Finalizing annotations and primer seqs

What was ordered from IDT



Herring SNP Primers IDT.xlsHerring SNP Primers IDT matched to contig seqs.txt
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>1_snp3_A12
CGTTCTGATTGGCTTACCCACTAAAATGTCATTCATATTCTTCAGTAAGCGTAGTTCATT
GTTCAACCACTKTTTGTCTTTTACACTTCGTCYTCATAGTCGAACAACCCTGAAATATTT
ACTTGGTSACGGTTACCTGAATTTTTAGGCAAGCCCCAAC
>2_snp3_B09
CCACCGTCCAGTAGAGGAATGAGGTGAAGATGAAGACACTAATGATGCTGAAGGGAAGGA
TATGGAATATGTAGGCCAAAAACATCTGCCACTTCTGATARAGGCCATCCTTACTCTCCT
GATCCGATATAGCCCTGAGTGCAGG
>3_snp1_B12
GGTCATCTGGAGGCATCTGGGTGAAAGGCCGTCGGCCCTGGGCAACAACACCATGCTGGT
TCAGTGGATGCCCCAGAATGACCTYCTGGGCCACTCCCAGATAAAGGCCTTTGTCGCCCA
CGGGGGAACGAACGGAGTTCAGGAG
>4_snp1_C03
GCTTTAGCAATTAGCTGCATTCATATTTTACATATCTTTGTTTGTTTACTACTGAAAATA
TGCTAGTTAAAACACAGATACAAAACMATGTGAGTTTATACAACCATAGATTTAACAGGT
ATAACAGATAACTCAATACAAGTCTTTTTTTATGTATAGGTAGAGTGGTCATTGTG
>5_snp1_C04
TGAGGAGACCCAGTGAGGTCTGCTGGACCACACCCCCTCTGTGTTATGGCACAGGGAGTG
GATCTATGKATGATGGATGGGAAGGCATTTGTCTATCTTTGTCAACGCCTGATG
>6_snp1_C07
TTTGCTACAAAACGCAGATGGTCCATCTCATAAGGTATATTGCACAAAATAATGAAGAAA
CAAACATATGTGCCATTAAGATGATACAAMTGCAAAACAAAAATCCAGTTTCACATCTGC
TATGTGGGACCCATTCAC
>7_snp1_C09
TAAGGAATGCCCACGTCTGCTTTGGGGAAGTGATGAGGTAAATAAGAGTGTTTATTGCCT
CAGTGCTGTMATTTGTGTGAAGTGCCACGTGTGTGTCTGTTCACGTTTCCCATGACTCCT
AAGGACAGGAACACAACACGCTTGTCC
>8_snp1_D01
GCAGTACCCTCAGTGGTGTAGGACAGGATATCAATTGGACTGTCAGCTGCCATCCTGTAY
TTGGCGTTGTAGGCTGGACCCTCCTCAGAGTCTTTGCCAGCAGAGATGGTGGCCTCCCAG
TTGTAGTAGTTGCTGTTGACCTTGGCAGACAC
>9_snp2_E09
GTGATTCCCTTGTGGTGGTTGTGGTCCACCAGACCTCCAATGACATAAGCTTTGGACTCA
TCCAGCTCCTTAAGCATGTTGGGYGAGTCGGAGGTGAGGTAGACCAGSTCCTCCTTACGC
ATCACTTCCTGAAAGTGCTCTGGC
>10_snp2_E11
CTCTCTGCCAGTGATGCTGAAGGGAAGACCACTGGCAACCCTGAGTCCTGAGGAGCTCGG
ACTRAAGATAGACTARGAGAGGAGAGTGGAGACTGTGATGAATTGACATCAAGACACTCT
TGTCAAGATGGTACACACACTGTGGCAG
>11_snp1_F02
GGATGCCAACAGCACTCTTAAAGCTCGTGTCCATCATCATGAGGGGAYGGGAGATCTCTG
ATGTCACAGTTTTGGAAGAGTTTGATGTAGAACACAACAAGCTCCTCATAGTTCTTAATG
GATATCCTCTCATTCACACCATGAAACCTCTGAGGGA
>12_snp1_G03
CCAACCCTGATGTCAGTTCCCAGAGACATGTACAGTACCTGGTTGTCTGACAGAGTCTGC
ATRGGCTCATAGAAACATACCACAGATGAGTGGAGCCCTACAGCAGTATGGATCCCTCAT
GCCCAACACAGTCAC
>13_snp1_G07
GTCTTTGGTGGCACTTCTGCCCACATTCAAGGGAAGAATGTTTCCRATTCTCTGGGTCTC
ATGGATAACAGCATCAGTGTAAGGCATGTTCTCCCTGTCAGTTAAGGAGGGCGGGCGTGA
GGATCCAACCACACGGTCAATCTCCT
>14_snp1_H04
CTTCGGCTTTTGCCGTGCCGAAGGAGTGGGTGCTGCTCCACGTGGTGCAGGGCCACATTG
GCGCRGGCAACTACAGTTACCTGCGACTAAACCACGACGGGCGCATCATCCTACACATGA
GCAGC

