>input_sequence_82789
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------ATGAGCAAGTGGTGGTGCATCGCC
TCCCTCCTGCTGTGCCTCGCGGTGGCGGTGGCGGGCAGGGGCATGCCTGCTCGCGACGACTGCGATACTGTTGCTCTTGC
TGCCGGTCGCAACGGCCAAGACGGTTCTGGTTTCGGTGAAACCAAGACCGCCTTTGCTGGGAGCAATGGTGGTGACGGCG
GGCTCTTCGGCGGTGCCGTCAACGGTGGCCCTCTCGGCGGGGGCATCGCCGGCTTTGGCCCGCACGGCGGCTTTGGTGCC
GGTGCCGGGCCGTTCGGTGGTTTCGGCGGTGGCTTCGGTGCTGGTGGTGGAGGTGGAGGAGGGGGAGGCGGCGGCGGCGG
CGTGATACCTTGA-------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
---------------------------------------------------------------
>chr3D_1_TraesCS3D01G538100
CTCAGAGGGTCCACCAGTCGTACTCGAGCACCGCGAGTTCAGCCGTGTGAAAGGACCCGAGCCAATATCATTGGCCGGTT
TCTCTGTCCCGGATGTCGGCCACCCAAGTCCCCCACCACCGTTGCCGGACGCCGTGGCACTCCCTCTGCGGCGGCCGCGG
CGCAGGGACGTCGGGGAAGCCGGAGAAGCTGCATCGTCGCGGCGGTGGCGGCGGCGGCTGATTGAGGAGGATCTGACGAA
GGAGGATGCGCGGCTCGCGTGGTGGCGCGGATCCGCGCTGCGGATCGGCGGCGGGGACCTCCGGCTACCGCCCGGCCATT
GGGAGGAGAGGGGTTGGTGGGGAACAATGGGGGGAGGCGCCGGCGGCACCGAGGGGGAGGAGGAGAGGCAGAGGAGGCGA
AGATAACGTGAAGGATTTTTACTCCAACGCCGCACGGTGGAGTAAATGTAGGCGGGATACGGCCTGGTGGATAGTTTTTC
CTCCTCTATTGGCTATTGGAGTTTGGTTAGGTGTGCGTTACTCCCCCTAACGCAGCATAGGGGATCGGTTACAGTTACCC
TTAGGCTGCGCATATATTAACTGCATGTTACTGCACGTCATGGGAGAAGTCAGAACAAGCACCGAGTCATCTCTGGTGAA
CAGAACAGACGACAATCTCCTTTGGCTGGTTTCTACAAGTGGTTAATAATCGGGAAAAGCGTGCACAGTGTTCACGTTTT
AGGCTGTCAAAACTAACACAGGGTAAAATCGTGTCAGCACCAAATCACCTGCGTTCCATCGCAATAACTTCTCATCAACC
TTTTGAATCCATGGACGGATGGACCTACTTCTTCATCTGCGAGTTATTGCGCCATGCATGGCAACAACTACCCGCTTGCC
GGCTGCCACC----ATTTAATTACTGTCACGCGCTCGCACCTGCCCATCT--------CGTCGTCGTCCTCTCTTTAAAC
CCCCCTGCCACTGCGTTACTCGCCTCATCCAACTCTCTGAGACCAACC----AGCCATGAGCAAGTGGTGGTGCATCGCC
TCCCTCCTGCTGTGCCTCGCGGTGGCGGTGGCGGGCAGGGGCATGCCTGCTCGCGACGACTGCGATACTGTTGCTCTTGC
TGCCGGTCGCAACGGCCAAGACGGTTCTGGTTTCGGTGAAACCAAGACCGCCTTTGCTGGGAGCAATGGTGGTGACGGCG
GGCTCTTCGGCGGTGCCGTCAACGGTGGCCCTCTCGGCGGGGGCATCGCCGGCTTTGGCCCGCACGGCGGCTTTGGTGCC
GGTGCCGGGCCGTTCGGTGGTTTCGGCGGTGGCTTCGGTGCTGGTGGTGGAGGTGGAGGAGGGGGAGGCGGCGGCGGCGG
CGTGATACCTTGAGGTGGCCGGGACACGAGCGCGTATGTAAACGTGGTAGTAGCTGT----ACGTGTGTCCCTGATTTCA
TTTACACGCATCTGTTAGTGTAATAAGAAGTCCTTTGATTAGCTGCGTGAGCATGCATGTATGAGTCATACGTGTCATCA
TGTCATTAGCCTCATCGTGTTCGTATCTGATTAGTTAATGTATAAATGAAAGCATTGGTGTGTGAGATGGTTTCTTGGTC
TGAGCATGGATGCATGAAGTTAGCCGTGTTGCGGTGTTT------GTATCATATTGATGCTTATTTATTAAGCTCCACTT
TTCGAAAATTTATTAAGCTCCAAAGTCCAAACAATATAGTGTCATTTTCCCTTGAACGTCCTTCATTCTTAAGCACCGCT
GACTTGCTAGAAATTACTCATTTGCATCTGCTAGTGATATGTTCTGATCTGAATCTTCCGTCATTCATACGCAGTACGAG
TATTATTGGTGAAAAGTCGCAAAACTTTATGATGTGCCACGAGAAAGATCCAACAGCTAAGTGAAATCGTCCGTGGCCTT
TTAGGGCATCTCTAACGGCAACCTGCAAATTTTCTCACGCATCCATCCGTGGATAGGGGAAACCAGTCTGCGGACACGGA
TGCGGAAGGCAGCCATCCATACTAGTCGCATATATTTCAAACTTTTTTTCAGCAAACAAGATAAAATTTATGCAAATACA
ATCGGTTTTCATGCAAGCTGGACGAAAACGGTAATATTTTGAACATATTTTAACTAAAAAGGTAAAATTATGTGTATGTA
CGGTCTCTCGGAGCTTCACTCCCATGACAGGTATACATTACACTAGTTTACGGCCGGCTGCAGCGGATCACTGGCCGAGG
GAATACTCCAGTTTTTTATACTTAGGCTTTAGGGATAGATACCCTCTCCTAAGAGGCCTTCAAAAGGGAGTTTGTGTTTT
CCTGCGAGAGACCAGGTATGGCACATTATCATGTAAAAATATTTCTCTAGTTTTGTATACAAT
>chr3B_819
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------ATGGACCTACTTCTTCATCTCCGAGTTATTGCGCCATGCATGGCAACAACCACCCGCTTGCC
GGCTGCCAAA----ATTTAATTACTGTCACGCGCTCGCACCTGCCCATCTGGCCATCTCGTCCTCCTCCTCCCTTTAAAC
CCCCCTGCCACTGCGTTACTCACCTCAGCCACCTCGCAGAGACAAACCCAAGAGCCATGAGCAAGTGGTGGTGCATCGCC
