Markers + reference

Ophiopogon

5 species · Asparagaceae · Asparagales

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Species 5
Genome length 156–157 kb
Candidate markers 271
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1278 0.0103 1.00 57.9 yes View details
psbM-trnD-GUC LSC 727 0.0098 0.99 62.6 yes View details
trnE-UUC-trnT-GGU LSC 493 0.0238 0.99 61.6 yes View details
trnT-UGU-trnL-UAA LSC 1011 0.0125 0.96 66.2 yes View details
accD-psaI LSC 392 0.0208 0.98 68.5 yes View details
infA LSC 237 0.0295 1.00 67.1 yes View details
rpl16 LSC 1438 0.0072 1.00 53.6 yes View details
rps3 LSC 663 0.0045 1.00 48.6 yes View details
ndhF-rpl32 SSC 974 0.0110 0.97 65.1 yes View details
ccsA SSC 972 0.0056 1.00 48.9 yes View details
ycf1 SSC 5529 0.0069 1.00 47.5 yes View details
rps3-rpl22 LSC 69 0.0778 1.00 83.3 yes View details
psbC-trnS-UGA LSC 148 0.0254 0.96 68.8 yes View details
petN-psbM LSC 893 0.0076 1.00 66.4 yes View details
psaJ-rpl33 LSC 521 0.0129 1.00 65.7 yes View details
rpl32-trnL-UAG SSC 948 0.0073 0.97 65.2 yes View details
psbI-trnS-GCU LSC 125 0.0163 0.96 62.4 yes View details
ccsA-ndhD SSC 223 0.0318 1.00 62.0 yes View details
ndhA SSC 2156 0.0061 1.00 62.0 yes View details
atpB LSC 1488 0.0032 1.00 61.2 yes View details
ndhC-trnV-UAC LSC 1640 0.0050 1.00 58.7 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1346–1356 1.000 80.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1357–1367 1.000 80.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1350–1360 1.000 76.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 1376–1386 1.000 75.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 1358–1368 1.000 75.7
psbI-trnS-GCU_p1 psbI-trnS-GCU CTTATCTAACGATCCGGGCC GGGTTCGAATCCCTCTCTCT 185–191 1.000 80.0
psbI-trnS-GCU_p2 psbI-trnS-GCU CTTATCTAACGATCCGGGCC ATTGGGAGAGATGGCTGAGT 254–260 1.000 79.6
psbI-trnS-GCU_p3 psbI-trnS-GCU CTTATCTAACGATCCGGGCC TTCGAATCCCTCTCTCTCCG 182–188 1.000 79.3
psbI-trnS-GCU_p4 psbI-trnS-GCU CTTATCTAACGATCCGGGCC GTGGACTAAAGCGGCAGATT 236–242 1.000 78.7
psbI-trnS-GCU_p5 psbI-trnS-GCU CTTATCTAACGATCCGGGCC TGGACTAAAGCGGCAGATTG 235–241 1.000 78.7
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA TGCTACTGCACTGTTCATTCT 893–1064 1.000 73.9
petN-psbM_p2 petN-psbM AGTATGGGGAAGGAGTGGAC TGCTACTGCACTGTTCATTCT 842–1013 1.000 73.1
petN-psbM_p3 petN-psbM GTATGGGGAAGGAGTGGACT TGCTACTGCACTGTTCATTCT 841–1012 1.000 73.1
petN-psbM_p4 petN-psbM TATGGGGAAGGAGTGGACTC TGCTACTGCACTGTTCATTCT 840–1011 1.000 72.7
petN-psbM_p5 petN-psbM AGTAAGTCTTGCTTGGGCTG TGCTACTGCACTGTTCATTCT 899–1070 1.000 72.5
psbM-trnD-GUC_p1 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TGCTATACACCTTGCTGGGA 852–865 1.000 61.9
psbM-trnD-GUC_p2 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC TTCAATTGGTCAGAGCACCG 826–839 1.000 61.5
psbM-trnD-GUC_p3 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC ACACCTTGCTGGGATTGTAG 846–859 1.000 61.3
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC CACCTTGCTGGGATTGTAGT 845–858 1.000 61.3
psbM-trnD-GUC_p5 psbM-trnD-GUC AGAATGAACAGTGCAGTAGC ATGCTATACACCTTGCTGGG 853–866 1.000 60.1
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU GCATCGACCCAGGAAGAATT GAACCGATGACTTACGCCTT 521–692 1.000 86.4
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU GCATCGACCCAGGAAGAATT CCATGGCGTTACTCTACCAC 500–671 1.000 86.0
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU GCATCGACCCAGGAAGAATT AAGCCCTTTCTTTTCTCGCA 946–1113 1.000 85.6
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU GGATCCTAGTTCGGGACTGA GAACCGATGACTTACGCCTT 989–1161 1.000 85.3
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU GGATCCTAGTTCGGGACTGA AAGCCCTTTCTTTTCTCGCA 1414–1582 1.000 85.0
psbC-trnS-UGA_p1 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGTGGCTGAGTGGTTGATAG 253–262 1.000 84.1
psbC-trnS-UGA_p2 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGTTGATAGCTCCGGTCTTG 242–251 1.000 84.1
psbC-trnS-UGA_p3 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GCTGAGTGGTTGATAGCTCC 249–258 1.000 84.0
psbC-trnS-UGA_p4 psbC-trnS-UGA CCTGTTCTTTCCATGACCCC GGCTGAGTGGTTGATAGCTC 250–259 1.000 84.0
psbC-trnS-UGA_p5 psbC-trnS-UGA TTCCATGACCCCTCTTAGCT GGTGGCTGAGTGGTTGATAG 245–254 1.000 83.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Ophiopogon bodinieri NC_051508.1 157078 View on NCBI ↗
Ophiopogon chingii NC_070129.1 156918 View on NCBI ↗
Ophiopogon jaburan NC_049870.1 156454 View on NCBI ↗
Ophiopogon japonicus NC_049869.1 156564 View on NCBI ↗
Ophiopogon planiscapus PV087159.1 156979 View on NCBI ↗