CLUSTAL X (1.81) multiple sequence alignment input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 ACTCATCTGGGACTCCATGTCAGCTTGCCGAAACATGGCACGACAAAAAA chr6D_1 ACTAATCTGGGACTCC-TGTCAGCTTGCCAAAACATGGCACGGCAAATAA chr6B_353 -------------------------------------------------- chr6A_634 -------------------------------------------------- SNPs ---S------------S------------S------------S----S-- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 TAACCAAATATAACACTATGTTAAGATTACTTGCTAACAGTCCCTTGACT chr6D_1 TAACCAAATATAACACTAAGTTA-GATTACTTGCTAACAGTCCCTTGACT chr6B_353 -------------------------------------------------- chr6A_634 -------------------------------------------------- SNPs ------------------S----S-------------------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 CGTCTTCTTGTACTCTCTATGTTCTTCTTTCAGTTGGAGATTCATGGCTT chr6D_1 CGTCTTCTTGTACTCTCTATGGTCTTCATTCAGTTGGGGATTCATGGCTT chr6B_353 -------------------------------------------------- chr6A_634 -------------------------------------------------- SNPs ---------------------S-----S---------S------------ forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 GTCGAGTCGTCAGATGAAAGTACAGGTTCTCCTGGACTGCCGGCCCACAC chr6D_1 GTCGAGTCGTCAGCTGAAGATACAGGTGCTCCTCGACTACCAGCCCACAC chr6B_353 -------------------------------------------------- chr6A_634 -------------------------------------------------- SNPs -------------S----SS-------S-----S----S--S-------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 ATCCACATATTAGCATGCTATATGCAGAAACACATAGCCTCATGCAAAAA chr6D_1 ATCCACATATTAGCATGCTATATGGAGAAACAGACAGCCTCAAGCAAGTA chr6B_353 -------------------------------------------------- chr6A_634 -------------------------------------------------- SNPs ------------------------S-------S-S-------S----SS- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 CTCAACTGAGTTGTCGCTTGTTCATCTTCATGTTGGCCTGCATATTTTTG chr6D_1 CTCAACCAAGTTGTCGCGTGTTCATATTCATGTTGGCCAGCATCTTTTCG chr6B_353 -------------------------------------------------- chr6A_634 -------------------------------------------------- SNPs ------SS---------S-------S------------S----S----S- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 ACCAAAAACATAGATAGCCACCCGTCATCTTTTCTTCACTCACACTATGA chr6D_1 ACCAGACACA---------------------------------------- chr6B_353 -------------------------------------------------- chr6A_634 -------------------------------------------------- SNPs ----S-S---SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_335 ---------------AGCCACCCGTCATCTTTTCT--------------- reverse_1484 -------------------------------------------------- forward_336 ---------------AGCCACCCGTCATCTTTTCTT-------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 CGGTCAATGATACACCTCACCAGACAAGCCCTCTAACCTTGACACACTTT chr6D_1 --GTCAAATATACACCTCCCCGGACTAGCCCTCCAACCTTGGCACACTTT chr6B_353 --GTCGATGATACAACCCATCGGAGAAGCCCTCAAACCTTGACACACTTT chr6A_634 -------------------------------------------------- SNPs SS-------------------S-----------S---------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 AACTCATCACCCAACACATCTTCTCTTTGTTGTCAGTGACATTACTTACT chr6D_1 AGCTCATCACCCAACACATCTTCTCTTTGTTGTCAGTGAGATTACTTACT chr6B_353 AAATTACTGAACA--ACATCTTGTCTTTGTTGTCAGTGGCATAAATTACC chr6A_634 -------------------------------------------------- SNPs -------------------------------------------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 