Markers + reference

Chionanthus

19 species · Oleaceae · Lamiales

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Species 19
Genome length 155–156 kb
Candidate markers 264
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 9 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH(GUG)-psbA LSC 446 0.0472 1.00 85.3 yes View details
matK-rps16 LSC 1653 0.0138 0.99 62.9 yes View details
trnS(GCU)-trnG(GCC) LSC 708 0.0150 1.00 75.0 yes View details
ndhC-trnM(CAU) LSC 1940 0.0118 1.00 66.5 yes View details
atpB-rbcL LSC 782 0.0144 1.00 63.4 yes View details
psbE-petL LSC 1183 0.0154 1.00 70.5 yes View details
ycf1 IRb 1164 0.0030 1.00 46.3 no View details
ndhF SSC 2217 0.0119 1.00 55.1 yes View details
ndhF-rpl32 SSC 478 0.0186 1.00 70.7 yes View details
rpl32-trnL(UAG) SSC 798 0.0189 1.00 67.7 yes View details
ycf1 SSC 5619 0.0138 1.00 56.7 yes View details
rps2-rpoC2 LSC 207 0.0249 1.00 79.9 yes View details
rpl2-trnH(GUG) IRa 81 0.0833 0.93 76.9 no View details
psbI-trnS(GCU) LSC 122 0.1077 0.98 76.1 yes View details
petA-psbJ LSC 948 0.0116 1.00 75.2 yes View details
atpH-atpI LSC 1071 0.0123 1.00 74.2 yes View details
trnE(UUC)-psbD LSC 2170 0.0092 1.00 72.9 yes View details
petD-rpoA LSC 181 0.0310 1.00 72.5 yes View details
ycf3-trnS(GGA) LSC 774 0.0100 1.00 70.7 yes View details
trnT(UGU)-trnL(UAA) LSC 653 0.0123 1.00 70.5 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
trnH(GUG)-psbA_p1 trnH(GUG)-psbA CTGCCTTAATCCACTTGGCT CCGTGCTAACCTTGGTATGG 403–596 1.000 88.2
trnH(GUG)-psbA_p2 trnH(GUG)-psbA ACTGCCTTAATCCACTTGGC CCGTGCTAACCTTGGTATGG 404–597 1.000 88.0
trnH(GUG)-psbA_p3 trnH(GUG)-psbA CTGCCTTAATCCACTTGGCT ACCGTGCTAACCTTGGTATG 404–597 1.000 87.7
trnH(GUG)-psbA_p4 trnH(GUG)-psbA ACTGCCTTAATCCACTTGGC ACCGTGCTAACCTTGGTATG 405–598 1.000 87.5
trnH(GUG)-psbA_p5 trnH(GUG)-psbA AATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 396–589 1.000 86.7
matK-rps16_p1 matK-rps16 GGATGGGGTGGGGTATTAGT AAAAGGGTATGTTGCTGCCA 2746–2838 1.000 88.4
matK-rps16_p2 matK-rps16 TGGATGGGGTGGGGTATTAG AAAAGGGTATGTTGCTGCCA 2747–2839 1.000 88.4
matK-rps16_p3 matK-rps16 GGATGGGGTGGGGTATTAGT GCCGTACGAGGAGAAAACTT 2332–2419 1.000 87.5
matK-rps16_p4 matK-rps16 TGGATGGGGTGGGGTATTAG GCCGTACGAGGAGAAAACTT 2333–2420 1.000 87.5
matK-rps16_p5 matK-rps16 GCGCCCCCAAAATTGATTTT AAAAGGGTATGTTGCTGCCA 2535–2624 0.789 79.0
psbI-trnS(GCU)_p1 psbI-trnS(GCU) GTAATCCCGGACGTGAAGAA TGGACTAAAGCGTCGGATTG 208–232 1.000 86.7
psbI-trnS(GCU)_p2 psbI-trnS(GCU) GTAATCCCGGACGTGAAGAA GTGGACTAAAGCGTCGGATT 209–233 1.000 86.7
psbI-trnS(GCU)_p3 psbI-trnS(GCU) GTAATCCCGGACGTGAAGAA ATTGGGAGAGATGGCTGAGT 227–251 1.000 85.8
psbI-trnS(GCU)_p4 psbI-trnS(GCU) GTAATCCCGGACGTGAAGAA GACTAAAGCGTCGGATTGCT 206–230 1.000 83.9
psbI-trnS(GCU)_p5 psbI-trnS(GCU) GTAATCCCGGACGTGAAGAA CTGAGTGGACTAAAGCGTCG 213–237 1.000 83.7
trnS(GCU)-trnG(GCC)_p1 trnS(GCU)-trnG(GCC) CAATCCGACGCTTTAGTCCA AGACCGAAAGACCCTTTAACT 797–825 1.000 70.2
trnS(GCU)-trnG(GCC)_p2 trnS(GCU)-trnG(GCC) AATCCGACGCTTTAGTCCAC AGACCGAAAGACCCTTTAACT 796–824 1.000 70.2
trnS(GCU)-trnG(GCC)_p3 trnS(GCU)-trnG(GCC) ATCAACGGAACCGGAAAGAG AGACCGAAAGACCCTTTAACT 861–889 1.000 68.7
trnS(GCU)-trnG(GCC)_p4 trnS(GCU)-trnG(GCC) CATCAACGGAACCGGAAAGA AGACCGAAAGACCCTTTAACT 862–890 1.000 67.9
trnS(GCU)-trnG(GCC)_p5 trnS(GCU)-trnG(GCC) TCATCAACGGAACCGGAAAG AGACCGAAAGACCCTTTAACT 863–891 1.000 67.9
atpH-atpI_p1 atpH-atpI AACAGAAGCGGCAGAAATCA TCCCTGTCATGTTCCTTGGA 1200–1219 1.000 82.8
atpH-atpI_p2 atpH-atpI CAGCAGCAATAACAGAAGCG TCCCTGTCATGTTCCTTGGA 1210–1229 1.000 82.2
atpH-atpI_p3 atpH-atpI TACCCTCTACAGCTTGACCC TCCCTGTCATGTTCCTTGGA 1285–1304 1.000 82.1
atpH-atpI_p4 atpH-atpI GCGATACCCTCTACAGCTTG TCCCTGTCATGTTCCTTGGA 1289–1308 1.000 82.1
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TCCCTGTCATGTTCCTTGGA 1217–1236 1.000 81.8
rps2-rpoC2_p1 rps2-rpoC2 AACTCCTGCCTCCATCATCT TTCGAGGGGGAAATGAGAGA 365–383 1.000 86.3
rps2-rpoC2_p2 rps2-rpoC2 TGCCTCCATCATCTCTTCCA TTCGAGGGGGAAATGAGAGA 359–377 1.000 86.3
rps2-rpoC2_p3 rps2-rpoC2 TCCTGCCTCCATCATCTCTT TTCGAGGGGGAAATGAGAGA 362–380 1.000 85.7
rps2-rpoC2_p4 rps2-rpoC2 GAACTCCTGCCTCCATCATC TTCGAGGGGGAAATGAGAGA 366–384 1.000 85.1
rps2-rpoC2_p5 rps2-rpoC2 CTCCTGCCTCCATCATCTCT TTCGAGGGGGAAATGAGAGA 363–381 1.000 84.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (19)

