Markers + reference

Dasyclonium

4 species · Rhodomelaceae · Ceramiales

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Species 4
Genome length 170–171 kb
Candidate markers 453
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 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 513 0.1914 1.00 76.9 yes View details
psaC-ycf22 Genome 975 0.2036 1.00 80.3 yes View details
orf5 Genome 1092 0.2131 0.99 84.4 yes View details
ycf58 Genome 465 0.1860 1.00 79.7 yes View details
Orf4 Genome 693 0.1994 1.00 78.8 yes View details
dnaB Genome 1827 0.1724 1.00 78.9 yes View details
moeB Genome 1086 0.1687 1.00 79.5 yes View details
syfB Genome 1989 0.1761 1.00 78.8 yes View details
orf5-cemA Genome 725 0.0952 0.98 84.3 yes View details
tilS Genome 981 0.1539 1.00 83.5 yes View details
ycf4 Genome 549 0.1087 1.00 82.8 yes View details
accB Genome 486 0.1259 1.00 82.2 yes View details
dsbD Genome 738 0.1495 1.00 81.0 yes View details
ompR-rns Genome 378 0.1574 1.00 80.7 no View details
ycf55 Genome 948 0.1294 1.00 80.4 yes View details
ssrA Genome 437 0.0816 1.00 80.4 yes View details
trnL-trnN Genome 127 0.2533 0.94 80.3 yes View details
rps1 Genome 795 0.1524 1.00 80.2 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf37_p1 ycf37 CCACTTTTAGTTCTCATTCTTGCT ATGCAGTAGGATGGGTACGT 1201 0.500 23.9
ycf37_p2 ycf37 TGCATTCATAATTGTTTGTCCACT ATGCAGTAGGATGGGTACGT 1220 0.250 13.6
ycf37_p3 ycf37 TGCATTCATAATTGTTTGTCCACT TGTGATGCAGTAGGATGGGT 1224 0.250 11.9
ycf37_p4 ycf37 TCCACTTTTAGTTCTCATTCTTGC ATGCAGTAGGATGGGTACGT 1202 0.250 11.8
ycf37_p5 ycf37 TGCATTCATAATTGTTTGTCCACT TGCAGTAGGATGGGTACGTA 1219 0.250 11.7
ycf55_p1 ycf55 TGTCCTACTGGAGCTTCTGT AGTTTTGACTAGCAGCAGCA 1793 0.250 45.4
ycf55_p2 ycf55 TGTCCTACTGGAGCTTCTGT TTGACTAGCAGCAGCAAAGT 1789 0.250 45.4
ycf55_p3 ycf55 TGTCCTACTGGAGCTTCTGT CTGGACTTGGAGCTGCATTT 2294 0.250 43.9
ycf55_p4 ycf55 TGTCCTACTGGAGCTTCTGT GGACTTGGAGCTGCATTTGT 2292 0.250 41.5
ycf55_p5 ycf55 TGTCCTACTGGAGCTTCTGT TGGACTTGGAGCTGCATTTG 2293 0.250 41.5
trnL-trnN_p1 trnL-trnN TAGCGTGTCTGCCAATTTCA CTACCACTGAGCTACTGAGGA 159–178 1.000 82.5
trnL-trnN_p2 trnL-trnN TAGCGTGTCTGCCAATTTCA TCTACCACTGAGCTACTGAGG 160–179 1.000 82.5
trnL-trnN_p3 trnL-trnN TAGCGTGTCTGCCAATTTCA ACCAATCGGTTAACAGCCG 184–203 1.000 81.4
trnL-trnN_p4 trnL-trnN TAGCGTGTCTGCCAATTTCA TACCACTGAGCTACTGAGGA 158–177 1.000 81.0
trnL-trnN_p5 trnL-trnN GTGTCTGCCAATTTCACCAC CTACCACTGAGCTACTGAGGA 155–174 1.000 80.6
dsbD_p1 dsbD GGTTCAAATCCTTCCTGGGG TAAACTTCCAACGTCGTGCA 1223 0.250 48.3
dsbD_p2 dsbD ATTTCACCACGTCCGCTTTA TAAACTTCCAACGTCGTGCA 1416 0.250 48.1
dsbD_p3 dsbD TTTCACCACGTCCGCTTTAT TAAACTTCCAACGTCGTGCA 1415 0.250 48.1
dsbD_p4 dsbD TAGCGTGTCTGCCAATTTCA TAAACTTCCAACGTCGTGCA 1430 0.250 48.1
dsbD_p5 dsbD TTCACCACGTCCGCTTTATC TAAACTTCCAACGTCGTGCA 1414 0.250 47.2
tilS_p1 tilS GGTGCACCTCTATGTCCTTG GCGGATACCTGTTACACCTG 2250 0.250 49.2
tilS_p2 tilS GCACCTCTATGTCCTTGTCG GCGGATACCTGTTACACCTG 2247 0.250 48.9
tilS_p3 tilS ATGGTGCACCTCTATGTCCT GCGGATACCTGTTACACCTG 2252 0.250 48.6
tilS_p4 tilS GGTGCACCTCTATGTCCTTG CTCGAACCCGGAACTAATCG 1640 0.250 48.5
tilS_p5 tilS GCACCTCTATGTCCTTGTCG CTCGAACCCGGAACTAATCG 1637 0.250 48.1
psaC-ycf22_p1 psaC-ycf22 AAATTGCTTCAGCGCCTAGA CGAGGATCATCAAACCTCTGA 1639–1643 0.500 48.7
psaC-ycf22_p2 psaC-ycf22 AATTGCTTCAGCGCCTAGAA CGAGGATCATCAAACCTCTGA 1638–1642 0.500 48.7
psaC-ycf22_p3 psaC-ycf22 AATTGCTTCAGCGCCTAGAA TCGAGGATCATCAAACCTCTG 1639–1643 0.500 48.7
psaC-ycf22_p4 psaC-ycf22 CAGGTCAAATTGCTTCAGCG CGAGGATCATCAAACCTCTGA 1645 0.250 35.3
psaC-ycf22_p5 psaC-ycf22 CAGGTCAAATTGCTTCAGCG TCGAGGATCATCAAACCTCTG 1646 0.250 35.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Dasyclonium adiantiforme PV491991.1 170385 View on NCBI ↗
Dasyclonium bifurcatum PV491994.1 170415 View on NCBI ↗
Dasyclonium flaccidum NC_035287.1 170203 View on NCBI ↗
Dasyclonium incisum PV491985.1 171416 View on NCBI ↗