>input_sequence_73613
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-----------------------------------------------------------------ATGGCGACTTCCATG
GTGACGGACTTCGGCGACGGCCACTGCATCGTGGCGTTCGACCAGGACCACGTCCACACCACCCTGACCTCCTCCGGCGG
CGTCGTCGACGAGTGGCTGGACCTCATCTACCGCATCCACCGCCGCCGCCTCGACCGCCTCGTCGTCGGCCTCGACGTCG
AGTGGCGCCCCTCGTTCCGCGGCCTCCCGCCGGGCCCCGTGGCGCTGCTGCAGCTGTGCGTCGGCCGCCGCTGCCTCGTC
TTCCAGATCCTCCGCGCCGACTACGTCCCGGACTCCCTCTTCGACTTCCTCGCCGACGGCCGCTTCACCTTCGTCGGCGT
CGGGGTCTACGGCGACGCGCAGAAGCTCAGCGCTCACTACGGGCTGGCGGTGACGAACACGGTGGACCTGCGCTACCTCG
CCGCGAACACGCTGGGGAAGCCGGCGCTGCGGCACACCGGGCTGCAGGGTCTCGTGTGGCAGGTGATGGGCGTATGGCCC
GAGAAACCGCACCACGTGCGGGTCAGCGCCTGGGACGCGCCGCGGCTGACGCGGGATCAACTGCAGTATGCTTGCGCCGA
CGCCTTTGCATCGTTCGAGGTTGGCCGGAGGCTGTACGACGGCGACTATTAG----------------------------
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>chr3D_1_TraesCS3D01G278900
TGGACGAGGGGTGTGCGCCCTGTACGGTTAACGCTATAACGGGCGCTTAGAGCGCCGTTTAGGATTTGCCGCTCTGCAAT
AGGCGTATGCAGAAACACAGACGGTCAGTGGGTTCCATCGTTTCTAAGGTTCCCTTTTAAATGGTGAGGCCCTCTTTATA
CACCATAGCCCTTTCTTTCATAAAAAGGTATTGCGAACTTGTATAGTTCACATTCTTTGGCTCTACCAATCCATTATAGA
GTAAACAACTCTTTTCACAATAAGAGTTATTTATACAGTGACGGTATTTAATTATGAAAGTTGGCTAAGTAGCTGA-CCT
GTTAGTCCGTTCTTTTCAGATAAAGGAGCATAAACCTTTTTCTTTTTATTACTATTTTCTCCGCTTAATGGATAACCATG
ATCATCCATGGAGTCAAGGAGATTGCAGTGCTAGAAGCGATCGCTTGTCGCGAAGCTATGTATCTTGTTGAGGACTTGCT
ACTTCAAAATTTTATTGTCGCCTTCGACTCGAAACAAGTGATAAGCGACATTGAGAAGGGAACGAACATTACCTATGGAC
ACATTATCAAGGAGGTCAAGCACTGAGCATCAAACTTCAATTGCAAATTCATTTTCAAAGGCCGAGCAACGAACACAGAT
GCAA----------------------------------------------------------------------------
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----------------ATAGACTAGCTAAATTTTCGAATTCTCTCGATGAGGGGCGT----CATGTTTGGTTTCAACTCC
ACGATATTTTTTGTATCCCACTTCATGTGACTTTTGATCAATAAAGTTTAGCCATTATATATCCT-------AAAAAGAA
CAGACGCATCGTCGTTTTTGTTGCCTCAAAAAGGAAAAGAAAAACTTTCCCTCAAAAAAAAA-GAAAAAAAAAACTCCCC
TGAAGAAAAGGAAAAGAAAAACAGACGCACCGTCGTACCGCTACAATATATACGGCCGAGACCCAGTAAGACAAATCTAC
TCTGGATTTCTGATCTAGTCTATCTATACCAAACAGTAGTTCGAAACCTCGGGAGGACGATCGAGATGGCGACTTCCATG
GTGACGGACTTCGGCGACGGCCACTGCATCGTGGCGTTCGACCAGGACCACGTCCACACCACCCTGACCTCCTCCGGCGG
CGTCGTCGACGAGTGGCTGGACCTCATCTACCGCATCCACCGCCGCCGCCTCGACCGCCTCGTCGTCGGCCTCGACGTCG
AGTGGCGCCCCTCGTTCCGCGGCCTCCCGCCGGGCCCCGTGGCGCTGCTGCAGCTGTGCGTCGGCCGCCGCTGCCTCGTC
TTCCAGATCCTCCGCGCCGACTACGTCCCGGACTCCCTCTTCGACTTCCTCGCCGACGGCCGCTTCACCTTCGTCGGCGT
