>input_sequence_78646
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-------------------------------------------ATGACGAAAATCTCCTTTGCTTCATCCTTTCTGCTGT
TGCCCCTTCTGATCATTCTACTTTCGACCATTCATAAACCTACAACATATGCCGAGTGTACTCCACCGCCTTGCCAAGGA
AGTTAGTATTACACCTAGCACCCTTCTTTGTTCTTACAATTTGTGCCATGTCTCCATTGAAC-TTT-TTATTTTGTGTTT
GGCCCCAAATTTATTTTTTATTGGAGTTGAAC-TTCAATGGTCCAAGAAATAACTGATAATCTGCATTTCATAC----AC
AGAACAAAGTTGGCCAGAGCTCGTCGGGAAAGACCCAAACACGGCGTACAATTGTATAAGGCATGATAACCCCCAAGTGA
ATAACATCACATTCTTGATTTCTGATGCTCTTCGTCCCAGGGCGGACAATGGCATGTGCTGCAACCATGTGCTTTTGGTG
ATTGGAAATATCCCCTCTGGTGGGGATGGCATCATCAAGGTGCCACATGTTGGATAG-----------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
----------------------------------------------------------
>chr3A_1_TraesCS3A01G003000
TGATGATGATTTTCTATATATAAAGCACATAACATGGATTTATTGCTAGTAATTTGATCAAGGTGGCAATAACTTTGTGG
CACTAGGTGGGGATGGCATCATTCAATAGCCAATAACTTTGTAGTAGTATAGTTTTCATTCAATAGCCGTACTCGGTGCA
TGTTGATTTATTGCTAGTAATTGTAAATATAAAAATCAACAATGGCCACATTAATTGAAAATATACCACATTAATTAAAG
ATAGAATGTACTTGCTTTGGGGTTCTATAAATAGGAAGCCCCCTCCCCAACAATATTCTAATATAGGAAAGCTTAAGTTC
TAGTAAAATGGCGAAAATCTCCTTTGCTTCATCCTTTCTCCTGTTGCCCCTTCTGATATCTTGTGATGATGCTAATCCAC
ATTAAGCTTGAACAAATAACTGCCTATCTCCTAACATGAACGACTTAACCCAAACTTTGTTTCCTAGAACGTATATGGAA
GACATGAATCCATACGGTGTACCAACGAATAATTAATAACAATATCAATTGAATATATCTAGTATATTTCTTCATTCAAT
AGCCAACATTCAGTGCACATTGATTTATTGCTAGTTATTGTAGATACACGGAC---CATCAATGGGCGCATTAATTGAAA
ATATGTCACATTAATTAAAGATAAATTATCCTTGATTTTTTTTTGCGGGAAAGGAACTTTTCATTGATCAACTATGATGA
TTACATTCAGATTCAACAATGCTAGCTATCTCCCTAGGGGAATTCCGGAGCCAGCATGCCGTGCGCTGTTGCGAGCGACC
CATACAAGCTAGGGTGTGGCTCGCCAAATTTGCGTGCCTGCTGATCTTAGCTAGACTAATGTTCCTTTCTTGAGCCAGAA
CTCTTCTGATCTCATTAACCCGGTACGCATACCTCGACCGGTCTTGATTTGGGGTTCTATAACTAGAAAGCCCGCCCCCT
TCCCCAACAGTATTCTTAACAAGAAAGATTAAGTTCTAGTAAAATGACGAAAATCTCCTTTGCTTCATCCTTTCTGCTGT
TGCCCCTTCTGATCATTCTACTTTCGACCATTCATAAACCTACAACATATGCCGAGTGTACTCCACCGCCTTGCCAAGGA
AGTTAGTATTACACCTAGCACCCTTCTTTGTTCTTACAATTTGTGCCATGTCTCCATTGAAC-TTT-TTATTTTGTGTTT
GGCCCCAAATTTATTTTTTATTGGAGTTGAAC-TTCAATGGTCCAAGAAATAACTGATAATCTGCATTTCATAC----AC
AGAACAAAGTTGGCCAGAGCTCGTCGGGAAAGACCCAAACACGGCGTACAATTGTATAAGGCATGATAACCCCCAAGTGA
ATAACATCACATTCTTGATTTCTGATGCTCTTCGTCCCAGGGCGGACAATGGCATGTGCTGCAACCATGTGCTTTTGGTG
ATTGGAAATATCCCCTCTGGTGGGGATGGCATCATCAAGGTGCCACATGTTGGATAGAATCATTCTCTACTTTTTTTATT
GTAATTTGATCAATAAATT------------------------------ATTTCATACAATTATTATATAACCAAAACAA
CCAAAGTATTTTCTCGAATAGAAGACTGAAAGACCATGAAAATATAATTAAGAAGGCTATTCTGATCCAATCTTATACAT
CGAATGAAAACCAAAGTAAGATCACGGTCATGCTAAAAGGTTAATTATTTAGTATGGGTCTGACTATAGGTAAATCGCCT
TATATTTTATTTTGGTCAAGTCCATTTGGGACCATTGGATTAGCTTCAATGATCGTTATTCTTCCACCTTTCTCTAGATT
TCTTCCTTCTCGAATCGTTCCTCCTCCACTGTTCACCTCCGGGTTGCCTCCCATCCCCTCCTTTGGGTGGTCTACGAACC
CGAATGTAATTTTTATTACTTATGGTGTTCTTTGTACCGGCTTGGTAGATGATGAATAGATCAAAAGTTTTCATTTTTT-
----TACTTTTGGGGATAGTGGTTATGGTCATTAAGGTGAACTAGCTAAACAAGTTGTAAGCTTGCACATCACCCTTGTA
AAGACTTATATCGGCAAAAGTCCGGTTGTCATGGAAACTGGTGAGGATTTGCTATTCCCTAGTGGGTGTGGGGTATTCTT
