Markers + reference

Glechoma

4 species · Lamiaceae · Lamiales

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Species 4
Genome length 152–152 kb
Candidate markers 274
Primer pairs 95

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 8 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 345 0.0275 0.93 74.6 yes View details
rps16-trnQ-UUG LSC 935 0.0071 1.00 57.6 yes View details
trnS-GCU-trnG-UCC LSC 718 0.0063 0.97 58.9 yes View details
rpoC1 LSC 2819 0.0027 1.00 45.2 yes View details
petN-psbM LSC 962 0.0089 1.00 65.1 yes View details
ycf1 IRb 1056 0.0000 1.00 36.8 no View details
ndhF SSC 2214 0.0034 1.00 50.3 yes View details
rpl32-trnL-UAG SSC 738 0.0061 1.00 48.7 yes View details
ccsA SSC 978 0.0041 1.00 48.4 yes View details
ccsA-ndhD SSC 263 0.0342 1.00 65.7 yes View details
rps15-ycf1 SSC 392 0.0119 0.98 63.1 yes View details
ycf1 SSC 5547 0.0038 1.00 41.8 yes View details
psbE-petL LSC 897 0.0030 1.00 66.5 yes View details
atpA-atpF LSC 113 0.0144 0.86 62.7 yes View details
trnF-GAA-ndhJ LSC 634 0.0032 1.00 61.0 yes View details
petB LSC 1365 0.0015 1.00 60.5 yes View details
ycf3-trnS-GGA LSC 841 0.0048 0.99 60.1 yes View details
rpl20-rps12 LSC 798 0.0013 1.00 60.1 yes View details
matK LSC 1533 0.0016 1.00 59.8 yes View details
clpP1 LSC 1934 0.0018 1.00 59.4 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 95 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 CTAGACCTAGCCGCTATCGA 370–405 1.000 85.3
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TCTAGACCTAGCCGCTATCG 371–406 1.000 85.3
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CTAGACCTAGCCGCTATCGA 384–419 1.000 85.2
trnH-GUG-psbA_p4 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TCTAGACCTAGCCGCTATCG 385–420 1.000 85.2
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CTAGACCTAGCCGCTATCGA 383–418 1.000 85.2
matK_p1 matK AGTGGAAATCTCATTTTGATCT TACTTGTCCCCGAGGTATCC 1730 1.000 40.2
matK_p2 matK AGTGGAAATCTCATTTTGATCT TGTCCCCGAGGTATCCATTT 1726 1.000 40.2
matK_p3 matK AGTGGAAATCTCATTTTGATCT TTGTCCCCGAGGTATCCATT 1727 1.000 40.2
matK_p4 matK AGTGGAAATCTCATTTTGATCTT TACTTGTCCCCGAGGTATCC 1730 1.000 40.2
matK_p5 matK AGTGGAAATCTCATTTTGATCT ACCCCCGAATCTTCTACCTT 1657 1.000 40.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAACAGGTCGTGTCCTTCAA GAAATTGAAATGGGGCGTGG 1084–1173 1.000 82.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CAACAGGTCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1026–1115 1.000 82.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1066–1155 1.000 81.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CAACAGGTCGTGTCCTTCAA GTCTCGCTATTCGGAGGTTC 1039–1128 1.000 81.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1008–1097 1.000 81.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACCACTAAACTATACCCGCT 755–773 1.000 63.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACCACTAAACTATACCCGCT 754–772 1.000 63.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACCACTAAACTATACCCGCT 809–827 1.000 62.5
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC ACCACTAAACTATACCCGCT 757–775 1.000 61.0
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACCAACGGAAAGAGAGGGAT ACCACTAAACTATACCCGCT 813–831 1.000 60.9
atpA-atpF_p1 atpA-atpF CCTACTTGAAGTACGGTGCC AAGGAGCTCTAGGAACCCTG 309–327 1.000 83.4
atpA-atpF_p2 atpA-atpF CCTACTTGAAGTACGGTGCC CAAGGAGCTCTAGGAACCCT 310–328 1.000 83.4
atpA-atpF_p3 atpA-atpF CCTACTTGAAGTACGGTGCC GGAGCTCTAGGAACCCTGAA 307–325 1.000 83.4
atpA-atpF_p4 atpA-atpF CCTACTTGAAGTACGGTGCC GGCATGTTGGGAGTGATGAA 238–256 1.000 83.3
atpA-atpF_p5 atpA-atpF GTCGCCTACTTGAAGTACGG AAGGAGCTCTAGGAACCCTG 313–331 1.000 82.7
rpoC1_p1 rpoC1 TCGGTCTTGATTCCCGTAGA GGAATAAATCCGAATTTGTATTCT 2944–2948 1.000 40.4
rpoC1_p2 rpoC1 TTTTCGGTCTTGATTCCCGT GGAATAAATCCGAATTTGTATTCT 2947–2951 1.000 40.4
rpoC1_p3 rpoC1 TCGGTCTTGATTCCCGTAGA GGAATAAATCCGAATTTGTATTC 2944–2948 1.000 40.4
rpoC1_p4 rpoC1 TCCCGTAGAAATTCCGGAAC GGAATAAATCCGAATTTGTATTCT 2933–2937 1.000 40.4
rpoC1_p5 rpoC1 CCCGTAGAAATTCCGGAACT GGAATAAATCCGAATTTGTATTCT 2932–2936 1.000 40.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Glechoma cf. hirsuta PP203124.1 151669 View on NCBI ↗
Glechoma hederacea PP203125.1 151816 View on NCBI ↗
Glechoma hirsuta PP203126.1 151802 View on NCBI ↗
Glechoma longituba MF967576.1 151768 View on NCBI ↗