GTACGATAATGCATGTCTAGCA----TCAACACAACTCACTATGTGGTTA chr6D_1 GTACGACAATACATGTCTAGCATCGATCAACACAACTCACCATATTGTTA chr6B_353 CAACGACACTACATGTCTAGCA----TCAAGACAACTCGCTATATGCTTA chr6A_634 -------------------------------------------------- SNPs ------S---S--------------------------------S------ forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 AGCATCAAAAGTCACTCCTTGCATCACTAAGTGTTCATTCAACTGATCTT chr6D_1 AGCATCGAAAGTCACTCTTTGCATCACTAGGTGTTCATTTAACTGAGCTT chr6B_353 AGCATCAATAGTCACTCCTTGCATCACTATGTGTCCAGGTAACCGAGCTT chr6A_634 -------------------------------------------------- SNPs -----------------------------S---------S------S--- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 TTCTTTTTAGGGGCAGCTAGATG-----CACGGAAAAAGCACAAATAATA chr6D_1 TTGCTTTTAGGGGAAGCTCGATG-----CACGGAAAAAGCACAAACAATA chr6B_353 TTGCTTTTAGGGGAAGCTAGATCATATCCATGGTAAAAGCACAAACAATA chr6A_634 -------------------------------------------------- SNPs --SS---------S-------------------------------S---- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 AACAACAGGAGCATGTGGCGCGCATCCAGGCGGTCAAACAATGAAGCTTG chr6D_1 AACAAGGGGAGCATGTGGCGCGCATCCAGGCGGTCAAACAATGAAGCTTG chr6B_353 AACAAGGGTAGCAAGTGGCGTGCATCCAGGCGGTCAAACAATGAAGCTTG chr6A_634 ------------------------------------------GAAGCTTG SNPs -----SS------------------------------------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 TACCGTAGTGGGCTTAAACAGTTCTTCTTCCAATGAAATCATGCAAGTAG chr6D_1 TACCGTAGTGGGCTTAAACTGTTCTACTTCCAAAGAAATCGTGCAAGTAG chr6B_353 TACCGTAGTGGGCTTAAACAGTTCTTCT---AATCAAATCTTGCACCTAG chr6A_634 TAACTTAGTGGTCTTAGACAGTTGTTCT---AATCAAATGTAGCAAGTAG SNPs ----------------------------------------S--------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 TAGCTAGTTGGCTTTGAAGCAAGTAGACATACATATAGATAAAGGGCAAG chr6D_1 TAGCTAGTTAGCTTTGAAGCAAGTAGACATACATATACATAAAGAACAAG chr6B_353 TAGCTAGTTGGCTTTGAAGCAAGTAGACATACATATACATAAAGAGCAAG chr6A_634 TAGATAGTTAATTTTGAAGCAAGTAGACATACATATACATAAAGAGCAAG SNPs -------------------------------------S------S----- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 TTGATGTCTGATCCATCTGCCATCTGTGCACATGCATTGCACACGCGCAA chr6D_1 TTGATGTCTGAT-------CCATCTGCTCACATGAATTGCACGCGCGCAG chr6B_353 TTGATGTCTGAT-------CCATCTGTGCACATGCATTGCACACGCGCAG chr6A_634 TTGATATCTGAT-------CCATCTGTGCACATGCATTGCACACGCGCAC SNPs ------------SSSSSSS------------------------------S forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 ATGTCGGATCGATACCGCTTGCGTGGCCCATGTGATGGTGGCCACGGGAT chr6D_1 ATGGCGGATCGATACCTCTTGCGTGGCCCATGTGGTGGTGGCCACGGGAT chr6B_353 ATGTCGGTTCGATACCTCTTCCGTGGCCCATGTGCTGGTGGCCACGGG-- chr6A_634 ATGTCGGATCGGTACCTCTTGCGTGGCCCGTGTGGTGGTAGCCACGGGTT SNPs ----------------S-----------------S--------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 ACTAGCTAAGATGGA--------TCAGATTCATGAGAGCAACCTTTAGGT chr6D_1 ACTAGCTAAGATGGA--------TCAGATTCATGAGCAGAACCTTTAGGT chr6B_353 --------------A--------TCAGATTCATG-GAGCACCCTTTACCT chr6A_634 ATTACCTAAGATGAATCAGATATTCAGATTCACGAGAGGAACCTTTTGCT SNPs -------------------------------------------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 AGCATCACCGGCCGGCCTCTTTATATATGTGTGTGTCCCTGTCTCCTCAA chr6D_1 AGCTTCACCGGCCGGCCTCTTTATATATCTGTGTGTCCCCGTCTCCTCAA chr6B_353 AGCTTCACCGGCC----TCTTTATATATGCGTGTGTCCCAGTCTCTTCAT chr6A_634 AGCTTCACCGGCC----TCTTTATATCTGCGTGTGTCCCCGACTCTTGGA SNPs ---S-----------------------------------S---------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 CCCATCCATTC------------AGCTACACACACCACAAAGCTAGTTAG chr6D_1 CCCATCCATCCAGCTACACAGTTAGCTACACACACCACAAAGCTAGTTAG chr6B_353 CCCATCCATCCAGCTACAC------------------------------- chr6A_634 TCCATC---CCAGCTACATTGTTAGCTACACACTACACA----------- SNPs ---------S---------------------------------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -----------------------------ATGGGTATGGGTTCTAATAAG chr6B_1_TraesCS6B01G014200 CTAAGGAGCAGCCAGCCACCTAGCTAGCTATGGGTATGGGTTCTAATAAG chr6D_1 CTAAGCAGCAGCCAGCCACCTAGCTAGCTATGGGTATGGGTTCCAATAAG chr6B_353 -------------------------------------------------- chr6A_634 -----CAGCAGCCAGCCACCTAGCTAGCCATGGGTGTTGGTTCCGCCGGC SNPs -----S-------------------------------------S------ forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 AGAAGCAGCGCCACCGTTGTTGTGTCATGCGTAGTCTTAGGCGTAGCCCT chr6B_1_TraesCS6B01G014200 AGAAGCAGCGCCACCGTTGTTGTGTCATGCGTAGTCTTAGGCGTAGCCCT chr6D_1 AGAAGCAGCGCCACCGTTGTTGTGTCGTGCGTAGTCTTAGGCGTAGCCCT chr6B_353 -------------------------------------------------- chr6A_634 GC---------------TGTTGTGTCGTGCGTCGTCCTAGGCTTAGCCCT SNPs --------------------------S----------------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 GCTCGTCGTC---------------------------------------- chr6B_1_TraesCS6B01G014200 GCTCGTCGTC---------------------------------------- chr6D_1 GCTCGTCGTC---------------------------------------- chr6B_353 -------------------------------------------------- chr6A_634 GCTCGTCGTTGGGGCGGCGGCAGCCAAGAGCAGCCCAAACTCCTGCAAGG SNPs -------------------------------------------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 -------------------------------------------------- chr6D_1 -------------------------------------------------- chr6B_353 -------------------------------------------------- chr6A_634 CGTTGTGCCGTGGCCGGGAGGACTACAAACCCTGCCACGCCGCGTGCCTG SNPs -------------------------------------------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 --------------GGAGCCCATGGGAGGAGAGAAGGAGAAAAGGAAATC chr6B_1_TraesCS6B01G014200 --------------GGAGCCCATGGGAGGAGAGAAGGAGAAAAGGAAATC chr6D_1 --------------GGAGCCCACGGGAGGAGAGAAGGAGAAAAGGAAATC chr6B_353 -------------------------------------------------- chr6A_634 TGGGCGTGCATCTGGGATCCCATGGGAGGACACAAGGAGAAACGGCAGTA SNPs -------------------------------------------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 GGAGGAATAGCTGCCCCACCTACCTGCTACGAGCGCTGCCGCCATGAGCC chr6B_1_TraesCS6B01G014200 GGAGGAATAGCTGCCCCACCTACCTGCTACGAGCGCTGCCGCCATGAGCC chr6D_1 GGAGGAATAGCTGCCCCACCTACCTGCTACGAGCGCTGCCGCCATGAGCC chr6B_353 -------------------------------------------------- chr6A_634 GGAGGAATTGGTGCCCCACCTACCTGCCGCGTGCGCTGCCGCCACGC--- SNPs -------------------------------------------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 CAAGGAGGACATCGACGCCTGCGTCAAACGGTGCCGGAGTGGGTTAAAAG chr6B_1_TraesCS6B01G014200 CAAGGAGGACATCGACGCCTGCGTCAAACGGTGCCGGAGTGGGTTAAAAG chr6D_1 CAAGGAGGACATCGACGCCTGCGTCAAACGGTGCCGGAGTGGGATAGAAG chr6B_353 -------------------------------------------------- chr6A_634 ---GGACGACATCGCCGCCTGCGTCAAACAGTGCCAGAGTGGGATACAGG SNPs -------------------------------------------S--S--- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 GAGAAGAAGCAAGAGGGGGAGGACTTGGGCTCCTGGCGGGGCCGGCGGAG chr6B_1_TraesCS6B01G014200 GAGAAGAAGCAAGAGGGGGAGGACTTGGGCTCCTGGCGGGGCCGGCGGAG