACCGCATCCCGTTG
CTCTACTTTGTTTCCGCTGTTGTTTAAAAC-TTCAGAACCAATGCATGAGACATGGCGTGTGTCCCTGTTTAACTTGTAT
TTTCTTAGTGTCAGTGTTTGTGAACTCTTTGGCAGATGATGAATCTGTTCCGCGTGCATTTTTTTTCTCCAAACCGCTG-
------------GCTGGAAATAATCTTTTTCGCGTGTGCTCTGCTTGGTCCC--AATCTGGT--GGCTCTACGTTTATAA
TGTTGTTGATGGATACCACTATGGTGCAAATGCAAGCGCTGTCCTTCTCATGTAATTTT---------------------
--------------------------------------------------------------------------------
-----------------------------------AGTTTGGAATGTGAAAGTCTGGGAGCAAATCCGCTCGGCTGCAAG
CCCGTTTTACCCTGGCCA-AATTACCCGTTGCTGGACGTGCCACGTAGCCTCAGGCGCACCGTGCGTTCGGCTCCGAAGA
GAATGAAGCCTCAA-CAAGCCACTGCACAGCAGATACACGGGAGAAACGAAGGAGGCGATGGCGACCATGGCCGGGCGCT
ACTGGTGCAGCTAC---AGCTCGCCT------TCTGCGCCGCCGCCCCAGCGGCAGCGCGGGCCTCCGCTGCAGCCGCGA
CACACGGGAGGACGGGGAAGGGGACTCCGGCGACCGAGCCTACGGGCGGCCGCGTCGGCGGCGGGGGAGCCCGTGAAGGC
GGCCACGGACGCCGAGTTCTTCCAGCCCGCCGACTCGAGGCCCATCATGCTCTTCGACGGCGTGTGCAACCTCTGCAACG
GCGGCGTCCGGTTCGTGCGGGAGCGCGACCCTGGCCGGAGCATCAGGTACATCCCCCTCCAGAGCGACTCCGGGAGGAAG
CTCCTGCGCCGGTCCGGCAGAAGCCCCGACGACATCTCCAGCGTCGTCCTCGTCGAGAAGGACAGGTAACCATCGCC---
----TCTAGCTGCTCTGCTATTGTTAATGGACATCAGCCATGGACCAAGT--ATCAGAAATGTTGTTGCT--GTGCAGGT
CCTACATCAAGTCTGAAGCTGTGCTGAGGATAATGGAGTACCTCAACCTGCCGTTCCCGCAGCTCGCCGCGTTCCTCAAA
ATTGCCCCTCTGTAAGCTCAATTCACACACACACG--GCATGCTTTCAATTGAACCACTGCAATTGCA-----AACTACT
AATTCTTGGCGGTGCCATGGCTAGGTTTGTGAGGGACTTCGCCTACGACAACGTCGCGAACAACCGGTATGTGGTGTTCG
GCCGGTCAGAGACAGAATCATGCGAGATACTCTGAATTGGTGCCGCAGATAAGCACCTCAGTGCTCTTGCTTATAGTATT
ATAGATAGAAGAATGGCCATACATTGAGAAGTTGTAGGCATGACAGATATGAGACAGAATCATGCGAGATACTCTGAATT
GATGCCGCAGATAAGCACCTCGGTGCTCCTGCTTATATATTATAGATAGAAGAATGGCCATACATTGAGAAGTTGTAGGC
ATGACAGATATGAGATGGCATGAACCACCATC--ATTACAACCAATCCAATTTTAGCACTACTACCCTG-CCTCACGTAG
CGCTCACCTATGGTAAGCATTTCTGCACTTGCTCCTCTGTC-TATGTCCAAGCACTATGTTCACGACGGAGAGCACTTCT
GATCAGAGGCCACGGAAGCGTACTTGTGGCTTCACCTTGCCCGCGACTCTTCCTTGGGCATTTAGGATTTTGGCTTTTGT
TGGGGCCGTGTGGTTGGCCCAAGAGAGGTCCACGTTGTGGAGAAAAATCCCGTGGCATGGCACGCTTTTGCTGCACAGGA
TCTGGATGGCCTCTTGCTCCGAGGACGTCCCCCGGATGTTGATGAATCTTGCGTCCGTTATGGCCACACCACCTTCCTGC
AAATGCAGCCAATATGG-TTTCAGT---------------------------TGAGGTAGTGGTGGTGACTGAATTCAAT
TGAGTGGGTTTCCTCACCCGTTCTGGACAGTTTCCCTGGGGGCAATAGAACTGGTCGATGTAGATAGGATACCGTACTTC
AGTCATGTTGAGGTCCGTGAAAAGGAACGTGTTCGCTTTGCCTCGCCCTCCCTGCATTTCTCATAACATCAT-ATAAGTT
TGGGGAAAATACTACCA-------------------------TGGTGTATGCAACCATGGGTTGGTATCTTT-GAACTGA
C----GGCACACACAT----------------GCATGTAGATGCGGCTTCAGTGTTACCTGCCACGATTTGATCCTGACA
CCGGTCATCGTATTAAAGAAGTTGCAGTTGGATACTGTAATTCTTTCCACCATCGTTTGTTTTTCACCGGCACC
>chr3D_1
TTCTGAAGAACAACGGCCTCGCTGTTGAGAAGAGTAAGAACCGTCTTCTTTCCTTGTAATGCAGATTATGTCTGATCATA
