##scaffold00084_181078 (primer9)
>IXFm1_9R
TATCGCGAAAGGCAGGGCAGGCAGCATCCAGCGGAGGGCTCGGCAAACGCGCTACGCCMCCCAGCAAAGCGGAAGTTAAGAAGGTGATTGAATCTCAATTARGACATTGACAACTCCTTTTAAGGTCTCTTTCACACACACAAAAAAAGCTACTTTCCCTTCCCTCCC
>IXFm2_9R
GAAAGGCAGGGCAGGCAGCATCCAGCGGAGGGCTCGGCAAACGCGCTACGCCMCCCAGCAAAGCGGAAGTTAAGAAGGTGATTGAATCTCAATTARGACATTGACAACTCCTTTTAAGGTCTCTTTCACACACACAAAAAAAGCTACTTTCCCTTCCCTCCCCCCAGTATCCAAAGCTCC
>IXFd05_9R
CATCCAGCGGAGGGCTCGGCAAACGCGCTACGCCMCCCAGCAAAGCGGAAGTTAAGAAGGTGATTGAATCTCAATTARGACATTGACAACTCCTTTTAAGGTCTCTTTCACACACACAAAAAAAGCTACTTTCCCTTCCCTCCCCCCAGTATCCAA
>IXF1d06_9R
GGCAGGGCAGGCAGCATCCAGCGGAGGGCTCGGCAAACGCGCTACGCCMCCCAGCAAAGCGGAAGTTAAGAAGGTGATTGAATCTCAATTARGACATTGACAACTCCTTTTAAGGTCTCTTTCACACACACAAAAAAAGCTACTTTC

##scaffold00024_965997 (primer12)
# Note this was an Indel polymorphism so both mother and offspring sequence was unreadable after the polymorphism. Nevertheless, fasta sequence was extracted for the purpoe of this file.
>IXF1d02_12F
TCGATCGATATTTTTCTTTTTCGTTTCCCGGAGCCGCCAACTTCGGCTGCGGCTGCGCTTCTGCGGCGCGCCCGCACTACCGCCAAATCGACG
>IXF1d04_12F
ATCGATCGATATTTTTCTTTTTCGTTTTCCTGACTCGCAGCTTTGACTGCAGCTTTGCTTCTGCGCCGCGCTTGTACGACCGACGAAGACGAC
>IXF1m1_12F
GATCGATATTTTTCTTTTTCTTTTCCCGGACCCGCCAACTCCGACTGCGGCTGTGGTGCTGCGGCGCGCTTGTACTACCGACAACGACGACGT
>IXF1m2_12F
GATCGATATTTTTCTTTTTCGTTTTCGGGAGTAGCCAACTCTGACTGCGGTTGCGCTGCTGCGGCGCGCTTGTACTACCGACAACGACGA

##scaffold01005_1090145 (Primer24)
>IXF1m1_24F
GCCATCCGACAATGGAGACGGTGGAGGCGAACTCGGTGATGGCGAGCATTCTCCACTAGCATCTGAATAACCACTATCGAAAGGATCCTCATACAGTTTAAAAGAAAAYTCTGCAGCAAAAAAAAMMAAAAWTWAAA
>IXF1m2_24F
AATGCCATCCGACAATGGAGACGGTGGAGGCGAACTCGGTGATGGCGAGCATTCTCCACTAGCATCTGAATAACCACTATCGAAAGGATCCTCATACAGTTTAAAAGAAAAYTCTGCAGCAAAAAAAAMMAAAAWTWAAA
>IXF1d04_24F
CCATCCGACAATGGAGACGGTGGAGGCGAACTCGGTGATGGCGAGCATTCTCCACTAGCATCTGAATAACCACTATCGAAAGGATCCTCATACAGTTTAAAAGAAAAYTCTGCAGCAAAAAAAAMMAAAAWTWAAA
>IXF1d21_24F
TCCGACAATGGAGACGGTGGAGGCGAACTCGGTGATGGCGAGCATTCTCCACTAGCATCTGAATAACCACTATCGAAAGGATCCTCATACAGTTTAAAAGAAAAYTCTGCAGCAAAAAAAAMNAAAAWTWAAA

