Markers + reference

Vuhuangia

2 species · Lamiaceae · Lamiales

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Species 2
Genome length 153–153 kb
Candidate markers 267
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 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 694 0.0029 1.00 56.2 yes View details
petN-psbM LSC 1022 0.0020 1.00 58.5 yes View details
trnE-UUC-trnT-GGU LSC 558 0.0018 1.00 58.7 yes View details
psaA-ycf3 LSC 646 0.0016 1.00 59.9 yes View details
rrn23 IRb 2810 0.0000 1.00 23.7 no View details
ndhF SSC 2232 0.0013 1.00 52.0 yes View details
ndhF-rpl32 SSC 414 0.0048 1.00 57.7 yes View details
ycf1 SSC 5664 0.0009 1.00 51.7 yes View details
rrn23 IRa 2810 0.0000 1.00 23.7 yes View details
trnV-GAC-rps12 IRa 1592 0.0006 0.99 60.0 yes View details
rpoA-rps11 LSC 71 0.0141 1.00 60.6 yes View details
matK-trnK-UUU LSC 694 0.0029 1.00 60.5 yes View details
rps12-trnV-GAC IRb 1592 0.0006 0.99 60.0 yes View details
trnT-UGU-trnL-UAA LSC 690 0.0014 1.00 59.6 yes View details
accD-psaI LSC 736 0.0014 1.00 59.5 yes View details
petA-psbJ LSC 1010 0.0010 1.00 59.5 yes View details
rpl20-rps12 LSC 814 0.0012 1.00 59.5 yes View details
ndhC-trnV-UAC LSC 954 0.0010 1.00 59.4 yes View details
rps16 LSC 1132 0.0009 1.00 59.3 yes View details
atpF LSC 1259 0.0008 1.00 59.2 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
trnK-UUU_p1 trnK-UUU TTCGTGTCAACCAATCCCAA TCCATGTCCTTGTTGAGTTGA 2744–2745 1.000 62.5
trnK-UUU_p2 trnK-UUU TCGTGTCAACCAATCCCAAT TCCATGTCCTTGTTGAGTTGA 2743–2744 1.000 60.7
trnK-UUU_p3 trnK-UUU TTCGTGTCAACCAATCCCAA TCCATGTCCTTGTTGAGTTGAA 2744–2745 1.000 60.0
trnK-UUU_p4 trnK-UUU TTCGTGTCAACCAATCCCAA ATCCATGTCCTTGTTGAGTTGA 2745–2746 1.000 58.3
trnK-UUU_p5 trnK-UUU TCGTGTCAACCAATCCCAAT TCCATGTCCTTGTTGAGTTGAA 2743–2744 1.000 58.2
matK-trnK-UUU_p1 matK-trnK-UUU AGGAAGTCGTGTTGTTGAGA TGGGGTTGCTAACTCAATGG 788–789 1.000 68.4
matK-trnK-UUU_p2 matK-trnK-UUU AGGAAGTCGTGTTGTTGAGA GGGGTTGCTAACTCAATGGT 787–788 1.000 68.4
matK-trnK-UUU_p3 matK-trnK-UUU GCACGATTATGAGCAAACACA TGGGGTTGCTAACTCAATGG 839–840 1.000 66.8
matK-trnK-UUU_p4 matK-trnK-UUU GCACGATTATGAGCAAACACA GGGGTTGCTAACTCAATGGT 838–839 1.000 66.8
matK-trnK-UUU_p5 matK-trnK-UUU AGCACGATTATGAGCAAACAC TGGGGTTGCTAACTCAATGG 840–841 1.000 64.6
rps16_p1 rps16 ATATACAAGCCGCTACCCCC ACCGGTTCCGAATTAGAGGA 1189–1190 1.000 70.8
rps16_p2 rps16 ATATACAAGCCGCTACCCCC CAATTCCATACCGGTTCCGA 1198–1199 1.000 69.4
rps16_p3 rps16 ATATACAAGCCGCTACCCCC TCAATTCCATACCGGTTCCG 1199–1200 1.000 69.4
rps16_p4 rps16 TATACAAGCCGCTACCCCC ACCGGTTCCGAATTAGAGGA 1188–1189 1.000 66.5
rps16_p5 rps16 TATATACAAGCCGCTACCCC ACCGGTTCCGAATTAGAGGA 1190–1191 1.000 65.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 763 1.000 70.3
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 762 1.000 70.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCAC 763 1.000 70.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCAC 762 1.000 70.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCGCACTTTTACCACT 817 1.000 69.1
atpF_p1 atpF CGTCGGCTCGAATAGTTACC GGGGCAAGGCGATAGAAAAA 1438 1.000 73.8
atpF_p2 atpF CGTCGGCTCGAATAGTTACC GGGCAAGGCGATAGAAAAAG 1437 1.000 71.3
atpF_p3 atpF TTTCGTCGGCTCGAATAGTT GGGGCAAGGCGATAGAAAAA 1441 1.000 70.7
atpF_p4 atpF TCGTCGGCTCGAATAGTTAC GGGGCAAGGCGATAGAAAAA 1439 1.000 69.9
atpF_p5 atpF GTCGGCTCGAATAGTTACCA GGGGCAAGGCGATAGAAAAA 1437 1.000 69.0
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA AGTTCCGACCGCTTTTCTAC 1111 1.000 79.5
petN-psbM_p2 petN-psbM ACTCGTAGTGTGGGGAAGAA GTTCCGACCGCTTTTCTACT 1110 1.000 79.5
petN-psbM_p3 petN-psbM TCGTAGTGTGGGGAAGAAGT AGTTCCGACCGCTTTTCTAC 1109 1.000 79.5
petN-psbM_p4 petN-psbM TCGTAGTGTGGGGAAGAAGT GTTCCGACCGCTTTTCTACT 1108 1.000 79.5
petN-psbM_p5 petN-psbM CGTAGTGTGGGGAAGAAGTG GTTCCGACCGCTTTTCTACT 1107 1.000 78.9

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
Vuhuangia flava PP357208.1 152634 View on NCBI ↗
Vuhuangia penduliflora PP357172.1 152600 View on NCBI ↗