chr6D_1 GAGAAGAAGCAAGAGGGGGAGGACTTGGGCTCTTGGCGGGTCCGACGGAG chr6B_353 -------------------------------------------------- chr6A_634 GAGAAGAAGCAAGAGAAGGAGCA--------------------------- SNPs --------------------------------S-------S---S----- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 GGACGGGAGCAAGAGGTAGAAGCAA------GAGGAGGAGGAGGAGGAGG chr6B_1_TraesCS6B01G014200 GGACGGGAGCAAGAGGTAGAAGCAA------GAGGAGGAGGAGGAGGAGG chr6D_1 GGAAGGGAGCAAGAGGTAGAAGCAA------GA---------GGAGGAGG chr6B_353 -------------------------------------------------- chr6A_634 ---------------GTAGAAGCAAGCGTAGGA---------GGAGGAGG SNPs ---S-----------------------------SSSSSSSSS-------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 AGCTGGGCTACTGGCGATGCCGACGGAGCGCGCAGGACGGGAAGTCGAAG chr6B_1_TraesCS6B01G014200 AGCTGGGCTACTGGCGATGCCGACGGAGCGCGCAGGACGGGAAGTCGAAG chr6D_1 AGCTGGGCTACTGGCGATGCCGACGGAGCGCGCCGGACGGGACGACGAAG chr6B_353 -------------------------------------------------- chr6A_634 AGCTGGCCTACTGGTGATGCCGACGGAGCGTGCCGGAAGGAAAGGCGGAG SNPs ---------------------------------S----------S----- forward_335 -------------------------------------------------- reverse_1484 ---------------------------------AGGACGGGAAGTCGAAG forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 AGAAAAAGAAGCAAGCGGACGCCGCCCCAGTCCAGCTGGGTTACGACCCA chr6B_1_TraesCS6B01G014200 AGAAAAAGAAGCAAGCGGACGCCGCCCCAGTCCAGCTGGGTTACGACCCA chr6D_1 AGAAAAAGAAGCAAGTGGACGCCGCCCCAGTCCAGCTGGGTTACGACCCA chr6B_353 -------------------------------------------------- chr6A_634 AGAAGAAGAAGCAAGCAGATGCCGCCCCAGTCCAGCTGAAATATGACCCA SNPs -------------------------------------------------- forward_335 -------------------------------------------------- reverse_1484 AGA----------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 GAATTCTGTTCCTTCATGTGCCGCCACATACATGACAAGGGGGACTGCCT chr6B_1_TraesCS6B01G014200 GAATTCTGTTCCTTCATGTGCCGCCACATACATGACAAGGGGGACTGCCT chr6D_1 GAATTCTGCTCCTTCATGTGCCGCCACATACATGACAAGGGGGACTGCCT chr6B_353 -------------------------------------------------- chr6A_634 GAAATCTGCTCCTTCGTGTGCCGCTACATACATGAAAAGGAGGACAGCCT SNPs --------S----------------------------------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 CCAAAAGTGCGAGGCAGGGCCAAATGAAGCAAGAGGGTGA---------- chr6B_1_TraesCS6B01G014200 CCAAAAGTGCGAGGCAGGGCCAAATGAAGCAAGAGGGTGATAAGTCGGTC chr6D_1 CCAAAAGTGCGAGGCAGCGCCAAACGAAGCTAGAGGGTGATAAGTCGGTC chr6B_353 -------------------------------------------------- chr6A_634 GAGAAGGTGTGAGGCAGCGCCAAACGAAGCAAGAGGGTGAGAAGTTGGTC SNPs -----------------S------S------------------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 TCCTTGCATCAACGGTGGAG------------------------------ chr6D_1 CCCTGGCACCGACGGAGGAG------------------------------ chr6B_353 -------------------------------------------------- chr6A_634 TCCTGGCGTCGACAGCGGTGGGCACGGAACTGGACGAAGAGAAGAGGGTG SNPs ----S-----S----S---------------------------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 ----------------------------------GGTGCTGCCTCCTGCA chr6D_1 ----------------------------------GGTGCTGCCTCCTGCA chr6B_353 -------------------------------------------------- chr6A_634 CACCGTCAACCTGAGCTATTTCTGCCGAGAAGCTGGTGCTGCCTCCTGCA SNPs -------------------------------------------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 CCGGGCCACATCGTTTGCTTTCCTAACAAGATGTTAATTTGGTCATCAAT chr6D_1 CCGGACTACATCGTTTGCTTTCCTAACAAGATGTTAATTAGGTCATCAAT