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

Species Accession Length (bp) Link
Chionanthus axillaris NC_042281.1 155550 View on NCBI ↗
Chionanthus brachystachys MK299388.1 155589 View on NCBI ↗
Chionanthus brassii NC_042282.1 155980 View on NCBI ↗
Chionanthus filiformis NC_042270.1 155853 View on NCBI ↗
Chionanthus implicatus NC_042283.1 155761 View on NCBI ↗
Chionanthus ligustrinus NC_042284.1 155912 View on NCBI ↗
Chionanthus macrobotrys NC_042384.1 154912 View on NCBI ↗
Chionanthus maxwellii NC_042385.1 155504 View on NCBI ↗
Chionanthus panamensis NC_042786.1 155812 View on NCBI ↗
Chionanthus parkinsonii NC_036979.1 155436 View on NCBI ↗
Chionanthus pedunculatus NC_042261.1 155578 View on NCBI ↗
Chionanthus polygamus NC_042386.1 155411 View on NCBI ↗
Chionanthus pubescens NC_042387.1 155800 View on NCBI ↗
Chionanthus quadristamineus NC_042373.1 155618 View on NCBI ↗
Chionanthus ramiflorus NC_042446.1 155649 View on NCBI ↗
Chionanthus retusus NC_035000.1 155687 View on NCBI ↗
Chionanthus rupicola NC_036980.1 155563 View on NCBI ↗
Chionanthus thorelii NC_042374.1 156057 View on NCBI ↗
Chionanthus virginicus NC_042447.1 155748 View on NCBI ↗