Markers + reference

Paederia

3 species · Rubiaceae · Gentianales

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Species 3
Genome length 154–154 kb
Candidate markers 272
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 269 0.0198 1.00 52.6 yes View details
rpoB-trnC-GCA LSC 1032 0.0006 1.00 38.8 yes View details
atpB LSC 1497 0.0009 1.00 46.8 yes View details
rbcL LSC 1437 0.0028 1.00 48.0 yes View details
petB LSC 1435 0.0014 1.00 59.6 yes View details
rpl16 LSC 1442 0.0009 1.00 41.1 yes View details
ycf1 IRb 1920 0.0003 1.00 45.6 no View details
rpl32-trnL-UAG SSC 653 0.0020 1.00 52.6 yes View details
ndhG SSC 531 0.0013 1.00 32.5 yes View details
ndhA SSC 2255 0.0009 1.00 45.3 yes View details
rps15-ycf1 SSC 373 0.0036 1.00 30.7 yes View details
ycf1 SSC 5613 0.0015 1.00 45.3 yes View details
trnS-GCU-trnG-UCC LSC 581 0.0034 1.00 61.7 yes View details
rpl16-rps3 LSC 131 0.0102 1.00 51.6 yes View details
rps4 LSC 606 0.0011 1.00 47.0 yes View details
matK-trnK-UUU LSC 691 0.0010 1.00 46.9 yes View details
matK LSC 1518 0.0009 1.00 46.8 yes View details
rps2 LSC 711 0.0009 1.00 46.8 yes View details
rps16 LSC 1097 0.0006 1.00 46.7 yes View details
trnE-UUC-trnT-GGU LSC 914 0.0007 1.00 46.7 yes View details
trnK-UUU-rps16 LSC 764 0.0000 1.00 46.6 yes View details
trnT-GGU-psbD LSC 1304 0.0005 1.00 46.6 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 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 GCTGCTATAGATGCCCCATC 323–324 1.000 80.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCTGCTATAGATGCCCCATC 337–338 1.000 80.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCTGCTATAGATGCCCCATC 336–337 1.000 80.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCTGCTATAGATGCCCCATC 338–339 1.000 80.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGTGCGAATCTTGGTATGGA 386–387 1.000 80.1
matK_p1 matK ACAAGTACAAGGCTTCAGAATG CCGCCTCCGAGGTATCTATT 1653 1.000 49.5
matK_p2 matK ACAAGTACAAGGCTTCAGAA CCGCCTCCGAGGTATCTATT 1653 1.000 48.6
matK_p3 matK ACAAGTACAAGGCTTCAGAATG CGCCTCCGAGGTATCTATTC 1652 1.000 45.7
matK_p4 matK ACAAGTACAAGGCTTCAGAAT CCGCCTCCGAGGTATCTATT 1653 1.000 45.5
matK_p5 matK CCATTTACAAGTACAAGGCTTCA CCGCCTCCGAGGTATCTATT 1659 1.000 44.8
matK-trnK-UUU_p1 matK-trnK-UUU AGAAAGACTGGCTGTTGAGA AACGGTAGAGTACTCGGCTT 771 1.000 65.9
matK-trnK-UUU_p2 matK-trnK-UUU AGAAAGACTGGCTGTTGAGA ACGGTAGAGTACTCGGCTTT 770 1.000 65.9
matK-trnK-UUU_p3 matK-trnK-UUU AGAAAGACTGGCTGTTGAGA TTGGGTTGCTAACTCAACGG 786 1.000 64.1
matK-trnK-UUU_p4 matK-trnK-UUU AAGACTGGCTGTTGAGATCT AACGGTAGAGTACTCGGCTT 768 1.000 64.1
matK-trnK-UUU_p5 matK-trnK-UUU AAGACTGGCTGTTGAGATCT ACGGTAGAGTACTCGGCTTT 767 1.000 64.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 GTCGTGGTCTTCCAAACCTT TTTCCTTGAAAGGGGTGCTC 986–989 1.000 79.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGTGGTCTTCCAAACCTT CTTGAAAGGGGTGCTCAACT 982–985 1.000 79.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 GTCGTGGTCTTCCAAACCTT GGAGCTTCGCCCTAATCAAA 917–920 1.000 79.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTTCCTTGAAAGGGGTGCTC 904–907 1.000 78.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTCCTTGAAAGGGGTGCTC 903–906 1.000 78.9
rps16_p1 rps16 TCACTACCCCCTCCCTTTTT TGAGCCAATGACTATTCCTGA 1195–1196 1.000 58.4
rps16_p2 rps16 ATTCGAAAGCGGTAAAGGGG TGAGCCAATGACTATTCCTGA 1255–1259 1.000 57.7
rps16_p3 rps16 TACAAGTCACTACCCCCTCC TGAGCCAATGACTATTCCTGA 1201–1202 1.000 57.6
rps16_p4 rps16 TCACTACCCCCTCCCTTTTT TTGAGCCAATGACTATTCCTGA 1196–1197 1.000 56.2
rps16_p5 rps16 TACAAGTCACTACCCCCTCC TTGAGCCAATGACTATTCCTGA 1202–1203 1.000 55.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA CAAACCGAAAGCAAAGACCC 688–694 1.000 79.9
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA CCAAACCGAAAGCAAAGACC 689–695 1.000 79.9
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC CAAACCGAAAGCAAAGACCC 687–693 1.000 79.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC CCAAACCGAAAGCAAAGACC 688–694 1.000 79.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA CCGAAAGCAAAGACCCCTTA 684–690 1.000 79.5

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
Paederia foetida NC_062416.1 153591 View on NCBI ↗
Paederia pertomentosa PP873175.1 153623 View on NCBI ↗
Paederia scandens NC_049155.1 153626 View on NCBI ↗