chr6B_353 -------------------------------------------------- chr6A_634 CCGGACTACATCGTTTGCTTTCCTAACAAGATGTTAATTAGGTCATCCAG SNPs ----S-S--------------------------------S---------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 CTCGTACGTTGTTATCATGGCTGTTGAGTACTTCCATTCTCCCCATATCC chr6D_1 CTTGTACGTTGTTATCATGGATGTCGAGTACTTCCATTTTCCCCATATCC chr6B_353 -------------------------------------------------- chr6A_634 CTTGTACGTTGTTATCATGGTTGTTGAGTAGTTCCATTTTCCCCATATCC SNPs --S-----------------S-----------------S----------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 ATGT--------GTGAGCACACAATCTTCTGTGTGTGCCACACTTTTGAA chr6D_1 ATGT--------GTGAGCACACGATCTTCTGTGTGTGCCACACTTTTGAA chr6B_353 -------------------------------------------------- chr6A_634 ATGTGTGACAGTGTGAGCACACAATCTTCTGTGTGTGCCACACTTTTGAA SNPs -------------------------------------------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 GCCACTGTACGTCGTTTTCCATTTTGAAATAAAAGGAGGTGATATAAGAA chr6D_1 GCCAC----CGTCGTTTTCCATTTTGAAATAAAAGGAGGTGACATAAGGA chr6B_353 -------------------------------------------------- chr6A_634 GCCACCATC----------------------------------------- SNPs -----SS-S---------------------------------S-----S- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 AACCGCAGGTATCTGTTTTGCGTTTTCGTTGTGCTGCCAATATGTTTGGC chr6D_1 AACTGCAGGTATATGT------------------TGCCAATATGTTCGAC chr6B_353 -------------------------------------------------- chr6A_634 --------------GTTTTCCCTTTTGGTTGTGCTGCCAATATGTTTGAC SNPs ---S--------S------S-S----S---------------------S- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 AACTGGTTTTGTGGCACCGATTGTAAGGTGATACAAAAGAAGATGCTTAA chr6D_1 AACTGGTTTTGTGTCATCGATTGTGAAGTGATACAAAAGAAGATGTTTAA chr6B_353 -------------------------------------------------- chr6A_634 AACAGATTTTGTGGCATCGATTGTAAGGTGATACAAAAGAAGATGTTTAG SNPs ----------------S----------------------------S---- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 GCGCTGATAAAACAACTTAATTTGTATGAGCATTAAGTGCATGCATGAAA chr6D_1 GCGCTGATCATACAACTGAATTTGTTTTAGCATTAAGTGCATACATGAGA chr6B_353 -------------------------------------------------- chr6A_634 GTGCTGATAATACAACTAAATTTGTTTTAGCACTAAGTACATGCATGAAA SNPs ----------S------S-------S-S---------------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 GCGTAAGACACAGGAGTAAACTTCTTTTGGCTAGCTTG---ATGGAAG-C chr6D_1 GCGTAAGACAGAGGAGTAAACTTTTTTTAGCTAGCTTGTTGATGGAAGCA chr6B_353 -------------------------------------------------- chr6A_634 GCGTAAGGCAGAGGAGTAAACTTCTTTTAGCTAGCTTGCTGATGGAAG-A SNPs ----------S-----------------S--------------------S forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 AAGCAAATGGATATACGTGTATCCAACTCGGGGATGCATCTGCGAGGTGC chr6D_1 AAGCAAGTGGATATATATGTATCAAACCTGGGCATCAATCTACGAGATGC chr6B_353 -------------------------------------------------- chr6A_634 AAGCAAGTGGATATATATGTATCCAACTTGGGGATGCATCAGCGAGATTC SNPs ------S--------SS-----------S-----------------S--- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 CACGAGCTCAAACGTGCATCAATGCATGGCAGTGCATATATCCAACGCCA chr6D_1 CATGAGCTCAAACTAGCATCAATGCATGACAGTGCATATATCGCGCCTGT chr6B_353 -------------------------------------------------- chr6A_634 CACGAGCTCAAACGTGCATCAATG-------------------------- SNPs ----------------------------S-------------SSS-SSSS forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 TGCGCACCTGTACACATGCATCAATGATATTTGTAGGACACGTAGAAGAT