Markers + reference

Gynochthodes

3 species · Rubiaceae · Gentianales

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Species 3
Genome length 153–153 kb
Candidate markers 268
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1228 0.0098 1.00 62.1 yes View details
petN-psbM LSC 762 0.0105 1.00 66.5 yes View details
trnT-UGU-trnL-UAA LSC 769 0.0078 1.00 63.7 yes View details
accD-psaI LSC 730 0.0082 1.00 57.4 yes View details
petA-psbJ LSC 917 0.0124 1.00 66.6 yes View details
psbB LSC 1527 0.0013 1.00 49.5 yes View details
rpoA LSC 1014 0.0020 1.00 53.0 yes View details
rpl32-trnL-UAG SSC 574 0.0081 1.00 64.0 yes View details
ndhA SSC 2193 0.0037 1.00 59.7 yes View details
rpl2-trnH-GUG IRa 85 0.0000 1.00 69.4 no View details
ccsA SSC 972 0.0007 1.00 63.4 yes View details
trnS-GCU-trnG-UCC LSC 1211 0.0028 1.00 62.3 yes View details
trnE-UUC-trnT-GGU LSC 769 0.0035 1.00 61.9 yes View details
trnF-GAA-ndhJ LSC 709 0.0019 0.99 61.0 yes View details
accD LSC 1575 0.0038 1.00 61.0 yes View details
psaA-ycf3 LSC 908 0.0022 1.00 60.2 yes View details
ycf4-cemA LSC 620 0.0022 1.00 60.1 yes View details
rpl20-rps12 LSC 758 0.0018 1.00 59.9 yes View details
rbcL LSC 1428 0.0014 1.00 59.6 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-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1364–1375 1.000 80.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AGCAATCTAAATGGGGCGTG 1423–1434 1.000 75.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1368–1379 1.000 75.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1394–1405 1.000 75.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 1356–1367 1.000 75.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA CATCGTTAGCTTGGAAGGCT 1343–1361 1.000 81.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC CATCGTTAGCTTGGAAGGCT 1342–1360 1.000 81.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA TCAAAACCGAACCCGAAACT 1273–1291 1.000 81.1
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC TCAAAACCGAACCCGAAACT 1272–1290 1.000 81.1
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA CGTTAGCTTGGAAGGCTAGG 1340–1358 1.000 80.9
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TCATTCTAGTTCCTACGGCCT 909–968 1.000 72.2
petN-psbM_p2 petN-psbM GGGGACACAATTCACATGGA TCATTCTAGTTCCTACGGCCT 931–990 1.000 71.7
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TCTAGTTCCTACGGCCTTTCT 905–964 1.000 71.7
petN-psbM_p4 petN-psbM AGGGGACACAATTCACATGG TCATTCTAGTTCCTACGGCCT 932–991 1.000 71.6
petN-psbM_p5 petN-psbM GGCTGCTTTAATGGTCGTCT TCATTCTAGTTCCTACGGCCT 893–952 1.000 71.4
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU TCTTTCGTAGTACCCCCAGG GAACCGATGACTTACGCCTT 901–933 1.000 79.7
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TCTTTCGTAGTACCCCCAGG TACCGCTGAGTTAAAAGGGC 866–898 1.000 78.9
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCTGCCTCCTTGAAAGAGAG GAACCGATGACTTACGCCTT 866–898 1.000 78.8
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TGTCCTGAACCACTAGACGA GAACCGATGACTTACGCCTT 845–877 1.000 78.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TCTTTCGTAGTACCCCCAGG CCGATGACTTACGCCTTACC 898–930 1.000 78.5
psaA-ycf3_p1 psaA-ycf3 ACGCGATCCCTATCTACCAA TTGAAGATCACGAGGCGTTT 991–1008 1.000 78.9
psaA-ycf3_p2 psaA-ycf3 ACGCGATCCCTATCTACCAA TTGGTTGAAGATCACGAGGC 995–1012 1.000 78.6
psaA-ycf3_p3 psaA-ycf3 CCTGGTTTAGCCCATTCCTC TTGAAGATCACGAGGCGTTT 1024–1041 1.000 78.5
psaA-ycf3_p4 psaA-ycf3 CCTGGTTTAGCCCATTCCTC TTGGTTGAAGATCACGAGGC 1028–1045 1.000 78.2
psaA-ycf3_p5 psaA-ycf3 ACGCGATCCCTATCTACCAA TGAAGATCACGAGGCGTTTC 990–1007 1.000 77.9
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ACCAATTTCGCCATATCCCC 819–831 1.000 79.8
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG GTTTCCATACCAAGGCCCAA 861–873 1.000 79.2
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG TAGCGTCTACCAATTTCGCC 827–839 1.000 79.2
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ACCAATTTCGCCATATCCCC 851–863 1.000 78.9
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT GTTTCCATACCAAGGCCCAA 893–905 1.000 78.3

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
Gynochthodes cochinchinensis NC_053818.1 153022 View on NCBI ↗
Gynochthodes officinalis NC_028009.1 153398 View on NCBI ↗
Gynochthodes parvifolia NC_054151.1 153069 View on NCBI ↗