Markers + reference

Pulmonaria

2 species · Boraginaceae · Boraginales

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Species 2
Genome length 151–151 kb
Candidate markers 273
Primer pairs 90

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 8 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1130 0.0009 1.00 59.3 yes View details
rps16-trnQ-UUG LSC 647 0.0031 1.00 60.5 yes View details
atpH-atpI LSC 978 0.0041 1.00 61.2 yes View details
trnE-UUC-trnT-GGU LSC 630 0.0032 1.00 60.6 yes View details
psbE-petL LSC 1054 0.0009 1.00 59.4 yes View details
petD LSC 1232 0.0024 1.00 60.2 yes View details
rpl16 LSC 1506 0.0013 1.00 59.5 yes View details
ycf1 IRb 1083 0.0000 1.00 32.9 no View details
rpl32-trnL-UAG SSC 480 0.0021 1.00 55.3 yes View details
ndhA SSC 2174 0.0014 1.00 55.9 yes View details
ycf1 SSC 5370 0.0006 1.00 45.7 yes View details
rps3-trnH-GUG IRa 87 0.0000 1.00 71.2 no View details
rps7-rps12 IRb 53 0.0189 1.00 63.3 yes View details
rps12-rps7 IRa 53 0.0189 1.00 63.3 yes View details
trnT-UGU-trnL-UAA LSC 659 0.0030 1.00 60.5 yes View details
ndhF-rpl32 SSC 593 0.0034 1.00 60.5 yes View details
trnT-GGU-psbD LSC 1172 0.0017 1.00 59.7 yes View details
ycf3-trnS-GGA LSC 792 0.0013 1.00 59.5 yes View details
ndhC-trnV-UAC LSC 775 0.0013 1.00 59.5 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16_p1 rps16 TGGATAGAGCAGAAAGGGGG TCAACTACGCACCCCTTCTA 1239 1.000 75.6
rps16_p2 rps16 GGGTGTCTACGGATTGGGTA TCAACTACGCACCCCTTCTA 1284 1.000 75.4
rps16_p3 rps16 TGGATAGAGCAGAAAGGGGG AATCAACTACGCACCCCTTC 1241 1.000 75.3
rps16_p4 rps16 TGGATAGAGCAGAAAGGGGG GAATCAACTACGCACCCCTT 1242 1.000 75.3
rps16_p5 rps16 GGGTGTCTACGGATTGGGTA AATCAACTACGCACCCCTTC 1286 1.000 75.1
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GTCTTTCAAGTCGCACGTTG GAGGTTCGAATCCTTCCGTC 727 1.000 79.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GGAGTAAGAATCCACAGCGG GAGGTTCGAATCCTTCCGTC 752 1.000 79.1
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATGTCTTTCAAGTCGCACGT GAGGTTCGAATCCTTCCGTC 729 1.000 78.5
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 720 1.000 78.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CATGTCTTTCAAGTCGCACG GAGGTTCGAATCCTTCCGTC 730 1.000 77.9
trnG-UCC_p1 trnG-UCC TCACCTGTTCGACAAAAGGT AATGGGATTGTTTGTGAAAC 889 1.000 40.1
trnG-UCC_p2 trnG-UCC TCACCTGTTCGACAAAAGGT AAATGGGATTGTTTGTGAAAC 890 1.000 40.1
trnG-UCC_p3 trnG-UCC TCACCTGTTCGACAAAAGGT AAAATGGGATTGTTTGTGAAAC 891 1.000 40.1
trnG-UCC_p4 trnG-UCC TTCACCTGTTCGACAAAAGGT AATGGGATTGTTTGTGAAAC 890 1.000 40.1
trnG-UCC_p5 trnG-UCC TTCACCTGTTCGACAAAAGGT AAATGGGATTGTTTGTGAAAC 891 1.000 40.1
atpH-atpI_p1 atpH-atpI GCAGCAATAACAGAAGCAGC TTTTGCAACTTTAGCTGCGG 1071 1.000 78.6
atpH-atpI_p2 atpH-atpI TACCCTCTACAGCTTGACCC TTTTGCAACTTTAGCTGCGG 1148 1.000 78.2
atpH-atpI_p3 atpH-atpI GCGATACCCTCTACAGCTTG TTTTGCAACTTTAGCTGCGG 1152 1.000 78.2
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA TTTTGCAACTTTAGCTGCGG 1081 1.000 78.1
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TTTTGCAACTTTAGCTGCGG 1080 1.000 77.6
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 717 1.000 79.0
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 715 1.000 79.0
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 771 1.000 78.9
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 696 1.000 78.6
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 694 1.000 78.6
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CCGCAACCAGTCATCCATAA 1302 1.000 79.3
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA CCGCAACCAGTCATCCATAA 1305 1.000 79.1
trnT-GGU-psbD_p3 trnT-GGU-psbD AACGGGCCCTTTTAACTCAG CCGCAACCAGTCATCCATAA 1321 1.000 79.1
trnT-GGU-psbD_p4 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GGACCAGCCTACAAAAACGA 1332 1.000 78.7
trnT-GGU-psbD_p5 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA GGACCAGCCTACAAAAACGA 1335 1.000 78.5

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
Pulmonaria australis PP024537.1 150977 View on NCBI ↗
Pulmonaria officinalis PP024538.1 150984 View on NCBI ↗