Markers + reference

Mosla

10 species · Lamiaceae · Lamiales

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Species 10
Genome length 153–153 kb
Candidate markers 267
Primer pairs 90

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 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 342 0.0121 1.00 33.9 yes View details
trnK-UUU-rps16 LSC 532 0.0053 0.99 39.3 yes View details
petN-psbM LSC 1031 0.0028 1.00 52.0 yes View details
rps4-trnT-UGU LSC 471 0.0063 1.00 49.9 yes View details
petA-psbJ LSC 1052 0.0043 1.00 53.4 yes View details
ndhD SSC 1530 0.0018 1.00 40.3 yes View details
ndhA SSC 2133 0.0028 1.00 37.5 yes View details
ycf1 SSC 5667 0.0031 1.00 39.1 yes View details
rps16-trnQ-UUG LSC 1031 0.0023 1.00 52.5 yes View details
trnT-GGU-psbD LSC 1311 0.0013 1.00 47.2 yes View details
ycf3-trnS-GGA LSC 836 0.0014 1.00 47.1 yes View details
rpl20-rps12 LSC 811 0.0012 1.00 47.0 yes View details
ycf3 LSC 1959 0.0010 1.00 46.7 yes View details
accD-psaI LSC 722 0.0024 0.99 46.2 yes View details
rpoC2 LSC 4197 0.0011 1.00 45.3 yes View details
rpoB-trnC-GCA LSC 1174 0.0011 1.00 45.2 yes View details
matK LSC 1545 0.0014 1.00 44.7 yes View details
rps16 LSC 1135 0.0011 1.00 44.7 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 90 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 AGACCTAGCTGCTATCGAAG 400–401 1.000 67.1
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGACCTAGCTGCTATCGAAG 414–415 1.000 67.0
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGACCTAGCTGCTATCGAAG 413–414 1.000 67.0
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGACCTAGCTGCTATCGAAG 415–416 1.000 67.0
trnH-GUG-psbA_p5 trnH-GUG-psbA GCCTTGATCCACTTGGCTAC AGACCTAGCTGCTATCGAAG 405–406 1.000 63.2
matK_p1 matK AGTGGAGATCCCATTTTGATCTT AACCCCCGAATCTTCTACCT 1663 1.000 50.4
matK_p2 matK AGTGGAGATCCCATTTTGATCTT ACCCCCGAATCTTCTACCTT 1662 1.000 50.4
matK_p3 matK GTGGAGATCCCATTTTGATCTT AACCCCCGAATCTTCTACCT 1662 1.000 47.0
matK_p4 matK GTGGAGATCCCATTTTGATCTT ACCCCCGAATCTTCTACCTT 1661 1.000 47.0
matK_p5 matK AGTGGAGATCCCATTTTGATCTTT ACCCCCGAATCTTCTACCTT 1662 1.000 44.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC TCCTTGAAAAAGGGGCTCAA 671–675 1.000 69.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC TTCCTTGAAAAAGGGGCTCA 672–676 1.000 69.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC CCTTGAAAAAGGGGCTCAAC 670–674 1.000 68.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC CTTGAAAAAGGGGCTCAACC 669–673 1.000 68.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGCCGAGTACTCTACCATTGA TCCTTGAAAAAGGGGCTCAA 661–665 1.000 67.3
rps16_p1 rps16 ATATACAAGCCGCTACCCCC GCAGCTGAACCGATGACTAT 1242–1244 1.000 70.3
rps16_p2 rps16 TATACAAGCCGCTACCCCC GCAGCTGAACCGATGACTAT 1241–1243 1.000 66.0
rps16_p3 rps16 TATATACAAGCCGCTACCCC GCAGCTGAACCGATGACTAT 1243–1245 1.000 64.6
rps16_p4 rps16 ATATACAAGCCGCTACCCCC AAGTGTAGATTGCGACGTCT 1266–1268 1.000 64.0
rps16_p5 rps16 TATATACAAGCCGCTACCCCC GCAGCTGAACCGATGACTAT 1243–1245 1.000 63.9
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 1099–1122 1.000 80.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG TTAGACATCAACTTGGGGCG 1160–1183 1.000 80.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GTCTCGCTATTCGGAGGTTC 1112–1135 1.000 80.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1092–1115 1.000 79.6
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTAGACATCAACTTGGGGCG 1153–1176 1.000 79.3
rpoC2_p1 rpoC2 CCCATTCGAAAACAATTGGATGA GGCAAACGGTTTGATTCGAC 282 1.000 54.0
rpoC2_p2 rpoC2 CCCATTCGAAAACAATTGGATGA GCAAACGGTTTGATTCGACA 281 1.000 53.4
rpoC2_p3 rpoC2 ATCAACGATTGGAATCCCTT GGCAAACGGTTTGATTCGAC 249 1.000 52.2
rpoC2_p4 rpoC2 ATCAACGATTGGAATCCCTT GCAAACGGTTTGATTCGACA 248 1.000 51.6
rpoC2_p5 rpoC2 CCCATTCGAAAACAATTGGATGA TCTAGTCAAGAAGCTCGTGC 320 1.000 51.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Mosla chinensis PZ101788.1 152544 View on NCBI ↗
Mosla dianthera NC_084319.1 152550 View on NCBI ↗
Mosla hangchowensis PZ101804.1 152543 View on NCBI ↗
Mosla japonica PZ101799.1 152646 View on NCBI ↗
Mosla longibracteata PZ101780.1 152530 View on NCBI ↗
Mosla longispica PZ101803.1 152545 View on NCBI ↗
Mosla pauciflora PZ101796.1 152532 View on NCBI ↗
Mosla scabra NC_084320.1 152562 View on NCBI ↗
Mosla soochowensis PZ101785.1 152544 View on NCBI ↗
Mosla tamdaoensis PZ101797.1 152514 View on NCBI ↗