Markers + reference

Isodon

86 species · Lamiaceae · Lamiales

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Species 86
Genome length 152–153 kb
Candidate markers 272
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

9 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 307 0.0189 1.00 54.2 yes View details
OOC40_pgp086-trnQ-UUG LSC 961 0.0103 0.98 60.8 yes View details
petN-psbM LSC 992 0.0094 1.00 71.1 yes View details
ycf1 IRb 1131 0.0011 1.00 32.8 no View details
ndhF SSC 2232 0.0063 1.00 48.7 yes View details
rpl32-trnL-UAG SSC 765 0.0147 1.00 60.4 yes View details
ccsA-ndhD SSC 232 0.0356 1.00 61.9 yes View details
psaC SSC 246 0.0053 1.00 28.5 yes View details
ycf1 SSC 5523 0.0084 1.00 52.1 yes View details
atpH-atpI LSC 1001 0.0084 1.00 69.3 yes View details
trnT-UGU-trnL-UAA LSC 686 0.0089 1.00 65.5 yes View details
trnF-GAA-ndhJ LSC 667 0.0076 1.00 62.8 yes View details
trnK-UUU-OOC40_pgp086 LSC 524 0.0095 1.00 61.6 yes View details
trnS-GCU-trnG-UCC LSC 761 0.0084 1.00 61.3 yes View details
psaA-ycf3 LSC 774 0.0062 1.00 59.2 yes View details
trnT-GGU-psbD LSC 1317 0.0061 1.00 58.5 yes View details
psbE-petL LSC 892 0.0053 1.00 57.2 yes View details
ycf3-trnS-GGA LSC 863 0.0060 1.00 57.1 yes View details
ndhA SSC 2123 0.0052 1.00 57.0 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 TCAGTGCTATGCATGGTTCC 680–769 1.000 88.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAGTGCTATGCATGGTTCCT 679–768 1.000 88.3
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCAGTGCTATGCATGGTTCC 694–783 1.000 88.2
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TCAGTGCTATGCATGGTTCC 693–782 1.000 88.2
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TCAGTGCTATGCATGGTTCC 695–784 0.988 87.6
trnK-UUU-OOC40_pgp086_p1 trnK-UUU-OOC40_pgp086 TCTAGCCGCACTTAAAAGCC AAAAGGAGCTCAACCCACAG 638–680 0.988 89.0
trnK-UUU-OOC40_pgp086_p2 trnK-UUU-OOC40_pgp086 CCGCACTTAAAAGCCGAGTA AAAAGGAGCTCAACCCACAG 633–675 0.988 88.9
trnK-UUU-OOC40_pgp086_p3 trnK-UUU-OOC40_pgp086 TCGCGGTCTTCCAAAGTTTA AAAAGGAGCTCAACCCACAG 705–747 0.988 86.5
trnK-UUU-OOC40_pgp086_p4 trnK-UUU-OOC40_pgp086 TCTAGCCGCACTTAAAAGCC AAAAAGGAGCTCAACCCACA 639–681 1.000 86.0
trnK-UUU-OOC40_pgp086_p5 trnK-UUU-OOC40_pgp086 CGCGGTCTTCCAAAGTTTAC AAAAGGAGCTCAACCCACAG 704–746 0.988 86.0
OOC40_pgp086-trnQ-UUG_p1 OOC40_pgp086-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 794–1082 0.988 89.1
OOC40_pgp086-trnQ-UUG_p2 OOC40_pgp086-trnQ-UUG TATCCTTCAAGTCGCACGTT GAGGTTCGAATCCTTCCGTC 802–1090 1.000 84.9
OOC40_pgp086-trnQ-UUG_p3 OOC40_pgp086-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 786–1074 1.000 84.6
OOC40_pgp086-trnQ-UUG_p4 OOC40_pgp086-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 798–1086 0.988 84.4
OOC40_pgp086-trnQ-UUG_p5 OOC40_pgp086-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 824–1112 0.988 84.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCACT 729–866 1.000 80.5
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCACT 728–865 1.000 80.5
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCGCACTTTTACCAC 729–866 1.000 80.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCGCACTTTTACCAC 728–865 1.000 80.4
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCGCACTTTTACCACT 783–920 1.000 78.9
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA TCCCTGTCATGTTCCTTGGA 1064–1152 1.000 87.0
atpH-atpI_p2 atpH-atpI AGCCAATCCAGCAGCAATAA TCCCTGTCATGTTCCTTGGA 1082–1170 1.000 86.5
atpH-atpI_p3 atpH-atpI GCCAATCCAGCAGCAATAAC TCCCTGTCATGTTCCTTGGA 1081–1169 1.000 86.0
atpH-atpI_p4 atpH-atpI TCCAGCAGCAATAACGGAAG TCCCTGTCATGTTCCTTGGA 1076–1164 1.000 85.7
atpH-atpI_p5 atpH-atpI AACGGAAGCAGCAGAAATCA TTTTTGCAACTTTAGCCGCG 1016–1104 1.000 85.2
petN-psbM_p1 petN-psbM ACTCGTAGTGTGGGGAAGAA AGTTCCTACCGCTTTTCTACT 615–1098 1.000 70.1
petN-psbM_p2 petN-psbM TCGTAGTGTGGGGAAGAAGT AGTTCCTACCGCTTTTCTACT 613–1096 1.000 70.1
petN-psbM_p3 petN-psbM ACTCGTAGTGTGGGGAAGAA TCATTCTAGTTCCTACCGCT 622–1105 1.000 69.9
petN-psbM_p4 petN-psbM TCGTAGTGTGGGGAAGAAGT TCATTCTAGTTCCTACCGCT 620–1103 1.000 69.9
petN-psbM_p5 petN-psbM CGTAGTGTGGGGAAGAAGTG AGTTCCTACCGCTTTTCTACT 612–1095 1.000 69.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (86)

