Markers + reference

Dactylis

2 species · Poaceae · Poales

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Species 2
Genome length 135–135 kb
Candidate markers 267
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 8 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0000 1.00 29.9 yes View details
trnK-UUU-rps16 LSC 559 0.0036 1.00 45.5 yes View details
trnG-UCC-trnT-GGU LSC 928 0.0022 1.00 60.0 yes View details
petN-trnC-GCA LSC 939 0.0032 1.00 60.6 yes View details
ycf3-trnS-GGA LSC 612 0.0065 1.00 62.5 yes View details
ndhC LSC 363 0.0000 1.00 25.8 yes View details
ndhC-trnV-UAC LSC 838 0.0024 1.00 60.1 yes View details
rbcL-psaI LSC 1228 0.0057 1.00 62.4 yes View details
petA LSC 963 0.0000 1.00 40.0 yes View details
clpP-psbB LSC 520 0.0019 1.00 49.2 yes View details
rps19-psbA LSC 136 0.0150 0.98 63.2 no View details
psaA-ycf3 LSC 659 0.0015 1.00 59.6 yes View details
rps16-trnQ-UUG LSC 769 0.0013 1.00 59.5 yes View details
trnT-UGU-trnL-UAA LSC 815 0.0012 1.00 59.5 yes View details
psbB LSC 1524 0.0013 1.00 59.5 yes View details
matK LSC 1536 0.0013 1.00 59.4 yes View details
rps16 LSC 1086 0.0009 1.00 59.3 yes View details
rpoA LSC 1023 0.0010 1.00 59.3 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA TGGGTATTTCTAGCTTTTCTTTCT AATACGTGTGCTTGGGAGTC 1167 1.000 40.0
psbA_p2 psbA TGGGTATTTCTAGCTTTTCTTTCTT AATACGTGTGCTTGGGAGTC 1167 1.000 40.0
psbA_p3 psbA TTGGGTATTTCTAGCTTTTCTTTCT AATACGTGTGCTTGGGAGTC 1168 1.000 40.0
psbA_p4 psbA GGGTATTTCTAGCTTTTCTTTCTTCA AATACGTGTGCTTGGGAGTC 1166 1.000 40.0
psbA_p5 psbA TGGGTATTTCTAGCTTTTCTTTCTTC AATACGTGTGCTTGGGAGTC 1167 1.000 40.0
trnK-UUU_p1 trnK-UUU AGATTGGTCTTTTCTATTTTCCGT CCATTGATTTTTGGATTTCGATCG 2645 1.000 40.2
trnK-UUU_p2 trnK-UUU GTCCGAGTTAAAAACTAAGATTGGT CCATTGATTTTTGGATTTCGATCG 2662 1.000 40.2
trnK-UUU_p3 trnK-UUU TGGTCTTTTCTATTTTCCGT CCATTGATTTTTGGATTTCGATCG 2641 1.000 40.2
trnK-UUU_p4 trnK-UUU TTGGTCTTTTCTATTTTCCGT CCATTGATTTTTGGATTTCGATCG 2642 1.000 40.2
trnK-UUU_p5 trnK-UUU TCCGAGTTAAAAACTAAGATTGGTC CCATTGATTTTTGGATTTCGATCG 2661 1.000 40.2
matK_p1 matK AAGTGGATTCGCCTACTCTT CAACACCCTGTTCTGACCAT 1740 1.000 63.9
matK_p2 matK AGTGGATTCGCCTACTCTTT CAACACCCTGTTCTGACCAT 1739 1.000 63.9
matK_p3 matK AAGTGGATTCGCCTACTCTTT CAACACCCTGTTCTGACCAT 1740 1.000 62.0
matK_p4 matK AAGTGGATTCGCCTACTCTT ATCCAACACCCTGTTCTGAC 1743 1.000 61.6
matK_p5 matK AGTGGATTCGCCTACTCTTT ATCCAACACCCTGTTCTGAC 1742 1.000 61.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 TGGACGAATTTGTTGCTCCA TCGAGCCGTATGAGGAGAAA 935–943 1.000 78.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 TGGACGAATTTGTTGCTCCA TTTCTCGAGCCGTATGAGGA 939–947 1.000 78.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TGAGGATCAGTCGTGGTCTT TCGAGCCGTATGAGGAGAAA 974–982 1.000 77.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 TGAGGATCAGTCGTGGTCTT TTTCTCGAGCCGTATGAGGA 978–986 1.000 77.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 TTTTTGCAGGCCAATTGCTC TCGAGCCGTATGAGGAGAAA 1369–1377 1.000 77.5
rps16_p1 rps16 TGGCACGACATAAATCCAAA GCTCCATAGACAGCAAGTTTG 1326–1327 1.000 47.2
rps16_p2 rps16 ACTAGTGATCTTCTCCACTCCT GCTCCATAGACAGCAAGTTTG 1255–1256 1.000 45.2
rps16_p3 rps16 AGTGATCTTCTCCACTCCTACT GCTCCATAGACAGCAAGTTTG 1252–1253 1.000 45.2
rps16_p4 rps16 TGGCACGACATAAATCCAAAT GCTCCATAGACAGCAAGTTTG 1326–1327 1.000 43.7
rps16_p5 rps16 TGGCACGACATAAATCCAAA GCTCCATAGACAGCAAGTTT 1326–1327 1.000 43.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 842 1.000 78.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 853 1.000 77.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 846 1.000 77.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 857 1.000 76.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 848 1.000 75.5

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
Dactylis glomerata NC_027473.1 134737 View on NCBI ↗
Dactylis glomerata subsp. glomerata PP335049.1 134958 View on NCBI ↗