Markers + reference

Rostellularia

2 species · Acanthaceae · Lamiales

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Species 2
Genome length 150–151 kb
Candidate markers 271
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 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
rps16-trnQ-UUG LSC 721 0.0526 0.76 75.1 yes View details
psbK-psbI LSC 454 0.0467 0.99 76.1 yes View details
rpoB-trnC-GCA LSC 1179 0.0360 0.94 80.5 yes View details
trnE-UUC-trnT-GGU LSC 733 0.0861 0.81 82.2 yes View details
ycf3-trnS-GGA LSC 683 0.0270 0.98 65.2 yes View details
rps4-trnT-UGU LSC 657 0.0435 0.84 77.6 yes View details
trnL-UAA-trnF-GAA LSC 218 0.1164 0.87 80.9 yes View details
trnF-GAA-ndhJ LSC 571 0.0280 1.00 59.9 yes View details
ndhG-ndhI SSC 305 0.0488 0.94 70.8 yes View details
rps15-ycf1 SSC 495 0.0525 0.92 82.9 yes View details
ndhI-ndhA SSC 79 0.0759 1.00 80.0 yes View details
petG-trnW-CCA LSC 125 0.0455 0.88 77.2 yes View details
trnR-UCU-atpA LSC 101 0.0421 0.94 74.5 yes View details
ndhK-ndhC LSC 58 0.0517 1.00 73.2 yes View details
petA-psbJ LSC 929 0.0221 0.98 73.1 yes View details
rpl22 LSC 393 0.0331 1.00 71.9 yes View details
trnG-GCC-trnfM-CAU LSC 126 0.0424 0.94 71.7 yes View details
trnI-GAU-trnA-UGC IRb 64 0.0312 1.00 70.5 yes View details
trnA-UGC-trnI-GAU IRa 64 0.0312 1.00 70.5 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 GCTTTCTGCCACATCGTTTC GAGGTTCGAATCCTTCCGTC 619–782 1.000 86.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGGATTCTGCCCTTCAAG GAGGTTCGAATCCTTCCGTC 648–811 1.000 85.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATTCTGCCCTTCAA GAGGTTCGAATCCTTCCGTC 649–812 1.000 82.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTC TTCGGAGGTTCGAATCCTTC 623–786 1.000 81.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATTCTGCCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 645–808 1.000 81.6
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT CGCCCCGGATCATTAGATAG 578–594 1.000 78.3
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG CGCCCCGGATCATTAGATAG 573–589 1.000 78.3
psbK-psbI_p3 psbK-psbI GCCAGTCATACCTGTGCTTT CGCCCCGGATCATTAGATAG 610–626 1.000 77.2
psbK-psbI_p4 psbK-psbI TGGCAAGCTGCTGTAAGTTT CGCCCCGGATCATTAGATAG 570–586 1.000 76.3
psbK-psbI_p5 psbK-psbI TTGGCAAGCTGCTGTAAGTT CGCCCCGGATCATTAGATAG 571–587 1.000 76.3
trnR-UCU-atpA_p1 trnR-UCU-atpA AAGAACTGCGTCCATTGTCT GAGGAAGCAGAAGCCCTTTT 250–255 1.000 78.1
trnR-UCU-atpA_p2 trnR-UCU-atpA AAGAACTGCGTCCATTGTCT AGGAAGCAGAAGCCCTTTTG 249–254 1.000 75.8
trnR-UCU-atpA_p3 trnR-UCU-atpA AAGAACTGCGTCCATTGTCT GGAAGCAGAAGCCCTTTTGA 248–253 1.000 75.8
trnR-UCU-atpA_p4 trnR-UCU-atpA AAGAACTGCGTCCATTGTCT TCAGGAACAAATGAACCGGT 218–223 1.000 74.0
trnR-UCU-atpA_p5 trnR-UCU-atpA AAAGAACTGCGTCCATTGTCT GAGGAAGCAGAAGCCCTTTT 251–256 1.000 73.3
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AGTTCTTCTGTCAAACCCCG CCGGATTTGAACTGGGGAAA 1345–1382 1.000 83.6
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GTCAAACCCCGGTCAATGAA CCGGATTTGAACTGGGGAAA 1336–1373 1.000 82.6
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCAAACCCCGGTCAATGAAC CCGGATTTGAACTGGGGAAA 1335–1372 1.000 82.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AGTTCTTCTGTCAAACCCCG GCAGGACAGAAGAGAAGCAG 1396–1433 1.000 81.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCCGGTCAATGAACCTACAA CCGGATTTGAACTGGGGAAA 1329–1366 1.000 81.9
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 768–837 1.000 87.7
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 805–874 1.000 87.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 765–834 1.000 86.5
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC CCGATGACTTACGCCTTACC 802–871 1.000 86.4
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC TTGAACCGATGACTTACGCC 807–876 1.000 85.3
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU AGAAGATGCGGGTTCGATTC GGGTAGAGCAGTTTGGTAGC 228–232 1.000 83.8
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU GAGAAGATGCGGGTTCGATT GGGTAGAGCAGTTTGGTAGC 229–233 1.000 83.8
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU AGAAGATGCGGGTTCGATTC GTTCAAATCCTGTCTCCGCA 179–183 1.000 83.7
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU GAGAAGATGCGGGTTCGATT GTTCAAATCCTGTCTCCGCA 180–184 1.000 83.7
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU AGAAGATGCGGGTTCGATTC TAGCTCGCAAGGCTCATAAC 212–216 1.000 82.6

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
Rostellularia mollissima NC_080237.1 150513 View on NCBI ↗
Rostellularia procumbens NC_062458.1 150454 View on NCBI ↗