Markers + reference

Coleus

4 species · Lamiaceae · Lamiales

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Species 4
Genome length 152–153 kb
Candidate markers 272
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 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
trnH-GUG-psbA LSC 294 0.0420 0.97 70.9 yes View details
trnK-rps16 LSC 528 0.0316 1.00 65.8 yes View details
atpH-atpI LSC 1049 0.0224 0.99 73.7 yes View details
petN-psbM LSC 989 0.0216 1.00 71.6 yes View details
trnE-UUC-trnT-GGU LSC 616 0.0260 1.00 72.6 yes View details
rpl16 LSC 1266 0.0194 1.00 58.1 yes View details
ycf1 IRb 1131 0.0019 1.00 36.7 no View details
ndhF SSC 2232 0.0163 1.00 55.4 yes View details
rpl32-trnL-UAG SSC 765 0.0286 0.97 71.4 yes View details
ndhD SSC 1503 0.0118 1.00 52.7 yes View details
ycf1 SSC 5577 0.0188 1.00 51.6 yes View details
ndhD-psaC SSC 117 0.0513 1.00 76.2 yes View details
ccsA-ndhD SSC 223 0.0800 1.00 75.2 yes View details
psbI-trnS-GCU LSC 145 0.0448 1.00 74.2 yes View details
psaA-pafI LSC 784 0.0166 0.99 72.5 yes View details
psbB-psbT LSC 173 0.0405 1.00 70.1 yes View details
trnL-UAG-ccsA SSC 90 0.0315 0.94 69.4 yes View details
rpl22-rps19 LSC 69 0.0700 1.00 69.1 yes View details
rps2-rpoC2 LSC 209 0.0383 1.00 68.0 yes View details
rps16-trnQ-UUG LSC 994 0.0206 0.96 67.9 yes View details
pafI-trnS-GGA LSC 862 0.0169 0.99 67.6 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCAGTGCTATGCATGGTTCC 744–760 1.000 83.2
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAGTGCTATGCATGGTTCCT 743–759 1.000 83.2
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCAGTGCTATGCATGGTTCC 758–774 1.000 83.1
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCAGTGCTATGCATGGTTCC 757–773 1.000 83.1
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCAGTGCTATGCATGGTTCC 759–775 1.000 83.1
trnK-rps16_p1 trnK-rps16 ATTCACTCAAGTGCTTCCCG AAAAGGAGCTCAACCCACAG 1022–1030 1.000 82.2
trnK-rps16_p2 trnK-rps16 ATTCACTCAAGTGCTTCCCG CCGGGATAAACGAAAGGGAG 1468–1477 1.000 81.4
trnK-rps16_p3 trnK-rps16 ATTCACTCAAGTGCTTCCCG GCCGTACGAGGAGAAAACTT 1222–1231 1.000 81.2
trnK-rps16_p4 trnK-rps16 ATTCACTCAAGTGCTTCCCG TCTATCCCAATGAGCCGTCT 1166–1174 1.000 81.2
trnK-rps16_p5 trnK-rps16 AGGTAGAAGATTCGGGGGTT AAAAGGAGCTCAACCCACAG 1341–1353 1.000 80.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCCACAACGGGTCATATCCT GAGGTTCGAATCCTTCCGTC 1038–1124 1.000 85.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1016–1102 1.000 85.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAACGGGTCATATCCTT GAGGTTCGAATCCTTCCGTC 1037–1123 1.000 80.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAACGGGTCATATCCT TTCGGAGGTTCGAATCCTTC 1042–1128 1.000 80.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCCACAACGGGTCATATCCT TAAGGCAACGGGTTTTGGTC 1068–1154 1.000 80.2
psbI-trnS-GCU_p1 psbI-trnS-GCU GCGTAATCCTGGACGTGAAG TTATTCGTACCGAGGGTTCG 169–225 1.000 76.1
psbI-trnS-GCU_p2 psbI-trnS-GCU GCGTAATCCTGGACGTGAAG TTCGAATCCCTCTCTTTCCG 153–209 1.000 75.6
psbI-trnS-GCU_p3 psbI-trnS-GCU GCGTAATCCTGGACGTGAAG GGGTTCGAATCCCTCTCTTT 156–212 1.000 74.6
psbI-trnS-GCU_p4 psbI-trnS-GCU GCGTAATCCTGGACGTGAAG GGTTCGAATCCCTCTCTTTCC 155–211 1.000 74.5
psbI-trnS-GCU_p5 psbI-trnS-GCU CGTAATCCTGGACGTGAAGA TTATTCGTACCGAGGGTTCG 168–224 1.000 74.4
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TCCCTGTCATGTTCCTTGGA 1118–1183 1.000 84.1
atpH-atpI_p2 atpH-atpI AGCCAATCCAGCAGCAATAA TCCCTGTCATGTTCCTTGGA 1136–1201 1.000 83.7
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC TCCCTGTCATGTTCCTTGGA 1135–1200 1.000 83.2
atpH-atpI_p4 atpH-atpI TCCAGCAGCAATAACGGAAG TCCCTGTCATGTTCCTTGGA 1130–1195 1.000 82.8
atpH-atpI_p5 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTTGCAACTTTAGCCGCG 1070–1135 1.000 82.2
rps2-rpoC2_p1 rps2-rpoC2 CCTCCAGCATCTCTTCCAAG CAATCATTTATAGGATTTAATGATTCC 282–293 1.000 45.0
rps2-rpoC2_p2 rps2-rpoC2 CCTCCAGCATCTCTTCCAAG CAGAACAATCATTTATAGGATTTAATG 287–298 1.000 44.9
rps2-rpoC2_p3 rps2-rpoC2 AAATGAACTCCTGCCTCCAG CAATCATTTATAGGATTTAATGATTCC 295–306 1.000 44.8
rps2-rpoC2_p4 rps2-rpoC2 AAATGAACTCCTGCCTCCAG CAGAACAATCATTTATAGGATTTAATG 300–311 1.000 44.7
rps2-rpoC2_p5 rps2-rpoC2 CCATGGCCAAAATGAACTCC CAGAACAATCATTTATAGGATTTAATG 309–320 1.000 44.6

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
Coleus amboinicus PX923121.1 152544 View on NCBI ↗
Coleus hadiensis NC_069583.1 152484 View on NCBI ↗
Coleus scutellarioides NC_057679.1 152603 View on NCBI ↗
Coleus xanthanthus NC_058328.1 152190 View on NCBI ↗