TGGGATCACGATAGTCATTGTATCCCTATCTGTCCACACCA-AAGAGAATGTGGAGTCACTTGAAGATGTTTGATACCTG
CATGATACAGTTCGAA----GAAATTATGCACACCAAACTGAAAAAAGTACAATGATAGAAGGTTAAATTTTTTTAGCAG
AAAAAAAAATTAATAGAAGGTAAACTTGCATACTGAAATACGCCCATGGATTTTTTTAATCCACATAACTTGCATGATAT
CAAAAGGGGTAATATGAAGGTAAAGTGAGCATCTACAACCGGACCACTCATATCCTCCCTAGACGTCTGGCCGGACAGGC
CGATCATTGCCCGGAG-AGGAGAGAGAAGGAAAAAAAACCACCCAACCAGACCCCTAC
>chr3B_190
TAGAA---------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
---------------------------------------------------AC---AATCAATGACAGCATTAATTGAAA
AC-------------------------------------------------------------ATATCCCATTCGCAATT
GATTGTC-------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------CTTGCTTTGGCGATCTATAACTAGAAAGCCCCCTCCCC
A----GACAATATTCTAAACAGGAAAGATTAAGTTCTAGTAAAATGGCGAAAATCTCCTTTGCTTCAACCTTTCTCCTGT
TGCCCCTTCTGATCATTCTACTTTCAACCATTCATAAACCTACAACATATGCCAAGTGTATACCACCGCCTTGCCAAGGA
AGTTAGTATTGCACCTAGCACCCTTCTTTGTTCTTACAATTTGCATCATATCCCCATTGAACTTTTTTTATTTTGTGTTT
GGACCCATTTTTATTTTTTGTTGGAGTTGAACTTTCAATTATCCAAGAAATAACCCATAATTTCCATTTCTTTACCATAC
AGAACAAAGTTGGCCAGAGCTCATTGGGAAAGACTCAAACACGGCGTACAATTGTATAAGGCGCGAGAACCCCCAAGTGA
ATAATATCACGTTCTTGATTTCTGATGCTCTTCGTCCTAGGGCGGACAATGGCATGTGTTGCAACCATGTGCTTTTGGTG
ATAGGAAATATCCCCTCCGGTGGTGATGGTGTCATCAAGGTGCCACATGTTGGATAGTACCATTCTCTACTTTTTTTATT
GTAATTTGATCAATAAA---------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
----------------------------------------------------------
>chr3D_472
TATG----------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
---------------------------------------------------------------------------TGGAA
CACGTGAATCCATGCGGTGTACTAATGAATAATTAATAACAATATCAATTGAATATATCTTATATCTTTCTTCATTCAAT
AGCCAACATTCAGTGCATATTGATTTATTGCTAGTCATTACTTTAAATATACAAATCATCAATGGCCGCATTAATTGAAA
ATATATCCCATTAATGCGGCGCTCTATAACTAGAAACCATCAATGGCCGCATTAATTGAAATTATATCCCATTCGCCATT
GATTGTC-------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------CTTGCTTTGGCGCTCTATAACTAGAAAGCCCCCTCCCC
A----AACAATATTCTAAACAGGAAAGGTTAAGTTCCAATAAAATGGAGAAAAGCTCCTTTGCTTCAACCTTTCTCCTGT
TGCCCCTTCTGATCATTCTACTTTCGACCATTCATAAACCTGCAACATACGGCGAGTGCATACCACCGCCTTGCCAAGGA
AGTTAGTATTGCACCTGGCACCCTGCTTTGTTCTTACAATTTGCATCATGTCTCCATTTAAC-TTTTTTATTTTGTGTTT
GGCCCCAATTTTATTTTTTGTTGGAGTTGAACTTTCAATGATCCAAGAAATAACCCGTAATTTCCATTTATTTACCATAC
AGAACAAAGTTGGCCAGAGCTCATTGGGAAAGACTCAAACACGGCATACAATTGTATAAGGCACGATAACCCCCAAGTGA
ATAGCATCACATTCTTGATTTCTGATGCTCTTCGTCCCAGGGCGGACAATGGCATGTGCTGCAACCATGTGCTTTTGGTG
ATTGGAAATATCCCCTCCGGTGGTGATGGTGTCATCAAGGTGCCACATGTTGGATAGAACCATTCTCTGCC-TTTTTATT
GTAATTTGATCAATAAAGTCTTTGCTGTGTTTGCACTTTTCTCCGTTTCATTTCATACAGTTCTTATATAGCCCAAACAA
CCAACATACTTTCTCAAACAGGAGACTGAAAGAACATGAAAATATAAGATGC----CTGTTCTGATCCAATCTTGTACAT
CACATCAAAACCAAAGGAAGACCG----CATGCTAAAAGGTTAACTATTTAGTATGGGACTGACTATAGGTAAGTCTCCT
TATATTTTATTTTGGTCAAGTCCAATTTGGACCACTCGTTTAGCTTCAACAATTGTTATTCTTTCATCTTTCTCTAGCTT
TCTTCCTCCTCGAATCGTTCTCCCTCATTTGTTCGCATCCGGGTTGCCTACCATCCCCACCTTCGGGTGGTCTATGGACA
