Markers + reference

Stenogyne

3 species · Lamiaceae · Lamiales

Back to catalogue

Species 3
Genome length 150–150 kb
Candidate markers 273
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-UCC LSC 694 0.0029 1.00 42.5 yes View details
atpH-atpI LSC 975 0.0027 1.00 60.5 yes View details
rpoB-trnC-GCA LSC 1104 0.0024 1.00 60.9 yes View details
petN-psbM LSC 502 0.0040 1.00 46.7 yes View details
atpB-rbcL LSC 802 0.0000 1.00 39.4 yes View details
rbcL-accD LSC 708 0.0019 1.00 45.8 yes View details
petA LSC 963 0.0007 1.00 49.7 yes View details
trnP-UGG-psaJ LSC 270 0.0025 1.00 39.8 yes View details
ycf1 IRb 1059 0.0000 1.00 40.0 no View details
ndhA SSC 2111 0.0025 1.00 59.1 yes View details
ycf1 SSC 5544 0.0008 1.00 53.0 yes View details
rpl2-trnH-GUG IRa 94 0.0000 1.00 71.2 no View details
psbT-psbN LSC 73 0.0183 1.00 69.8 yes View details
trnC-GCA-petN LSC 835 0.0012 1.00 60.7 yes View details
rpl32-trnL-UAG SSC 736 0.0018 1.00 59.9 yes View details
rpl2 IRb 1482 0.0009 1.00 59.3 yes View details
rpl2 IRa 1482 0.0009 1.00 59.3 yes View details
ccsA SSC 972 0.0007 1.00 59.2 yes View details
rps16 LSC 1141 0.0006 1.00 59.1 yes View details
atpA LSC 1524 0.0004 1.00 59.0 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 ATATACAAGTCGCTACCCCC TATGGACAGCTGAACCAGTG 1251 1.000 59.4
rps16_p2 rps16 ATATACAAGTCGCTACCCCC ATGGACAGCTGAACCAGTGA 1250 1.000 58.1
rps16_p3 rps16 ATATACAAGTCGCTACCCCC GTCTATGGACAGCTGAACCA 1254 1.000 57.1
rps16_p4 rps16 ATATACAAGTCGCTACCCCC TGTCTATGGACAGCTGAACC 1255 1.000 57.1
rps16_p5 rps16 ATATACAAGTCGCTACCCCC CTATGGACAGCTGAACCAGT 1252 1.000 57.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGGTTACTAGAACGAATCACA 775–780 1.000 58.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGGTTACTAGAACGAATCACA 774–779 1.000 58.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGGTTACTAGAACGAATCACA 829–834 1.000 56.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA CGGTTACTAGAACGAATCACAC 774–779 1.000 55.7
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC CGGTTACTAGAACGAATCACAC 773–778 1.000 55.7
atpA_p1 atpA GGTTCAAATCCTATTGGACGC TGTTGGGAGCGATGAAAGAA 1761 1.000 62.0
atpA_p2 atpA TCCGAGACACTTGATTCCTT TGTTGGGAGCGATGAAAGAA 1689 1.000 61.0
atpA_p3 atpA GGTTCAAATCCTATTGGACGC ATGTTGGGAGCGATGAAAGA 1762 1.000 60.2
atpA_p4 atpA TCCGAGACACTTGATTCCTT ATGTTGGGAGCGATGAAAGA 1690 1.000 59.2
atpA_p5 atpA TCCGAGACACTTGATTCCTTT TGTTGGGAGCGATGAAAGAA 1689 1.000 59.2
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT CCCGTCATGTTCCTTGGATT 1109–1118 1.000 79.0
atpH-atpI_p2 atpH-atpI AATAACGGAAGCGGCAGAAA CCCGTCATGTTCCTTGGATT 1110–1119 1.000 77.8
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACTTTAGCCGCG 1063–1072 1.000 75.9
atpH-atpI_p4 atpH-atpI AGGTCCAATAGAAGCAAGCC CCCGTCATGTTCCTTGGATT 1149–1158 1.000 75.8
atpH-atpI_p5 atpH-atpI GTCCAATAGAAGCAAGCCCT CCCGTCATGTTCCTTGGATT 1147–1156 1.000 75.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CATTGCTTCATTCGCATCCC CCGGATTTGAACTGGGGAAA 1184–1190 1.000 79.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CATTGCTTCATTCGCATCCC TTTGGTAATCAGGCGACACC 1203–1209 1.000 78.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CATTGCTTCATTCGCATCCC AAAAGGATTTGCAGTCCCCC 1166–1172 1.000 76.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CATTGCTTCATTCGCATCCC CGCGTTTTTGGTAATCAGGC 1209–1215 1.000 76.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CATTGCTTCATTCGCATCCC GCGTTTTTGGTAATCAGGCG 1208–1214 1.000 76.5
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 549–948 1.000 83.4
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTCTTCCCCACACTACGAGT 547–946 1.000 83.4
trnC-GCA-petN_p3 trnC-GCA-petN GTATCATTTTGGCGGCATGG ACTTCTTCCCCACACTACGA 601–1000 1.000 82.9
trnC-GCA-petN_p4 trnC-GCA-petN GTATCATTTTGGCGGCATGG TTCTTCCCCACACTACGAGT 599–998 1.000 82.9
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CACTTCTTCCCCACACTACG 550–949 1.000 82.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Stenogyne bifida NC_029818.1 150129 View on NCBI ↗
Stenogyne haliakalae NC_029817.1 149736 View on NCBI ↗
Stenogyne kanehoana NC_029821.1 150115 View on NCBI ↗