>input_sequence_82078
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-----------------------------------------------------------------ATGAAAGACGATCAA
TTCCTTCGATTTCGTCTCTTCAAGGATCGACTCAACTCCAAGAGCAACCTCTTCAAGAAGACCATCAC------------
-------------CCCCAACGGCCACTGCCCCAT---ATGCAACGCTCCAGTTGATGACGACCTTCACATGTTCATTCAG
TACCCCATAGGCATCCAAATTTGGGATGCCCTATTCCTCTTGGTGCCGCCCTCCATCGAGCTCATTTGGGATACCCCCAT
GTTGTCGAACCTCCACGGTGACATTAGGTCGTCGATTGCTCTCTCCTTGCTATGGAAAATTTGGGATTCCAGAAACATTC
TTGTCTTTTGCAACGAACTCCACTCCGCAAGGACCAATGTTAGAAATTTAGCTAGTGACTTCACTCTTTGA---------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-----------------------------------
>chr3D_1_TraesCS3D01G360600
AATTAGCACACACCCCACCCCTTCATAACTAGGATGCACAATATCAACATCAACACACACACAAAATAACATCAACAAAT
AGCAAAGTCATACAAGCCTAAGCTATGCTTAGGTGGATTAACTTCAAAGCGACCAAAATGATGATCAACACGCTACATTA
ATGACAGTATATGCATCAATCATTTCTTGACATCATAAGTATAAAGAGAAATGTTTTTCAACAACAACGACTTCAGAAAG
GGAACGACGCTTAAGCGCCGTCGTCGCCAGAGCCAACCATCAAAGGCTTGATCTTGGGTTTTTACCCTGAAGATTAAGTC
CCAGCAAATCCGAGCAATGCCTCATAAAACCAAT----------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------TGCTCCATCGTTTTGTCTGTGGCG
ACAAAACATAATCACATAATCGTCGTTGCCGCCGGTTATGAAGATCCAAGATCCCCCGTACAGTCACTGCAATCGCCTAG
CTGAGCAGGACCATC-CATCACCTGCGCGCATGAGCAAAGAACCGCCATATTAGGACACGGCAGGCCGATGATGTCGCCT
GCGTACCTAGAGACATGATTGTGGCCACTGACATGTTGCCACCAGAGACCACCGATCCGGACAAAATATGCACCGCTGCT
GCTTCACAACCATGCCCTCTACCTCAAACCACCATTCATAGATTGCATCTCATCATTGAGGGATACCAGACGAAAGACCT
CCCTACCGCCGCCTTCATTGACCAGTGTCAGGGCTTAGGTCGACCACTAGTCTCAAGCAGCGGCAAGGGGAAGGGAAGAT
GGAGAGGTAGGAGATGGTGGCTTATATTTCGGTGTCTACGGCTATCAAAAGCTATCAAAAGGGAGGCACATATGCTATGT
GTTGCAAG--TTTTTTTTACTTTGCATTATGTCTGCGACAATAATGTTGTACTTTGTACAATGTCTCATAAATACATGTT
TGAAAAAAAATCTGAATAAGTTCTTACATGTGTAACAAAAATTTATACACCTACATATCCTAGTTATGAAAGACGATCAA
TTCCTTCGATTTCGTCTCTTCAAGGATCGACTCAACTCCAAGAGCAACCTCTTCAAGAAGACCATCAC------------
-------------CCCCAACGGCCACTGCCCCAT---ATGCAACGCTCCAGTTGATGACGACCTTCACATGTTCATTCAG
TACCCCATAGGCATCCAAATTTGGGATGCCCTATTCCTCTTGGTGCCGCCCTCCATCGAGCTCATTTGGGATACCCCCAT
GTTGTCGAACCTCCACGGTGACATTAGGTCGTCGATTGCTCTCTCCTTGCTATGGAAAATTTGGGATTCCAGAAACATTC
TTGTCTTTTGCAACGAACTCCACTCCGCAAGGACCAATGTTAGAAATTTAGCTAGTGACTTCACTCTTTGAACTTTCAGA
TACGAAAATGTCTCTAA-AAGGATGCCTTCATGTCATGGCGTCAATACCTCTCCTCACGCTCTAGCGCACAATTGCAAAG
CTCGCCTTGTAGTCGTTTTTGAGTAATGCATTCGCGTAGGGATTCTCTCCCC-TAGTGATTGGTCA-AAAAATCAATTCC
TTTGGTTAAAATAATTCATACATGTCTGAAAAAGCAAGACATATATATTCACCAAAACTGAATCTTGTTACCATTAGTTA
GCACCCTCCTC-TTTACCTCTTGTGCTTGGTTGAGAGGCCACAAACTCCACCAAGGCCCAATCACAAGCATCCACTTTCT
TTTTGCTCATCTTCTCAAGGCCTCCAACGGTGGAGGCGGAATAAACTCCGGCCGCTTTTTGTAGCCGCCCGGAATTTGAT
ACTCCCCCGGTCCTCCCCTATATAGGCACGCCTCCTTCCACCTCCCCCCTTCGCCACTTTCCTGCCTTCCTCCATTGCTC
GCCAGGCCGTCCTTAAGCCAACTCAGGTAGCAGCAACTAGAGCCGACATGATGGCGGAGGCGTGGATGGACGTGCTGCCG
