Markers + reference

Torenia

12 species · Linderniaceae · Lamiales

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Species 12
Genome length 153–154 kb
Candidate markers 271
Primer pairs 100

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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 546 0.0225 0.96 72.2 yes View details
trnS-GCU-trnG-CGA LSC 788 0.0170 0.89 62.2 yes View details
ndhC-trnV-UAC LSC 1136 0.0144 1.00 59.7 yes View details
trnV-UAC-trnM-CAU LSC 188 0.0077 0.99 47.1 yes View details
petA-psbJ LSC 1058 0.0163 0.99 59.4 yes View details
psbE-petL LSC 927 0.0169 0.99 58.1 yes View details
petB LSC 1387 0.0095 0.99 50.0 yes View details
ndhF SSC 2259 0.0099 1.00 52.5 yes View details
rpl32-trnL-UAG SSC 827 0.0182 0.98 65.8 yes View details
ycf1 SSC 5568 0.0145 1.00 45.4 yes View details
ycf1-trnN-GUU IRa 547 0.0163 1.00 70.5 yes View details
psaA-ycf3 LSC 727 0.0135 1.00 71.2 yes View details
ndhA-ndhH SSC 1 0.3030 1.00 68.8 yes View details
trnG-CGA-trnR-UCU LSC 244 0.0270 0.93 67.4 yes View details
trnK-UUU-rps16 LSC 856 0.0147 1.00 65.2 yes View details
rpl22-rps19 LSC 77 0.0288 0.97 65.2 yes View details
trnM-CAU-atpE LSC 228 0.0349 1.00 64.4 yes View details
rps16-trnQ-UUG LSC 1047 0.0153 0.99 62.8 yes View details
atpF-atpH LSC 380 0.0161 1.00 62.4 yes View details
trnT-UGU-trnL-UAA LSC 664 0.0085 0.99 62.2 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 100 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 CCGTGCTAACCTTGGTATGG 543–695 1.000 86.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 557–709 1.000 86.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 556–708 1.000 86.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 558–710 1.000 86.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 544–696 1.000 86.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TCCTTGAAAAAGGGGCTCAA 978–999 1.000 77.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTCCTTGAAAAAGGGGCTCA 979–1000 1.000 77.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCCTTGAAAAAGGGGCTCAA 977–998 1.000 77.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCCTTGAAAAAGGGGCTCA 978–999 1.000 77.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CTTGAAAAAGGGGCTCAACC 975–996 1.000 77.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTGG 1178–1276 1.000 85.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1120–1218 1.000 85.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAAATTGAAATGGGGCGTGG 1192–1290 1.000 83.6
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1134–1232 1.000 83.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAAATTGAAATGGGGCGTGG 1170–1268 1.000 80.4
trnS-GCU-trnG-CGA_p1 trnS-GCU-trnG-CGA CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 770–857 1.000 60.6
trnS-GCU-trnG-CGA_p2 trnS-GCU-trnG-CGA AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 769–856 1.000 60.6
trnS-GCU-trnG-CGA_p3 trnS-GCU-trnG-CGA CAATCCGACGCTTTAGTCCA AACCGAAAGACCCTTTAACT 808–895 1.000 60.5
trnS-GCU-trnG-CGA_p4 trnS-GCU-trnG-CGA AATCCGACGCTTTAGTCCAC AACCGAAAGACCCTTTAACT 807–894 1.000 60.5
trnS-GCU-trnG-CGA_p5 trnS-GCU-trnG-CGA ACGGAAAGAGAGGGATTCGA AACCGAAAGACCCTTTAACT 862–949 1.000 59.1
trnG-CGA-trnR-UCU_p1 trnG-CGA-trnR-UCU ACCCTTAGCCTTCCAAGCTA AGAAGACCTCTGTCCTATCCA 310–403 1.000 72.6
trnG-CGA-trnR-UCU_p2 trnG-CGA-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 304–397 1.000 72.5
trnG-CGA-trnR-UCU_p3 trnG-CGA-trnR-UCU ACCCTTAGCCTTCCAAGCTA AGGTTTAGAAGACCTCTGTCCT 316–409 1.000 71.9
trnG-CGA-trnR-UCU_p4 trnG-CGA-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 310–403 1.000 71.8
trnG-CGA-trnR-UCU_p5 trnG-CGA-trnR-UCU CAAAACGCTGAATCGACGTC AGAAGACCTCTGTCCTATCCA 337–430 1.000 71.3
atpF-atpH_p1 atpF-atpH TTAAATCCGAAACTCCCGGC CCGAGGCAGAGGGAAAAATA 565–594 1.000 76.6
atpF-atpH_p2 atpF-atpH TTAAATCCGAAACTCCCGGC GCAGAGGGAAAAATACGAGGT 560–589 1.000 74.2
atpF-atpH_p3 atpF-atpH TTAAATCCGAAACTCCCGGC GGGTTGGTTGTAGCATTAGC 494–523 1.000 73.1
atpF-atpH_p4 atpF-atpH TTAAATCCGAAACTCCCGGC GAGGCAGAGGGAAAAATACGA 563–592 1.000 72.2
atpF-atpH_p5 atpF-atpH TTAAATCCGAAACTCCCGGC AGGCAGAGGGAAAAATACGAG 562–591 1.000 72.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (12)

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

Species Accession Length (bp) Link
Torenia anagallis NC_082123.1 153459 View on NCBI ↗
Torenia asiatica NC_082124.1 154006 View on NCBI ↗
Torenia benthamiana NC_045273.1 153526 View on NCBI ↗
Torenia concolor NC_045272.1 153853 View on NCBI ↗
Torenia crustacea NC_082125.1 153668 View on NCBI ↗
Torenia flava NC_073112.1 153867 View on NCBI ↗
Torenia fordii MW309811.1 154007 View on NCBI ↗
Torenia fournieri NC_056129.1 153938 View on NCBI ↗
Torenia oblonga NC_082126.1 153669 View on NCBI ↗
Torenia polygonoides NC_073113.1 153477 View on NCBI ↗
Torenia thouarsii NC_082127.1 153013 View on NCBI ↗
Torenia violacea NC_072147.1 154007 View on NCBI ↗