Markers + reference

Fraxinus

24 species · Oleaceae · Lamiales

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Species 24
Genome length 155–156 kb
Candidate markers 265
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH(GUG)-psbA LSC 437 0.0322 1.00 67.4 yes View details
rps16-trnQ(UUG) LSC 1644 0.0074 1.00 56.6 yes View details
atpB-rbcL LSC 780 0.0143 1.00 58.6 yes View details
psbE-petL LSC 1187 0.0074 1.00 54.0 yes View details
rpl16 LSC 1284 0.0063 0.99 46.5 yes View details
ycf1 IRb 1164 0.0018 1.00 45.7 no View details
ndhF-rpl32 SSC 428 0.0168 1.00 53.5 yes View details
rpl32-trnL(UAG) SSC 862 0.0102 0.99 57.3 yes View details
ycf1 SSC 5625 0.0076 1.00 53.0 yes View details
atpA-atpF LSC 70 0.0393 0.99 67.1 yes View details
rpl22-rps19 LSC 65 0.0282 1.00 65.1 yes View details
rpl2-trnH(GUG) IRa 76 0.0388 0.96 62.5 no View details
psaA-ycf3 LSC 718 0.0054 1.00 58.9 yes View details
trnS(GCU)-trnG(GCC) LSC 704 0.0058 0.98 57.7 yes View details
trnM(CAU)-psbD LSC 1312 0.0057 1.00 56.1 yes View details
trnL(UAG)-ccsA SSC 90 0.0223 1.00 54.5 yes View details
trnM(CAU)-trnL(UAA) LSC 680 0.0054 1.00 54.1 yes View details
trnF(GAA)-ndhJ LSC 668 0.0053 1.00 52.4 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 80 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 CCGTGCTAACCTTGGTATGG 508–574 1.000 87.0
trnH(GUG)-psbA_p2 trnH(GUG)-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 509–575 1.000 86.8
trnH(GUG)-psbA_p3 trnH(GUG)-psbA CTGCCTTAATCCACTTGGCT ACCGTGCTAACCTTGGTATG 509–575 1.000 86.5
trnH(GUG)-psbA_p4 trnH(GUG)-psbA ACTGCCTTAATCCACTTGGC ACCGTGCTAACCTTGGTATG 510–576 1.000 86.3
trnH(GUG)-psbA_p5 trnH(GUG)-psbA AATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 501–567 1.000 85.5
rps16-trnQ(UUG)_p1 rps16-trnQ(UUG) CGGATCTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1504–1748 1.000 85.6
rps16-trnQ(UUG)_p2 rps16-trnQ(UUG) ATCTGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1501–1745 1.000 85.6
rps16-trnQ(UUG)_p3 rps16-trnQ(UUG) AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1490–1734 1.000 85.2
rps16-trnQ(UUG)_p4 rps16-trnQ(UUG) CCACAACGGATCTGTCCTTC GAGGTTCGAATCCTTCCGTC 1510–1754 1.000 84.1
rps16-trnQ(UUG)_p5 rps16-trnQ(UUG) GGATCTGTCCTTCAAGTCGC GAGGTTCGAATCCTTCCGTC 1503–1747 1.000 83.4
trnS(GCU)-trnG(GCC)_p1 trnS(GCU)-trnG(GCC) CAATCCGACGCTTTAGTCCA AGACCGAAAGACCCTTTAACT 787–818 1.000 67.0
trnS(GCU)-trnG(GCC)_p2 trnS(GCU)-trnG(GCC) AATCCGACGCTTTAGTCCAC AGACCGAAAGACCCTTTAACT 786–817 1.000 67.0
trnS(GCU)-trnG(GCC)_p3 trnS(GCU)-trnG(GCC) ATCAACGGAACCGGAAAGAG AGACCGAAAGACCCTTTAACT 851–882 1.000 66.3
trnS(GCU)-trnG(GCC)_p4 trnS(GCU)-trnG(GCC) CATCAACGGAACCGGAAAGA AGACCGAAAGACCCTTTAACT 852–883 1.000 65.5
trnS(GCU)-trnG(GCC)_p5 trnS(GCU)-trnG(GCC) TCATCAACGGAACCGGAAAG AGACCGAAAGACCCTTTAACT 853–884 1.000 65.5
atpA-atpF_p1 atpA-atpF ACTAATTTCGTCGGCTCGAA TGTTGGGAGCGATGAAAGAA 124–134 1.000 78.8
atpA-atpF_p2 atpA-atpF ACTAATTTCGTCGGCTCGAA ATATTGGCATGTTGGGAGCG 133–143 1.000 77.5
atpA-atpF_p3 atpA-atpF ACTAATTTCGTCGGCTCGAA ATGTTGGGAGCGATGAAAGA 125–135 1.000 76.9
atpA-atpF_p4 atpA-atpF ACTAATTTCGTCGGCTCGAA CATGTTGGGAGCGATGAAAG 126–136 1.000 76.5
atpA-atpF_p5 atpA-atpF AATTTCGTCGGCTCGAATGG TGTTGGGAGCGATGAAAGAA 121–131 1.000 76.1
trnM(CAU)-psbD_p1 trnM(CAU)-psbD GTGGTAGAGTAACGCCATGG GGACCAGCCTACAAAAACGA 1290–1475 1.000 84.7
trnM(CAU)-psbD_p2 trnM(CAU)-psbD TCAGTGGTAGAGTAACGCCA GGACCAGCCTACAAAAACGA 1293–1478 1.000 84.5
trnM(CAU)-psbD_p3 trnM(CAU)-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAAACGGTCCCT 1280–1465 1.000 83.6
trnM(CAU)-psbD_p4 trnM(CAU)-psbD TCAGTGGTAGAGTAACGCCA ACAAAAACGAAACGGTCCCT 1283–1468 1.000 83.5
trnM(CAU)-psbD_p5 trnM(CAU)-psbD GGCGTAAGTCATCGGTTCAA GGACCAGCCTACAAAAACGA 1267–1452 1.000 83.0
psaA-ycf3_p1 psaA-ycf3 GCCCATTCCTCGAAAGAAGT ATTGGTTGAAGATCACGGGG 529–852 1.000 83.7
psaA-ycf3_p2 psaA-ycf3 GCCCATTCCTCGAAAGAAGT TGGTTTGATCAAGCAGCTGA 602–925 1.000 82.4
psaA-ycf3_p3 psaA-ycf3 GCCCATTCCTCGAAAGAAGT CGGAGGCTTGGTTTGATCAA 610–933 1.000 80.9
psaA-ycf3_p4 psaA-ycf3 TGTTCTTGAGAAATGGCCCG ATTGGTTGAAGATCACGGGG 554–877 1.000 80.8
psaA-ycf3_p5 psaA-ycf3 TTTTACTTCTGGTTCCGGCG ATTGGTTGAAGATCACGGGG 482–805 1.000 80.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (24)