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

Species Accession Length (bp) Link
Isodon adenanthus NC_067642.1 152602 View on NCBI ↗
Isodon albopilosus NC_067643.1 152701 View on NCBI ↗
Isodon alborubrus NC_067644.1 152709 View on NCBI ↗
Isodon amethystoides MT473767.1 152639 View on NCBI ↗
Isodon angustifolius NC_067645.1 152694 View on NCBI ↗
Isodon atroruber NC_067647.1 152187 View on NCBI ↗
Isodon aurantiacus NC_067648.1 152693 View on NCBI ↗
Isodon barbeyanus NC_067649.1 152654 View on NCBI ↗
Isodon bifidocalyx NC_067670.1 152285 View on NCBI ↗
Isodon brachythyrsus NC_067650.1 152697 View on NCBI ↗
Isodon bulleyanus NC_067651.1 152645 View on NCBI ↗
Isodon calcicola NC_067652.1 152594 View on NCBI ↗
Isodon chionanthus NC_067706.1 152498 View on NCBI ↗
Isodon coetsa NC_067646.1 152714 View on NCBI ↗
Isodon coetsa var. cavaleriei ON858844.1 152674 View on NCBI ↗
Isodon coetsa var. coetsa ON858843.1 152745 View on NCBI ↗
Isodon coetsoides NC_067653.1 152692 View on NCBI ↗
Isodon dawoensis NC_067654.1 152709 View on NCBI ↗
Isodon delavayi NC_067655.1 152661 View on NCBI ↗
Isodon effusus NC_067694.1 152298 View on NCBI ↗
Isodon enanderianus NC_067656.1 152680 View on NCBI ↗
Isodon eriocalyx NC_067779.1 152657 View on NCBI ↗
Isodon excisoides NC_067657.1 152646 View on NCBI ↗
Isodon excisus NC_067780.1 152643 View on NCBI ↗
Isodon flabelliformis NC_067696.1 152298 View on NCBI ↗
Isodon flavidus NC_067658.1 152257 View on NCBI ↗
Isodon flexicaulis NC_067701.1 152662 View on NCBI ↗
Isodon forrestii NC_067659.1 152643 View on NCBI ↗
Isodon gibbosus NC_067660.1 152720 View on NCBI ↗
Isodon grandifolius var. atuntzeensis ON858856.1 152693 View on NCBI ↗
Isodon grandifolius var. grandifolius ON858868.1 152577 View on NCBI ↗
Isodon hirtellus NC_067661.1 152623 View on NCBI ↗
Isodon hsiwenii ON858858.1 152633 View on NCBI ↗
Isodon inflexus NC_067781.1 152701 View on NCBI ↗
Isodon interruptus NC_067662.1 152652 View on NCBI ↗
Isodon irroratus NC_067663.1 152688 View on NCBI ↗
Isodon japonicus NC_067782.1 152238 View on NCBI ↗
Isodon japonicus var. glaucocalyx ON858864.1 152660 View on NCBI ↗
Isodon japonicus var. japonicus ON858865.1 152674 View on NCBI ↗
Isodon kangtingensis NC_067664.1 152299 View on NCBI ↗
Isodon leucophyllus NC_067665.1 152693 View on NCBI ↗
Isodon longitubus NC_067695.1 152660 View on NCBI ↗
