Markers + reference

Dianella

2 species · Asphodelaceae · Asparagales

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Species 2
Genome length 158–158 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 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoB-trnC LSC 1274 0.0071 0.99 60.2 yes View details
trnT-psbD LSC 1112 0.0054 0.99 62.6 yes View details
trnF-ndhJ LSC 481 0.0146 1.00 59.8 yes View details
ndhC-trnV LSC 1859 0.0054 0.99 52.4 yes View details
petA-psbJ LSC 842 0.0095 1.00 64.2 yes View details
ycf2 IRb 6951 0.0014 1.00 44.2 yes View details
rps15 SSC 270 0.0074 1.00 49.6 yes View details
ndhI SSC 543 0.0018 1.00 49.8 yes View details
ccsA SSC 1011 0.0030 1.00 46.5 yes View details
ycf2 IRa 6951 0.0014 1.00 44.2 no View details
trnG-trnfM LSC 168 0.0179 1.00 62.8 yes View details
trnC-petN LSC 722 0.0055 1.00 61.9 yes View details
petN-psbM LSC 1024 0.0049 1.00 61.8 yes View details
ccsA-trnL SSC 35 0.0286 1.00 61.8 yes View details
ndhI-ndhG SSC 365 0.0137 1.00 61.7 yes View details
rps4 LSC 606 0.0033 1.00 60.6 yes View details
psaA-ycf3 LSC 657 0.0030 1.00 60.5 yes View details
infA-rps8 LSC 144 0.0139 1.00 60.5 yes View details
atpH-atpI LSC 492 0.0061 1.00 60.2 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
trnG_p1 trnG CCTTTGTTCGACAAACGTTCC TGGACGCTTTTCTTTCCTATCT 932–934 1.000 50.0
trnG_p2 trnG CTTTGTTCGACAAACGTTCCA TGGACGCTTTTCTTTCCTATCT 931–933 1.000 49.1
trnG_p3 trnG TTTGTTCGACAAACGTTCCA TGGACGCTTTTCTTTCCTATCT 930–932 1.000 47.8
trnG_p4 trnG GTTCGACAAACGTTCCATTCA TGGACGCTTTTCTTTCCTATCT 927–929 1.000 47.5
trnG_p5 trnG TGTTCGACAAACGTTCCATTC TGGACGCTTTTCTTTCCTATCT 928–930 1.000 47.5
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 554–556 1.000 79.7
atpH-atpI_p2 atpH-atpI CGCAATACCTTCTACGGCTT ATAGGGGAATCCATGGAGGG 642–644 1.000 79.5
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 610–612 1.000 79.1
atpH-atpI_p4 atpH-atpI AACGGAAGCGGCAGAAATAA ATAGGGGAATCCATGGAGGG 552–554 1.000 78.6
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA ATAGGGGAATCCATGGAGGG 555–557 1.000 78.6
rpoB-trnC_p1 rpoB-trnC AACCTACAGAACCCCTCGAA TAAAGGATTTGCAGTCCCCC 1395 1.000 77.0
rpoB-trnC_p2 rpoB-trnC AATTCTTCCGACAAGCCCTG TAAAGGATTTGCAGTCCCCC 1422 1.000 75.8
rpoB-trnC_p3 rpoB-trnC ACCTACAGAACCCCTCGAAT TAAAGGATTTGCAGTCCCCC 1394 1.000 75.2
rpoB-trnC_p4 rpoB-trnC AACCTACAGAACCCCTCGAA TTTGTTGATCAGGCGACACC 1432 1.000 75.1
rpoB-trnC_p5 rpoB-trnC AACCTACAGAACCCCTCGAA GACACCCGGATTTGAACTGG 1418 1.000 74.5
trnC-petN_p1 trnC-petN GGGGGACTGCAAATCCTTTA AGTCCACTCCTTCCCCATAC 855–857 1.000 75.2
trnC-petN_p2 trnC-petN GGGGGACTGCAAATCCTTTA GTCCACTCCTTCCCCATACT 854–856 1.000 75.2
trnC-petN_p3 trnC-petN GGGGGACTGCAAATCCTTTA AGCCCAAGCGAGACTTACTA 796–798 1.000 75.0
trnC-petN_p4 trnC-petN GGGGGACTGCAAATCCTTTA GAGTCCACTCCTTCCCCATA 856–858 1.000 74.8
trnC-petN_p5 trnC-petN GGGGGACTGCAAATCCTTTA CTAGAGTCCACTCCTTCCCC 859–861 1.000 74.4
petN-psbM_p1 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTGTTCATTCT 1128–1131 1.000 68.4
petN-psbM_p2 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTCATTCT 1127–1130 1.000 68.4
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTCT 1186–1189 1.000 68.1
petN-psbM_p4 petN-psbM TATGGGGAAGGAGTGGACTC TGCTACTGCACTGTTCATTCT 1126–1129 1.000 67.9
petN-psbM_p5 petN-psbM GGGGAAGGAGTGGACTCTAG TGCTACTGCACTGTTCATTCT 1123–1126 1.000 67.6
trnT-psbD_p1 trnT-psbD GTGGTAGAGTAACGCCATGG GGACCAGCCTACAAAAACGA 1271–1272 1.000 79.5
trnT-psbD_p2 trnT-psbD TCAGTGGTAGAGTAACGCCA GGACCAGCCTACAAAAACGA 1274–1275 1.000 79.3
trnT-psbD_p3 trnT-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1261–1262 1.000 78.4
trnT-psbD_p4 trnT-psbD GTGGTAGAGTAACGCCATGG CCCTCCGTAACCAATCATCC 1245–1246 1.000 78.3
trnT-psbD_p5 trnT-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1264–1265 1.000 78.2

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
Dianella amoena PV409674.1 157959 View on NCBI ↗
Dianella tasmanica NC_082904.1 157736 View on NCBI ↗