Markers + reference

Digitaria

3 species · Poaceae · Poales

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Species 3
Genome length 138–139 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

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 939 0.0130 0.99 53.6 yes View details
trnS-GCU-psbD LSC 983 0.0129 1.00 57.5 yes View details
trnG-GCC-trnfM-CAU LSC 304 0.0307 1.00 64.2 yes View details
trnG-UCC-trnM-CAU LSC 1074 0.0168 1.00 65.2 yes View details
trnT-GGU-trnE-UUC LSC 462 0.0202 1.00 67.3 yes View details
trnD-GUC-psbM LSC 1062 0.0188 0.97 57.4 yes View details
rpl16 LSC 1481 0.0128 1.00 52.8 yes View details
ndhF-rpl32 SSC 824 0.0138 1.00 68.3 yes View details
rpl32-trnL-UAG SSC 525 0.0198 0.99 67.4 yes View details
rpl14-rpl16 LSC 103 0.0458 0.99 71.4 yes View details
atpA-trnR-UCU LSC 169 0.0280 0.85 68.5 yes View details
ccsA-ndhD SSC 208 0.0224 1.00 67.6 yes View details
psaA-ycf3 LSC 638 0.0073 1.00 65.8 yes View details
trnT-UGU-trnL-UAA LSC 594 0.0147 0.99 65.1 yes View details
ycf4-cemA LSC 384 0.0106 0.99 65.1 yes View details
trnC-GCA-rpoB LSC 1252 0.0085 0.97 62.8 yes View details
psaJ-rps18 LSC 756 0.0081 0.97 62.5 yes View details
atpB-rbcL LSC 755 0.0071 1.00 61.7 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
trnK-UUU_p1 trnK-UUU TCAAAACTCAGATTGCTCCT TCGATTTTTGGATTTCGATCGT 2611–2621 1.000 41.4
trnK-UUU_p2 trnK-UUU TCAAAACTCAGATTGCTCCTT TCGATTTTTGGATTTCGATCGT 2611–2621 1.000 41.4
trnK-UUU_p3 trnK-UUU TTCAAAACTCAGATTGCTCCT TCGATTTTTGGATTTCGATCGT 2612–2622 1.000 41.4
trnK-UUU_p4 trnK-UUU TCAAAACTCAGATTGCTCCTTTC TCGATTTTTGGATTTCGATCGT 2611–2621 1.000 41.4
trnK-UUU_p5 trnK-UUU CAAAACTCAGATTGCTCCTTTCT TCGATTTTTGGATTTCGATCGT 2610–2620 1.000 41.4
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1004–1013 1.000 81.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1015–1024 1.000 80.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CTCGGAGGTTCGAATCCTTC 1008–1017 1.000 80.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC CTCGGAGGTTCGAATCCTTC 1019–1028 1.000 79.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TACTCGGAGGTTCGAATCCT 1010–1019 1.000 78.2
trnS-GCU-psbD_p1 trnS-GCU-psbD ATTAGCAATCCGCCGCTTTA CTTCGTAACCAGTCGTCCAT 1097–1110 1.000 75.9
trnS-GCU-psbD_p2 trnS-GCU-psbD GCTTTAGTCCACTCAGCCAT CTTCGTAACCAGTCGTCCAT 1083–1096 1.000 72.9
trnS-GCU-psbD_p3 trnS-GCU-psbD AGTCCACTCAGCCATCTCTC CTTCGTAACCAGTCGTCCAT 1078–1091 1.000 72.1
trnS-GCU-psbD_p4 trnS-GCU-psbD GATTCGAACCCTCGGTACAA CTTCGTAACCAGTCGTCCAT 1133–1146 1.000 70.9
trnS-GCU-psbD_p5 trnS-GCU-psbD TTAGCAATCCGCCGCTTTAG CTTCGTAACCAGTCGTCCAT 1096–1109 1.000 70.5
trnG-GCC-trnfM-CAU_p1 trnG-GCC-trnfM-CAU CGTAGCGAGCGTAGTTCAAT CGAGGCTCATAACCTTGAGG 445 0.333 50.1
trnG-GCC-trnfM-CAU_p2 trnG-GCC-trnfM-CAU CGTAGCGAGCGTAGTTCAAT CAGTTTGGTAGCTCACGAGG 460 0.333 49.6
trnG-GCC-trnfM-CAU_p3 trnG-GCC-trnfM-CAU CGTAGCGAGCGTAGTTCAAT CTACAGAGCGGAGTAGAGCA 478 0.333 49.3
trnG-GCC-trnfM-CAU_p4 trnG-GCC-trnfM-CAU CGTAGCGAGCGTAGTTCAAT TACAGAGCGGAGTAGAGCAG 477 0.333 49.3
trnG-GCC-trnfM-CAU_p5 trnG-GCC-trnfM-CAU CGTAGCGAGCGTAGTTCAAT GAGCGGAGTAGAGCAGTTTG 473 0.333 49.0
trnG-UCC-trnM-CAU_p1 trnG-UCC-trnM-CAU ACGAATCGCACTTTTACCACT CGCTAAGTGAGAAGCCCTTT 1186–1807 1.000 72.1
trnG-UCC-trnM-CAU_p2 trnG-UCC-trnM-CAU ACGAATCGCACTTTTACCAC CGCTAAGTGAGAAGCCCTTT 1186–1807 1.000 72.0
trnG-UCC-trnM-CAU_p3 trnG-UCC-trnM-CAU ACGAATCGCACTTTTACCACT CCTTCCGTCTTACCAAAGCA 1215–1836 1.000 71.4
trnG-UCC-trnM-CAU_p4 trnG-UCC-trnM-CAU ACGAATCGCACTTTTACCACT TGCCTTCCGTCTTACCAAAG 1217–1838 1.000 71.4
trnG-UCC-trnM-CAU_p5 trnG-UCC-trnM-CAU ACGAATCGCACTTTTACCAC CCTTCCGTCTTACCAAAGCA 1215–1836 1.000 71.3
trnT-GGU-trnE-UUC_p1 trnT-GGU-trnE-UUC AAAGGGCTTCTCACTTAGCG GCTGCCTCCTTGAAAGAGAG 581–586 1.000 79.0
trnT-GGU-trnE-UUC_p2 trnT-GGU-trnE-UUC AAAGGGCTTCTCACTTAGCG TGTCCTGAACCACTAGACGA 560–565 1.000 78.9
trnT-GGU-trnE-UUC_p3 trnT-GGU-trnE-UUC CTTTGGTAAGACGGAAGGCA GCTGCCTCCTTGAAAGAGAG 550–555 1.000 78.5
trnT-GGU-trnE-UUC_p4 trnT-GGU-trnE-UUC TGCTTTGGTAAGACGGAAGG GCTGCCTCCTTGAAAGAGAG 552–557 1.000 78.5
trnT-GGU-trnE-UUC_p5 trnT-GGU-trnE-UUC CTTTGGTAAGACGGAAGGCA TGTCCTGAACCACTAGACGA 529–534 1.000 78.4

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
Digitaria californica MT083940.1 138346 View on NCBI ↗
Digitaria glauca MK593550.1 138962 View on NCBI ↗
Digitaria sanguinalis OK637269.1 138079 View on NCBI ↗