Markers + reference

Lamium

8 species · Lamiaceae · Lamiales

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Species 8
Genome length 150–151 kb
Candidate markers 274
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1059 0.0040 1.00 38.3 yes View details
rps16-trnQ(UUG) LSC 987 0.0283 0.98 68.6 yes View details
rpoB-trnC(GCA) LSC 1107 0.0249 1.00 66.0 yes View details
ndhC-trnV(UAC) LSC 900 0.0285 1.00 68.3 yes View details
petA-psbJ LSC 1040 0.0317 1.00 77.8 yes View details
psbE-petL LSC 930 0.0254 1.00 65.1 yes View details
petB LSC 1381 0.0177 0.99 58.7 yes View details
ycf1 IRb 1119 0.0094 1.00 51.4 no View details
ndhF SSC 2223 0.0190 1.00 57.5 yes View details
ndhF-rpl32 SSC 488 0.0329 0.98 75.8 yes View details
ndhG SSC 531 0.0112 1.00 41.8 yes View details
ycf1 SSC 5463 0.0250 1.00 58.7 yes View details
trnH(GUG)-psbA LSC 196 0.0851 1.00 84.2 yes View details
ndhE-ndhG SSC 192 0.0660 1.00 74.6 yes View details
psbB-psbT LSC 189 0.0324 1.00 73.3 yes View details
trnE(UUC)-trnT(GGU) LSC 585 0.0219 0.97 71.4 yes View details
trnG(GCC)-trnfM(CAU) LSC 138 0.0383 1.00 70.8 yes View details
psbZ-trnG(GCC) LSC 242 0.0308 0.93 69.0 yes View details
rbcL-accD LSC 705 0.0243 0.99 67.3 yes View details
rps8-rpl14 LSC 160 0.0358 1.00 67.3 yes View details
psbT-psbN LSC 73 0.0424 1.00 66.9 yes View details
rpl32-trnL(UAG) SSC 396 0.0349 1.00 66.7 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 105 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 CAACCGTGCTAACCTTGGTA 315–348 1.000 87.8
trnH(GUG)-psbA_p2 trnH(GUG)-psbA GATCCACTTGGCTACATCCG ATCAACCGTGCTAACCTTGG 317–350 1.000 87.7
trnH(GUG)-psbA_p3 trnH(GUG)-psbA CAATCCACTGCCTTGATCCA CAACCGTGCTAACCTTGGTA 329–362 1.000 87.6
trnH(GUG)-psbA_p4 trnH(GUG)-psbA AATCCACTGCCTTGATCCAC CAACCGTGCTAACCTTGGTA 328–361 1.000 87.6
trnH(GUG)-psbA_p5 trnH(GUG)-psbA ACAATCCACTGCCTTGATCC CAACCGTGCTAACCTTGGTA 330–363 1.000 87.6
psbA_p1 psbA GATCCACTTGGCTACATCCG GAAAGCCGTGTGCAATGAAA 1628–1674 1.000 81.3
psbA_p2 psbA CAATCCACTGCCTTGATCCA GAAAGCCGTGTGCAATGAAA 1642–1688 1.000 81.2
psbA_p3 psbA AATCCACTGCCTTGATCCAC GAAAGCCGTGTGCAATGAAA 1641–1687 1.000 81.2
psbA_p4 psbA ACAATCCACTGCCTTGATCC GAAAGCCGTGTGCAATGAAA 1643–1689 1.000 81.2
psbA_p5 psbA GATCCACTTGGCTACATCCG CTAGTTCCGGGTTCGAATCC 1534–1578 1.000 80.7
rps16-trnQ(UUG)_p1 rps16-trnQ(UUG) GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 1045–1089 1.000 86.7
