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["Additional file 4: Table S2 SNPs used to develop CAPS markers"]
["Code","SNPa","CAPSb","Forward primer sequence (5'-3')","Reverse primer sequence (5'-3')","PCR fragment (bp)",null,"Restricted enzyme"]
[1,"AX-108823502","TaBL1","ACTGAACAAGGAAACAAGCAGA","TCTGGTCCATCTAAAGGGATTAC",null,800,null,"MluC I"]
[2,"AX-108919436","TaBL2","ACGAAAATACACAGGCGAGTAGA","GAGTTGGGGAAATATCAGGTGCT",454,null,"Mse I"]
[3,"AX-109048732","TaBL3","CCCTCCCGAAACTAAGTATCATT","GACTGACAAGAGCAAGTGATGC",623,null,"Bfa I"]
[4,"AX-108783920","TaBL4","TGCATATATTCTTCAGGCCGT","CAATGTATGAACGCAATACACC",438,null,"Nsi I"]
[5,"AX-108895529","TaBL5","CGGTGGATGTTATGTCCCTA","GCCTACATAGTCGTTGATCGCT",335,null,"Sau 96I"]
[6,"AX-109435898","TaBL6","GTGGATAAAACACAAACCAACAG","CTTCAACATATCCCTGGATATATG",691,null,"Hae II"]
[7,"AX-108863641","TaBL7","ACTAAGCAATGGATGTGAGGTAA","CCGACCATTGACTATCACAATAA",974,null,"Nla III"]
[8,"AX-109428194","TaBL8","TAGATCTTATACAATCACCCCGC","CCCATATTGTAAGACGTTTTTGC",973,null,"MluC I"]
[9,"AX-109468761","TaBL9","CTCAATGGTGAAGTCTCTGGC","AAGCTAGCACGCTGCTTCC",834,null,"Afl II"]
[10,"AX-109027972","TaBL10","TGCAATGTTTGACTTCGGC","CAGTGGCAACTAGACACGAGG",803,null,"Sac I"]
[11,"AX-109864320","TaBL11","CCTCATAACCTCTACCCAACCAC","CAGGAGGAAATAGAGCATTGC",683,null,"Dra I"]
[12,"AX-109916563","TaBL12","GGCAGGATGTTGTCAGTCTG","ACTCAACCAAAGTTTTATCAGTGG",646,null,"HpyCH 4III"]
[13,"AX-109855943","TaBL13","GTGGATGAAGAGAATGGTGGTG","GCAACATGACTGCGCCTTC",527,null,"Dpn I"]
[14,"AX-109347571","TaBL14","GCTAGCTAGCCGGCTAGACGT","CCCTACCACACTTGAAGGGTT",447,null,"Msp I"]
[15,"AX-108773562","TaBL15","CATATAGGAGTGGGAGGCGC","GTGGCGAGGACCGTAGACA",701,null,"Taq I"]
[16,"AX-108848127","TaBL16","CTTCTGTGTTCTTTGTACTACCTTGA","TGCCGCCTCATCTTCTTGA",577,null,"Taq I"]
[17,"AX-109817727","TaBL17","CAGCTTTCCATTTTGTCGAAC","CCACTTCTCTTTCTATTATGACATG",612,null,"Nsp I"]
[18,"AX-109300654","TaBL18","CAAGCATTCACACTGCATTATAGG","TGTAGAACTCGAAGATGCCGTAC",875,null,"Nla III"]
[19,"AX-108762202","TaBL19","GAGTCAGATGGATACAGGGTGAG","AACGCCCATTGAAGAGTGG",918,null,"BstB I"]
[20,"AX-109828493","TaBL20","GTAACTTCATCGGACAGCCAC","AATCAATTGAAAAATGACACCG",590,null,"Hae III"]
[21,"AX-108793110","TaBL21","TCACTCGGCCGATATCAATGTA","CCAAAAAGATGAGGAGATATGAAG",704,null,"Nco I"]
[22,"AX-109830729","TaBL22","CCTCAGCTCCCCAAGCTCAC","GTTCAACATGTTGTTGTTCTTATCC",926,null,"MluC I"]
[23,"AX-109322335","TaBL23","GATGCCTAACTTTGAAGTTCTTTTG","GTCTACAACCTTATCTTTTCACCGA",607,null,"Nla III"]
[24,"AX-109363969","TaBL24","GGATGACCAAGCCAATGTCC","GGTCCGGATGACATTGACGA",418,null,"BspH I"]
[25,"AX-109039756","TaBL25","CTCGCATCGCATGTTGGTT","GTCCTGCCGACTAGGATTACAG",317,null,"Aci I"]
[26,"AX-109939515","TaBL26","GCCTGTTTTATTTCAGTCATATGT","CTTCATCCCGTACATCACCG",713,null,"SnaB I"]
[27,"AX-108996126","TaBL27","GTGCATGATATATTCTTTGATGCC","CCATACAATCCTATCCGTGTTTTA",561,null,"Bfa I"]
[28,"AX-109301653","TaBL28","GTGGAGTAACTAAAGTGGACCA","GTGGTTGAGCTTGAGCTTGAG",479,null,"Pvu I"]
[29,"AX-109516011","TaBL29","GTGATAGGCGGGATTGTTTT","GCAGGAGCATGAGTCAATGA",800,null,"Dpn II"]
