Markers + reference

Beccarinda

2 species · Gesneriaceae · Lamiales

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Species 2
Genome length 153–154 kb
Candidate markers 266
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 300 0.1154 0.95 86.8 yes View details
trnS-GCU-trnS-CGA LSC 749 0.0275 0.97 62.2 yes View details
rpoB-trnC-GCA LSC 2098 0.0208 0.98 56.8 yes View details
trnT-UGU-trnL-UAA LSC 631 0.0351 0.99 65.0 yes View details
trnF-GAA-ndhJ LSC 668 0.0598 0.90 84.7 yes View details
cemA-petA LSC 341 0.0294 1.00 56.3 yes View details
ndhF-trnL-UAG SSC 1522 0.0265 0.99 62.8 yes View details
ccsA-ndhD SSC 246 0.0717 0.91 76.6 yes View details
ndhI SSC 492 0.0122 1.00 51.1 yes View details
ycf1 SSC 3510 0.0168 1.00 52.6 yes View details
ycf1-trnN-GUU IRa 2185 0.0170 0.99 55.7 yes View details
ycf4-cemA LSC 869 0.0280 0.95 73.2 yes View details
psbH-petB LSC 854 0.0215 0.98 72.7 yes View details
psbE-petL LSC 892 0.0249 0.99 72.4 yes View details
psaA-ycf3 LSC 884 0.0213 0.96 70.2 yes View details
accD-psaI LSC 739 0.0207 0.98 68.8 yes View details
ndhD-psaC SSC 92 0.0326 1.00 68.4 yes View details
rps11-rpl36 LSC 102 0.0297 0.99 68.3 yes View details
ndhC-trnV-UAC LSC 1031 0.0169 0.97 67.1 yes View details
petB-petD LSC 916 0.0131 1.00 66.3 yes View details
psbN-psbH LSC 87 0.0230 1.00 65.7 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 105 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 362–366 1.000 88.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 376–380 1.000 88.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 375–379 1.000 88.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 377–381 1.000 88.2
trnH-GUG-psbA_p5 trnH-GUG-psbA TTTAGTCATGGGCGAACGAC TTCCCTCTAGACCTAGCTGC 429 0.500 57.1
trnS-GCU-trnS-CGA_p1 trnS-GCU-trnS-CGA CAATCCGACGCTTTAGTCCA ACCACTAAACTATACCCGCT 804 0.500 41.1
trnS-GCU-trnS-CGA_p2 trnS-GCU-trnS-CGA AATCCGACGCTTTAGTCCAC ACCACTAAACTATACCCGCT 803 0.500 41.1
trnS-GCU-trnS-CGA_p3 trnS-GCU-trnS-CGA ACGGAAAGAGAGGGATTCGA ACCACTAAACTATACCCGCT 858 0.500 40.0
trnS-GCU-trnS-CGA_p4 trnS-GCU-trnS-CGA AGCAATCCGACGCTTTAGTC ACCACTAAACTATACCCGCT 806 0.500 38.3
trnS-GCU-trnS-CGA_p5 trnS-GCU-trnS-CGA CGACGCTTTAGTCCACTCAG ACCACTAAACTATACCCGCT 799 0.500 38.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA GACCCATCCTCGCATGAATT ATCCTAGATGCGAACGAGGA 2765–2769 1.000 82.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GACCCATCCTCGCATGAATT TCCTAGATGCGAACGAGGAT 2764–2768 1.000 82.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA GACCCATCCTCGCATGAATT TGTTGTTTGATCAGGCGACA 2596–2600 1.000 82.0
rpoB-trnC-GCA_p4 rpoB-trnC-GCA GACGATATCGAGCTGGAACC ATCCTAGATGCGAACGAGGA 2936–2940 1.000 81.7
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GACGATATCGAGCTGGAACC TCCTAGATGCGAACGAGGAT 2935–2939 1.000 81.7
psaA-ycf3_p1 psaA-ycf3 TGAGAAATGACCCGGTTTGG ATCAAGCCGCTGAGTATTGG 1075–1081 1.000 83.0
psaA-ycf3_p2 psaA-ycf3 TGAGAAATGACCCGGTTTGG GGAAACAGGCTATAGCGCTT 1057–1063 1.000 83.0
psaA-ycf3_p3 psaA-ycf3 GCCCATTCCTCGAAAGAAGT ATCAAGCCGCTGAGTATTGG 1056–1062 1.000 82.9
psaA-ycf3_p4 psaA-ycf3 GCCCATTCCTCGAAAGAAGT GGAAACAGGCTATAGCGCTT 1038–1044 1.000 82.9
psaA-ycf3_p5 psaA-ycf3 TGAGAAATGACCCGGTTTGG TTGAAGATCACGAGGCGTTT 1004–1010 1.000 82.3
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA TTTTCCGGCGATACGAATGT GCTTCCATTGAGTCTCTGCA 1531–1558 1.000 81.1
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA TTTTCCGGCGATACGAATGT TTTTCGCTCTCTGAACGCTT 1501–1528 1.000 80.9
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA TTTTCCGGCGATACGAATGT TTTTTCGCTCTCTGAACGCT 1502–1529 1.000 80.9
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA AAACTTGACCTGTTGACCCC GCTTCCATTGAGTCTCTGCA 1556–1583 1.000 80.6
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA AAACTTGACCTGTTGACCCC TTTTCGCTCTCTGAACGCTT 1526–1553 1.000 80.4
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ GGGATAGCTCAGCTGGTAGA AGTTGGATAGGATGGCCCTT 736–810 1.000 87.0
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA AGTTGGATAGGATGGCCCTT 700–774 1.000 86.8
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ CTACATTGGGAATGGTCGGG AGTTGGATAGGATGGCCCTT 753–827 1.000 86.7
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ TGCTACATTGGGAATGGTCG AGTTGGATAGGATGGCCCTT 755–829 1.000 86.6
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ GGATGGGATGCTACATTGGG AGTTGGATAGGATGGCCCTT 763–837 1.000 86.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Beccarinda cordifolia NC_070426.1 153197 View on NCBI ↗
Beccarinda tonkinensis NC_072338.1 154113 View on NCBI ↗