##scaffold00687_215401 (primer51)
>IXm1F51 51F
TGCTAATGCCGCAGTCTGTGTGGGTAGCACAGTGAAACGTGGTTTTTAAAAATGTGCCGTTCAAAYAATCTATTAATTGTAATTTGTAGTTTCCTACCTGCAGGCTGAATGCGAAAATCCCCAGGAACACATTTCCAAAATAAAATAGANAATCAGAWTTCATTTCTACTTATTGCACCTACAATTTAAASCCGAATGATCGCGTT
>IXm2R51 51R
TTCTGATTCTCTATTTTATTTTGGAATGTGTTCCTGGGGATTTTCGCATTCAGCCTGCAGGTAGGAAACTACAAATTACAATTAATAGATTNTTTGAACGGCACATTTTTAAAAACCACGTTTCACTGTGCTACCCACACAGAYTGCGGCATTAGCAGTTAGTGATGCAAYCTACATCCCGGATTTGGTGTGTACGGGTATCTGGGGAATTCTAT
>IXd21F51 51F
TGCTAATGCCGCAGTCTGTGTGGGTAGCACAGTGAAACGTGGTTTTTAAAAATGTGCCGTTCAAAYAATCTATTAATTGTAATTTGTAGTTTCCTACCTGCAGGCTGAATGCGAAAATCCCCAGGAACACATTTCCAAAATAAAATAGANAATCAGAWTTCATTTCTACTTATTGCACCTACAATTTAAASCCGAATGATCGCGTTTGGATAGCTN
>IXd21R51 51R
GATTCTGATTYTCTATTTTATTTTGGAAATGTGTTCCTGGGGATTTTCGCATTCAGCCTGCAGGTAGGAAACTACAAATTACAATTAATAGATTRTTTGAACGGCACATTTTTAAAAACCACGTTTCACTGTGCTACCCACACAGAYTGCGGCATTAGCAGTTAGTGATGCAAYCTACATCCCGGATTTGGTGTGTACGGGTATCTGGGGAANA
>IXd22F51 51F
ATGCCGCAGTCTGTGTGGGTAGCACAGTGAAACGTGGTTTTTAAAAATGTGCCGTTCAAAYAATCTATTAATTGTAATTTGTAGTTTCCTACCTGCAGGCTGAATGCGAAAATCCCCAGGAACACATTTCCAAAATAAAATAGARAATCAGAWTTCATTTCTACTTATTGCACCTACAATTTAAASCCGAATGATCGCGTTGGATAGCT
>IXd22R51 51R
TGATTCTGATTNTCTATTTTATTTTGGAAATGTGTTCCTGGGGATTTTCGCATTCAGCCTGCAGGTAGGAAACTACAAATTACAATTAATAGATTRTTTGAACGGCACATTTTTAAAAACCACGTTTCACTGTGCTACCCACACAGAYTGCGGCATTAGCAGTTAGTGATGCAAYCTACATCCCGGATTTGGTGTGTACGGGTATCTGGGGAAA

##scaffold01005_615383 (primer52)
>IXm1F52 52F
TGTAGAAGGTCTTGTTCAAGTGGTTTTTTGAATGTTTTGTTTCATTAACAATCTATGGCCAATTAAACAGGGTGCATAMATAATAACTTTAAAAGCGGATTTACCCAAGCTATCCGATGACATCAGGAATAACGCTCGCGTGCTGCAGATATCACGTTCCCTCTTGATTAGRAAAATGATACTCCCGGATTTTCACTTGTTTACTTCTAGTTTTATCTAAACAAACAAATAAAATAAGTGGTACAATTCTAGCCTAGCTTAATATTGCATGGGGTAGCAAAAAAAAT
>IXm2R52 52R
TTTACATGTAGAAGGTCTTGTTCAAGTGGTTTTTTGAATGTTTTGTTTCATTAACAATCTATGGCCAATTAAACAGGGTGCATAMATAATAACTTTAAAAGCGGATTTACCCAAGCTATCCGATGACATCAGGAATAACGCTCGCGTGCTGCAGATATCACGTTCCCTCTTGATTAGRAAAATGATACTCCCGGATTTTCACTTGTTTACTTCTAGTTTTATCTAAACAAACAAATAAAATAAGTGGTACAATTCTAGCCTAGCTTAATATTGCATGGGGTAGCAAAAAN
>IXd24F52 52F
TGTAGAGGTCTTGTTCAGTGGTTTTTTGAATGTTTTGTTTCATTAACNATCTATGGCCAATTAAACAGGGTGCATAMATAATAACTTTAAAAGCGGATTTACCCAAGCTATCCGATGACATCAGGAATAACGCTCGCGTGCTGCAGATATCACGTTCCCTCTTGATTAGRAAAATGATACTCCCGGATTTTCACTTGTTTACTTCTAGTTTTATCTAAACAAACAAATAAAATAAGTGGTACAATTCTAGCCTAGCTTAATATTGCATGGGGTAGCAAAAA
>IXd24R52 52R
CAGTGGTTTTTTGAATGTTTTGTTTCATTAACAATCTATGGCCAATTAAACAGGGTGCATAMATAATAACTTTAAAAGCGGATTTACCCAAGCTATCCGATGACATCAGGAATAACGCTCGCGTGCTGCAGATATCACGTTCCCTCTTGATTAGRAAAATGATACTCCCGGATTTTCACTTGTTTACTTCTAGTTTTATCTAAACAAACAAATAAAATAAGTGGTACAATTCTAGCCTAGCTTAATATTGCATGGGGTAGCAAAAAA