[30,"AX-108762525","TaBL30","CAATTCAATGATGACAGTGCAG","AGGTATACTCTTCCGTGACACAA",382,null,"HpyCH 4IV"]
[31,"AX-109487901","TaBL31","GGTTTTCCTTCTGTCATCTTCGT","GTGTCATGTT TTTCAAGGGGTC",442,null,"Alw I"]
[32,"AX-108743617","TaBL32","CATGCATATTTTGGCTCCG","ACCATTCAAAGCTATCGGCAC",785,null,"Alu I"]
[33,"AX-108751549","TaBL33","TTGTGATTTTGCTACGAAGGC","TCCCCGCAAAGAGAAAAA",989,null,"Hae III"]
[34,"AX-109034274","TaBL34","CTTGTATGCCTTGCATCTATTTCTG","GGCGCTTCTTCTTCTTCGTC",719,null,"Bfa I"]
[35,"AX-109366792","TaBL35","GCGACGTGCGGATGAAAAT","CAAAGCAAGCTACAACACAAATGG",505,null,"Hinf I"]
[36,"AX-110037447","TaBL36","CGGTGACCTTGCTGAACTG","CCTGACCATCGAAGAGATGTT",374,null,"CviQ I"]
[37,"AX-108987517","TaBL37","GATGAGACGTGGTTGGTGGG","GTCCCGCTGCTGAATGTAC",390,null,"Bfa I"]
[38,"AX-108762678","TaBL38","CTCTTTTCTCTTTGCCTGTGTCC","GGAGTGCTCAAGTCCTCTGCAC",366,null,"Afl III"]
[39,"AX-108796554","TaBL39","GCGTCTCTCCATCATTGAATT","CTACCCATGACGGCTTAAAAA",621,null,"Hpa II"]
[40,"AX-109972147","TaBL40","CGTATTTAAAGCTGCGTGGG","GAGCAAACAAATTGATGCGC",795,null,"Taq I"]
[41,"AX-109344528","TaBL41","GGCACATAACGTCATGGAGAC","GCCGAGCCGAGCAAACTTT",403,null,"BstY I"]
[42,"AX-109299632","TaBL42","CGACGGTAACTTCTTGTCTTCTC ","TGCTGTTTAGATTGGAGTTCTGC",583,null,"Nla III"]
[43,"AX-108828412","TaBL43","GGAGATATTTTCCGAAGGACAG","GGGAATCTAACAGTCTCCCCA",699,null,"Bfa I"]
[44,"AX-109031908","TaBL44","GTGGCCATCAAGCCGCTAT","CGGTGTACATCCTAAATTTTGATCC",576,null,"HpyCH 4V"]
[45,"AX-108863110","TaBL45","GTCGTGGATAATTATGTTGTGAAC","GAGCCGACATATCATCTCGA",702,null,"HpyCH 4III"]
[46,"AX-109441692","TaBL46","GGTACCGATGCTTTTCCCG","GAGCCGACATATCATCTCGA",547,null,"BspE I"]
[47,"AX-109419012","TaBL47","GGAGAAAAAAAAACCGAAATGAT ","CGGTAAAACAATACTGCATATAGG",648,null,"Taq I"]
[48,"AX-108769105","TaBL48","GGCCCACCCTTTTTTTGTG","CTGGCGAACTAGAGACCAGC",613,null,"Hpa II"]
[49,"AX-109415466","TaBL49","CATCGCTGACTGGGGCTC","GGGAACACAGTTGGAAGCC",639,null,"Taq I"]
[50,"AX-109527589","TaBL50","GGCCCAATAACAAAATAAAAAGC","CCGAGAAAGAGACATAGAAAACTAA",434,null,"Dra I"]
[51,"AX-109497011","TaBL51","CAGCACCACAGAGTACCAACC","GTCAGCATCTGGTACCTGGG",951,null,"Bfa I"]
[52,"AX-110042240","TaBL52","CCATCGACGAACGATGAAAC","CGCTGATGGC ATTCCTCGTA",469,null,"Bfa I"]
[53,"AX-109984991","TaBL53","CTCTACAATGTACCAAGCAGTGA ","GTTGACATCTTCACGAAGCCT",436,null,"BstU I"]
[54,"AX-109420619","TaBL54","CAAATGAACACGGTGTGCCC","CCTCTTACCAAGAAAGTGTCGTG",650,null,"Stu I"]
[55,"AX-109816616","TaBL55","CAACCAAGCCTACAACATTCAC","GAATGGTGGTGTGCACTACAAC",524,null,"Ase I"]
[56,"AX-109517725","TaBL56","GTCCTCTCACCACCGGTTC","GCAGAAATACTAGATAAAGCATGGC",532,null,"HpyCH 4V"]
[57,"AX-109520937","TaBL57","GCCAACTGTCGTGGTTCTAAGA","GTGATGAGGATACAGACCTGGGA",585,null,"Taq I"]
[58,"AX-109879762","TaBL58","CATACAACTCGGAGTACACTGGAAC","GATGTTATGCTGATTGCTGGTTG",594,null,"Apo I"]
[59,"AX-109839332","TaBL59","CTTTCCACTTGAGTTGACTAGGTTG","CTATTTTCTCTCGCGTCTCCATC",666,null,"Bfa I"]
[60,"AX-110045982","TaBL60","GTAGCCCGTCCCATAAGCG","GGACTTGATG ACCGATGGTG",510,null,"Dra I"]
[]
["a SNP, ID numbers from Wheat660K SNP chip."]
["b CAPS, the tentative names for CAPS markers."]