Markers + reference

Collinsonia

3 species · Lamiaceae · Lamiales

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Species 3
Genome length 153–153 kb
Candidate markers 267
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 342 0.0331 1.00 65.1 yes View details
rps16-trnQ-UUG LSC 1059 0.0123 1.00 61.4 yes View details
rps4-trnT-UGU LSC 453 0.0191 1.00 67.2 yes View details
psbE-petL LSC 856 0.0113 1.00 65.9 yes View details
ndhF-rpl32 SSC 419 0.0191 1.00 57.9 yes View details
rps15-ycf1 SSC 400 0.0200 1.00 61.3 yes View details
ycf1 SSC 5661 0.0084 1.00 44.6 yes View details
trnT-UGU-trnL-UAA LSC 686 0.0078 1.00 68.8 yes View details
rpl20-rps12 LSC 810 0.0091 1.00 65.1 yes View details
trnG-GCC-trnfM-CAU LSC 173 0.0193 1.00 64.0 yes View details
petA-psbJ LSC 1041 0.0077 1.00 63.9 yes View details
trnC-GCA-petN LSC 161 0.0124 1.00 63.8 yes View details
ndhC-trnV-UAC LSC 993 0.0105 0.99 62.3 yes View details
ycf4-cemA LSC 660 0.0081 1.00 61.8 yes View details
petA LSC 963 0.0048 1.00 61.8 yes View details
petG-trnW-CCA LSC 127 0.0210 1.00 60.4 yes View details
psbC LSC 1422 0.0019 1.00 59.9 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 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 TTCCCTCTAGACCTAGCTGC 408 1.000 81.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 422 1.000 81.6
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 421 1.000 81.6
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 423 1.000 81.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 460 1.000 80.5
trnK-UUU_p1 trnK-UUU ATACATAGAATTTCGATATGACAG TCCATGTCCTTGTTGAGTTGA 2655–2688 1.000 41.8
trnK-UUU_p2 trnK-UUU ATACATAGAATTTCGATATGACAG TCCATGTCCTTGTTGAGTTGAA 2655–2688 1.000 41.8
trnK-UUU_p3 trnK-UUU TCTATACATAGAATTTCGATATGACAG TCCATGTCCTTGTTGAGTTGA 2658–2691 1.000 41.8
trnK-UUU_p4 trnK-UUU ATACATAGAATTTCGATATGACAG ATCCATGTCCTTGTTGAGTTGA 2656–2689 1.000 41.8
trnK-UUU_p5 trnK-UUU TCTATACATAGAATTTCGATATGACA TCCATGTCCTTGTTGAGTTGA 2658–2691 1.000 41.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 1097–1139 1.000 84.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GTCTCGCTATTCGGAGGTTC 1110–1152 1.000 84.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1090–1132 1.000 83.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTCTCGCTATTCGGAGGTTC 1103–1145 1.000 83.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG CGGGTTTTGGTCTCGCTATT 1119–1161 1.000 83.2
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ACTTCTTCCCCACACTACGA 269–277 1.000 82.5
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTCTTCCCCACACTACGAGT 267–275 1.000 82.5
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CACTTCTTCCCCACACTACG 270–278 1.000 81.9
trnC-GCA-petN_p4 trnC-GCA-petN GTATCATTTTGGCGGCATGG TTCTTCCCCACACTACGAGT 319–327 1.000 81.6
trnC-GCA-petN_p5 trnC-GCA-petN GTATCATTTTGGCGGCATGG ACTTCTTCCCCACACTACGA 321–329 1.000 81.5
psbC_p1 psbC AGGTATTCGTGCTTGGATGG AGTGATTCCTACTTCAATTCAAGGA 1504 1.000 40.2
psbC_p2 psbC AAATTCGTGCAGCGGAAGAT AGTGATTCCTACTTCAATTCAAGGA 1568 1.000 40.2
psbC_p3 psbC TCTCAGGAAATTCGTGCAGC AGTGATTCCTACTTCAATTCAAGGA 1575 1.000 40.2
psbC_p4 psbC AGGTATTCGTGCTTGGATGG GTGATTCCTACTTCAATTCAAGGA 1503 1.000 40.2
psbC_p5 psbC AGGTATTCGTGCTTGGATGG AGTGATTCCTACTTCAATTCAAGG 1504 1.000 40.2
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU AGAAGATGCGGGTTCGATTC CTTGAGGTCACGGGTTCAAA 235–239 1.000 82.6
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU GAGAAGATGCGGGTTCGATT CTTGAGGTCACGGGTTCAAA 236–240 1.000 82.6
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU AGAAGATGCGGGTTCGATTC GGGTAGAGCAGTTTGGTAGC 271–275 1.000 82.3
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU GAGAAGATGCGGGTTCGATT GGGTAGAGCAGTTTGGTAGC 272–276 1.000 82.2
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU ATGCGGATATGGTCGAATGG GGGTAGAGCAGTTTGGTAGC 312–316 1.000 81.5

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
Collinsonia sinensis PP357190.1 152653 View on NCBI ↗
Collinsonia szechuanensis PP357222.1 152622 View on NCBI ↗
Collinsonia verticillata PP357184.1 152520 View on NCBI ↗