##scaffold03258_520152 (primer6)
>RM30m1_6F
CGRAAGAGTGCTTTTTCATTAGTTGTGTAACAACAAAGAAGAACTTTCGAAATTGTTTGAAAGTGCAGCATCTCTGCAGGATTGCGGGCTGGGCCTTAC
>RM30d25_6F
AGTGCTTTTTCATTAGTTGTGTAACAACAAAGAGAACTTTCGAAATTGTTTGAAAGTGCAGCATCTCTGCAGGATTGCGGGCTGGGCCTTACCCGCCAGACAGCGTC
>RM30d01_6F
CGGARAGATGTGCTTTTTCATTAGTTGTGTACAACAAAGAAAACTTTCGAAATTGTTTGAAAGTGCAGCATCTCAGCAAGATTGCGGGCTGAGGCCTTACCCGCCAGACAGCGTCCACTTCAT
>RM30d24_6F
GCACGGARAGATGTGCTTTTTCATTAGTTGTGGTAACAACAAAGTAGAACTTTCGAAATTGGTTTGAAAGTGCAGCATCTCTGCAGGATTGCGGGCTGGGGCCTTACCCGCCAGACAGCG

##scaffold01654_178568 (primer8)
#Note: LOH was detected in IXF1 and RM30 line, sequenced fragment did not capture exact RAD tag but the adjecent region. For both lines daughter sequences were same as the mother sequence
>IXm2_8F
TGGGACAGAGCTGCAGACGGTGCCGGGTCGGCTTGCGCTCRCACACGCACTCGCATGCACGCCATCAAATCTAAAATAATTTGTTGTTTTTTGTTTTTMTTTTTTTTTTTC
>IXm1_8F
CTAGTGGGACAGTAGCTGCAGACGGTGCCGAGGTCGGCTTGCGCTCRCACACGCACTCGCATGCACGCCATCAAATCTAAAATAATTTGTTGTTTTTTGTTTTTMTTTTTTTTTT
>IXF1d05_8F
CTCRCACACGCACTCGCACGCACGCCATCAAATCTAAAATAATTTGTTGTTTTTTGTTTTTMTTTTTTTTTTTCTTCGGTCGTGACATTTT
>RM30m1_8F
GGGACAGAGCTGCAGACGGTGCCGGGTCGGCTTGCGCTCACACACGCACTCGCATGCACGCCATCAAATCTAAAATAATTTGTTGTTTTTTGTTTTTCTTTTTTTTTT
>RM30m2_8F
CTCACACACGCACTCGCATGCACGCCATCAAATCTAAAATAATTTGTTGTTTTTTGTTTTTCTTTTTTTTTT
>RM30d04_8F
GGGACAGAGCTGCAGACGGTGCCGGGTCGGCTTGCGCTCACACACGCACTCGCATGCACGCCATCAAATCTAAAATAATTTGTTGTTTTTTGTTTTTCTTTTTTTTTT