TGAATGTGATTTTTATTGCTTATGGTGTTCTTTGTACCACCTTGATAGATAATGAAT-GATCAGAAGTTTTCAACAACAA
AAAATACTTTTGGGAACAGTGGTTATGTTAATTAAGGTGAACTGGCTAAACAAGTTGTTAGCTTGCCCATCACCCTTGTA
AATACTGATATCCGCAATAGTTTGGTTGTCATGGAAGTTGGTGAGGATTTGCTCAATCCTAGTGAGTATGAGGTATTCTT
TGGAATCAACATAGTCATCATATCCCCATCTGTCCACACGCCAAGAGAATGATTAGTAACTTGAAGATGCGTGATATCTG
CATTATAAATCATCGTATACGAAATTGCGCATGCCAAACTGAAAAAAAA-----GATAGAAGGTTAAAAAAATCAGCATA
TTTT-----TTTATAGAAGGTAAACTTGCATACTAAAACACGTCCATGGCTATTTTTAATCTACATAACTTGCAAAATAT
CCAAAGGGATACTATAAATCTAAAGTGAGCATCTACAACCGGACCACTCATATCCTCCCCAATCGTCCAGCCGGACAGCC
CGATCATTGTCTGGCATAGGAGAGAGAAGAGAAA------------------------
>SNPs
-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS-----
S--S---------S--------S--S----------------------------------SS---S--------------
-----------------S-----------------S---SSSSSS-SSSSS--------------S--------------
----S--S-------SSSSSSSSSSS--S-SSSS-SSSS-SSS--SSS-S-SSS-SSSSSSSSS-SSS-S-S-SSS-SSS
SSSSS-SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS----S-----S-S------------------S-S---S
SSSSS----S------S----S------------------------S--------------------S-------S----
------------------------------------------------------------SS------------------
----------S--------------------------------SSS----------------------------------
--------S----------S--------------------S-------------SS-----S-S------S-SS------
----------------------S-S---------S----------------------------S----------------
--------------------------------------------------------------------------------
-----------------S-----S-----SS----------------------------S--------------------
-----------------S-----------------------------------------S--S-------S--S------
----SS--S------S--S--S-----------S-------------SSSSSSSSS--S---------------S-----
-SS--S----------S----S-SSSSS----------------S-------------S--------------S--S---
------------------------S--S------S-S-S----------SS--S---------S--S----------S--
-------S------------SS----SSS-----S-S------------S--------S----S----------S-S--S
S------S---------S--------------------SS----S-----S------S-----S---------SSSSSS-
--------------S-S----------S-S-------------S--------------S-------S-------------
--S---S-----S----S---SS-------------SS---------------SSSS-------S--S--S---------
---S----SS--------SS------S------------SS----------SSS---S-----------SS-----S---
---S---S-SSSSSSS----------SS---SS--------------SSSSSSS--------------SSSS-SSSSSSS
SSSSSSSSS--S----------------------S---S---S------S-S---------S------------SS----
-S------S--S---S--SS---------------------------------------S-SS----SS---------S-
---------S-S--SS-------------SS---SSSSSSSSSSSSSSSSSSSSSSSS
>forward_849
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-----------------------------TTGCGTGCCTGCTGATCTTA-------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
----------------------------------------------------------
>reverse_2515
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
----------------------------------AAAACCACCCAACCAGACCC----
