Markers + reference

Triodia

15 species · Poaceae · Poales

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Species 15
Genome length 134–136 kb
Candidate markers 273
Primer pairs 100

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1095 0.0070 1.00 55.5 yes View details
rps16-trnQ-UUG LSC 1259 0.0089 1.00 68.5 yes View details
trnG-UCC-trnM-CAU LSC 1018 0.0081 1.00 66.2 yes View details
trnY-GUA-trnD-GUC LSC 342 0.0118 1.00 63.9 yes View details
psbM-petN LSC 804 0.0089 1.00 59.1 yes View details
petN-trnC-GCA LSC 795 0.0077 1.00 52.2 yes View details
rbcL-psaI LSC 881 0.0077 1.00 62.5 yes View details
psaJ-rpl33 LSC 399 0.0068 1.00 43.7 yes View details
rpl33-rps18 LSC 252 0.0226 1.00 70.4 yes View details
ndhF-rpl32 SSC 907 0.0119 1.00 66.6 yes View details
rpl32-trnL-UAG SSC 520 0.0199 1.00 66.3 yes View details
trnD-GUC-psbM LSC 1028 0.0093 1.00 74.5 yes View details
ndhC-trnV-UAC LSC 949 0.0056 0.97 68.8 yes View details
psbE-petL LSC 1288 0.0062 1.00 66.2 yes View details
petA-psbJ LSC 905 0.0061 1.00 63.3 yes View details
ycf4-cemA LSC 349 0.0097 0.99 62.9 yes View details
ccsA-ndhD SSC 192 0.0159 1.00 61.3 yes View details
psaA-ycf3 LSC 628 0.0037 1.00 61.2 yes View details
ycf3-trnS-GGA LSC 578 0.0067 1.00 61.0 yes View details
petB LSC 1433 0.0027 1.00 60.0 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
rps16_p1 rps16 TGAGGATCAGTCGTGGTCTT TGATCCATTCCGGTAAGGGT 2288–2405 0.933 82.5
rps16_p2 rps16 TGAGGATCAGTCGTGGTCTT TGCAGAGTCTTCCCCGATAA 1927–1962 1.000 82.1
rps16_p3 rps16 GGAATTACACCGGACACTCC TGATCCATTCCGGTAAGGGT 2119–2236 0.800 77.5
rps16_p4 rps16 GGAATTACACCGGACACTCC TGCAGAGTCTTCCCCGATAA 1760–1793 0.867 76.7
rps16_p5 rps16 GGAATTACACCGGACACTCC TTGCAGAGTCTTCCCCGATA 1761–1794 0.867 76.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1149–1338 1.000 86.0
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATCTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1160–1349 1.000 84.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1153–1342 1.000 81.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA CGCATAAAACGAAATGGGGC 1211–1400 0.933 79.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GCATAAAACGAAATGGGGCG 1210–1399 0.933 79.9
trnG-UCC-trnM-CAU_p1 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT TGAACCGATGACTTATGCCT 424–1164 1.000 47.6
trnG-UCC-trnM-CAU_p2 trnG-UCC-trnM-CAU ACGAATCACACTTTTACCACT GCCGTGGCATTACTCTACC 1142–1210 0.933 44.6
trnG-UCC-trnM-CAU_p3 trnG-UCC-trnM-CAU AGAACGAATCACACTTTTACCAC GCCGTGGCATTACTCTACC 1145–1213 0.933 43.6
trnG-UCC-trnM-CAU_p4 trnG-UCC-trnM-CAU GAACGAATCACACTTTTACCACT GCCGTGGCATTACTCTACC 1144–1212 0.933 43.6
trnG-UCC-trnM-CAU_p5 trnG-UCC-trnM-CAU AACGAATCACACTTTTACCACT GCCGTGGCATTACTCTACC 1143–1211 0.933 42.7
trnY-GUA-trnD-GUC_p1 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GCGGTGCTCTAACCAATTGA 453–536 1.000 81.7
trnY-GUA-trnD-GUC_p2 trnY-GUA-trnD-GUC GGGGACGGACTGTAAATTCG GCGGTGCTCTAACCAATTGA 420–503 1.000 79.7
trnY-GUA-trnD-GUC_p3 trnY-GUA-trnD-GUC GGGACGGACTGTAAATTCGT GCGGTGCTCTAACCAATTGA 419–502 1.000 79.5
trnY-GUA-trnD-GUC_p4 trnY-GUA-trnD-GUC AATTCTTCCTGGGTCGATGC GGCGGTGCTCTAACCAATT 454–537 1.000 77.0
trnY-GUA-trnD-GUC_p5 trnY-GUA-trnD-GUC TGGGGACGGACTGTAAATTC GCGGTGCTCTAACCAATTGA 421–504 1.000 76.3
trnD-GUC-psbM_p1 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC TCATTTTGGCTGGCTGTTTT 1160–1208 1.000 72.5
trnD-GUC-psbM_p2 trnD-GUC-psbM TAGGTATGCCATACACCCCG TCATTTTGGCTGGCTGTTTT 1193–1241 1.000 71.6
trnD-GUC-psbM_p3 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC AATCATTTTGGCTGGCTGTT 1162–1210 1.000 70.6
trnD-GUC-psbM_p4 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC ATCATTTTGGCTGGCTGTTT 1161–1209 1.000 70.6
trnD-GUC-psbM_p5 trnD-GUC-psbM TCAATTGGTTAGAGCACCGC TCATTTTGGCTGGCTGTTTTT 1160–1208 1.000 70.4
psbM-petN_p1 psbM-petN AAAACAGCCAGCCAAAATGA AGTATGGGGGAGAAGTGGAC 849–889 1.000 73.0
psbM-petN_p2 psbM-petN AAAACAGCCAGCCAAAATGA GTATGGGGGAGAAGTGGACT 848–888 1.000 73.0
psbM-petN_p3 psbM-petN AAAACAGCCAGCCAAAATGA TATGGGGGAGAAGTGGACTC 847–887 1.000 72.5
psbM-petN_p4 psbM-petN AAAACAGCCAGCCAAAATGA GGGGGAGAAGTGGACTCTAG 844–884 1.000 72.2
psbM-petN_p5 psbM-petN AACAGCCAGCCAAAATGATT GTATGGGGGAGAAGTGGACT 846–886 1.000 71.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (15)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Triodia basedowii NC_042860.1 135278 View on NCBI ↗
Triodia chichesterensis NC_042861.1 135284 View on NCBI ↗
Triodia concinna NC_042862.1 135218 View on NCBI ↗
Triodia glabra NC_042863.1 135251 View on NCBI ↗
Triodia lanigera NC_042872.1 135453 View on NCBI ↗
Triodia longiceps NC_042864.1 134425 View on NCBI ↗
Triodia mallota NC_042865.1 135261 View on NCBI ↗
Triodia plurinervata NC_042866.1 135386 View on NCBI ↗
Triodia rigidissima NC_042867.1 135657 View on NCBI ↗
Triodia schinzii NC_042870.1 135016 View on NCBI ↗
Triodia scintillans NC_042871.1 135301 View on NCBI ↗
Triodia stipoides NC_037157.1 134874 View on NCBI ↗
Triodia tomentosa NC_042868.1 135375 View on NCBI ↗
Triodia vanleeuwenii NC_042869.1 135318 View on NCBI ↗
Triodia wiseana NC_037161.1 134962 View on NCBI ↗