##scaffold02723_2112 (primer30)
>RM30m1_30F
GCNTTCACGACCGCCGAACCTATGACAAGGATCGTTACTTCTGCAGTTCGCACATCTATTTCTCGCATAAACGAATCGTCYGAACACGTTTGCAATGAAGATCCGGGTGGAACCTTAAATTCTTATGAATATCGCCGCCAACATCACAGTGAAAATCCGAGCATGTTTCACAGCCTTGATCGTCTTCGCAGTAAATCTGGCGGCNATGTCA
>RM30m2_30F
ACCGCCGAACCTATGACAAGGATCGTTACTTCTGCAGTTCGCACATCTATTTCTCGCATAAACGAATCGTCYGAACACGTTTGCAATGAAGATCCGGGTGGAACCTTAAATTCTTATGAATATCGCCGCCAACATCACAGTGAAAATCCGAGCATGTTTCACAGCCTTGATCGTCTTCGCAGTAAATCTGGCGGCNATGTC
>RM30d04_30F
ACGAAACAGCNTTCACGACCGCCGAACCTATGACAAGGATCGTTACTTCTGCAGTTCGCACATCTATTTCTCGCATAAACGAATCGTCYGAACACGTTTGCAATGAAGATCCGGGTGGAACCTTAAATTCTTATGAATATCGCCGCCAACATCACAGTGAAAATCCGAGCATGTTTCACAGCCTTGATCGTCTTCGCAGTAAATCTGGCGGCNATGTC

##scaffold02581_769135 (primer41)
>RMm2_41R
ANCCGGAAAGCTGGCTGGCCTGGTCCTCNAGGTCCAACTGGGCCCAAAGGAGATACCGGAAACGACGGTTGGCACATTTTANATTTCATGTGTTGCGTATGTTCGTTTTGATACAATCAANAATTTTGCTTACAAAAGGGCCTGCAGGTAAAGAAGGCCCTACAGGGCCAGAAGGTCCAACNGGTCCGAGGGGTAAATAACAACAAMAAAA
>RMd04_41R
GGTCCTCNAGGTCCAACTGGGCCCAAAGGAGATACCGGAAACGACGGTTGGCACATTTTANATTTCATGTGTTGCGTATGTTCGTTTTGATACAATCAANAATTTTGCTTACAAAAGGGCCTGCAGGTAAAGAAGGCCCTACAGGGCCAGAAGGTCCAACNGGTCCGAGGGGTAAATAACAACAAMA

##scaffold02581_777742 (primer42)
>RM30m1_42F
CCTGCAGGTCCGACAGGGCCAATAGNACCAGGAGCACCAGGAGCTCCATCTTTGCCTGGGTATCCTGGTGCACCAGGTGGGCCAGGAATCTTGGATGGGAGTGTGATTCCAGGAGCACCAACATCTCCTTTAGGCCCTTGCGGTCCAGGGGCTCCGGGATATCCGTCTTTGCCAGGGGYWCCTGGGGCTCCAGGAGCTCCATCCGCACCATTGCGWCCAGCA
>RM30d21_42F
TGTGGGCCGACTGGGCCTGCAGGTCCGACAGGGCCAATAGNACCAGGAGCACCAGGAGCTCCATCTTTGCCTGGGTATCCTGGTGCACCAGGTGGGCCAGGAATCTTGGATGGGAGTGTGATTCCAGGAGCACCAACATCTCCTTTAGGCCCTTGCGGTCCAGGGGCTCCGGGATATCCGTCTTTGCCAGGGGYWCCTGGGGCTCCAGGAGCTCCATCCGCACCATTGCGWCCAGCATCTC
>RM30d04_42F 
TCTTGTGGGCCGACTGGGCCTGCAGGTCCGACAGGGCCAATAGNACCAGGAGCACCAGGAGCTCCATCTTTGCCTGGGTATCCTGGTGCACCAGGTGGGCCAGGAATCTTGGATGGGAGTGTGATTCCAGGAGCACCAACATCTCCTTTAGGCCCTTGCGGTCCAGGGGCTCCGGGATATCCGTCTTTGCCAGGGGYWCCTGGGGCTCCAGGAGCTCCATCCGCACCATTGCGNCCAGCATCTCC