CCGCCGGCGCCCTACTTCGCCGGGCAGCCGTGTTGGGCCGTGCAGCAGGAGCGTCGCGGAGGCGGCGCCTGGACGCTGGA
GGAGAACAAGGTGTTCGAGGAGGCGCTCGCGGCGATCGACCTGGACGCGCCGGACCGGTGGGAGATGGTCGCGCTGATGT
TGCCCAGGAAGACGGTCGCCGACGTGGTGAACCACTACCGGGCCCTCGAGAACGACGTCGGGTTCATCGAGGCCGGGCTG
GTCCCGTTCCCTCACTACGACAGCTCGTCCCCTTCGTCCGGGTTCACTCTGGACTGGGACGGGGGCGCCGCCGGCGCCGG
CGGGTTCCGGCGCGGCTACTGCCTCAAGCGCGGGCGCGCCGACCAGGAGCGGAAGAAGGGCGTCCCGTGGACGGAGGAGG
AGCACCGGTAAGCCGCCGTCTTGGTGATCTTCTTC
>chr3B_1
AATTAGCACATATCCCACCCCTTCATAACAAGGATGCACAATATCAACATCAACACACAGACAAAATCACATCGACAAAT
AACAAAGTCATACAAGCCTAAGCTATGCTTAGATTGATTAACTTCAAAGCGACCAAAATGATGATCAACAATCTACATTA
ACAACCGTATATGCATCAATCATCTCTTGACATCATAAGTATAACGAGAAATTTTCTTCAACAACAACGACTTCAGGT-G
GGAACGACGCTCAAGCATCGTGGTCGCCAAATCCACCCAACGAAGGCTTGATCTTGAGTTTTTACCCTGAAGATTAAGTC
CCAGCAAATCGGAGCAATGCCTCAACAAGGTAATGACACATTGCCAGGTATAACCAATTAGGGCCAGACCTCGGGTCAGC
CTGGAGCTCGAGATCGATACTTGAGAAGCACCGCCAAATCGAAGTCATCATGTGTTGTCACCACCACTTTCTTATCCCAA
TAGTTACATGCGCAATACGGTCTTAGACATGAAATGCCACACAAGTGACCATGCTTGCACAAGCAGGCAATCCAGCCACA
ACAAGATATAGTCGACACCAAAGGCTCGAATAATAAAGGTTGCCGTTGCACATGTGACGGAGATTGACGAGATAGAAAGG
TCAATGACAACGCCAAAATCCCAATTGAGGGCTTCGGTAACCCCACACTGTCCTCATGCTCCGTGGTTATGTCTGTGGCG
ACAGAACATAATA--------GTCGTTGCCGCCAATTATGAAGATACAAGATCCCCCGTACCGTCACTGCAATTGCGTAG
CAGAGCAGGACTA-GACATCACCTGCGCGCACGAGCAGAGAACCGCCATATTAGGACATAACAGGCTGATGCTGCCGCCC
ATATACCTAGAGACATGATTGTGGCCACCGACATCTCGCCACCAGAGACCACTGACCTGGACAGAATATCCACCGCTGCT
ACTACACAACCATGCCCTCTACATTAAACCACCATTCATAGATTGCATCTCATCATTGAGGGCTACCAGACGAAAGCCCT
CCCTACCGCCACCTTCATTGACCAGTGTCAGGGTTTAGGGCGACCACTAGTCTCAAGCAGCGGCAAGGGGAAGCGGGGAT
GGAGAGGCAGGAGATGGTGGCTTATGTTTCGGTACCTACGA----------CTATCAAAAGGGAGGCACATATTCTATGT
GGTGCAAGATTTTCTTGTACTTTGCATTATGTCTGCCACAATAA------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
------------------------------------------------------------------ACATGTTCATTTAA
TGCCCCGCAGCCATCCAGACCTAGGATGCCCTACTCCTCCCGGTATCGCCCTCCATCGAGCTCATTTGGGATGTCCCCAC
GCTGCTGGACCTCCATGGTGATATTTGGTCGTCGGTTGTTCTCTCCTTGCTATGGAATATTTGGGATTCCAGAAACAAT-
TTGTCTTTCGCAACGAACTCCACTCCGTAAGGACTAGCGCTAGAAATTTAGCTAGTGACTTCACTCTTTGAACTTTCAGA
TACGAAAACGTCTCTAAGAAGGATGCCTCCATATCATAGCGTCAATACCTCTCCTCACA--CTAGCACACAATTGCAAAG
CTTGCCATTTGGTCGCCTTTGAATAATGCATTCGA-TAGGGATCATCTCCCCCTAGTGATTGGTCACAAAAATCAATTCC
TTCGGTTAAAATAATTCACACATGTCTGAAAAAGCAAGACATATAT--TCAACAAAACTGAATCTTGTTACCATTAGTTA
GCACTCTCCTC-TTTACCTCTTGTGCTTGGTTGAGAGGCCACAAACTCCACCAAGGCCCAATCACAAGCACCCACTTTCT
TTTTGCTCATCTTCTCAAGGCCTCCAACGGTGGAGGCGGAATAAACTCCGGCCACTTTTTGTAGCCGCCCGGAATTTGAT
ACTCCCCCGGTCCTCCCCTATATAGGCATGCCTCCTTCCACCTCTCCCCTTCGCCACTTTCCTGCCTTCCTCCATTGCTC
GCC-----GCCCTTAAGCCAGCTCAGGTA---GCAACTAGAGCCGACATGATGGCGGAGGCGTGGGTGGACGTGCTGCCG
CCGCCGGCGCCCTACTTCGCCGGGCAGCCGTGCTGGGCCGTACAGCAAGAGCGTCGTGGAGGCGGCGCCTGGACACTGGA