CGGGGTCTACGGCGACGCGCAGAAGCTCAGCGCTCACTACGGGCTGGCGGTGACGAACACGGTGGACCTGCGCTACCTCG
CCGCGAACACGCTGGGGAAGCCGGCGCTGCGGCACACCGGGCTGCAGGGTCTCGTGTGGCAGGTGATGGGCGTATGGCCC
GAGAAACCGCACCACGTGCGGGTCAGCGCCTGGGACGCGCCGCGGCTGACGCGGGATCAACTGCAGTATGCTTGCGCCGA
CGCCTTTGCATCGTTCGAGGTTGGCCGGAGGCTGTACGACGGCGACTATTAGGTTAAGGGTGCCAATGCCATCTGCTTAG
TTTTCTAGGGTTATTA---GGTGAATAGTGTTACCTTTTGCTTTGCATCCCAAGCATGTCG-TATGGAGTTTGCCCTGGT
GTTGGAACTT-GAAACTTTACAGAACTTGAAACTTTACAAGATACTTCCTCCGTTTTTAAATATAAGTTCTTTAGAGATT
TCAATATGA------ACTACATACGGATAGACACATTTTAGAGTGTAGATTTACTCATTTTGCTAGTAAGTATGTAGGTC
ATATTGAAATCTCTAAAAGTTCTTATATTTAGGAACGGAGGA---------GGTAGAAAG-TATATCTGGTGAAACGAAT
TGAAAATCA-----------------------------TGTTTCAAATATTCCAAAATTTTGACAAAAAAGC--TAGTGT
TACATGAACCATAGTAGGT-------------ATATAAAATCAAATCAATTTTGCTTGGGAGGTGTGAAAAA-AAATCAG
CATCACTTTCCGTAACTCATATTTTCAT--GTCTCGCTTTTGGTTGCCAAATTCATGTCCTTTATCATAGCTCCCATAAT
ACCGCCTCTCTCATTTTTCAGTCTTTTTC-GTAACATTTGGTTTCCACTTCCTATGAAAACTTTGTTTCCAC--ATAGTA
GTATTCTCTTGAAATAGACTTTCGCCTCACTTTATATAGAAAGTAAC--------ATGATATAAGATAG-----------
-TCTTACAAAATATATCAAAGAGAAGACCGTACAACAAAAATTGCACCGCAAAAAACACACACAAATCCCCTTAACAGCG
CAA-TTCATCACCGCCTTCAAGTCCATCAAGCGCACCCCAAGGGTAAGGCCCGCTGCGAGCCAGGATCACTCACCACCAC
ACCGGTTGCCGGCCACA---------------------------------------------------------------
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--------CGACCAAGAAGTGCAGCCACCACCGTCACCATGAGACTCG--------------------------------
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-----------------------------------------------------------------------ACCGGCCCC
TGCACCCGGCTCACGCCCGCCTACGCCTTGGACGGTTTCAAAGTTCTGGGTTGATTCTTGACTATTCAGAGTTGAAATAT
GGACTTCTCTCTTTGAGA--ATGGCACAGAACATCTAAAA
>chr3B_1
TGGACGAGGGGTGTGCGCCTTGTACTGTTAGCGCTATAACGGGTGCTTAGAGCGCCGTTTAGGATTTGCCGTTCTGCAAC
AGCCGTATGCAGAAACACAAACGGTCAGTGGGTTCCATGGTTTCTATGGTTCCCTTTTAAACGGTGAGGCCCTCTTTATA
CACCGGAGCCCTTTCTTTCATCAAAAGGTATTGCAAACTTGTATAGTTCACATTCTTTGGCTCTACCAATTCATTATAGA
GTGAATAGCTCTTTTCACAATAAGAGTTATTTATATAGTGACGGTATTTAATTATGAAAGTTGGCTAAGTAGCTGACCCT
GTTAGTCCATTCTTTTAAGATAAAGGAGCATAAGCCATTTTCTTTTTATTACTATTTCCTCCTCTTAATGGATAACCATG
ATCGTCCATGGAGTCAAGGAGGTTGCGATGCTAGAAGCGATCGCCTGTCGCGAAGCTATGTATCTTATTGGGGATTTGCT
ACTTCAAAATTTTATTATTGCCTCCGACTCGAAACAGGTGATAAGCGACATTGAGAAGGGAAAGAACAATACCTATGGAC
ACATTATCAAGGAGGTCAAGCAATGAGCATCAAACTTGAATTGCAAATTCATTTTCGAAGGCCGAGCAACGAACACAGAT
GCAA----------------------------------------------------------------------------
