Markers + reference

Vertebrata

3 species · Rhodomelaceae · Ceramiales

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Species 3
Genome length 167–169 kb
Candidate markers 453
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 453 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf37 Genome 504 0.2824 1.00 76.8 yes View details
ycf80 Genome 1431 0.2110 1.00 80.0 yes View details
ycf58 Genome 456 0.2900 1.00 77.7 yes View details
ConsOrf4 Genome 732 0.2696 1.00 78.8 yes View details
infB Genome 2271 0.2018 1.00 77.9 yes View details
accB Genome 513 0.1956 1.00 80.3 yes View details
dnaB Genome 1794 0.2122 1.00 78.1 yes View details
moeB Genome 1071 0.2275 1.00 79.6 yes View details
syfB Genome 1968 0.2484 1.00 78.6 yes View details
ompR Genome 726 0.1805 0.98 80.5 yes View details
trnL-trnN Genome 114 0.3127 0.99 83.7 yes View details
ycf22 Genome 648 0.1878 1.00 82.2 yes View details
carA Genome 1179 0.1979 1.00 81.8 yes View details
ConsOrf5 Genome 1092 0.2686 1.00 80.3 yes View details
ycf29 Genome 627 0.1760 1.00 79.8 yes View details
trnR-trnV Genome 35 0.3039 0.97 79.7 yes View details
ConsOrf5-trnM Genome 530 0.1258 1.00 79.5 yes View details
argB Genome 861 0.1963 1.00 79.5 yes View details
ycf23 Genome 840 0.2175 1.00 79.3 yes View details
trpA Genome 813 0.1888 1.00 79.2 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf37_p1 ycf37 CATTCGCACCAAAAATCCGT AAACACGGGATATAGCGCAG 762 0.333 49.5
ycf37_p2 ycf37 CATTCGCACCAAAAATCCGT TGCGCTAGAAAACAGCTTCT 1135 0.333 49.2
ycf37_p3 ycf37 CATTCGCACCAAAAATCCGT AAAACACGGGATATAGCGCA 763 0.333 48.0
ycf37_p4 ycf37 TCATTCGCACCAAAAATCCG AAACACGGGATATAGCGCAG 763 0.333 47.2
ycf37_p5 ycf37 CATTCGCACCAAAAATCCGT TGTGATGCTGTAGGATGGGT 1182 0.333 47.2
carA_p1 carA TTATGGTGCGAATGGGATGC ACAACAGAAGCACCAGAAGG 1476 0.333 47.7
carA_p2 carA TTATGGTGCGAATGGGATGC GGACAACAGAAGCACCAGAA 1478 0.333 47.6
carA_p3 carA AACTTATGGTGCGAATGGGA ACAACAGAAGCACCAGAAGG 1479 0.333 46.7
carA_p4 carA AACTTATGGTGCGAATGGGA GGACAACAGAAGCACCAGAA 1481 0.333 46.7
carA_p5 carA TTATGGTGCGAATGGGATGC GCACCAGAAGGACACTTACC 1467 0.333 46.4
trnL-trnN_p1 trnL-trnN TAGCGTGTCTGCCAATTTCA ACTCCCCAGGAAGGATTTGA 217–219 1.000 88.7
trnL-trnN_p2 trnL-trnN TAGCGTGTCTGCCAATTTCA CCCCAGGAAGGATTTGAACC 214–216 1.000 87.6
trnL-trnN_p3 trnL-trnN TAGCGTGTCTGCCAATTTCA ACCACTGAGCTACTGAGGAA 163–165 1.000 87.0
trnL-trnN_p4 trnL-trnN GTGTCTGCCAATTTCACCAC ACTCCCCAGGAAGGATTTGA 213–215 1.000 86.8
trnL-trnN_p5 trnL-trnN TCTAGCGTGTCTGCCAATTT ACTCCCCAGGAAGGATTTGA 219–221 1.000 86.3
trnR-trnV_p1 trnR-trnV AGAAGGTCCCTGTCCTGATC CTGGTTCAAGTCCAGTACCG 83–96 1.000 90.3
trnR-trnV_p2 trnR-trnV AGAAGGTCCCTGTCCTGATC TTACAAGCAGGTGGTCACTG 100–113 1.000 88.9
trnR-trnV_p3 trnR-trnV GTCCCTGTCCTGATCCCTTA TTACAAGCAGGTGGTCACTG 95–108 1.000 88.6
trnR-trnV_p4 trnR-trnV AGAAGGTCCCTGTCCTGATC CAGGTGGTCACTGGTTCAAG 93–106 1.000 87.8
trnR-trnV_p5 trnR-trnV GTCCCTGTCCTGATCCCTTA CTGGTTCAAGTCCAGTACCG 90–91 0.667 73.5
trpA_p1 trpA CGATTAGTTCCGGGTTCGAG ATAAAAAGCAAGTGCCCCCA 1065 0.333 51.8
trpA_p2 trpA CGATTAGTTCCGGGTTCGAG TAAAAAGCAAGTGCCCCCAT 1064 0.333 51.8
trpA_p3 trpA ACCTCCAGAAAGAGCGACTA ATAAAAAGCAAGTGCCCCCA 1255 0.333 51.4
trpA_p4 trpA ACCTCCAGAAAGAGCGACTA TAAAAAGCAAGTGCCCCCAT 1254 0.333 51.4
trpA_p5 trpA CGATTAGTTCCGGGTTCGAG AGAAGCTATGGACAGCAGGA 1251 0.333 51.0
ycf23_p1 ycf23 CAAATTGCTTCCGCTCCAAG CCCTCTCTCAAACCATAAGCA 1289 0.333 40.2
ycf23_p2 ycf23 CAAATTGCTTCCGCTCCAAG GATGTTCCCTCTCTCAAACCA 1295 0.333 39.6
ycf23_p3 ycf23 AAATTGCTTCCGCTCCAAGA CCCTCTCTCAAACCATAAGCA 1288 0.333 39.5
ycf23_p4 ycf23 AATTGCTTCCGCTCCAAGAA CCCTCTCTCAAACCATAAGCA 1287 0.333 39.5
ycf23_p5 ycf23 GAAACTGCATGCCCTACTGA CCCTCTCTCAAACCATAAGCA 1238 0.333 39.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Vertebrata australis NC_035283.1 167318 View on NCBI ↗
Vertebrata isogona NC_035278.1 167445 View on NCBI ↗
Vertebrata thuyoides NC_035273.1 168951 View on NCBI ↗