GGAGAACAAGGTGTTCGAGGAGGCGCTCGCGGCGATCGACCTGGACGCGCCGGACCGGTGGGAGATGGTCGCGCTGATGC
TGCCCAGGAAGACGGTCGCCGACGTGGTGAACCACTACCGGGCCCTCGAGAACGACGTCGGGTTCATCGAGGCCGGGCTG
GTCCCGTTTCCTCACTACGACAGCTCGTCCCCTTCGTCCGGGTTCACTCTGGACTGGGACGGCGGCGCCGCCGGCGCCGG
CGGGTTCAGGCGCGGCTACTGCCTCAAGCGCGGGCGCGCCGACCAGGAGCGGAAGAAGGGCGTCCCGTGGACGGAGGAGG
AGCACCGGTAAGCCGCCATCTTCATGATCTTCTTC
>chr3A_355
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------TGCTCCATCATTCTGTCTGTGGCG
ACAAAACATAATCA--------TCGTTGCCGCTGATTATGAAGATCCAAGATCCCCCGTACCGGCACTGCAATCGCCTAG
CAGAGCAGGAGCGTGTCGTCACCTCCGCGCCCAAGTAAGAC------------------AACAGGCAGATGCTGCCGCAC
GCGTACCTAGTGATAGGATTGTGGCCACCGAC--GTCGTCACCAGAGACCGCCTACCCATACACAAAATCCACCATTGCT
GCTGCACAACCATGCTCTATGCCTCAAGCCATCGCTCATAGGTTGCATCTCATCATTGAGGGCTACCAGACGAAAGACCT
CCCTACCGCAGCCTTCATTGACCAGTGTCGGGGCTTAGGCCAACCACTAGTACCAAGCAATGGCAAGGGGAAGGGAGGAT
GGAGAGGTGGGAGATGGCGGCTTAGGTTTCGATGCCTACG----------GCTATCAAAAGGGAGGCACATATGCTATGT
GGTGCAAG--TTTTTTTTACTTTGCATTATATCTGCCACAATAATGTTGTACTTTGTACAATGTCTCATAAAAACATGTT
TCAAAAACAATCTGAATAACTTCTTACATGTGTAACAAAAAATTGTACACCTACATATCCTAGTTATGGAACATGATCAA
TTCCTTCGATTTCGTCTCTTCAAGGATCGACTCAATTCCAAGAGCAACCTCTTCAAGAAAACCATCACCCCTTTTGCAAA
AAAAAAAAATTCACCCCAACGGCCACTGCTGCCCTAGATGCGAGGCTCCAGTTGATGACGACCTTCACATGTTCA----G
TACCCAGTAGCCATCCAGATGTGGGATGGCCTACTTCACCCGGTGCCACCCTCCATCGAGCTCATTTGGGTTGTCCCCAC
GCTGTCGGATCTCCATGACGATATTTCGCCATCGATTGCTCTTTCCTTGTTATGGAAGATTTGGGATTCCAGAAACATGC
TTGTCTTTGGCAACGAACTCCACTTTGCAAGGACCAATGTTAGAAATTTAGCTAGCGACTTCACTCTTTGAACTTT---A
TACGAAAGTGTCTCTAAGAAGGATGCCTTCATGCCATGGCGTCAATACCTCTCTTCACGCTCTAGCGCACAATTGGAAAG
CTCGCCTTTTACTCGTCTTTGAGTAATGCATTCGGGTATGTATCCTCTCCCCTTAGTGATTTGTCA-AAAATTCAATTCC
TCCGGTTAAAATAATTCATACATGTCTGAAAAAGCAAGACATATAT--TCAACAAAACTGAATCTTGTTACTATTAGCTA
GCACTCTCCTCTTTTACCTCTTGTGCTTGGTTGAGAGGCCACAAACTCCACCAAGGCCCAATCACAAGCATCCACTTTCT
TTTTGCTCATCTCCTCAAGGCCTCCAACGGTGGAGGCGGAATAAACTCCGGCCACTTTTTGTAGCCGCCCGGAATTTGAT
ACTCCCCCGGTCCTCCCCTATATAGGCGCGCCTCCTTCCACCTCCCCCCTTCGCCACTTTCCTGCCTTCCTCCATTGCTC
GCC-----GTCCCTAAGCCAGCTCAGGTAGCAGCAACTAGAGCCGACATGATGGCGGAGGCGTGGGCGGACGTGCTGCCG
CCGCCGGCGCCCTACTTCGCCGGGCAGCCGTGCTGGGCCGTGCAGCCGGAGCGTCGCGGAGGGGGCGCGTGGACGCTGGA
GGAGAACAAGGTGTTCGAGGAGGCGCTCGCGGCGATCGACCTGGACGCGCCGGACCGGTGGGAGATGGTCGCGCTGATGC
TGCCCCGGAAGACGGTCGCCGACGTGGTGAACCACTACCGGGCCCTCGAGAACGACGTGGGGTTCATCGAGGCCGGGCTG
GTCCCGTTCCCTCACTACGACAGCTCGTCCCCTTCGTCCGGGTTCACCCTGGACTGGGACGGCGGCGCCGCCGGCGCCGG
CGGGTTCAGGCGCGGCTACTGCCTCAAGCGCGGGCGCGCCGACCAGGAGCGGAAGAAGGGCGTCCCGTGGACGGAGGAGG
AGCACCGGTAAGCCGCCATCTTCGTGATCTTCTTC
>SNPs
----------S-S----------------S-----------------------------S-------S-----S------
-S------------------------------S-S-----------------------------------SS--------
