Markers + reference

Rytidosperma

2 species · Poaceae · Poales

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Species 2
Genome length 129–133 kb
Candidate markers 269
Primer pairs 100

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 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-psbD LSC 1015 0.0101 0.97 66.5 yes View details
psbC LSC 1422 0.0021 1.00 56.1 yes View details
trnY-GUA-trnD-GUC LSC 356 0.0169 1.00 63.4 yes View details
trnC-GCA-rpoB LSC 752 0.0080 1.00 63.3 yes View details
rpoC1 LSC 2052 0.0024 1.00 44.8 yes View details
rbcL LSC 1431 0.0084 1.00 61.8 yes View details
petA-psbJ LSC 940 0.0088 0.97 66.5 yes View details
petB LSC 1433 0.0056 1.00 62.2 yes View details
ndhF-rpl32 SSC 1017 0.0087 0.90 65.6 yes View details
rpl32-trnL-UAG SSC 323 0.0217 1.00 51.3 yes View details
rpoC1-rpoC2 LSC 193 0.0259 1.00 67.4 yes View details
trnT-UGU-trnL-UAA LSC 706 0.0059 0.96 66.0 yes View details
rpl14-rpl16 LSC 103 0.0194 1.00 63.7 yes View details
rps16-trnQ-UUG LSC 853 0.0091 0.77 63.6 yes View details
rps19-psbA LSC 122 0.0244 0.67 62.6 no View details
trnG-UCC-trnM-CAU LSC 612 0.0065 1.00 62.5 yes View details
trnD-GUC-psbM LSC 926 0.0022 0.98 62.0 yes View details
trnG-GCC-trnfM-CAU LSC 324 0.0154 1.00 61.9 yes View details
trnW-CCA-trnP-UGG LSC 131 0.0153 1.00 61.3 yes View details
psbB LSC 1527 0.0046 1.00 61.3 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU TGAAAACTCAGATTGCTCTTTTCT GTCCGGTGTAATTCCATCGA 2635–2639 1.000 40.5
trnK-UUU_p2 trnK-UUU TGAAAACTCAGATTGCTCTTTTCT CGTCCGGTGTAATTCCATCG 2636–2640 1.000 40.5
trnK-UUU_p3 trnK-UUU TGAAAACTCAGATTGCTCTT GTCCGGTGTAATTCCATCGA 2635–2639 1.000 40.5
trnK-UUU_p4 trnK-UUU TTGAAAACTCAGATTGCTCT GTCCGGTGTAATTCCATCGA 2636–2640 1.000 40.5
trnK-UUU_p5 trnK-UUU TGAAAACTCAGATTGCTCTTTTC GTCCGGTGTAATTCCATCGA 2635–2639 1.000 40.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 732–927 1.000 82.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 743–938 1.000 82.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 736–931 1.000 81.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 747–942 1.000 81.2
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 738–933 1.000 80.0
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA GCCGGACCATCCTACAAAAA 1133–1160 1.000 80.9
trnS-GCU-psbD_p2 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACAAAAACGAAACGGTCCCT 1120–1147 1.000 80.3
trnS-GCU-psbD_p3 trnS-GCU-psbD ACGGAAAGAGAGGGATTCGA GCCGGACCATCCTACAAAAA 1182–1209 1.000 79.9
trnS-GCU-psbD_p4 trnS-GCU-psbD GACGGAAAGAGAGGGATTCG GCCGGACCATCCTACAAAAA 1183–1210 1.000 79.4
trnS-GCU-psbD_p5 trnS-GCU-psbD ACGGAAAGAGAGGGATTCGA ACAAAAACGAAACGGTCCCT 1169–1196 1.000 79.3
psbC_p1 psbC TGTTTCCCAGGAAATCCGTG TGGCTCGGCTAGATGGAATA 1604 1.000 79.3
psbC_p2 psbC TGTTTCCCAGGAAATCCGTG AAAGAATGAATGGCTCGGCT 1614 1.000 78.3
psbC_p3 psbC GCAGCGGAAGATCCTGAATT TGGCTCGGCTAGATGGAATA 1585 1.000 77.5
psbC_p4 psbC TGTTTCCCAGGAAATCCGTG AACCGAGCCAGAACAGAAAA 1585 1.000 76.7
psbC_p5 psbC TGTTTCCCAGGAAATCCGTG ACCGAGCCAGAACAGAAAAA 1584 1.000 76.7
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU GTCGACCCAAGCGGATATAC TCTACAGAGCGGAGTAGAGC 516–542 1.000 79.9
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU GCGAGCGTAGTTCAATGGTA TCTACAGAGCGGAGTAGAGC 476–502 1.000 79.8
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU CGTAGCGAGCGTAGTTCAAT TCTACAGAGCGGAGTAGAGC 480–506 1.000 79.1
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU TAGCGAGCGTAGTTCAATGG TCTACAGAGCGGAGTAGAGC 478–504 1.000 78.8
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU GTCGACCCAAGCGGATATAC CGAGGCTCATAACCTTGAGG 482–508 1.000 78.5
trnG-UCC-trnM-CAU_p1 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT CCGGTGCATTACTCTACCAC 741–762 1.000 51.6
trnG-UCC-trnM-CAU_p2 trnG-UCC-trnM-CAU AGAACGAATCACACTTTTACCAC CCGGTGCATTACTCTACCAC 744–765 1.000 50.6
trnG-UCC-trnM-CAU_p3 trnG-UCC-trnM-CAU GAACGAATCACACTTTTACCACT CCGGTGCATTACTCTACCAC 743–764 1.000 50.6
trnG-UCC-trnM-CAU_p4 trnG-UCC-trnM-CAU AACGAATCACACTTTTACCACT CCGGTGCATTACTCTACCAC 742–763 1.000 49.7
trnG-UCC-trnM-CAU_p5 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT ACCGGTGCATTACTCTACCA 742–763 1.000 48.6

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
Rytidosperma pallidum NC_037166.1 132765 View on NCBI ↗
Rytidosperma semiannulare NC_036701.1 129095 View on NCBI ↗