Markers + reference

Echium

2 species · Boraginaceae · Boraginales

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Species 2
Genome length 150–150 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

13 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
trnH-GUG-psbA LSC 269 0.0856 0.83 85.2 yes View details
trnK-UUU-rps16 LSC 700 0.0215 1.00 59.0 yes View details
trnS-GCU-trnG-UCC LSC 729 0.0434 0.95 76.6 yes View details
atpF-atpH LSC 365 0.0537 0.97 85.8 yes View details
pafI-trnS-GGA LSC 905 0.0167 0.99 66.0 yes View details
rps4-trnT-UGU LSC 346 0.0405 1.00 68.4 yes View details
trnT-UGU-trnL-UAA LSC 612 0.0209 0.94 61.3 yes View details
petA-psbJ LSC 781 0.0196 0.98 72.0 yes View details
psbE-petL LSC 1089 0.0250 0.99 68.7 yes View details
petL-petG LSC 172 0.0174 1.00 55.7 yes View details
ycf1 IRb 1083 0.0009 1.00 46.9 no View details
rpl32-trnL-UAG SSC 535 0.0430 1.00 68.2 yes View details
ycf1 SSC 5412 0.0137 1.00 46.6 yes View details
petG-trnW-CCA LSC 126 0.0763 0.94 88.4 yes View details
atpA-atpF LSC 56 0.0600 0.89 71.4 yes View details
trnG-GCC-trnfM-CAU LSC 148 0.0338 1.00 70.1 yes View details
trnT-GGU-psbD LSC 1171 0.0146 0.99 68.0 yes View details
trnR-ACG-trnN-GUU IRb 594 0.0135 1.00 66.4 yes View details
trnN-GUU-trnR-ACG IRa 594 0.0135 1.00 66.4 yes View details
trnF-GAA-ndhJ LSC 628 0.0091 0.87 66.3 yes View details
rpl33-rps18 LSC 148 0.0141 0.96 64.5 yes View details
ndhC-trnV-UAC LSC 632 0.0095 1.00 64.2 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 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 GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 341–388 1.000 84.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 355–402 1.000 84.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 354–401 1.000 84.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 356–403 1.000 84.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GGAATCACAATCCACTGCCT CCGTGCTAACCTTGGTATGG 362–409 1.000 84.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC GCTTCTCCCTAATCAAACGGA 824–826 1.000 71.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AGCTTCTCCCTAATCAAACGG 825–827 1.000 71.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GCTTCTCCCTAATCAAACGGA 763–765 1.000 70.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GCTTCTCCCTAATCAAACGGA 762–764 1.000 70.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGCTTCTCCCTAATCAAACGG 763–765 1.000 70.4
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC ATTAGCAATCCGCCGCTTTA GGGGTAATAGAACGAATCACACT 798–814 1.000 62.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CCATCAACGGAAAGAGAGGG GGGGTAATAGAACGAATCACACT 853–869 1.000 61.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA GGGGTAATAGAACGAATCACACT 847–863 1.000 60.9
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AGCCATCAACGGAAAGAGAG GGGGTAATAGAACGAATCACACT 855–871 1.000 58.9
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CCATCAACGGAAAGAGAGGG GGGGTAATAGAACGAATCACAC 853–869 1.000 58.8
atpA-atpF_p1 atpA-atpF ATGCCATCGCCTACTTGAAG GTGGAAATAGAAGCCGAGCA 460–466 1.000 81.6
atpA-atpF_p2 atpA-atpF AAGTGGTTACTACCTGGGCT GTGGAAATAGAAGCCGAGCA 981–987 1.000 80.8
atpA-atpF_p3 atpA-atpF TCGGCTCGAATGGTTACCA GCGATGAAAGAAATAATTGATTAG 94–100 1.000 46.5
atpA-atpF_p4 atpA-atpF CGGCTCGAATGGTTACCA GCGATGAAAGAAATAATTGATTAG 93–99 1.000 46.5
atpA-atpF_p5 atpA-atpF TCGGCTCGAATGGTTACC GCGATGAAAGAAATAATTGATTAG 94–100 1.000 46.5
atpF-atpH_p1 atpF-atpH TGGCCCAAAGAAACGAAAGA GGCTGGTTGTAGCATTAGCA 450–468 1.000 82.7
atpF-atpH_p2 atpF-atpH GTGGCCCAAAGAAACGAAAG GGCTGGTTGTAGCATTAGCA 451–469 1.000 82.1
atpF-atpH_p3 atpF-atpH TGGCCCAAAGAAACGAAAGA TGGGCTGGTTGTAGCATTAG 452–470 1.000 81.4
atpF-atpH_p4 atpF-atpH AGTGGCCCAAAGAAACGAAA GGCTGGTTGTAGCATTAGCA 452–470 1.000 81.4
atpF-atpH_p5 atpF-atpH GTGGCCCAAAGAAACGAAAG TGGGCTGGTTGTAGCATTAG 453–471 1.000 80.8
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CCGCAACCAGTCATCCATAA 1294–1301 1.000 80.9
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA CCGCAACCAGTCATCCATAA 1297–1304 1.000 80.7
trnT-GGU-psbD_p3 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGACCAGCCTACAAAAACGA 1324–1331 1.000 80.2
trnT-GGU-psbD_p4 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GGACCAGCCTACAAAAACGA 1327–1334 1.000 80.0
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1314–1321 1.000 79.2

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
Echium plantagineum OL335188.1 149776 View on NCBI ↗
Echium vulgare subsp. vulgare PP024536.1 150254 View on NCBI ↗