Markers + reference

Rhynchotechum

2 species · Gesneriaceae · Lamiales

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Species 2
Genome length 155–155 kb
Candidate markers 268
Primer pairs 85

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoC1-trnC-GCA LSC 4399 0.0050 1.00 51.5 yes View details
psbC LSC 1422 0.0113 1.00 55.8 yes View details
cemA LSC 693 0.0014 1.00 56.4 yes View details
psbB LSC 1527 0.0098 1.00 57.6 yes View details
petB-petD LSC 934 0.0075 0.99 49.4 yes View details
ccsA SSC 963 0.0021 1.00 46.7 yes View details
ycf1 SSC 5481 0.0053 1.00 41.8 yes View details
ccsA-ndhD SSC 243 0.0537 1.00 76.8 yes View details
ndhD-psaC SSC 92 0.0217 1.00 65.0 yes View details
infA-rps8 LSC 108 0.0185 1.00 63.1 yes View details
ycf4-cemA LSC 870 0.0069 1.00 62.7 yes View details
atpH-atpI LSC 1062 0.0057 0.99 62.6 yes View details
matK-trnK-UUU LSC 707 0.0057 1.00 62.0 yes View details
accD-psaI LSC 716 0.0056 1.00 62.0 yes View details
petA-psbJ LSC 1080 0.0046 1.00 61.4 yes View details
petN-psbM LSC 1020 0.0030 1.00 60.9 yes View details
rpl16-rps3 LSC 1048 0.0038 1.00 60.9 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU CCATGATCGTGAGCAAATGC AACGGTAGAGTACTCGGCTT 838–839 1.000 78.1
matK-trnK-UUU_p2 matK-trnK-UUU CCATGATCGTGAGCAAATGC ACGGTAGAGTACTCGGCTTT 837–838 1.000 78.1
matK-trnK-UUU_p3 matK-trnK-UUU CCATGATCGTGAGCAAATGC GGGTTGCTAACTCAACGGTA 851–852 1.000 75.8
matK-trnK-UUU_p4 matK-trnK-UUU CCATGATCGTGAGCAAATGC TTCGGGTTGCTAACTCAACG 854–855 1.000 75.5
matK-trnK-UUU_p5 matK-trnK-UUU TGAAACCATGATCGTGAGCA ACGGTAGAGTACTCGGCTTT 842–843 1.000 75.3
atpH-atpI_p1 atpH-atpI TCCGATAGAAGCAAGCCCTA TCCCTGTCATGTTCCTTGGA 1232–1235 1.000 78.0
atpH-atpI_p2 atpH-atpI AACGGAAGCAGCAGAAATCA TCCCTGTCATGTTCCTTGGA 1193–1196 1.000 77.9
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TCCCTGTCATGTTCCTTGGA 1251–1254 1.000 77.8
atpH-atpI_p4 atpH-atpI TCCAGGTCCGATAGAAGCAA TCCCTGTCATGTTCCTTGGA 1238–1241 1.000 77.6
atpH-atpI_p5 atpH-atpI GATAGAAGCAAGCCCTACGG TCCCTGTCATGTTCCTTGGA 1229–1232 1.000 77.5
rpoC1-trnC-GCA_p1 rpoC1-trnC-GCA ACCCAGTTCCAACAATGCAT ATTCAGGAAGAACAGGTGGT 229 1.000 69.8
rpoC1-trnC-GCA_p2 rpoC1-trnC-GCA AACTGCCTGACGTTGCATAT ATTCAGGAAGAACAGGTGGT 189 1.000 69.7
rpoC1-trnC-GCA_p3 rpoC1-trnC-GCA ACTGCCTGACGTTGCATATT ATTCAGGAAGAACAGGTGGT 188 1.000 69.7
rpoC1-trnC-GCA_p4 rpoC1-trnC-GCA CAACCCAGTTCCAACAATGC ATTCAGGAAGAACAGGTGGT 231 1.000 68.7
rpoC1-trnC-GCA_p5 rpoC1-trnC-GCA AACCCAGTTCCAACAATGCA ATTCAGGAAGAACAGGTGGT 230 1.000 68.2
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA TCATTCTAGTTCCTACCGCCT 1112–1116 1.000 72.3
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT TCATTCTAGTTCCTACCGCCT 1110–1114 1.000 72.3
petN-psbM_p3 petN-psbM ACTCGTAGTGTGGGGAAGAA TCTAGTTCCTACCGCCTTTCT 1108–1112 1.000 71.8
petN-psbM_p4 petN-psbM TCGTAGTGTGGGGAAGAAGT TCTAGTTCCTACCGCCTTTCT 1106–1110 1.000 71.8
petN-psbM_p5 petN-psbM CGTAGTGTGGGGAAGAAGTG TCATTCTAGTTCCTACCGCCT 1109–1113 1.000 71.7
psbC_p1 psbC AGGTATTCGTGCTTGGATGG ACATTGGATCCCCTGTCTCA 1480–1482 1.000 78.2
psbC_p2 psbC TATTCGTGCTTGGATGGCG ACATTGGATCCCCTGTCTCA 1477–1479 1.000 70.4
psbC_p3 psbC GGTATTCGTGCTTGGATGGC ACATTGGATCCCCTGTCTCA 1479–1481 1.000 70.2
psbC_p4 psbC AAGGTATTCGTGCTTGGATGG ACATTGGATCCCCTGTCTCA 1481–1483 1.000 70.0
psbC_p5 psbC GATGGCGGCTCAAGATCAG ACATTGGATCCCCTGTCTCA 1465–1467 1.000 69.8
accD-psaI_p1 accD-psaI TAAGCTCCACGCCTTTTTCC CCATTGCAATTGCCGGAAAT 811 1.000 76.4
accD-psaI_p2 accD-psaI TAAGCTCCACGCCTTTTTCC AAGAAGCCATTGCAATTGCC 817 1.000 75.8
accD-psaI_p3 accD-psaI GGTTCACAAGCGGCTGAATA CCATTGCAATTGCCGGAAAT 903 1.000 75.7
accD-psaI_p4 accD-psaI GGTTCACAAGCGGCTGAATA AAGAAGCCATTGCAATTGCC 909 1.000 75.1
accD-psaI_p5 accD-psaI TAAGCTCCACGCCTTTTTCC GCCGGAAATACTAGGCCTAC 800 1.000 73.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Rhynchotechum nirijuliense NC_070428.1 154629 View on NCBI ↗
Rhynchotechum vestitum NC_070429.1 154513 View on NCBI ↗