-SS--S-----------------S--------------------S-------S--S--------------------SSS-
-----------S----SS---S-------S-S---S---S-S--------------S-----------------------
----------S-------------SS--SSS-------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------S-----------
--------------SSSSSSS-------------S--------------------------S------------------
-S------------S----------------S--------------------------SSS-----S----S--S----S
----------------------------S-------S------------------S-------S-----S----------
---S----------------------------------------------------------S-----------------
---------------------------------------S------------------------------------S---
-------------------------S--------S-----SSSSSSSSSS------------------------------
-S----------------------------------S-----------------------------------S-------
-S-----S-----------S---------------------S--S-----------------------S--S-S------
-----------------------------------S-----------------------S--------------------
-----------------------------SS-SS-------S-S---------------------------------S--
------S---S------S--S------------S-----SS-------------------------------SS-----S
-S-----S-------S-----S---S-------------------------------S----------------------
--------S-----------------------------------------------------------------------
--------------------------------------------------------------------------------
--------S-------S-----------------S--------S------------------------------------
--S-------------------------------------------SS---S----------------------------
----S---------------------------------------------------------------------------
-----------------------------------------------------S--------------------------
--------------------------------------------------------------------------------
---SSSSS------------S--------------------------------------------S--------------
--------------------------------S-----------------------------------------------
-------------------------------------------------------------------------------S
--------------------------------------------------------------------------------
--------------------------------------------------------------S-----------------
-------S------------------------------------------------------------------------
-----------------S----S------------
>forward_861
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-----------------------------------------ACCGCCATATTAGGACACGG-------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-----------------------------------
>reverse_2246
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-----GCCGTCCTTAAGCCAACTCA-------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
-----------------------------------
