Markers + reference

Consolida

3 species · Ranunculaceae · Ranunculales

Back to catalogue

Species 3
Genome length 156–156 kb
Candidate markers 267
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 241 0.0304 1.00 47.0 yes View details
trnK-UUU-rps16 LSC 604 0.0177 1.00 52.5 yes View details
rps16-trnQ-UUG LSC 1288 0.0109 1.00 41.6 yes View details
trnG-UCC-trnR-UCU LSC 169 0.0355 1.00 53.3 yes View details
trnD-GUC-trnY-GUA LSC 402 0.0149 1.00 37.8 yes View details
trnT-UGU-trnL-UAA LSC 733 0.0091 1.00 54.0 yes View details
psbE-petL LSC 1022 0.0078 1.00 43.0 yes View details
rpl16 LSC 1513 0.0070 1.00 37.9 yes View details
ycf1 IRb 1677 0.0004 1.00 34.8 no View details
ccsA-ndhD SSC 316 0.0422 1.00 54.3 yes View details
ndhG-ndhI SSC 391 0.0239 1.00 43.2 yes View details
ycf1 SSC 5316 0.0075 1.00 31.7 yes View details
petN-psbM LSC 1224 0.0071 1.00 64.9 yes View details
rbcL-accD LSC 729 0.0073 1.00 61.7 yes View details
trnC-GCA-petN LSC 864 0.0062 1.00 58.0 yes View details
atpB-rbcL LSC 712 0.0037 1.00 55.1 yes View details
ndhH-rps15 SSC 140 0.0190 1.00 52.1 yes View details
trnF-GAA-ndhJ LSC 674 0.0099 1.00 51.7 yes View details
trnS-GCU-trnG-UCC LSC 705 0.0066 1.00 51.4 yes View details
trnL-CAA-ndhB IRb 581 0.0000 1.00 50.6 yes View details
ndhB-trnL-CAA IRa 581 0.0000 1.00 50.6 yes View details
rpl22 LSC 540 0.0099 1.00 49.8 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
trnH-GUG-psbA_p1 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT GCTGCTGTTGAAGTTCCAAC 303–305 1.000 80.8
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TGCTGTTGAAGTTCCAACCA 301–303 1.000 80.7
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC GCTGCTGTTGAAGTTCCAAC 304–306 1.000 80.6
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TGCTGTTGAAGTTCCAACCA 302–304 1.000 80.5
trnH-GUG-psbA_p5 trnH-GUG-psbA AATCCACTTGGCTACATCCG GCTGCTGTTGAAGTTCCAAC 296–298 1.000 79.3
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GAGTTCAACCAACCTACGGG 716–720 1.000 80.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGAGTTCAACCAACCTACGG 717–721 1.000 80.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GAGTTCAACCAACCTACGGG 715–719 1.000 80.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGAGTTCAACCAACCTACGG 716–720 1.000 80.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCAACCAACCTACGGGAAC 712–716 1.000 79.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTGTCAATCGAATCCACGGA GAAATTGAAATGGGGCGTGG 2107–2469 1.000 82.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCAATCGAATCCACGGAACC GAAATTGAAATGGGGCGTGG 2104–2466 1.000 82.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TGTGTTGGATTGGCACTTGA GAAATTGAAATGGGGCGTGG 1930–2289 1.000 82.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GTGTCAATCGAATCCACGGA CTTACAGCAGCTTGCCAAAC 2608–2976 1.000 81.9
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCAATCGAATCCACGGAACC CTTACAGCAGCTTGCCAAAC 2605–2973 1.000 81.8
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACCGAAAGACCCCTTAACT 812–829 1.000 68.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACCGAAAGACCCCTTAACT 811–828 1.000 68.1
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AACCGAAAGACCCCTTAACT 866–883 1.000 66.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AAACCGAAAGACCCCTTAACT 813–830 1.000 66.3
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AAACCGAAAGACCCCTTAACT 812–829 1.000 66.3
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 249 1.000 66.2
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 252 1.000 66.0
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 255 1.000 65.5
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 258 1.000 65.2
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 253 1.000 63.8
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 927 1.000 80.5
trnC-GCA-petN_p2 trnC-GCA-petN CACCAGCACCAGGAAGATTT TTAAAGCAGCCCAAGCAAGA 1009 1.000 80.4
trnC-GCA-petN_p3 trnC-GCA-petN CAGCACCAGGAAGATTTCGA TTAAAGCAGCCCAAGCAAGA 1006 1.000 80.3
trnC-GCA-petN_p4 trnC-GCA-petN ACCAGCACCAGGAAGATTTC TTAAAGCAGCCCAAGCAAGA 1008 1.000 79.4
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 921 1.000 79.0

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
Consolida ajacis NC_041534.1 155900 View on NCBI ↗
Consolida orientalis NC_047292.1 155915 View on NCBI ↗
Consolida regalis PX380652.1 156019 View on NCBI ↗