chr6D_1 ACT-----------CATGCTTCAATGATATTTGTAGGACACGTAGAAGAT chr6B_353 -------------------------------------------------- chr6A_634 -------------------------------------------------- SNPs SSSSSSSSSSSSSS-----S------------------------------ forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 --CGCACCTGTACACATGCATC---------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 TTCCTA--------CATAGCCATTGATCCAGAATACAAACTTTAACATCC chr6D_1 TTCCAACATATCACCATAGCCATTGATCCAGACTAGAAACTTTAACATCC chr6B_353 -------------------------------------------------- chr6A_634 -------------------------------------------------- SNPs ----S---------------------------S--S-------------- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 ACCCATCCTCTCGCTGTAGCCATATATCCATAATGTTATACCAGCCTTGA chr6D_1 ACCCATCCTCCCGCTGTAGCCATATATCCATAGTGCCGTACCAGCTTGGA chr6B_353 -------------------------------------------------- chr6A_634 -------------------------------------------------- SNPs ----------S---------------------S--SSS-------S-S-- forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 TGTAAAAATGACGTAGGCTCAGTCATTCCAGTAGCTATAATTTGACATAT chr6D_1 TGTAAAATGGACGTAAGCCAG----------------------------- chr6B_353 -------------------------------------------------- chr6A_634 -------------------------------------------------- SNPs -------SS------S--SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 AACTTATATTCGTTGGTAAAATCTGTCATATAGATGCGACAAAAAATAAG chr6D_1 -------------------------------------------------- chr6B_353 -------------------------------------------------- chr6A_634 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 TGTGTATTTACGTATGTATGTATGAAAGAACACACTTTCATAACCCACAA chr6D_1 -------------------------------------------------- chr6B_353 -------------------------------------------------- chr6A_634 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 AAGAAAGAACATGCTTTTATAAACATGAACCAAACTAAATAGCTCGTCAA chr6D_1 -------------------------------------------------- chr6B_353 -------------------------------------------------- chr6A_634 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 GATGGAAATCAAATTCAAGCGCACATGTTTTCTGATTTGCTGTTGGTCAA chr6D_1 -------------------------------------------------- chr6B_353 -------------------------------------------------- chr6A_634 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 -------------------------------------------------- chr6B_1_TraesCS6B01G014200 AACACACACTACTCTACTGTATAATTTACAATTTTGCTAGAACTCATCTA chr6D_1 -------------------------------------------------- chr6B_353 -------------------------------------------------- chr6A_634 -------------------------------------------------- SNPs SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS forward_335 -------------------------------------------------- reverse_1484 -------------------------------------------------- forward_336 -------------------------------------------------- reverse_2253 -------------------------------------------------- input_sequence_78202 ------------------------ chr6B_1_TraesCS6B01G014200 GATGAGATATAATTTGGTCTCATT chr6D_1 ------------------------ chr6B_353 ------------------------ chr6A_634 ------------------------ SNPs SSSSSSSSSSSSSSSSSSSSSSSS forward_335 ------------------------ reverse_1484 ------------------------ forward_336 ------------------------ reverse_2253 ------------------------