Markers + reference

Myosotis

11 species · Boraginaceae · Boraginales

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Species 11
Genome length 149–149 kb
Candidate markers 262
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 262 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
tRNA-Ser-tRNA-Ser LSC 785 0.0062 1.00 69.8 yes View details
atpA LSC 1524 0.0006 1.00 34.5 yes View details
tRNA-Thr-psbD LSC 1284 0.0064 0.99 66.6 yes View details
pafI-tRNA-Ser LSC 892 0.0043 1.00 62.5 yes View details
psbE-petL LSC 1161 0.0041 1.00 46.5 yes View details
tRNA-Pro-psaJ LSC 555 0.0090 1.00 72.5 yes View details
rpl33 LSC 207 0.0025 1.00 26.2 yes View details
rps18-rpl20 LSC 265 0.0100 0.98 60.9 yes View details
ycf1 SSC 5382 0.0024 1.00 43.1 yes View details
rpl32-ndhF SSC 701 0.0048 1.00 69.2 yes View details
ycf1 IRa 1080 0.0010 1.00 42.6 no View details
atpA-atpF LSC 67 0.0457 0.91 84.6 yes View details
tRNA-Glu-tRNA-Thr LSC 744 0.0032 1.00 64.8 yes View details
ndhC-tRNA-Val LSC 715 0.0030 1.00 60.1 yes View details
tRNA-Thr-tRNA-Leu LSC 707 0.0033 1.00 60.0 yes View details
petA-psbJ LSC 839 0.0013 1.00 60.0 yes View details
psaA-pafI LSC 815 0.0017 0.98 59.8 yes View details
accD-psaI LSC 557 0.0032 0.97 56.8 yes View details
atpB-rbcL LSC 723 0.0028 1.00 56.0 yes View details
ycf1-rps15 SSC 326 0.0081 0.95 55.4 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
tRNA-Ser-tRNA-Ser_p1 tRNA-Ser-tRNA-Ser ATTAGCAATCCGCCGCTTTA TGAATCAAACCGAAAGACCCT 899–921 1.000 72.3
tRNA-Ser-tRNA-Ser_p2 tRNA-Ser-tRNA-Ser TAGCAATCCGCCGCTTTAAT TGAATCAAACCGAAAGACCCT 897–919 1.000 72.3
tRNA-Ser-tRNA-Ser_p3 tRNA-Ser-tRNA-Ser ACGGAAAGAGAGGGATTCGA TGAATCAAACCGAAAGACCCT 948–970 1.000 71.2
tRNA-Ser-tRNA-Ser_p4 tRNA-Ser-tRNA-Ser TTAGCAATCCGCCGCTTTAA TGAATCAAACCGAAAGACCCT 898–920 1.000 70.6
tRNA-Ser-tRNA-Ser_p5 tRNA-Ser-tRNA-Ser ACAACAACGGAAAGAGAGGG TGAATCAAACCGAAAGACCCT 954–976 1.000 70.3
atpA_p1 atpA AGCCTTCCAAGCTAACGATG GTAATTGAGCGTGAGAGCCA 2453–2477 1.000 80.7
atpA_p2 atpA AGCCTTCCAAGCTAACGATG GTGGAAATAGAAGCCGAGCA 2230–2254 1.000 80.7
atpA_p3 atpA CCTAGCCTTCCAAGCTAACG GTAATTGAGCGTGAGAGCCA 2456–2480 1.000 80.5
atpA_p4 atpA AGCCTTCCAAGCTAACGATG TTGGGGGCGCTAAAAGAAAT 1966–1990 1.000 80.5
atpA_p5 atpA CCTAGCCTTCCAAGCTAACG GTGGAAATAGAAGCCGAGCA 2233–2257 1.000 80.4
atpA-atpF_p1 atpA-atpF CCGTCGCCTACTTGAAGTAC TTGGGGGCGCTAAAAGAAAT 198–214 1.000 86.2
atpA-atpF_p2 atpA-atpF ACTAATTTCGTCGGCTCGAA TTGGGGGCGCTAAAAGAAAT 115–131 1.000 84.2