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----------------ATAGACTAGCTAAATTTTCGAATTCTCTGGATGAGGGGCAT----CATGTTTGGTTTCACCCCC
GTGATATTTTTTTTATCCCACTTCATGTGACTTTTGATCAACAAAGTTTAGCCATTACCCTAG---------AAAAAAAA
CAGACGCATCGCCGTTTTTGTTGCCTCAAAAAGGAAAAGAAAAACTTTCCCTCAAAAAAAAAGGAAAAGAAAAACTCCCC
TAAAGAAAAGGAAAAGAAAAACAGACGCACCGTCGTACCGCTACAATATATACGGC------------------------
---GGATTTCTGATCTACTCTATCTATACCAAACAGCAGTTCGAAACCTCGGGAGGACGATCGAGATGGCGACTTCCATG
GTGACGGACTTCGGCGACGGCCACTGCATCGTGGCGTTCGACCAGGACCACGTCCACACCACCCTGACCTCCTCCGGCGG
CGTCGTCGACGAGTGGCTGGACCTCATCTACCGCATCCACCGCCGCCGCCTCGAGCGCCTCGTCGTCGGCCTCGACGTCG
AGTGGCGCCCCTCGTTCCGCGGCCTCCCGCCGGGCCCCGTCGCGCTGCTGCAGCTGTGCGTCGGCCGCCGCTGCCTCGTC
TTCCAGATCCTCCGCGCCGACTACGTCCCGGACTCCCTCTTCGACTTCCTCGCCGACGGCCGCTTCACCTTCGTCGGCGT
CGGGGTCTACGGCGACGCGCAGAAGCTCAGCGCTCACTACGGGCTGGCGGTGACGAACACGGTGGACCTGCGCTACCTCG
CCGCGAACACGCTGGGGAAGCCGGCGCTGCGGCACACCGGGCTGCAGGGCCTCGTGTGGCAGGTGATGGGCGTGTGGCCC
GAGAAGCCGCACCACGTGCGGGTCAGCGCCTGGGACGCGCCGCGGCTGACGCGGGATCAACTGCAGTATGCTTGCGCCGA
CGCCTTTGCATCGTTCGAGGTTGGCCGGAGGCTGTACGACGGCGACTATTAGGTTAAGGGTGACAATGCCATCTGTTTAG
TTTTCTAGGGTTATTATTAGGTGAATAGTGTTACATTTTGCTTTGCATCACAAGCATGTCGACATGGAGTTTGCCCTGGT
GTTGGAACTT-GAAACTTTACA-----------------AGATACTCCCTCCGTTTTTAAATATAAGTTCTTTA------
------------TGGACTACATACTGATAGCCATATTTTAGAGTGCAAATTCACTCATTTTGCTAGTATGGATGTAGTTC
ATATTGAAATCTCTAAAAA-------ATTTAGGAACGGAGGGAGTACAAGGGGTAGAGAG-GATATCGGGTGAAACGAAT
TGAAAATCATGTTTATCAAAAAATAAATATGAAAAACATGTTTCAAATATTCCAAAATTTTGACAAAAAAGC--TAGTGT
AACATAATCCACAAGTTTCATAAAAATGCAAGATATAAAATCAAATCAATTTCGCTTGGGAGGTGTGAAAAAAAAATCAG
CATCACTTTCAATAACTCATATTTTCAT--GCCTCACTTTTGGTTGCCAAATTTATGTCCTTCATCATAGCTCCCATAAT
ACAGCCTCTCTCATTTTTCAGGCTTTTTT-GGAACATTTGGTTTCCACTTCCTATGAAAACTTTGTTTCCAC--ATAGTA
GTAGTCTCTTGAAATAGACTTTCACCTCGCTTTATATAGAAAGTAACACGGCCGAATGATATAAGATAG-----------
-TCTTACAAAATATATCGAAGAGAAAATTGTACAACAAAAATTGCACCGCAAAAAACACATACAAATCCCCTTAACAACG
CAA-TTCATCACCGCCTTCGAGTCCATCAAGCGCACT-CAAGGGTAAGGCCTGGTGTGAGCCAGGATCACTTACCGCCAC
ACCGGTTGCCGGCCACA---------------------------------------------------------------
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--------CGACCAAGAAGTGCAGCCACCACCGTCACCATAAGACTCG--------------------------------
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-----------------------------------------------------------------------ACC------
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>chr3A_84