##scaffold01115_5223 (primer43)
>RMm2_43R
TCAGCTCAATTTTTCATTCTTTTCGAATTCAACGCCGCAATTAACGCGAACTTATTTGATTGCTTTGTTACATGTTTTATCTTTTACTTTTTTTTTTATGCAACTTAACATTTCCACGAAAAATATCTGCAGATAACAACAACATTCGAAAGCTGAAAGACCGCAATCAGAANG
>RMd21_43F
TTTTCGTGGAATGTTAAGTTGCATAAAAAAAAAAGTAAAAGATAAAACATGTAACAAAGCAATCAAATAAGTTCGCGTTAATTGCGGCGTTGAATTCGAAAAGAATGAAAAATTGAGCTGACCTTTCTTGGGAGAAGNGGGKGGCGTTTCCATTGCGGATGATGNGGTCGGATTAAGGACGAAACC
>RMd22_43F
ATATTTTTCGTGGAATGTTAAGTTGCATAAAAAAAAAAGTAAAAGATAAAACATGTAACAAAGCAATCAAATAAGTTCGCGTTAATTGCGGCGTTGAATTCGAAAAGAATGAAAAATTGAGCTGACCTTTCTTGGGAGAAGNGGGNGGCGTTTCCATTGCGGATGATGTGGTCGGATTAAGGACGAACC

##scaffold00640_105924 (primer2)
>RM2m1_2R
CTCGTATTCACACTAAATAGAACCTGCAGTTCAACCGGTGAAACTATGAACGAAATGCAACTTAAGATGTTGATCGGTTCGAATTTTTAAATTTTTCTTTGWCGTCACCA
>RM2d23_2R
ATCTCGTATTCACACTAAATAGAACCTGGCAGTTCAACCGAGTGAAACTATGAACGAAATGCAACTTAAGATGTTGATCGAGTTCGAATTTTTAAATTTTTCTTTGWCGTCACC
>RM2d04_2F
GGCATTTCGTTCATAGTTTCACCGAGTTGAACCGCATAGTTCTATTTAGTGTGAATACGAGATCTTCAGATTTAAGCAATTTGAATTATTTTCGTCTTTCGAGTTCTTTTCCTCTGCAGTA

##scaffold03102_238072 (primer3)
>RM2m1_3R
GGGCGGCGATATTACAACATAGGAAACCAAGAGAATCTGCAGTKCTGTYGAACTGCTCTACAAAATGATTGTAAACATTGTATTTCTATGCATAGTTTGTTGCCTAACGCAATCCAATCAATACAAAGTCGYTCAGATTTTTAGTCATATCCCTCTCCAAYCCTTGCCTCCTTGCGTATCTTCCCCCCTTCTGGGCGGAAGAAGATAATACTACAAGGCCTCTG
>RM2d06_3R
GCATGTAGTGGGCGGCGATATTACAACATAGGAAACCAAGAGAATCTGCAGTKCTGTYGAACTGCTCTACAAAATGATTGTAAACATTGTATTTCTATGCATAGTTTGTTGCCTAACGCAATCCAATCAATACAAAGTCGYTCAGATTTTTAGTCATATCCCTCTCCAAYCCTTGCCTCCTTGCGTATCTTCCCCCCTTCTGGGCGGAAGAAGATAATACTACAAGGCCTCTGCTACATCACTAATTTTTTCT
>RM2d04_3R
CTCGCGCATGTAGTGGGCGGCGATATTACAACATAGGAAACCAAGAGAATCTGCAGTKCTGTYGAACTGCTCTACAAAATGATTGTAAACATTGTATTTCTATGCATAGTTTGTTGCCTAACGCAATCCAATCAATACAAAGTCGYTCAGATTTTTAGTCATATCCCTCTCCAAYCCTTGCCTCCTTGCGTATCTTCCCCCCTTCTGGGCGGAAGAAGATAATACTACAAGGCCTCTGCTACATCACT

##scaffold00512_163074 (primer14)
>CH876m1_14F
CAGTGCTGYTTTGATTTTCCTGTCGTCAGGCTTCAATAGTAACCCAAATCAAAGAAAGCCTCTTCTACCTCGCGGTGAAAAATGCAAATTCAGCAAATCCCATTT
>CH876d25_3F
TGYTTGATTTTCCAGTCGTCAGCTTCAAAAGTAACCCAAATCAAGAAGCCTCTTCTACCTCGCGTGAAAAAACAAATTCAGCAAATCCCATTTCGGCA
>CH876d04_14F
YTTGATTTTCCCTGTCGTCTGCTTCAAAAAGTAACCCAAATCAAGAAGCCTCTTCTACCTCGCGTGAAAAATGCAAATTCAGCAAATCCCATTTCGGCATTTGTTGATTGT