TATATCGTGGGCAGCATTGCTGCCATGAACATTCTCCACA----------------------------------------
-------------------------TTTGTCATTATTTACTCTGAACTTTCCTCTTTTAACCTTGTCGTGTGTAGAGATT
AGAACATCCACGGTGGAAATAAACGACGAATCGAGAGGCCGCCCATTCCAAAAGGCCAAGGTAACAGAGAAGAAGAAACG
ATGTTTTATCAGCAGTGTGCCTTATTTCTTTGTTTGTCAATATATGCCAGTTCTCTTATGTATGAAGTGTTACCG-----
------AGACTGACTTACCTATGGATTCACACAGATTGAGATAGAGTTGGGAAAGAGCGAGAAATTCGACGAGTTGATGG
CCTCTGCTGCGGCAGATGCCGAAGAAGGCGAGGAGGAGGCCTGAAGAACCAAACAAAGCCGTAGCGACTGCATCCTGTTG
CTCTACTTTGTTATCGCTGTTGTTTAAAACTTTCAAAACCAATGCACGAGACATGGCGTGTGTCCCTGTTTAACTTGTAT
TTTCGTAGTGTCAGTGTTTGTGAACTCTTTGTCTGATGAT-AATCTGTTTCGCGTGCATTTC-TTGCTCCAAACCACTGG
CTGGTTCGTATTGCTGGAAATAATCTTTTTCGCGTGTGCTCCGTTTGGTCCTATAATCTGGT--GGCTCTACGTTTATAA
TCTTGTTGATTGATATTACTATGGTGCGAATGTACAGGCTGTGCTTCTCATGTAATTTTATTTTCCGTTTGGAC------
--------------------------------------------------------------------------------
-------------------------------------TTTGGAATGTGAAATTCTGGAAGCAAAT----------GCAAA
CCCGTTTTACCCTGGCC-AAATTACCGGTTGCTGGACGTGCCACGTAGCCTGATGCGCACCGCGCGTTGGGCTGCGAAGA
GAATGAAGCTTCAAACAAGCCACCGCACAGCAGGTACACGAGAGGAAGGAAAGAGGCGATGGCGACCATGGCCGGGCGCT
ACTGCTGCAGCTACTACAGCTCGCCC------TCTGCGCCGCCGCCCCAGCGGCAGCGCGGGCCTCCGCTGCAGCTGCAA
CCGGCGGGAGGACGAGGACGGGGACTCCGGCGACCGAGCCTACGGGCGGTCGCGTCGGCGGCGGCGGAGCCCGTGAAGGC
GGCCACGGACGCCGAGTTCTTCCAGCCCGCCGACTCGAGGCCTATCATGCTCTTCGACGGCGTGTGCAACCTGTGCAACG
GCGGCGTCCGGTTCGTGCGGGAGCACGACCCCGGCCGGAGCATCAGGTACGTCCCCCTCCAGAGCGACTCCGGGAGGAAG
CTCCTGCGCCGGTCCGGCAGAAGCCCCGACGACATCTCCAGCGTCGTCCTCGTCGAGAAGGACAGGTAACCATCGCC---
----TCTAGCTGCTCTGCTATTGTCAATGGACATCAGCCATGGACCAAGT--GTGAGAAATGTTTTTTGGAAGTGCAGGT
CATACATCAAGTCTGATGCCGTGCTGAGGATAATGGAGTACCTGAACCTGCCGTTCCCGCAGCTCGCCGCGTTCCTCAAA
ATTGCCCCCCTGTAAGCTCAATTCACA----------------TTTCAACTGAACCACTGCAATATAAGTAGCAATTACT
GATTCGTTGCGATGCCATGGCTAGGTTTGTGAGGGACTTCGCCTACGACAACGTCGCGAACAACCGGTATGTGGTGTTCG
GCCGGTCAGAGACAGAATCATGCGAGATACTCTGAATTGCTGCCACAGAT------------------------------
--------------------------------------------------------------------------------
-------------AGCACCTCGGTGCTCCTGCTTATATATTATAGATAGAAGAATGGCCATACATTGAGAAGTTGTAGGC
ATGACAGATATGAGATGGCATGAACCACCATCATATTACAACCAATCCAATTTTAGCACTGCTACCCTG-CCTCACGTGT
CGCTCACCTACGGTAAGCATTTCTGCACTTGCTCCTCTGTCTTATGTCCAAGCACTATGTTCACAACGGAGAGCACTGGG
GATCAGAGGCCGCGGAAGCGTACTTGTGGCTTCACCGTGCCCGCGACGCTTCCTTGAGCATTTAGGATTTTGGCTTTTGT
TGGGGCCGTGTGGTTGGCCCAAGAGAGGTCCACGTTGTGGAGAAAAATCCCGTGGCACGGCACGCTTTTGCTGCACAGGA
TCTGGATGGCCTCTTGCTCCGAGGACGTCCCCCGGATGTTGATGAATCTCGCGTCCGTTATGGCCACACCACCTTCCTGC
AAACGCAACCAATATGATTTTCAGTTTCAATCGTTGTCTTTCAGGATGCATCTGATGTAGTGGTGGTGACTGAATTCAAT