HerringHRM.fa

>1
CGTTCTGATTGGCTTACCCACTAAAATGTCATTCATATTCTTCAGTAAGCGTAGTTCATTGTTCAACCACT[G/T]TTTGTCTTTTACACTTCGTC[C/T]TCATAGTCGAACAACCCTGAAATATTTACTTGGT[C/G]ACGGTTACCTGAATTTTTAGGCAAGCCCCAAC
>2
GCTTCTTCAAGGGACTGCTCCGTTGTGTCGAAGCTGAGTCCACCGATGAACAGTTTTCCCTCGTCAGACATATT[G/T]CTGGTTTAAACTCG[G/T]CTGCTGTTGAGCTGGAATGTTCTGCGTGAT[A/G]TCCCAGTTAAGGACGGTGTCGC
>3
GGTCATCTGGAGGCATCTGGGTGAAAGGCCGTCGGCCCTGGGCAACAACACCATGCTGGTTCAGTGGATGCCCCAGAATGACCT[C/T]CTGGGCCACTCCCAGATAAAGGCCTTTGTCGCCCACGGGGGAACGAACGGAGTTCAGGAG
>4
GCTTTAGCAATTAGCTGCATTCATATTTTACATATCTTTGTTTGTTTACTACTGAAAATATGCTAGTTAAAACACAGATACAAAAC[A/C]ATGTGAGTTTATACAACCATAGATTTAACAGGTATAACAGATAACTCAATACAAGTCTTTTTTTATGTATAGGTAGAGTGGTCATTGTG
>5
TGAGGAGACCCAGTGAGGTCTGCTGGACCACACCCCCTCTGTGTTATGGCACAGGGAGTGGATCTATG[G/T]ATGATGGATGGGAAGGCATTTGTCTATCTTTGTCAACGCCTGATG
>6
TTTGCTACAAAACGCAGATGGTCCATCTCATAAGGTATATTGCACAAAATAATGAAGAAACAAACATATGTGCCATTAAGATGATACAA[A/C]TGCAAAACAAAAATCCAGTTTCACATCTGCTATGTGGGACCCATTCAC
>7
TAAGGAATGCCCACGTCTGCTTTGGGGAAGTGATGAGGTAAATAAGAGTGTTTATTGCCTCAGTGCTGT[A/C]ATTTGTGTGAAGTGCCACGTGTGTGTCTGTTCACGTTTCCCATGACTCCTAAGGACAGGAACACAACACGCTTGTCC
>8
GCAGTACCCTCAGTGGTGTAGGACAGGATATCAATTGGACTGTCAGCTGCCATCCTGTA[C/T]TTGGCGTTGTAGGCTGGACCCTCCTCAGAGTCTTTGCCAGCAGAGATGGTGGCCTCCCAGTTGTAGTAGTTGCTGTTGACCTTGGCAGACAC
>9
GTGATTCCCTTGTGGTGGTTGTGGTCCACCAGACCTCCAATGACATAAGCTTTGGACTCATCCAGCTCCTTAAGCATGTTGGG[C/T]GAGTCGGAGGTGAGGTAGACCAG[C/G]TCCTCCTTACGCATCACTTCCTGAAAGTGCTCTGGC
>10
CTCTCTGCCAGTGATGCTGAAGGGAAGACCACTGGCAACCCTGAGTCCTGAGGAGCTCGGACT[A/G]AAGATAGACTA[A/G]GAGAGGAGAGTGGAGACTGTGATGAATTGACATCAAGACACTCTTGTCAAGATGGTACACACACTGTGGCAG
>11
GGATGCCAACAGCACTCTTAAAGCTCGTGTCCATCATCATGAGGGGA[C/T]GGGAGATCTCTGATGTCACAGTTTTGGAAGAGTTTGATGTAGAACACAACAAGCTCCTCATAGTTCTTAATGGATATCCTCTCATTCACACCATGAAACCTCTGAGGGA
>12
CCAACCCTGATGTCAGTTCCCAGAGACATGTACAGTACCTGGTTGTCTGACAGAGTCTGCAT[A/G]GGCTCATAGAAACATACCACAGATGAGTGGAGCCCTACAGCAGTATGGATCCCTCATGCCCAACACAGTCAC
>13
GTCTTTGGTGGCACTTCTGCCCACATTCAAGGGAAGAATGTTTCC[A/G]ATTCTCTGGGTCTCATGGATAACAGCATCAGTGTAAGGCATGTTCTCCCTGTCAGTTAAGGAGGGCGGGCGTGAGGATCCAACCACACGGTCAATCTCCT
>14
CTTCGGCTTTTGCCGTGCCGAAGGAGTGGGTGCTGCTCCACGTGGTGCAGGGCCACATTGGCGC[A/G]GGCAACTACAGTTACCTGCGACTAAACCACGACGGGCGCATCATCCTACACATGAGCAGC


Attached is the Sanger summary file.  Sequences (n=14) we proceeded
   with are highlighted yellow.

   A note of concern: some sequences, although apparently scorable via
   HRMA, contained multiple polymorphisms per template after Sanger.
    Each putative SNP is included in the sequence.  I cannot say which
   is the variant you want to test for S/NS.

   Let me know if you have any questions,

   Eric







ContigsHerring_hrm selection.fa
Note Full Contig file location:

File with primers and annotations

96HerringSNP_primers_blast.txt

herring_genotype_table.xlsx

Microsoft Excel.pdf