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

Species Accession Length (bp) Link
Fraxinus americana NC_042449.1 155602 View on NCBI ↗
Fraxinus angustifolia NC_042271.1 155574 View on NCBI ↗
Fraxinus angustifolia subsp. angustifolia ON641283.1 155579 View on NCBI ↗
Fraxinus baroniana PQ456185.1 155691 View on NCBI ↗
Fraxinus chiisanensis NC_037171.1 155541 View on NCBI ↗
Fraxinus chinensis PQ456186.1 155378 View on NCBI ↗
Fraxinus chinensis subsp. rhynchophylla PQ456190.1 155592 View on NCBI ↗
Fraxinus excelsior NC_037446.1 155622 View on NCBI ↗
Fraxinus excelsior subsp. excelsior PP336750.1 155574 View on NCBI ↗
Fraxinus hupehensis NC_052770.1 155689 View on NCBI ↗
Fraxinus insularis MK299392.1 155700 View on NCBI ↗
Fraxinus lanuginosa NC_042424.1 155628 View on NCBI ↗
Fraxinus latifolia NC_042450.1 155606 View on NCBI ↗
Fraxinus malacophylla NC_063328.1 155621 View on NCBI ↗
Fraxinus mandshurica NC_041463.1 155530 View on NCBI ↗
Fraxinus nigra MK299394.1 155345 View on NCBI ↗
Fraxinus ornus subsp. ornus PP336751.1 155680 View on NCBI ↗
Fraxinus paxiana PQ456184.1 155692 View on NCBI ↗
Fraxinus pennsylvanica NC_043874.1 155543 View on NCBI ↗
Fraxinus quadrangulata NC_042451.1 155541 View on NCBI ↗
Fraxinus sieboldiana MK299395.1 155703 View on NCBI ↗
Fraxinus sogdiana PQ456188.1 155597 View on NCBI ↗
Fraxinus velutina NC_082971.1 155610 View on NCBI ↗
Fraxinus xanthoxyloides NC_042452.1 155694 View on NCBI ↗