TGAATTGGTTTCCTCACCCGTTTTGGACAGTTTCCCTGGGGGCAATAGAACTGGTCGATGTCGATAGGATACCGTACTTG
AGTCATGTTGAGGTCCCTGAAAAGGAACGTGTTCGCTTTGCCTCGCCCTCCCTGCATTTCTCATAACATCAT-ATAAGTT
TGGGGAACATACTACCA-------------------------TGGTGTATGCAACCATCAGTTGGTATCTTTTGAACTGA
T----GGCACACACAT----------------GCGTGTAGATGCGGCTTCAGTGTTACCTGCCACGATTTGATCCTGACA
CCGGTCATCGTATTGAAGAAGTTGCAGTTGGATACTGTAATTCTTTCCACCAGCGCTGGTTTTTCACTGGCACC
>chr3B_186
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-------------------------TTTATCATCATGTACTCTCAACTTTCCTCTTTTAACCTTGGTGTGTGTAGAGATT
AGGACATCCACGGTGGAAATAAACGACGAATCGAGAGGCCGCCCATTCCAAAAGGCTAAGGTAAGAGAG-----------
------TAACAACAGTTTGGCTTA-CTCTTTGTCTGTCAATG--TGCTAATTCTCTTATGTATGAAGTTCCACTTCTCGA
CAAGTAAAACTGACTCGGCGACTGATTCATGCAGATTGAGATAGAGTTGGGAAAGAGCGAGAAATTCGACGAGTTGATGG
CCTCTGCTGCGGCAGATGCCGAAGAAGGCGAGGAGGAGGCCTGAAGAACCAAACAAAGCCGTAGCGACCACATCCTGTTG
CTCTACTTTGTTATCGCTGTTGTTTAAAAC-TTCAAAACCAATGCACCAGACATGGCGTGTGTTCTTGTTTAACTTGTAT
TTTCGTAGTGTCAGTGTTTGTGAACTCTTTGGCAGATGAT-AATCAGTTTCGTGTGCATTTC-TTTCTCCGAACTGCTG-
------------GCTGGAAGTAATCTTTTTCGCGTGTGCTCCGTTTGGTCCT--AATCCGGAGAGGCTCTACGTTTGTAA
TTTTGTTGATTGATACCACTATGGTGCGAATGCAGGCGCTGTGTTTCTCATGTAATTTTCTTTTTGAGCATCATAAACTT
TATTCATCAAATGATAGCTAAATCGTTTACATAATGATGAAGAATAAAGTCAGGGATGACAGTTTCCCATGCTTCAGACT
TGCCAGAACTAATACAACGTTTCTCATGTAATTTTAGTTTGGAATGTGAAATTCTGGAAGCAAATCCGCTCGGCTGCAAG
CCCGTTTTACCCCGGCCAAAATTACCCGTTGCTGGACGTGCCACGTAGCCTCAGGCGCACCGTGCCTTCGGCTCTGAAGA
GAAATGAAGCTTGGACAAGCCACTGCACAGCAGATACACGAGAGAAGGGAAGGAGGCGATGGCGACCATGGCCGGGCGCT
ACTGCTGCAGCTAC---AGCTCGCCCTCTGCCTCTGCGCCGCCGCCCCATCGGCAGCGCGGGCCTCCGCTGCAGCCGCGA
CCCACGGGAGGACGGGGAAGGGGACTCCGGCGGCCGAGCCTACGGGCGGTCGCGTCGGCGGCGGCGGAGCCCGTGAAGGC
TGCCACCGACGCCGAGTTCTTCCAGCCCGCCGACTCGAGGCCCATCATGCTCTTCGACGGCGTGTGCAACCTCTGCAACG
GCGGCGTCCGGTTCGTGCGGGAGCACGACCCCGGCCGGAGCATCAGGTACATCCCCCTCCAGAGCGACTCCGGGAGGAAG
CTCCTGCGCAGGTCCGGCAGAAGCCCCGACGACATCTCCAGCGTCGTCCTCGTCGAGAAGGACAGGTAACCAAACCGAGT
CTGGTCGAGCTGCTCTGCCTTTGTCCATCGACATCAGCCATGGCCAAGTGTGGTGAGAAATGTTCTTTGCCCCT-CAGGT
CATACATCAAGTCTGACGCCGTGCTGAGGATAATGGAGTACCTGAACCTGCCGTTCCCGCAGCTCGCCGCGTTCCTCAAA
ATTGCCCCTTTGTAAGCTCAATTCACACACACACACTGCATGCTTTCAATTGAACCACTGCAATTGCA-----AACTACT
AATTCGTGGCGATGCCATGGCTAGGTTTGTGAGGGACTTCGCCTACGACAACGTCGCGAACAACCGGTATGTGGTTTTCG
GCCGGTCAGAGACAGAATCATGCGAGATACTCTGAATTGCTGCCATAGAT------------------------------
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-------------AGCACCTCGGTGCTCCTGCTTATAT--TATAGATAGAAGAATGGACATATTGC--GAAGTTGTAGGC
ATGACAGATATGAGATGGCATGAACCGCCATC--ATTACTACCAATCCAATCTTAGCACTGCTACCCTG-CCTCATGTGG
CGCTCACCTACGGTAAGCATTTCTGCACTTACTCCTCTGTC-TATGTCCAAGCACTATGTTCACAACGGAGAGCGCTGGG
