Markers + reference

Delphinium

26 species · Ranunculaceae · Ranunculales

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Species 26
Genome length 154–155 kb
Candidate markers 268
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-trnQ-UUG LSC 760 0.0203 0.99 74.9 yes View details
rpoB-trnC-GCA LSC 1101 0.0129 0.98 70.1 yes View details
trnT-GGU-psbD LSC 1553 0.0161 0.98 78.3 yes View details
trnP-UGG-psaJ LSC 688 0.0271 0.99 80.9 yes View details
rpl16 LSC 1529 0.0136 1.00 67.3 yes View details
ycf1 IRb 1704 0.0065 1.00 55.6 no View details
ndhF-trnL-UAG SSC 861 0.0182 0.99 71.0 yes View details
ycf1 SSC 5310 0.0138 1.00 59.1 yes View details
rpl33-rps18 LSC 173 0.0389 0.99 76.4 yes View details
petA-psbJ LSC 443 0.0210 0.98 73.8 yes View details
trnS-GCU-trnG-UCC LSC 698 0.0139 0.98 72.8 yes View details
ycf3-trnS-GGA LSC 867 0.0118 1.00 71.3 yes View details
atpF-atpH LSC 423 0.0145 1.00 70.6 yes View details
ndhC-trnV-UAC LSC 1070 0.0140 1.00 70.0 yes View details
rps8-rpl14 LSC 244 0.0203 1.00 69.9 yes View details
trnC-GCA-petN LSC 886 0.0119 1.00 69.4 yes View details
trnT-UGU-trnL-UAA LSC 698 0.0120 1.00 68.1 yes View details
rbcL-accD LSC 706 0.0081 0.99 68.1 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-trnQ-UUG_p1 trnK-UUU-trnQ-UUG AAAGCCGAGTACTCTACCGT GAGGTTCGAATCCTTCCGTC 386–823 1.000 90.0
trnK-UUU-trnQ-UUG_p2 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT GAGGTTCGAATCCTTCCGTC 385–822 1.000 90.0
trnK-UUU-trnQ-UUG_p3 trnK-UUU-trnQ-UUG TCTAGCCGCACTTAAAAGCC GAGGTTCGAATCCTTCCGTC 400–837 1.000 89.3
trnK-UUU-trnQ-UUG_p4 trnK-UUU-trnQ-UUG CCGCACTTAAAAGCCGAGTA GAGGTTCGAATCCTTCCGTC 395–832 1.000 89.1
trnK-UUU-trnQ-UUG_p5 trnK-UUU-trnQ-UUG AAGCCGAGTACTCTACCGTT CTCGGAGGTTCGAATCCTTC 389–826 1.000 89.0
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AACCGAAAGACCCCTTAACT 792–863 1.000 76.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AACCGAAAGACCCCTTAACT 791–862 1.000 76.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA AAACCGAAAGACCCCTTAACT 793–864 1.000 74.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC AAACCGAAAGACCCCTTAACT 792–863 1.000 74.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC AGCAATCCGACGCTTTAGTC AACCGAAAGACCCCTTAACT 794–865 1.000 74.0
atpF-atpH_p1 atpF-atpH CGACCCAAGGAAACGAAAGA AATTTACGGACTGGTCGTGG 501–519 1.000 89.0
atpF-atpH_p2 atpF-atpH TTAAATCCGAAACTCCCGGC AATTTACGGACTGGTCGTGG 531–546 0.962 85.0
atpF-atpH_p3 atpF-atpH CGACCCAAGGAAACGAAAGA ACAATTTACGGACTGGTCGT 503–521 1.000 83.1
atpF-atpH_p4 atpF-atpH CGACCCAAGGAAACGAAAGA GGTCGTGGCATTAGCACTTT 489–507 1.000 83.0
atpF-atpH_p5 atpF-atpH TTAAATCCGAAACTCCCGGC ACAATTTACGGACTGGTCGT 533–548 0.962 79.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG CCGGATTTGAACTGGGGAAA 1132–1272 0.962 81.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG TTTCTTGATCAGGCGACACC 1151–1291 0.962 81.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG AAAAGGATTTGCAGTCCCCC 1114–1254 0.962 79.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ACATTCCCTCATTTCCATCCC CCGGATTTGAACTGGGGAAA 1134–1274 0.962 76.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATTCCCTCATTTCCATCCCG GACACCCGGATTTGAACTGG 1137–1277 0.962 75.8
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 930–959 1.000 88.7
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 924–953 1.000 87.3
trnC-GCA-petN_p3 trnC-GCA-petN TTTATCGTTTTGGCGGCATG TTAAAGCAGCCCAAGCAAGA 983–1012 1.000 86.7
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 948–977 1.000 86.4
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 984–1013 1.000 85.5
trnT-GGU-psbD_p1 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA ACAAAAACGAAACGGTCCCT 1628–1739 1.000 88.2
trnT-GGU-psbD_p2 trnT-GGU-psbD GCCCTTTTAACTCAGCGGTA GACCGGACCAACCTACAAAA 1642–1753 1.000 88.1
trnT-GGU-psbD_p3 trnT-GGU-psbD ACAGGCCCTTTTAACTCAGC ACAAAAACGAAACGGTCCCT 1632–1743 0.923 81.7
trnT-GGU-psbD_p4 trnT-GGU-psbD ACAGGCCCTTTTAACTCAGC GACCGGACCAACCTACAAAA 1646–1757 0.923 81.6
trnT-GGU-psbD_p5 trnT-GGU-psbD ACAGGCCCTTTTAACTCAGC TAGACCGGACCAACCTACAA 1648–1759 0.923 81.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (26)

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

Species Accession Length (bp) Link
Delphinium albocoeruleum PQ845753.1 154258 View on NCBI ↗
Delphinium anthriscifolium PX380653.1 154808 View on NCBI ↗
Delphinium beesianum PX380655.1 154228 View on NCBI ↗
Delphinium brunonianum NC_051554.1 153926 View on NCBI ↗
Delphinium caeruleum PX380657.1 154314 View on NCBI ↗
Delphinium candelabrum var. monanthum MW246165.1 153995 View on NCBI ↗
Delphinium ceratophorum MK253460.1 154245 View on NCBI ↗
Delphinium densiflorum PX644816.1 153918 View on NCBI ↗
Delphinium denudatum PV364607.1 154228 View on NCBI ↗
Delphinium ecalcaratum PP078686.1 154887 View on NCBI ↗
Delphinium elatum var. sericeum PX380658.1 154296 View on NCBI ↗
Delphinium gyalanum PX380660.1 154320 View on NCBI ↗
Delphinium kingianum PX380666.1 154149 View on NCBI ↗
Delphinium maackianum NC_047293.1 154484 View on NCBI ↗
Delphinium montanum OK148444.1 154185 View on NCBI ↗
Delphinium pachycentrum PX380667.1 154147 View on NCBI ↗
Delphinium platyonychinum PX380668.1 153936 View on NCBI ↗
Delphinium pylzowii var. trigynum PX380669.1 153769 View on NCBI ↗
Delphinium spirocentrum PX380670.1 154137 View on NCBI ↗
Delphinium tangkulaense PP234555.1 154316 View on NCBI ↗
Delphinium tatsienense PX380671.1 154222 View on NCBI ↗
Delphinium tenii PX380672.1 154145 View on NCBI ↗
Delphinium thibeticum PX380673.1 154177 View on NCBI ↗
Delphinium trichophorum PX644817.1 154117 View on NCBI ↗
Delphinium wangii PX380676.1 154210 View on NCBI ↗
Delphinium yunnanense NC_056321.1 154053 View on NCBI ↗