Markers + reference

Danthonia

3 species · Poaceae · Poales

Back to catalogue

Species 3
Genome length 134–134 kb
Candidate markers 274
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 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnG-GCC-trnfM-CAU LSC 345 0.0078 0.99 50.2 yes View details
trnG-UCC-trnM-CAU LSC 1518 0.0064 0.97 56.6 yes View details
trnT-UGU-trnL-UAA LSC 787 0.0093 1.00 59.6 yes View details
rbcL-psaI LSC 808 0.0058 1.00 53.9 yes View details
rpl33-rps18 LSC 335 0.0154 0.90 52.6 yes View details
rps11-rpl36 LSC 164 0.0314 0.97 63.9 yes View details
ndhF SSC 2217 0.0041 1.00 49.0 yes View details
ndhF-rpl32 SSC 924 0.0084 0.98 55.1 yes View details
rpl32-trnL-UAG SSC 314 0.0255 1.00 63.3 yes View details
ndhG SSC 531 0.0025 1.00 34.6 yes View details
rps19-psbA LSC 123 0.0163 1.00 63.8 no View details
trnK-UUU-rps16 LSC 578 0.0012 0.95 63.5 yes View details
rps16 LSC 1085 0.0049 1.00 62.1 yes View details
psbE-petL LSC 1001 0.0047 1.00 61.9 yes View details
petA-psbJ LSC 910 0.0037 1.00 61.7 yes View details
petN-trnC-GCA LSC 916 0.0044 1.00 61.5 yes View details
ycf3-trnS-GGA LSC 585 0.0046 1.00 61.5 yes View details
rpl20-Daca_g44 LSC 695 0.0058 1.00 60.8 yes View details
petB LSC 1446 0.0028 1.00 60.7 yes View details
trnD-GUC-psbM LSC 894 0.0022 1.00 60.4 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-rps16_p1 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGTGCTCAACCTACAAGAACT 679–712 1.000 70.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 TAGTCGCACTTAAAAGCCGA GGTGCTCAACCTACAAGAACT 680–713 1.000 69.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAAGAACT 677–710 1.000 69.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 CGCACTTAAAAGCCGAGTAC GGTGCTCAACCTACAAGAACT 676–709 1.000 68.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 GTCGCACTTAAAAGCCGAGT GGTGCTCAACCTACAAGAACT 678–711 1.000 68.1
rps16_p1 rps16 GGTACTAGTGACCCTCTCCC TCTCGATACCACTTTGCAATGA 1168–1191 1.000 63.9
rps16_p2 rps16 AGTGACCCTCTCCCACTTTT TCTCGATACCACTTTGCAATGA 1162–1185 1.000 63.1
rps16_p3 rps16 CTAGTGACCCTCTCCCACTT TCTCGATACCACTTTGCAATGA 1164–1187 1.000 62.6
rps16_p4 rps16 GGTACTAGTGACCCTCTCCC CTCGATACCACTTTGCAATGA 1167–1190 1.000 60.3
rps16_p5 rps16 GGTACTAGTGACCCTCTCCC TCTCGATACCACTTTGCAATG 1168–1191 1.000 60.3
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU GCGAGCGTAGTTCAATGGTA TCTACAGAGCGGAGTAGAGC 496–519 1.000 80.3
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU CGTAGCGAGCGTAGTTCAAT TCTACAGAGCGGAGTAGAGC 500–523 1.000 79.5
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU TAGCGAGCGTAGTTCAATGG TCTACAGAGCGGAGTAGAGC 498–521 1.000 79.3
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU GCGAGCGTAGTTCAATGGTA CGAGGCTCATAACCTTGAGG 462–485 1.000 78.9
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU GCGAGCGTAGTTCAATGGTA CAGTTTGGTAGCTCACGAGG 477–500 1.000 78.4
trnG-UCC-trnM-CAU_p1 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT TCTTACCGGGGCATTACTCT 1604–1652 1.000 54.0
trnG-UCC-trnM-CAU_p2 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT GTCTTACCGGGGCATTACTC 1605–1653 1.000 53.5
trnG-UCC-trnM-CAU_p3 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT GACTTATGTCTTACCGGGGC 1612–1660 1.000 53.4
trnG-UCC-trnM-CAU_p4 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT TACCGGGGCATTACTCTACC 1601–1649 1.000 53.0
trnG-UCC-trnM-CAU_p5 trnG-UCC-trnM-CAU GAACGAATCACACTTTTACCACT TCTTACCGGGGCATTACTCT 1606–1654 1.000 52.9
trnD-GUC-psbM_p1 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG ATTAACCCTTTTGGCTGGCT 1063–1064 1.000 74.0
trnD-GUC-psbM_p2 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG CCTTTTGGCTGGCTGTTTTT 1057–1058 1.000 73.9
trnD-GUC-psbM_p3 trnD-GUC-psbM TTCAATTGGTCAGAGCACCG TTAACCCTTTTGGCTGGCTG 1062–1063 1.000 71.3
trnD-GUC-psbM_p4 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC ATTAACCCTTTTGGCTGGCT 1064–1065 1.000 69.8
trnD-GUC-psbM_p5 trnD-GUC-psbM GTTCAATTGGTCAGAGCACC CCTTTTGGCTGGCTGTTTTT 1058–1059 1.000 69.8
petN-trnC-GCA_p1 petN-trnC-GCA AGCCCAAGCGAGACTTACTA AGTTCAAATCTGGGTGCCG 965 1.000 70.9
petN-trnC-GCA_p2 petN-trnC-GCA AGACCACCATTAAAGCAGCC AGTTCAAATCTGGGTGCCG 981 1.000 70.8
petN-trnC-GCA_p3 petN-trnC-GCA AGCCCAAGCGAGACTTACTA CCAGTTCAAATCTGGGTGCC 967 1.000 70.4
petN-trnC-GCA_p4 petN-trnC-GCA AGACCACCATTAAAGCAGCC CCAGTTCAAATCTGGGTGCC 983 1.000 70.3
petN-trnC-GCA_p5 petN-trnC-GCA CCACTCCTCCCCCATACTAC AGTTCAAATCTGGGTGCCG 1021 1.000 69.8

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
Danthonia californica NC_025232.1 134191 View on NCBI ↗
Danthonia decumbens MT083937.1 133905 View on NCBI ↗
Danthonia spicata NC_050415.1 134245 View on NCBI ↗