CGTGTGCATAG---------------------------------------------------------------------
--------------ACACAGACCGTCAGTGGGTTCCATCGTTTCTATGGTTCTTT------TGATGAGGCCCTTTTTATA
CACAGGAACCCTTTCTTTCGTCAAAAGGTATTGCGAACTTGTATAGTTCATATTCTTTGGCTCTACTTTTCCATTATAAA
GTAAATATGTCTTTTCACAATAAGAGTTATCCATACAATGATAGTATTTAATTACTAAAGTTGGCTAAGTGGCTGAGCCT
GTTAGTCTGTTCTTTTAAGATAAAGGAGCATAATCATTTTTCTTTTTATTACTATTTTCTCTGCTTAATGGATAACCACG
ATCATCCATGGAGTCAAGAAGGTTGCAGCAGTAGAAGCGATCGCCTGTCACGAA-CTTTGTATCTTGTTGAGAATTTGCT
ACTTCAAAATTTTGTTGTTGCCTCCGACTCGAAACAAGTGATAAGCGACATTGAGAAGGAAACAGACAGTACCTATGGAC
ACATTATCAAGGAGGTCAAACATTGAGCATCAAACTTCAAGTACAAATACATTTTCGAAGGCCGAGCAACCAACACAGAT
TCAGATAGCAAAAATGCTAAACACACGGGCATTCTACGGAGCTGTTACGGGGCTAACGATAAAATCTCTCCATNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGGAACTCGTAAAACCCAGTAATAAGTTTGTGAATG
TAGCATTGTTGTTCAGATAGACTAGCTAAAATTTTGAATTCTTTGGACGAGGGGCTCGTGCCATATTTGGTTTCAACCCC
ATGATATTTTTTGTATCCCACTTCTTGTGGCTTTTGATCAATAAAATTTAGCTATTACCCTCAAAAAAGGAAAAGAAAAA
CAGACGCACCGTCGTTTTTGTTGCCTC------------------------------AAAAAGGAAAAGAAAAACTCCCC
TAAAGAAAAGGAAAAGAAAAACAGACGCACCGTCGTACCGCTACAATATATACGGCCGAGACCCAGCAAGACAAATCTAC
TCTGGATTTCTGATCTAGTCTATCTATACCAAACAGCAGTTCGAAACCTCGGGAGGACGATCGAGATGGCGACTTCCATG
GTGACGGACTTCGGCGACGGCCACTGCATCGTGGCGTTCGGCCAGGACCACGTCCACACCACCCTGACCTCCTCCGGCGG
CGTCGTCGACGAGTGGCTGGACCTCGTCTACCGCATCCACCGCCGCCGCCTCGACCGCCTCGTCGTCGGCCTCGACGTCG
AGTGGCGCCCCTCGTTCCGCGGCCTCCCGCCGGGCCCCGTCGCGCTGCTGCAGCTGTGCGTCGGCCGCCGCTGCCTCGTC
TTCCAGATCCTCCGCGCCGACTACGTCCCGGACTCCCTCTTCGACTTCCTCGCCGACGGCCGCTTCACCTTCGTCGGCGT
CGGGGTCTACGGCGACGCGCAGAAGCTCAGCGCTCACTACGGGCTGCAGGTGACGAACGCGGTGGACCTGCGCTACCTCG
CCGCGAACAT------------------------------------------------GCAGGTGATGGGCGTGTGGCCC
GAGAAGCCGCACCACGTGCGGGTCAGCGCCTGGGACGCGCCGCGGCTGACGCGGGACCAACTGCAGTATGCTTGCGCCGA
CGCCTTTGCATCGTTCGAGGTCGGCCGGAGGCTCTACGACGGCGAATATTAGGTCAAGGGTGCCAATGCCATCCGCTTAG
TTTTCTAGGA---TTATTAGGTAAATAGTGTTATCTT-TGCTTTGCA-CCCAAGCATGTCGATATTTAGTTTGCCCTGGT
GTTGAACTTT-TAAACTTTACA-----------------AGATACTCCTTCCGTTTTTAAATATAAGCTCTTTAGAGATT
TCAATATGGACATGGACTAAATACGGATAAACATATTTTAAAGTGTAGATTCACTCATTTTGCTAGTACATATATAAGTC
ATATTGAAATCTTTAAAAGGGTTTATATTTAAGAACGGAGGGAGTACAAGGTAGAGAGTAT---ATCTGGTGAAATGAAT
TGAAAAT-----------------------------CATGTTTCAAATATTCCAAAATTTTGACAAAAAAGC--TAGTGT
AACATAATCCACAG------------------------------------------------------------------
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>chr3A_1389
