Markers + reference

Cyanotis

2 species · Commelinaceae · Commelinales

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Species 2
Genome length 169–171 kb
Candidate markers 272
Primer pairs 95

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 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnR-UCU LSC 3182 0.1138 0.58 71.7 yes View details
petN-psbM LSC 2963 0.0665 0.50 63.5 yes View details
trnE-UUC-trnT-GGU LSC 1621 0.1849 0.87 87.4 yes View details
rps4-trnT-UGU LSC 1273 0.1354 0.68 80.9 yes View details
ndhC-rbcL LSC 1843 0.1368 0.95 83.1 yes View details
accD-psaI LSC 1158 0.1510 0.72 79.5 yes View details
clpP LSC 3417 0.0539 0.79 69.6 yes View details
rps3-rpl22 LSC 774 0.2024 0.96 83.6 yes View details
ycf1-ndhF SSC 641 0.3160 0.42 72.2 yes View details
ndhF-rpl32 SSC 1315 0.1951 0.96 85.0 yes View details
psaC-ndhE SSC 983 0.1324 0.82 82.2 yes View details
rpoB-trnC-GCA LSC 1406 0.0647 0.98 80.4 yes View details
rpl33-psaJ LSC 760 0.1162 0.80 79.3 yes View details
rpl2-trnH-GUG IRa 48 0.0208 0.95 79.2 no View details
rps2-rpoC2 LSC 248 0.1203 0.97 78.2 yes View details
rps16-trnQ-UUG LSC 1007 0.0440 0.88 78.0 yes View details
rpl16-rps3 LSC 1480 0.0608 0.91 78.0 yes View details
psbJ-rpoA LSC 421 0.0643 1.00 77.4 yes View details
trnQ-UUG-psbK LSC 1119 0.0901 0.70 76.8 yes View details
matK-trnK-UUU LSC 1275 0.0543 0.89 76.7 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU TCGTGAAGAAAGAACCGCAA GACAATGGTGTGTCGATCGA 2009–2061 1.000 86.9
matK-trnK-UUU_p2 matK-trnK-UUU TTCGTGAAGAAAGAACCGCA GACAATGGTGTGTCGATCGA 2010–2062 1.000 86.9
matK-trnK-UUU_p3 matK-trnK-UUU AAGAGACTTCGTGGATCCGA GACAATGGTGTGTCGATCGA 1978–2030 1.000 86.0
matK-trnK-UUU_p4 matK-trnK-UUU AGAGACTTCGTGGATCCGAA GACAATGGTGTGTCGATCGA 1977–2029 1.000 86.0
matK-trnK-UUU_p5 matK-trnK-UUU TGAAATTTCCCCAAGACCCG GACAATGGTGTGTCGATCGA 1831 0.500 59.3
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCCGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1098–2053 1.000 85.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCCGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1096–2051 1.000 85.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AATCCACAGCCGATCATGTC GAGGTTCGAATCCTTCCGTC 1104–2059 1.000 85.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GAATCCACAGCCGATCATGT GAGGTTCGAATCCTTCCGTC 1105–2060 1.000 85.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGAATCCACAGCCGATCATG GAGGTTCGAATCCTTCCGTC 1106–2061 1.000 83.4
trnQ-UUG-psbK_p1 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA TCGAATAAAGTACAGAATTAAGACAGA 936–1212 1.000 49.3
trnQ-UUG-psbK_p2 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA CGAATAAAGTACAGAATTAAGACAGA 935–1211 1.000 49.3
trnQ-UUG-psbK_p3 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA TCGAATAAAGTACAGAATTAAGACAG 936–1212 1.000 49.3
trnQ-UUG-psbK_p4 trnQ-UUG-psbK ACCAAAACCCGTTGCCTTAC TCGAATAAAGTACAGAATTAAGACAGA 935–1211 1.000 49.3
trnQ-UUG-psbK_p5 trnQ-UUG-psbK GACCAAAACCCGTTGCCTTA TCGAATAAAGTACAGAATTAAGACA 936–1212 1.000 49.3
trnS-GCU-trnR-UCU_p1 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA AGCATTAAACTGGTATTAGAAGCA 1328 0.500 20.0
trnS-GCU-trnR-UCU_p2 trnS-GCU-trnR-UCU ACTCAGCCATCTCTCCCAAT AGCATTAAACTGGTATTAGAAGCA 1304 0.500 20.0
trnS-GCU-trnR-UCU_p3 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA AAGCATTAAACTGGTATTAGAAGCA 1329 0.500 20.0
trnS-GCU-trnR-UCU_p4 trnS-GCU-trnR-UCU GCTTTAGTCCACTCAGCCAT AGCATTAAACTGGTATTAGAAGCA 1314 0.500 20.0
trnS-GCU-trnR-UCU_p5 trnS-GCU-trnR-UCU ATTAGCAATCCGCCGCTTTA GCATTAAACTGGTATTAGAAGCA 1327 0.500 20.0
rps2-rpoC2_p1 rps2-rpoC2 TGTATGGGGCCATTTTTGGA TGAAATGAATTTACATGAGACAT 376 1.000 47.7
rps2-rpoC2_p2 rps2-rpoC2 TGTATGGGGCCATTTTTGGA ATGAAATGAATTTACATGAGACA 377 1.000 47.6
rps2-rpoC2_p3 rps2-rpoC2 GGAGATGTATGGGGCCATTT TGAAATGAATTTACATGAGACAT 381 1.000 47.6
rps2-rpoC2_p4 rps2-rpoC2 CTTTGCGGAGATGTATGGGG ATGAAATGAATTTACATGAGACA 388 1.000 47.4
rps2-rpoC2_p5 rps2-rpoC2 CTTTGCGGAGATGTATGGGG TGAAATGAATTTACATGAGACAT 387 1.000 47.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GTGGACATTCCCTCATTCCC TTACCACTTGGCTATGTCGC 1462–1643 1.000 85.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCCTCATTCCCATCATTCCG TTACCACTTGGCTATGTCGC 1453–1634 1.000 85.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCTCATTCCCATCATTCCGG TTACCACTTGGCTATGTCGC 1452–1633 1.000 85.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GTGGACATTCCCTCATTCCC AAAGGATTTGCAGTCCCCTG 1484–1665 1.000 85.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCTCATTCCCATCATTCCGG AAAGGATTTGCAGTCCCCTG 1474–1655 1.000 84.7

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
Cyanotis ciliata MK133255.1 170870 View on NCBI ↗
Cyanotis speciosa NC_071226.1 169409 View on NCBI ↗