Markers + reference

Ventilago

2 species · Rhamnaceae · Rosales

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Species 2
Genome length 162–163 kb
Candidate markers 270
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 990 0.0408 0.62 66.3 yes View details
trnR-UCU-atpA LSC 714 0.0632 0.49 70.7 yes View details
psaA-ycf3 LSC 973 0.0277 0.78 74.0 yes View details
trnF-GAA-ndhJ LSC 821 0.0463 0.95 85.2 yes View details
petA-psbJ LSC 1115 0.2692 0.63 75.0 yes View details
ycf1 IRb 1116 0.0364 0.96 68.5 yes View details
ndhF SSC 2250 0.0133 1.00 50.1 yes View details
ndhF-rpl32 SSC 717 0.1202 0.62 84.2 yes View details
ndhA SSC 2635 0.0171 0.89 56.0 yes View details
rps15-ycf1 SSC 369 0.0528 0.92 71.7 yes View details
ycf1 SSC 5766 0.0143 1.00 51.5 no View details
rpl2-trnH-GUG LSC 356 0.1167 0.72 70.6 no View details
ndhK-ndhC LSC 7 0.1429 1.00 75.9 yes View details
ycf1-ndhF SSC 72 0.3710 0.86 75.3 yes View details
trnK-UUU-rps16 LSC 1001 0.0302 0.99 73.8 yes View details
rps3-rpl22 LSC 169 0.0741 0.80 72.4 yes View details
rpl32-trnL-UAG SSC 1201 0.0172 0.92 71.3 yes View details
rps4-trnT-UGU LSC 479 0.0194 0.97 69.6 yes View details
rpl14-rpl16 LSC 138 0.0511 0.99 69.0 yes View details
petN-psbM LSC 861 0.0083 0.98 65.1 yes View details
psbK-psbI LSC 448 0.0277 0.97 64.4 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-rps16_p1 trnK-UUU-rps16 AGTCGCGGTCTTACAAACTC ATTTCAAAGAAAGCGGGGGT 1181–1212 1.000 81.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 GTCGCGGTCTTACAAACTCT ATTTCAAAGAAAGCGGGGGT 1180–1211 1.000 81.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCGATGGTATGGACGAATCC ATTTCAAAGAAAGCGGGGGT 1159–1190 1.000 81.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 CAGTCGCGGTCTTACAAACT ATTTCAAAGAAAGCGGGGGT 1182–1213 1.000 80.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGTCGCGGTCTTACAAAC ATTTCAAAGAAAGCGGGGGT 1183–1214 1.000 80.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG TGTCCAATAGAAATGGGGCG 865–1141 1.000 84.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GTCCAATAGAAATGGGGCGT 864–1140 1.000 84.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 804–1080 1.000 84.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TGTCCAATAGAAATGGGGCG 848–1124 1.000 84.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GTCCAATAGAAATGGGGCGT 847–1123 1.000 84.5
psbK-psbI_p1 psbK-psbI CTTTTGTTTGGCAAGCTGCT AGGATTACGCCCTGGATCAT 569–579 1.000 81.1
psbK-psbI_p2 psbK-psbI GTTTGGCAAGCTGCTGTAAG AGGATTACGCCCTGGATCAT 564–574 1.000 81.1
psbK-psbI_p3 psbK-psbI TGGCAAGCTGCTGTAAGTTT AGGATTACGCCCTGGATCAT 561–571 1.000 79.1
psbK-psbI_p4 psbK-psbI TTGGCAAGCTGCTGTAAGTT AGGATTACGCCCTGGATCAT 562–572 1.000 79.1
psbK-psbI_p5 psbK-psbI TTTGGCAAGCTGCTGTAAGT AGGATTACGCCCTGGATCAT 563–573 1.000 79.1
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG GGAAGCCCTTTTGAAAGAAGC 492–858 1.000 65.8
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT GGAAGCCCTTTTGAAAGAAGC 491–857 1.000 65.7
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GGAAGCCCTTTTGAAAGAAGC 431–797 1.000 65.1
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG TCAGGAACAGATGGAACGTT 468–834 1.000 64.3
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG TTCAGGAACAGATGGAACGT 469–835 1.000 64.3
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT GCTACTGCACTGTTCGTTCT 1022–1474 1.000 78.4
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT GCTACTGCACTGTTCGTTCT 961–1413 1.000 76.9
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCGTTC 1023–1475 1.000 76.1
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCGTTC 962–1414 1.000 74.6
petN-psbM_p5 petN-psbM ATAGTAAGTCTCGCTTGGGC GCTACTGCACTGTTCGTTCT 1023–1475 1.000 72.5
psaA-ycf3_p1 psaA-ycf3 GCCCATTCCTCGAAAGAAGT ATCAAGCTGCCGAGTATTGG 937–1151 1.000 84.4
psaA-ycf3_p2 psaA-ycf3 GCCCATTCCTCGAAAGAAGT AGCGCAGAATTGGTTGAAGA 879–1093 1.000 84.0
psaA-ycf3_p3 psaA-ycf3 GCCCATTCCTCGAAAGAAGT CGATCAAGCTGCCGAGTATT 939–1153 1.000 83.5
psaA-ycf3_p4 psaA-ycf3 GAGAAATGACCTGGTCTGGC ATCAAGCTGCCGAGTATTGG 955–1169 1.000 83.2
psaA-ycf3_p5 psaA-ycf3 GAGAAATGACCTGGTCTGGC AGCGCAGAATTGGTTGAAGA 897–1111 1.000 82.8

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
Ventilago harmandiana NC_065258.1 162898 View on NCBI ↗
Ventilago leiocarpa NC_053785.1 161880 View on NCBI ↗