TCCCTCCTGCTGTGCCTCGCCGTGGCGGTGGCCGGCAGGGGCATGCCTGCCGGGGACGACTGCGACACCGTTGCTCTTGC
TGCCGGTCGCAACAACCAAGACGGTGCTGGTTTCGGCGAAGCCAAGACCGCCTTTGCTGGGAGCAACGGTGGTGACGGCG
GCCTCTTCGGCGGTGCCGTCAACGGTGGCCCTCTCGGCGGGGGCGTCGCTGGCTTTGGTCCGCACGGCGGGTTTGGTGCC
GGCGCTGGGCCCTTCGGTGGGTTTGGCGGCGGCTTCGGCGCTGGTGGCGGAGGTGGAGGAGGGGGAGGCGGT------GG
CGTGATACCTTGAGGTGGCCGGGATACGAGCGCGTTTGTGAACGTGGTAGTAGCTGTACGTACGTGTGTCCCTGCTTTCA
TTTACATGCATCTGTTAGTGTGATAAGAAGTCCTTTGATTAGCTGCGTGAGCATGCATGTGTGGCTCGTACGTGTCATGA
TGTCATTGGCCTCCGGGTGTGCGTATCTGATTGGTTAAGGTATAA-TGAAAGCAGTGGTGTGTGAGATGGTGTCTTGGTC
TGAGCATGCATGCATAAAGTTAGCCGTGTTGCATTGTTTGTACTAGTATCATATTGATGCTAATTAATTAAGCTCCA---
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
---------------------------------------------------------------
>chr3A_819
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------ATGGACCGACTTCTTCATCTCCGAGTTATTGCGCCATGCATGGCAACAACCACCCGCTTGCC
GGCTGCCACCTTCCATTTAATTACTGTCACGCGCTCGCACCTGT--------CCATCTCGTCCTCCTCCTCCCTTTAAAC
CCCCCTGCCACCGCGTTACTCGGCTCACACACCTCTCTGAGACCAACC----AGCCATGAGCAAGTGGTGGTGCATCGCC
TCCCTCGTACTGTGCCTCGCCGTGGTGGCGGCGGGCAGGGGTATGCCTGCCGGCGACGACTGCGATATTGTCGTTAATGC
GGCCGGTCGTAACAATCAAGACGGTGATGGTTTCGATGAAGCCAAGACTGCCTTTGCTGGGAGCACTGGTGGTGACGGCG
GGCTCTTCGGTGGTGCCATCAACGGTGGCCCGCTCGGCGGGGGCATCGCCGGCTTTGGCCCTCACGGCGGGTTTGGGGCT
GGCGCCGGGCCGTTCGGTGGTTTCGGCGGCGGCTTCGGCGCTGGTAGCGGAGGTGGAGGAGGGGGAGGCGGA---GGCGG
CGTGATACCTTGAGGTGGCCGGTACACGAGCGCGTATGTGAACGTCGTAGTAGCTGAAT----GTGTGTCCCTGCTTTCA
ATTACATGTATCTGTTAGTGTAATAAGAAGTCCTTGGATTAGCTGCGTGAGCATGCATGTATGGCTCGTACGTGTCACAA
AGTCATTGGCCACAGCGTGTGCATATCTGA--------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
---------------------------------------------------------------
>SNPs
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSS--------------------S-----------------------------S-----------
--------------------------------------------------------------S--S-----S--------
---------------------------S---S------------------------------------------------
--------------------S-----------------------------SS----------------------------
-------------SS----------S--------------S---------------------------------------
----------------------------------------------------------------------S---------
--S--------------------------S--------S--------S-----------------------SSSS-----
---------------------------------------S----------------------------------S-----
------S--------------------------------------------------------SS--S----------S-
-------S------S-----S-----------S-----S------S--------S----------------S--------
--------S------S----------------SS---------------------------S---S-----------SSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS
>forward_540
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
----------------------------------------CTCCCCCTAACGCAGCATAG--------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
---------------------------------------------------------------
>reverse_2159
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------------------------------TA
CGGTCTCTCGGAGCTTCA--------------------------------------------------------------
--------------------------------------------------------------------------------
---------------------------------------------------------------