atpA-atpF_p3 atpA-atpF CGTCGCCTACTTGAAGTACA TTGGGGGCGCTAAAAGAAAT 197–213 1.000 82.0
atpA-atpF_p4 atpA-atpF CCGTCGCCTACTTGAAGTAC TGGGGGCGCTAAAAGAAATA 197–213 1.000 80.3
atpA-atpF_p5 atpA-atpF CCGTCGCCTACTTGAAGTAC AATATTGGCATGTTGGGGGC 210–226 1.000 79.6
tRNA-Glu-tRNA-Thr_p1 tRNA-Glu-tRNA-Thr TTCGTAGTACCACCCTACCC GAACCGATGACTTACGCCTT 873–907 1.000 83.9
tRNA-Glu-tRNA-Thr_p2 tRNA-Glu-tRNA-Thr AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 817–851 1.000 83.9
tRNA-Glu-tRNA-Thr_p3 tRNA-Glu-tRNA-Thr AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 815–849 1.000 83.9
tRNA-Glu-tRNA-Thr_p4 tRNA-Glu-tRNA-Thr AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 794–828 1.000 83.5
tRNA-Glu-tRNA-Thr_p5 tRNA-Glu-tRNA-Thr TTCGTAGTACCACCCTACCC CCATGGCGTTACTCTACCAC 852–886 1.000 83.4
tRNA-Thr-psbD_p1 tRNA-Thr-psbD GTGGTAGAGTAACGCCATGG CCGCAACCAGTCATCCATAA 1386–1427 1.000 82.4
tRNA-Thr-psbD_p2 tRNA-Thr-psbD TCAGTGGTAGAGTAACGCCA CCGCAACCAGTCATCCATAA 1389–1430 1.000 82.2
tRNA-Thr-psbD_p3 tRNA-Thr-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1406–1447 1.000 80.7
tRNA-Thr-psbD_p4 tRNA-Thr-psbD GGCGTAAGTCATCGGTTCAA CCGCAACCAGTCATCCATAA 1363–1404 1.000 80.7
tRNA-Thr-psbD_p5 tRNA-Thr-psbD GTGGTAGAGTAACGCCATGG GACCGGACCAACCTACAAAA 1420–1461 1.000 80.5
psaA-pafI_p1 psaA-pafI GTTCTTGAAAAATGGCCCGG ATTGCAGAGGCTTGGTTTGA 1034–1058 1.000 81.5
psaA-pafI_p2 psaA-pafI GTTCTTGAAAAATGGCCCGG TTGCAGAGGCTTGGTTTGAT 1033–1057 1.000 81.5
psaA-pafI_p3 psaA-pafI GCCCATTCCTCGAAAGAAGT ATTGCAGAGGCTTGGTTTGA 1010–1034 1.000 81.3
psaA-pafI_p4 psaA-pafI GCCCATTCCTCGAAAGAAGT TTGCAGAGGCTTGGTTTGAT 1009–1033 1.000 81.3
psaA-pafI_p5 psaA-pafI GTTCTTGAAAAATGGCCCGG ATCAAGCCGCTGAGTATTGG 1015–1039 1.000 81.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (11)

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

Species Accession Length (bp) Link
Myosotis angustata PQ310502.1 149201 View on NCBI ↗
Myosotis australis subsp. australis PQ310498.1 149228 View on NCBI ↗
Myosotis capitata PQ310499.1 149091 View on NCBI ↗
Myosotis colensoi PQ310503.1 149183 View on NCBI ↗
Myosotis goyenii subsp. infima PQ310500.1 149198 View on NCBI ↗
Myosotis rakiura PQ310501.1 149091 View on NCBI ↗
Myosotis retrorsa PQ310505.1 149137 View on NCBI ↗
Myosotis saxatilis PQ310506.1 149195 View on NCBI ↗
Myosotis tenericaulis PQ310507.1 149156 View on NCBI ↗
Myosotis traversii subsp. traversii PQ310508.1 149297 View on NCBI ↗
Myosotis venticola PQ310509.1 149270 View on NCBI ↗