GTCAA-AGGCCGCGGAACCGTACTTGTGGCTTCACCGTGCCCGCGACGCGTCCTTGGGCATTTAGGATTTTGGCTTTTGT
TGGGGCCGTGTGGTTGGCCCAAGAGAGGTCAACGTTGTGGAGAAAAATCCCGTGGCACGGCGCGCTTTTGCTGCACAGGA
TCTGGATGGCCTCTTGCTCCGAGGACGTCCCCCGGATGTTGATGAACCTCGCGTCTGTTATGGCCACACCACCTTCCTGC
AAACGCAGCCAATATGG-TTTCAGT---------------------------TGAGGTAGTGGTGGTGACTGAATTCAAT
TGAGTGGGTTTCCTCACCCGTTCTGGACAGTTTGCCTGGGGGCAATAGAACTGGTCAATGTCGATAGGATACCGTACTTC
AGTCATGTTGAGGTCCCTGAAAAGGAACGTGTTCGCTTTGCCTCGCCCTCCCTGCATTTCTCATAACATCATTATAAGTT
TGGGGAACATACTACATGGCGTA----------------------TGCATGCAACCATCAGTTGGTATCTTT-GAACTGA
TGCAAGGCACACACAT----------------GCATGTAGATGCGGCTTCAGTGTTACCTGCCACGATTTGATCCTGACA
CCGGTCATCGTACTAAAGAAGTTGCAGTTGGATAGTGTAATTCTTTCCACCAGCGCTGGTTTTTCACCGGCACC
>chr3B_1974
CATAACT-------------------------------------------------------------------------
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--------------------------ACCATC--CTTACAGCCAATCCAATTTTAACACCACTACCCTGACCTTACATGG
CGCTCACCTAAGGTAAGAATTTTTGCACT-GCTCCTCTGTC-TATGTCCAAGCACTATGTTCACAACAAAGAGCACTCGG
GATCAACGGCCCAAGAACTGCACTTGTGGCTTCACCTTGCCCGCGACGCTCCCATGGGCATTCATAATCTTGGCTTTTGG
TGGAGCAGTGTGTTTACACCATGATAGGTCGACATTATCGAGATAGATGTCGTGGCACGGCACGCTATTGCTGCACATGA
TCTTGATAGCCTCTCGCTCGGAGGACGTCCCATGGATGTTGATGAACCTCGCGTCCGTTATGGCCACACCACCTTGCTGC
AAAGGCAACCAATATAA-TTTCAGTCTCAACCATTGCCCTGAAGATGGAGCGGTCAAT-GTGGTGGTGACTGAG-----T
TGAGTAGGTTTCCTTACCCGTTCTGGACAGTTTCCATGTGGACAATAGAACTGGTCGATGTCGATAGGATGTTGGACTTC
AGTCATGTTGAGGTCCCTGAAAATGAATCCGCTCGCTTTGCCTTGCCCGCCCTGCATTTAC---AACATCAT-ATATGTT
ATCAGGGGAATTAATAGTGGTATATATGCCTATGGCTTGCAGTGGTGTGTGCAACCATCAGTTGATATCTTT-GATCTGA
TGCAAGGCACACACATGCACAACACAGAGAAGGCATGTAGATGCTGCTTCAGTGTTACCTGCCAAGATTTGATCCTGACA
CCGTTCGTCGTGTTAAAGAAGTTGCAGTTGGATACTGTAATCCTCTCCACCATCGCTGGGCCTTCACCAGCACC
>SNPs
----------------------------------------S-S----------S-------S---S------------S-
-SSSSSSSSSSSSSS-SSSS---S-S-SSSSS--SSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSS-------------S--------------------------S--------------
-----------S-----------S--------S-----------------------------S-----S-----------
------S----------------S--------S---S--S------S--S------S---------S---S----S----
---S----------S---S---SSS--------------------------S----------------------------
----------------S----------------------------------------------------------S----
------------SS---------------------S----------S---------------------------------
----S-----------------------------------S--------S-----------SS-----------------
-----------------------------------------S-S-------S----------------------------
