Markers + reference

Drymocallis

3 species · Rosaceae · Rosales

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Species 3
Genome length 154–155 kb
Candidate markers 269
Primer pairs 95

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 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnR-UCU-atpA LSC 645 0.0052 1.00 51.4 yes View details
rpoB-trnC-GCA LSC 1190 0.0034 1.00 54.0 yes View details
petN-psbM LSC 1273 0.0021 1.00 60.4 yes View details
psaI-ycf4 LSC 424 0.0047 1.00 48.0 yes View details
cemA LSC 690 0.0010 1.00 33.5 yes View details
petA-psbJ LSC 966 0.0048 1.00 61.2 yes View details
clpP LSC 2103 0.0025 1.00 59.3 yes View details
rpl14 LSC 369 0.0054 1.00 56.3 yes View details
trnR-ACG-trnN-GUU IRb 472 0.0056 1.00 47.2 yes View details
ycf1 IRb 1107 0.0000 1.00 33.6 no View details
ycf1 SSC 5745 0.0022 1.00 47.8 yes View details
rpl2-trnH-GUG IRa 42 0.0000 1.00 71.2 no View details
ndhF-rpl32 SSC 599 0.0034 0.97 65.8 yes View details
ycf3-trnS-GGA LSC 695 0.0019 1.00 62.6 yes View details
rps16-trnQ-UUG LSC 907 0.0023 0.98 61.2 yes View details
trnT-UGU-trnL-UAA LSC 872 0.0031 1.00 60.8 yes View details
rps16 LSC 1133 0.0024 1.00 60.4 yes View details
psaA-ycf3 LSC 756 0.0018 1.00 60.2 yes View details
rbcL-accD LSC 650 0.0010 1.00 59.6 yes View details
ndhD SSC 1503 0.0009 1.00 59.3 yes View details
trnE-UUC-trnT-GGU LSC 529 0.0025 1.00 58.9 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 AAGTAAGACGGTGGAGAAGT TGTACCAACCGAACCAATGA 1299–1301 1.000 55.4
rps16_p2 rps16 AGTAAGACGGTGGAGAAGTAGA TGTACCAACCGAACCAATGA 1298–1300 1.000 54.5
rps16_p3 rps16 AAGTAAGACGGTGGAGAAGT TGGGTTCCAAACTGAAGGAA 1245–1247 1.000 53.8
rps16_p4 rps16 AAGACGGTGGAGAAGTAGAA TGTACCAACCGAACCAATGA 1295–1297 1.000 53.0
rps16_p5 rps16 AGACGGTGGAGAAGTAGAAA TGTACCAACCGAACCAATGA 1294–1296 1.000 53.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 953–998 1.000 83.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 951–996 1.000 83.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GATGTAAGACTCCACAGCGG GAGGTTCGAATCCTTCCGTC 967–1012 1.000 82.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATGTAAGACTCCACAGCG GAGGTTCGAATCCTTCCGTC 968–1013 1.000 82.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TAAGACTCCACAGCGGATCA GAGGTTCGAATCCTTCCGTC 963–1008 1.000 82.1
trnR-UCU-atpA_p1 trnR-UCU-atpA ATTGGAGTGAAAAGCGTCCA AAGACGTTTACCGAGGAAGC 811–818 1.000 79.0
trnR-UCU-atpA_p2 trnR-UCU-atpA TGGAGTGAAAAGCGTCCATT AAGACGTTTACCGAGGAAGC 809–816 1.000 79.0
trnR-UCU-atpA_p3 trnR-UCU-atpA TTGGAGTGAAAAGCGTCCAT AAGACGTTTACCGAGGAAGC 810–817 1.000 79.0
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGAGTGAAAAGCGTCCATT GAGGAAGCGGAAACCCTTTT 797–804 1.000 76.6
trnR-UCU-atpA_p5 trnR-UCU-atpA TTGGAGTGAAAAGCGTCCAT GAGGAAGCGGAAACCCTTTT 798–805 1.000 76.6
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TATTGCCTCATTTCCACCCC CCGGATTTGAACTGGGGAAA 1278–1280 1.000 76.2
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TATTGCCTCATTTCCACCCC AAAAGGATTTGCAGTCCCCC 1260–1262 1.000 74.0
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CATTTCCACCCCCAAGCAT CCGGATTTGAACTGGGGAAA 1270–1272 1.000 71.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATATTGCCTCATTTCCACCCC CCGGATTTGAACTGGGGAAA 1279–1281 1.000 71.5
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GTTCCTCTGTTAAGCCCTGA CCGGATTTGAACTGGGGAAA 1354–1356 1.000 70.6
petN-psbM_p1 petN-psbM AGTAAATCTCGCTTGGGCTG GTAAAAACAGTCAGCCAAGGC 1379–1382 1.000 72.2
petN-psbM_p2 petN-psbM AGTAAATCTCGCTTGGGCTG CGTAAAAACAGTCAGCCAAGG 1380–1383 1.000 70.1
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT GTAAAAACAGTCAGCCAAGGC 1319–1322 1.000 69.6
petN-psbM_p4 petN-psbM AGTAAATCTCGCTTGGGCTG TAAAAACAGTCAGCCAAGGC 1378–1381 1.000 68.6
petN-psbM_p5 petN-psbM ATGGGGAAGAAGTGGACTCT CGTAAAAACAGTCAGCCAAGG 1320–1323 1.000 67.6
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGAGATGTCCTGGACCAC GAACCGATGACTTACGCCTT 618 1.000 79.1
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GAGAGATGTCCTGGACCACT GAACCGATGACTTACGCCTT 617 1.000 79.1
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU AGAGAGATGTCCTGGACCAC CCATGGCGTTACTCTACCAC 597 1.000 78.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GAGAGATGTCCTGGACCACT CCATGGCGTTACTCTACCAC 596 1.000 78.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GAGAGATGTCCTGGACCACT TGGCGTTACTCTACCACTGA 593 1.000 78.5

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
Drymocallis fissa NC_087030.1 154738 View on NCBI ↗
Drymocallis glandulosa NC_087028.1 154789 View on NCBI ↗
Drymocallis saviczii NC_050966.1 154487 View on NCBI ↗