GTGGACCTGCGCTACCTCGCCGCGAAC-----------------------------------------------------
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----------------------------------------------------------ACGGTGGACCTGCGCTACCTCG
CCACGAACACGCTGGGGAAGCCGGCGCTGCGGCACACCGGGCTGCAGGGCCTTGTGTGGCAGGTGATAGGCGTGTGGCCT
GAGAAGCCGCACCACGTGCGGGTCAGCGCCTGGGACGCGCCGCGGTTGACGCGGGACCAACTGCAGTATGCTTGCGCCGA
CGCCTTTGCATCGTTCGAGGTCGGCCGGAGGCTCTACGACAGCGAATATTAGGTCAAGGGTGCCAATGCCATCTGCTTAG
TTTTCTAGGG---TTATTAGGTGAATAGTGTTACCTTTTGCTTTGCATCCCAAGCATGTCGATATGGAGTTTGCCCTGGT
GTTGGAACTTAGAAACTTTACA-----------------AGATATTCCCTCTGTTTTTAAATATAAGCTCTTTAGAGATT
TCAATATGA------ACTACATACGGATAGACATATTTTAGAGTGTAGATTCACTCATTTT-------------------
--ATTGAAATATCTGAAAGGGCTTATATTTAGAAACGGATGGAGTACAAGGTAGAGAGTATTATATCTGGTGAAACGAAT
TGAAAAT-----------------------------CATGTTTCAAATATTCCAAAATTTTGACAAAAAACCTATAGTGT
TATATAACCCACAAGTTTCAGAAACGTGCAAGATATAAAATCAAATCAATATCACTTGGGAGGTGTGAAAAG-AAATCAA
CATCACTTTAAATAACTCATATTTTCATATGTCTCACTTTTGGTTGCCAAATTTATGTCCTTTATCATAGCTCCCATAAT
ACCGCCTCTCTCATTTT-CAGGCTTTTTTTGGAACATTTGGTTTCCACTTCCTATGAAAACTTTGTTTCCACATATAGTA
GTAGTCTCTTGAAATAGACTTCCGGCTCGCTTTATATAGAAAGCAACACGGCCGAATGATATAACATAGTGAGAAAGTCT
TTCTTACAAAATATATTAAAGAGGAAACCGTATAACAGAAATTGCACCGCAAAAAACACACACAAATCCCCTTAACAACG
CAATTTCATCACCGCCTTCGAGTCTATCAAGCGCACC-CAATGGTAAGGCCCGTTGCGAGACAGGATCACTTACCGCCAC
ACCGGTTGCCGGCCACACGACCAAGAAGTGCAGCCATCAATGGCGGAGACAGAGGGGACCAGTAGGGGCCCTGGCCCCCT
TAAGATTATTGATTTGCTGCTAATTACTAGATGAACAGTGTACATTTTATAAAAAATATATGTATTAGTATTGTTTGGCC
CCTGTTATTGAAACTTTGAGTTATTTGGCCCCCCTGATCCTTAATTTCTGACTCCGCCACTGGCAGCCATCACCTTCACC
ATGAGAGTCGACCAAAAAGTGCAGCCACCACCGCCACCATGAGACTCGCTGGAGAGCCAAACGGGCAGTCCACCACCCGC
GGGCAGGCCTGGCATCCTGGACCAAACCCCTCACCGAAATCAAAACACGAGGACGTTGCCAACAAGAGGCGAAGCAACCG
CCTCACGCAAATCCAGCAAGTCTCCACCTTGACTTGACGAAGGTGGCCAAGCCACACGAAGAGGCCAACCCACCGGCCCC
TGCACCCGGCTCACGCCCGCCTACGCCTTGGACGG-----------TGGGTTGATTCTTGACTATTCAGAGTTGAAATAT
GGACTTCTCTCTTTTGAGATATGGCACAAAACATCTAAAA
>SNPs
-------------------------S----S------------S---------------------------S-------S
--S-------------------------------------------S---------------------------------
----SS---------------S----------------------------------------------------------
-----S-S------------------------------------------------------------------------
----------------S----------------S----------------------------------------------
---------------------S----------------------S-----------------------------S-----
------------------S----S--------------------------------------------S-----------
----------------------S---------------------------------S-----------------------
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--------------------------------------------S----------S---------------------S--
-S-------------------------------------------------------SSSSSSSS------------S--
--------------------------------------------------------------------S-----------
-S----------------------------------------------------------------S-------------
------------------------------------S-------------------------------------------
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----------------------------------------S---------------------------------------
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-------------------------------------------------S-----------------------S------
-----S--------------------------------------------------------------------------
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----------------------SSSSSSSSSSSSSSSSS-------S---------------------------------
---------------------------------S-----------------S----------------S-----------
-------------------SS--------------------S---------------S----------------------
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-----S-S---S--SSSSS---------------------------------S---------------------------
----------SS-----------------------S-----------------S--------------------------
---------------------S------S--S------------------------------------------------
---S------------------------S---------------------------------------------------
-------------------------S---------------------------------------------------S--
-------------------S-----------------S---------------S-----------------S---S----
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-----------------------------------SSSSSSSSSSS----------------------------------
--------------SSSS----------S-----------
>forward_1267
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-----------------------------------------------ATATACGGCCGAGACCCAGT-------------
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>reverse_2854
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-----------------------------------------------------CTGCGAGCCAGGATCACTC--------
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