-S--------S----------------S------S-------S-------------------------------------
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---------------------------------------------------S-----S----------------------
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----------------------------------------S------S--------------------------------
----S--------------------S------------------------------------------------------
-S-----------------------------------------------S--------------S---------------
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------------------------S------S------------------------------------------------
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------------------------S---------------------------S-S---------S--SSS----------
-S--------------S--S-----------------------S------------------------------------
----------------------------------S---------------------------------------------
-----S-----S--------------------------------------------------------------------
---------------------------------------S----S-----SSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSS-------------------------------------------------------------------
------------------------------------------------------------------------------S-
----------S-----------------------------------------------------S------------SSS
-----------S-----------------------------------S--------------------------------
---------------------------------------------------------S----------------------
-------------------------------------------------S------------------------------
---S----------------------------------------------------------------------------
-------------------------------------------------------------S------------------
----------------S---------------------------------------------------------------
-------S--------------------------------------------------SS--------------------
S-------------------------------------------------------------------------------
-------------------------------------------------------S-S----------------
>forward_176
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----------------------------------------------------------------------------CAGG
GAACGTCAGCCAGTTA----------------------------------------------------------------
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>reverse_2319
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------------------------------------------------------------------------------CT
GATCAGAGGCCACGGAAG--------------------------------------------------------------
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