Isodon lophanthoides NC_067783.1 152208 View on NCBI ↗
Isodon lophanthoides var. graciliflorus ON858870.1 152208 View on NCBI ↗
Isodon loxothyrsus NC_067667.1 152640 View on NCBI ↗
Isodon lungshengensis NC_067668.1 152253 View on NCBI ↗
Isodon macrocalyx NC_067666.1 152297 View on NCBI ↗
Isodon macrophyllus NC_067669.1 152596 View on NCBI ↗
Isodon medilungensis NC_067705.1 152714 View on NCBI ↗
Isodon megathyrsus NC_067671.1 152568 View on NCBI ↗
Isodon mucronatus NC_067704.1 152637 View on NCBI ↗
Isodon muliensis NC_067700.1 152695 View on NCBI ↗
Isodon nervosus NC_058575.1 152669 View on NCBI ↗
Isodon oreophilus NC_067672.1 152274 View on NCBI ↗
Isodon oresbius NC_067673.1 152626 View on NCBI ↗
Isodon parvifolius NC_067674.1 152713 View on NCBI ↗
Isodon pharicus NC_067675.1 152698 View on NCBI ↗
Isodon phyllopodus NC_067707.1 152240 View on NCBI ↗
Isodon phyllostachys NC_067677.1 152699 View on NCBI ↗
Isodon pleiophyllus NC_067678.1 152651 View on NCBI ↗
Isodon polystachys NC_067697.1 152681 View on NCBI ↗
Isodon racemosus NC_067698.1 152683 View on NCBI ↗
Isodon ramosissimus NC_067709.1 152473 View on NCBI ↗
Isodon rosthornii NC_067699.1 152322 View on NCBI ↗
Isodon rubescens NC_053708.1 152761 View on NCBI ↗
Isodon rugosiformis NC_067679.1 152650 View on NCBI ↗
Isodon rugosus NC_067680.1 152677 View on NCBI ↗
Isodon schimperi NC_067708.1 152450 View on NCBI ↗
Isodon scoparius NC_067681.1 152610 View on NCBI ↗
Isodon scrophularioides NC_067682.1 152268 View on NCBI ↗
Isodon sculponeatus NC_067683.1 152298 View on NCBI ↗
Isodon secundiflorus NC_067703.1 152680 View on NCBI ↗
Isodon serra NC_064127.1 152312 View on NCBI ↗
Isodon setschwanensis NC_067702.1 152669 View on NCBI ↗
Isodon shikokianus var. occidentalis ON858908.1 152677 View on NCBI ↗
Isodon smithianus NC_067684.1 152672 View on NCBI ↗
Isodon tenuifolius NC_067685.1 152656 View on NCBI ↗
Isodon ternifolius NC_067686.1 152824 View on NCBI ↗
Isodon trichocarpus NC_067693.1 152299 View on NCBI ↗
Isodon umbrosus var. leucanthus ON858906.1 152682 View on NCBI ↗
Isodon villosus NC_067687.1 152172 View on NCBI ↗
Isodon wardii NC_067688.1 152678 View on NCBI ↗
Isodon weisiensis NC_067689.1 152693 View on NCBI ↗
Isodon wikstroemioides NC_067690.1 152652 View on NCBI ↗
Isodon xerophilus NC_067692.1 152466 View on NCBI ↗
Isodon yuennanensis NC_067691.1 151923 View on NCBI ↗