Markers + reference

Campylaephora

2 species · Ceramiaceae · Ceramiales

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Species 2
Genome length 172–172 kb
Candidate markers 459
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 459 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
syfB Genome 2046 0.1075 1.00 77.9 yes View details
moeB Genome 1083 0.1154 1.00 78.8 yes View details
rpl19 Genome 354 0.0932 1.00 72.9 yes View details
infB Genome 2286 0.0862 1.00 76.1 yes View details
orf621 Genome 1917 0.1127 1.00 77.9 yes View details
trpA Genome 792 0.0745 1.00 83.3 yes View details
orf365 Genome 1098 0.1157 1.00 81.8 yes View details
QQR83_pgp086 Genome 780 0.0962 1.00 78.9 yes View details
ycf23 Genome 843 0.0854 1.00 78.4 yes View details
rps10-tufA Genome 20 0.1053 0.95 77.8 yes View details
QQR83_pgt016-QQR83_pgt017 Genome 17 0.1765 1.00 77.8 yes View details
QQR83_pgt017-ycf4 Genome 50 0.1702 0.94 77.7 yes View details
rpl19-QQR83_pgt008 Genome 217 0.1535 0.93 77.5 yes View details
tilS Genome 984 0.0894 1.00 77.4 yes View details
pgmA Genome 1569 0.0841 1.00 77.1 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
syfB_p1 syfB GAATCCTCCCACCCCAGATA ACAAAATCCGGCTTATGGCT 2633–2639 1.000 85.4
syfB_p2 syfB GGGTGTAGCCAAGTGGTAAG ACAAAATCCGGCTTATGGCT 2686–2692 1.000 85.3
syfB_p3 syfB GGTGTAGCCAAGTGGTAAGG ACAAAATCCGGCTTATGGCT 2685–2691 1.000 85.3
syfB_p4 syfB GAATCCTCCCACCCCAGATA AGGAAAGTCCGGGCTCTAAT 2960–2965 1.000 85.1
syfB_p5 syfB GGTGTAGCCAAGTGGTAAGG TCCGGCTTATGGCTTACTCT 2679–2685 1.000 84.8
moeB_p1 moeB GAAGGACTTGAACCCTCGAC ACTTGGTACGACCTGAAGAAG 1738 0.500 46.0
moeB_p2 moeB GAAGGACTTGAACCCTCGAC CTTGGTACGACCTGAAGAAGT 1737 0.500 46.0
moeB_p3 moeB GAGTTGCCTTACCAGCCATT ACTTGGTACGACCTGAAGAAG 1975 0.500 45.4
moeB_p4 moeB GAGTTGCCTTACCAGCCATT CTTGGTACGACCTGAAGAAGT 1974 0.500 45.4
moeB_p5 moeB TACACGCCTTGAAGGACTTG CTTGGTACGACCTGAAGAAGT 1747 0.500 45.4
rpl19_p1 rpl19 CTACAGCGACAAAGCCAGAA AGTGGTGATGCAAGCTTTCA 1478–1483 1.000 85.1
rpl19_p2 rpl19 CTACAGCGACAAAGCCAGAA TCAGTGGTGATGCAAGCTTT 1480–1485 1.000 85.1
rpl19_p3 rpl19 TCAGCATTATCGCCAAGCAT AGTGGTGATGCAAGCTTTCA 1694 0.500 59.7
rpl19_p4 rpl19 TCAGCATTATCGCCAAGCAT TCAGTGGTGATGCAAGCTTT 1696 0.500 59.7
rpl19_p5 rpl19 TCAGCATTATCGCCAAGCAT TGGTTGCACCAGGAAAAAGT 1369 0.500 58.6
rpl19-QQR83_pgt008_p1 rpl19-QQR83_pgt008 AGCTTCTTCTTGTGCAAGCA TCAGTGGTGATGCAAGCTTT 1311–1316 1.000 84.7
rpl19-QQR83_pgt008_p2 rpl19-QQR83_pgt008 AGCTTCTTCTTGTGCAAGCA AGTGGTGATGCAAGCTTTCA 1309–1314 1.000 84.6
rpl19-QQR83_pgt008_p3 rpl19-QQR83_pgt008 AGCTTCTTCTTGTGCAAGCA TGGTTGCACCAGGAAAAAGT 984–989 1.000 84.6
rpl19-QQR83_pgt008_p4 rpl19-QQR83_pgt008 AGCTTCTTCTTGTGCAAGCA TACCGGCTGCAATAGGAGTA 1365–1370 1.000 84.1
rpl19-QQR83_pgt008_p5 rpl19-QQR83_pgt008 AGCTTCTTCTTGTGCAAGCA TGCTGGCTTAGGAACAATGG 1394–1399 1.000 83.4
rps10-tufA_p1 rps10-tufA AGATGTTGCAGAAGACGAGG TGTTTCTGGTTCAGCCCTTC 1337 0.500 56.8
rps10-tufA_p2 rps10-tufA AGATGTTGCAGAAGACGAGG AACTGTTGGAGCAGGAGTTG 656 0.500 56.8
rps10-tufA_p3 rps10-tufA AGATGTTGCAGAAGACGAGG CTGTTGGAGCAGGAGTTGTT 654 0.500 56.8
rps10-tufA_p4 rps10-tufA AGATGTTGCAGAAGACGAGG ACTGTTGCAACTGGTCGAAT 1141 0.500 56.7
rps10-tufA_p5 rps10-tufA AGATGTTGCAGAAGACGAGG GGAGGAAGAACTGTTGGAGC 664 0.500 55.5
infB_p1 infB ACCTTCTGATTGTGCTGACA AATGCCGAGACGTTCTACAG 2715 1.000 76.6
infB_p2 infB GTGCTGACATTCCATCTCTGT AATGCCGAGACGTTCTACAG 2704 1.000 76.0
infB_p3 infB TGTGCTGACATTCCATCTCTG AATGCCGAGACGTTCTACAG 2705 1.000 75.9
infB_p4 infB TCACCTTCTGATTGTGCTGA AATGCCGAGACGTTCTACAG 2717 1.000 74.2
infB_p5 infB TCACCTTCTGATTGTGCTGAC AATGCCGAGACGTTCTACAG 2717 1.000 74.2

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
Campylaephora boydenii NC_079843.1 171790 View on NCBI ↗
Campylaephora sungminbooi NC_031211.1 171923 View on NCBI ↗