Markers + reference

Cynodon

2 species · Poaceae · Poales

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Species 2
Genome length 134–134 kb
Candidate markers 282
Primer pairs 90

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 282 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-psbD LSC 925 0.0000 1.00 46.0 yes View details
psbD LSC 1062 0.0094 1.00 64.3 yes View details
psbC LSC 1422 0.0000 1.00 40.0 yes View details
trnG-UCC-trnT-GGU LSC 972 0.0093 1.00 61.7 yes View details
rpoB LSC 3228 0.0012 1.00 56.0 yes View details
petA-psbJ LSC 861 0.0070 1.00 62.8 yes View details
psbE-petL LSC 752 0.0213 1.00 71.3 yes View details
rpl22 LSC 450 0.0000 1.00 23.7 yes View details
rrn16-trnV-GAC IRa 229 0.0000 1.00 22.1 yes View details
trnS-UGA LSC 88 0.1294 0.97 90.8 yes View details
rpl22-rps19 IRb 78 0.0769 1.00 84.6 yes View details
trnV-GAC IRa 72 0.0556 1.00 81.9 yes View details
trnV-GAC IRb 72 0.0417 1.00 76.5 yes View details
matK-trnK-UUU LSC 671 0.0030 1.00 60.5 yes View details
ndhC-trnV-UAC LSC 950 0.0021 1.00 60.0 yes View details
trnT-GGU-trnE-UUC LSC 546 0.0037 1.00 59.7 yes View details
rpl16 LSC 1458 0.0014 1.00 59.5 yes View details
rrn16 IRa 1492 0.0013 1.00 59.5 yes View details
rrn16 IRb 1492 0.0000 1.00 40.0 no 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
matK-trnK-UUU_p1 matK-trnK-UUU CATAATCGTGGGCAAATGCA CAGGAGCGTTCGGTGTAATT 880 1.000 71.0
matK-trnK-UUU_p2 matK-trnK-UUU ACATAATCGTGGGCAAATGC CAGGAGCGTTCGGTGTAATT 881 1.000 71.0
matK-trnK-UUU_p3 matK-trnK-UUU CATAATCGTGGGCAAATGCA AGGAGCGTTCGGTGTAATTT 879 1.000 69.5
matK-trnK-UUU_p4 matK-trnK-UUU ACATAATCGTGGGCAAATGC AGGAGCGTTCGGTGTAATTT 880 1.000 69.5
matK-trnK-UUU_p5 matK-trnK-UUU CATAATCGTGGGCAAATGCAT CAGGAGCGTTCGGTGTAATT 880 1.000 67.0
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA ACTCTACCAAGGGCTATAGTCA 986–988 1.000 59.6
trnS-GCU-psbD_p2 trnS-GCU-psbD GAAAGTCCCAAACGATCCGA ACTCTACCAAGGGCTATAGTCA 1059–1061 1.000 59.2
trnS-GCU-psbD_p3 trnS-GCU-psbD TCGAAAGTCCCAAACGATCC ACTCTACCAAGGGCTATAGTCA 1061–1063 1.000 59.2
trnS-GCU-psbD_p4 trnS-GCU-psbD AAAGTCCCAAACGATCCGAG ACTCTACCAAGGGCTATAGTCA 1058–1060 1.000 59.2
trnS-GCU-psbD_p5 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT ACTCTACCAAGGGCTATAGTCA 972–974 1.000 56.7
psbD_p1 psbD TGCTCGGAAATGGTTGAAGT GTCACGACCAGCTAAAACGA 1129–1130 1.000 76.8
psbD_p2 psbD TGCTCGGAAATGGTTGAAGT TCACGACCAGCTAAAACGAA 1128–1129 1.000 74.5
psbD_p3 psbD GTGCTCGGAAATGGTTGAAG GTCACGACCAGCTAAAACGA 1130–1131 1.000 74.0
psbD_p4 psbD TATGAGGTGCTCGGAAATGG GTCACGACCAGCTAAAACGA 1136–1137 1.000 74.0
psbD_p5 psbD GGTGCTCGGAAATGGTTGAA GTCACGACCAGCTAAAACGA 1131–1132 1.000 72.9
psbC_p1 psbC TTCGTTTCCCAGGAAATCCG TGGCTCGGCTAGATGGAATA 1607 1.000 78.5
psbC_p2 psbC GCAGCGGAAGATCCTGAATT TGGCTCGGCTAGATGGAATA 1586 1.000 77.3
psbC_p3 psbC TTCGTTTCCCAGGAAATCCG ATGAATGGCTCGGCTAGATG 1612 1.000 74.8
psbC_p4 psbC GCAGCGGAAGATCCTGAATT ATGAATGGCTCGGCTAGATG 1591 1.000 73.6
psbC_p5 psbC TTCGTTTCCCAGGAAATCCG ATGGCTCGGCTAGATGGAAT 1608 1.000 73.4
trnS-UGA_p1 trnS-UGA TATTCCATCTAGCCGAGCCA ATAGCGAAAGTGGACTTGCA 288–291 1.000 80.0
trnS-UGA_p2 trnS-UGA TATTCCATCTAGCCGAGCCA TAGCGAAAGTGGACTTGCAT 287–290 1.000 80.0
trnS-UGA_p3 trnS-UGA TATTCCATCTAGCCGAGCCA AGCGAAAGTGGACTTGCATC 286–289 1.000 77.1
trnS-UGA_p4 trnS-UGA TATTCCATCTAGCCGAGCCA GCGAAAGTGGACTTGCATCT 285–288 1.000 77.1
trnS-UGA_p5 trnS-UGA TATTCCATCTAGCCGAGCCA CGAAAGTGGACTTGCATCTG 284–287 1.000 76.7
trnG-UCC-trnT-GGU_p1 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT GGTCTTTCCGTGGCATTACT 1114 1.000 51.6
trnG-UCC-trnT-GGU_p2 trnG-UCC-trnT-GGU ACGAATCACACTTTTACCACT TCCGTGGCATTACTCTACCA 1108 1.000 51.3
trnG-UCC-trnT-GGU_p3 trnG-UCC-trnT-GGU AGAACGAATCACACTTTTACCAC GGTCTTTCCGTGGCATTACT 1117 1.000 50.6
trnG-UCC-trnT-GGU_p4 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT GGTCTTTCCGTGGCATTACT 1116 1.000 50.6
trnG-UCC-trnT-GGU_p5 trnG-UCC-trnT-GGU GAACGAATCACACTTTTACCACT TCCGTGGCATTACTCTACCA 1110 1.000 50.3

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
Cynodon dactylon NC_034680.1 134297 View on NCBI ↗
Cynodon dactylon x Cynodon transvaalensis MK175053.1 134350 View on NCBI ↗