Markers + reference

Clerodendrum

5 species · Lamiaceae · Lamiales

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Species 5
Genome length 152–152 kb
Candidate markers 272
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 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 311 0.0733 0.98 79.1 yes View details
rps16-trnQ-UUG LSC 1248 0.0208 1.00 69.2 yes View details
trnS-GCU-trnG-UCC LSC 642 0.0261 1.00 66.6 yes View details
petA-psbJ LSC 885 0.0191 1.00 68.6 yes View details
ndhF SSC 2226 0.0111 1.00 50.6 yes View details
ccsA SSC 954 0.0120 1.00 53.3 yes View details
ycf1 SSC 5571 0.0174 1.00 55.6 yes View details
rps2-rpoC2 LSC 212 0.0415 0.99 70.7 yes View details
trnT-UGU-trnL-UAA LSC 684 0.0173 1.00 66.9 yes View details
ndhC-trnV-UAC LSC 859 0.0156 1.00 66.9 yes View details
psbI-trnS-GCU LSC 116 0.0302 1.00 66.6 yes View details
trnL-UAG-ccsA SSC 105 0.0225 1.00 66.6 yes View details
atpH-atpI LSC 1049 0.0152 0.98 62.7 yes View details
rps19-rpl2 IRb 60 0.0302 0.88 62.3 yes View details
trnC-GCA-petN LSC 568 0.0123 0.98 62.2 yes View details
trnK-UUU-rps16 LSC 660 0.0178 0.98 62.1 yes View details
trnT-GGU-psbD LSC 1166 0.0139 0.99 61.2 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG GTCGTGGGTATCTGGTTCAC 527–589 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGTGGGTATCTGGTTCACTG 525–587 1.000 90.4
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GTCGTGGGTATCTGGTTCAC 541–603 1.000 90.1
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GTCGTGGGTATCTGGTTCAC 540–602 1.000 90.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG GAGTGGGAGCTTAGTTTCCG 977–1039 1.000 87.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAG GCCGTACGAGGAGAAAACTT 976–1090 0.800 77.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAG TCTATCCCAATGAGCCGTCT 920–1031 0.800 77.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAG AAGATCTTCGGAAAGTGGGC 858–969 0.800 77.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAG GATCTTCGGAAAGTGGGCTT 856–967 0.800 77.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAG AGCCGTCTATCGAATCGTTG 908–1019 0.800 77.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1258–1339 1.000 86.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1262–1343 1.000 81.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1288–1369 1.000 81.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1250–1331 1.000 80.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AGTCGCACGTTGCTTTCTAC GAGGTTCGAATCCTTCCGTC 1257–1338 1.000 80.2
psbI-trnS-GCU_p1 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA TGGACTAAAGCGTCGGATTG 204–219 1.000 83.7
psbI-trnS-GCU_p2 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA GTGGACTAAAGCGTCGGATT 205–220 1.000 83.7
psbI-trnS-GCU_p3 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA TTAGCTTGGGAGAGATGGCT 227–242 1.000 82.2
psbI-trnS-GCU_p4 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA GACTAAAGCGTCGGATTGCT 202–217 1.000 80.9
psbI-trnS-GCU_p5 psbI-trnS-GCU GTAATCCTGGACGCGAAGAA CTGAGTGGACTAAAGCGTCG 209–224 1.000 80.5
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 709–736 1.000 56.6
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 708–735 1.000 56.6
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 712–739 1.000 55.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 711–738 1.000 55.5
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 710–737 1.000 55.5
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTGCAACTTTAGCCGCAG 836–1134 1.000 84.7
atpH-atpI_p2 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTGCAACTTTAGCCGCAG 854–1152 1.000 84.3
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTGCAACTTTAGCCGCAG 853–1151 1.000 83.7
atpH-atpI_p4 atpH-atpI TCCAGCAGCAATAACGGAAG TTTTGCAACTTTAGCCGCAG 848–1146 1.000 83.4
atpH-atpI_p5 atpH-atpI ATCCAGCAGCAATAACGGAA TTTTGCAACTTTAGCCGCAG 849–1147 1.000 82.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Clerodendrum colebrookianum NC_069069.1 152073 View on NCBI ↗
Clerodendrum cyrtophyllum MZ958825.1 152052 View on NCBI ↗
Clerodendrum lindleyi NC_056199.1 151678 View on NCBI ↗
Clerodendrum paniculatum NC_073114.1 152225 View on NCBI ↗
Clerodendrum trichotomum NC_057680.1 151549 View on NCBI ↗