rps16-trnQ(UUG)_p2 rps16-trnQ(UUG) AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1038–1082 1.000 85.7
rps16-trnQ(UUG)_p3 rps16-trnQ(UUG) ATCGTGTCTTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1050–1094 1.000 85.6
rps16-trnQ(UUG)_p4 rps16-trnQ(UUG) TGTCTTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 1046–1090 1.000 83.9
rps16-trnQ(UUG)_p5 rps16-trnQ(UUG) GTCTTTCAAGTCGCACGTTG TTCGGAGGTTCGAATCCTTC 1049–1093 1.000 82.0
rpoB-trnC(GCA)_p1 rpoB-trnC(GCA) GACATTGCCTCGTTTGCATC CCGGATTTGAACTGGGGAAA 1197–1238 1.000 84.1
rpoB-trnC(GCA)_p2 rpoB-trnC(GCA) TAGACATTGCCTCGTTTGCA CCGGATTTGAACTGGGGAAA 1199–1240 1.000 83.5
rpoB-trnC(GCA)_p3 rpoB-trnC(GCA) GACATTGCCTCGTTTGCATC TTTGGTAATCAGGCGACACC 1216–1257 1.000 83.2
rpoB-trnC(GCA)_p4 rpoB-trnC(GCA) TAGACATTGCCTCGTTTGCA TTTGGTAATCAGGCGACACC 1218–1259 1.000 82.6
rpoB-trnC(GCA)_p5 rpoB-trnC(GCA) GACATTGCCTCGTTTGCATC AAAAGGATTTGCAGTCCCCC 1179–1220 1.000 82.0
trnE(UUC)-trnT(GGU)_p1 trnE(UUC)-trnT(GGU) CATAGTACCCTACCCCCAGG GAACCGATGACTTACGCCTT 695–784 1.000 87.2
trnE(UUC)-trnT(GGU)_p2 trnE(UUC)-trnT(GGU) CATAGTACCCTACCCCCAGG CCATGGCGTTACTCTACCAC 674–763 1.000 86.9
trnE(UUC)-trnT(GGU)_p3 trnE(UUC)-trnT(GGU) CATAGTACCCTACCCCCAGG TGGCGTTACTCTACCACTGA 671–760 1.000 86.8
trnE(UUC)-trnT(GGU)_p4 trnE(UUC)-trnT(GGU) CATAGTACCCTACCCCCAGG CCGATGACTTACGCCTTACC 692–781 1.000 86.0
trnE(UUC)-trnT(GGU)_p5 trnE(UUC)-trnT(GGU) GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 660–749 1.000 85.6
psbZ-trnG(GCC)_p1 psbZ-trnG(GCC) GGGTTAGTCTTTCTGGTGGG AATCGAACCCGCATCTTCTC 327–345 1.000 84.0
psbZ-trnG(GCC)_p2 psbZ-trnG(GCC) GGGTTAGTCTTTCTGGTGGG GAATCGAACCCGCATCTTCT 328–346 1.000 83.9
psbZ-trnG(GCC)_p3 psbZ-trnG(GCC) GGGTTAGTCTTTCTGGTGGG GAACCCGCATCTTCTCCTTG 323–341 1.000 79.5
psbZ-trnG(GCC)_p4 psbZ-trnG(GCC) GGGTTAGTCTTTCTGGTGGG TACCATTCGACCATATCCGC 289–307 1.000 79.1
psbZ-trnG(GCC)_p5 psbZ-trnG(GCC) AGTCTTTCTGGTGGGTATCCT AATCGAACCCGCATCTTCTC 322–340 1.000 78.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

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

Species Accession Length (bp) Link
Lamium album NC_036971.1 150505 View on NCBI ↗
Lamium album subsp. album PP203135.1 150514 View on NCBI ↗
Lamium amplexicaule PQ231089.1 150650 View on NCBI ↗
Lamium barbatum PV802395.1 150887 View on NCBI ↗
Lamium galeobdolon subsp. flavidum PP203136.1 151309 View on NCBI ↗
Lamium orvala PP336767.1 151368 View on NCBI ↗
Lamium purpureum PZ055112.1 150474 View on NCBI ↗
Lamium takeshimense MN240520.1 150626 View on NCBI ↗