Markers + reference

Prostanthera

4 species · Lamiaceae · Lamiales

Back to catalogue

Species 4
Genome length 153–153 kb
Candidate markers 273
Primer pairs 75

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 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rbcL-accD LSC 683 0.0302 0.99 66.4 yes View details
accD LSC 1512 0.0233 0.98 62.1 yes View details
ycf2 LSC 6426 0.0075 0.99 42.5 yes View details
ycf1 SSC 1208 0.0069 0.99 48.5 no View details
ndhF-rpl32 SSC 512 0.0371 0.98 68.8 yes View details
rpl32-trnL SSC 512 0.0387 0.98 69.4 yes View details
ycf1 SSC 5568 0.0252 0.99 55.2 yes View details
ycf2 LSC 6456 0.0098 0.99 44.4 no View details
rpl23-trnI-CAU LSC 194 0.2202 0.96 85.8 yes View details
ccsA-ndhD SSC 232 0.0510 0.98 78.1 yes View details
ycf3-trnS-GGA LSC 835 0.0251 0.99 66.7 yes View details
petB-petD LSC 186 0.0573 1.00 66.6 yes View details
ndhC-trnV-UAC LSC 1051 0.0213 0.99 66.3 yes View details
trnI-CAU-rpl23 LSC 190 0.1544 0.88 65.0 yes View details
trnI-CAU-ycf2 LSC 88 0.1098 1.00 63.4 yes View details
ycf2-trnI-CAU LSC 88 0.1098 1.00 63.4 yes View details
rps16-trnQ-UUG LSC 1030 0.0128 0.96 62.9 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAAATTGAAATGGGGCGTGG 1162–1178 1.000 83.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1104–1120 1.000 83.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1145–1161 1.000 83.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1087–1103 1.000 82.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAAATTGAAATGGGGCGTGG 1163–1179 1.000 82.4
ycf3-trnS-GGA_p1 ycf3-trnS-GGA AATGCCTCCCTTTCTCCTGA CCCTCGGTAAACAAAAGCCT 1009–1014 1.000 79.2
ycf3-trnS-GGA_p2 ycf3-trnS-GGA ATGCCTCCCTTTCTCCTGAA CCCTCGGTAAACAAAAGCCT 1008–1013 1.000 79.2
ycf3-trnS-GGA_p3 ycf3-trnS-GGA AATGCCTCCCTTTCTCCTGA ACGGAAAGAGAGGGATTCGA 1030–1035 1.000 78.7
ycf3-trnS-GGA_p4 ycf3-trnS-GGA ATGCCTCCCTTTCTCCTGAA ACGGAAAGAGAGGGATTCGA 1029–1034 1.000 78.7
ycf3-trnS-GGA_p5 ycf3-trnS-GGA ATGCCTCCCTTTCTCCTGAA TTCCAATGCTACGCCTTGAA 979–984 1.000 78.5
ndhC-trnV-UAC_p1 ndhC-trnV-UAC TGCCAAAATAGGAATAAGACTTGA AGAAGGTCTACGGTTCGAGT 1154–1167 1.000 46.3
ndhC-trnV-UAC_p2 ndhC-trnV-UAC TGCCAAAATAGGAATAAGACTTGA GAAGGTCTACGGTTCGAGTC 1153–1166 1.000 46.3
ndhC-trnV-UAC_p3 ndhC-trnV-UAC TGCCAAAATAGGAATAAGACTTG AGAAGGTCTACGGTTCGAGT 1154–1167 1.000 46.3
ndhC-trnV-UAC_p4 ndhC-trnV-UAC TGCCAAAATAGGAATAAGACTTGA GTTCGAGTCCGTATAGCCCT 1142–1155 1.000 46.3
ndhC-trnV-UAC_p5 ndhC-trnV-UAC TGCCAAAATAGGAATAAGACTTGAT AGAAGGTCTACGGTTCGAGT 1154–1167 1.000 46.3
rbcL-accD_p1 rbcL-accD TCATGGTATGCACTTCCGTG TCACTATCACTGCTGTTCGC 1791–1796 0.500 61.4
rbcL-accD_p2 rbcL-accD TTGAATGCTACTGCGGGTAC TCACTATCACTGCTGTTCGC 1991–1996 0.500 61.3
rbcL-accD_p3 rbcL-accD TCTTCACATTCACCGTGCAA TCACTATCACTGCTGTTCGC 1839–1844 0.500 61.2
rbcL-accD_p4 rbcL-accD TTCTTCACATTCACCGTGCA TCACTATCACTGCTGTTCGC 1840–1845 0.500 61.2
rbcL-accD_p5 rbcL-accD AATGCTACTGCGGGTACATG TCACTATCACTGCTGTTCGC 1988–1993 0.500 61.0
accD_p1 accD AGGGGGCAAGAAAACTCT AAATAATGGAACTTGGCGCG 1531–1552 1.000 44.8
accD_p2 accD AGGGGGCAAGAAAACTCT AAAATAATGGAACTTGGCGCG 1532–1553 1.000 44.8
accD_p3 accD AGGGGGCAAGAAAACTCT AATAATGGAACTTGGCGCGC 1530–1551 1.000 44.7
accD_p4 accD AGGGGGCAAGAAAACTCT ATAATGGAACTTGGCGCGC 1529–1550 1.000 44.7
accD_p5 accD AGGGGGCAAGAAAACTCT TAAAATAATGGAACTTGGCGCG 1533–1554 0.750 33.0
petB-petD_p1 petB-petD TGCACTTTCCAATGATACGT GTTCAAGTCACACACTCCCA 254 1.000 63.0
petB-petD_p2 petB-petD TGCACTTTCCAATGATACGT AGTTCAAGTCACACACTCCC 255 1.000 60.6
petB-petD_p3 petB-petD ATGCACTTTCCAATGATACGT GTTCAAGTCACACACTCCCA 255 1.000 59.5
petB-petD_p4 petB-petD AATGCACTTTCCAATGATACGT GTTCAAGTCACACACTCCCA 256 1.000 57.4
petB-petD_p5 petB-petD ATGCACTTTCCAATGATACGT AGTTCAAGTCACACACTCCC 256 1.000 57.1

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
Prostanthera althoferi subsp. althoferi OR699041.1 152865 View on NCBI ↗
Prostanthera althoferi x Prostanthera campbellii NC_084413.1 152778 View on NCBI ↗
Prostanthera campbellii NC_084414.1 152754 View on NCBI ↗
Prostanthera wilkieana NC_084412.1 152812 View on NCBI ↗