Markers + reference

Toona

7 species · Meliaceae · Sapindales

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Species 7
Genome length 157–160 kb
Candidate markers 279
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 10 remaining regions by MarkerSeek score (out of 279 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 442 0.0593 1.00 76.6 yes View details
trnK-UUU-rps16 LSC 784 0.0185 0.99 65.1 yes View details
trnS-GCU-trnG-UCC LSC 791 0.0081 0.97 51.3 yes View details
psbC-trnS-UGA LSC 237 0.0207 1.00 40.7 yes View details
ycf4-cemA LSC 942 0.0063 0.99 41.5 yes View details
psbE-petL LSC 1280 0.0060 1.00 38.5 yes View details
trnW-CCA-trnP-UGG LSC 175 0.0359 1.00 50.8 yes View details
trnP-GGG-psaJ LSC 363 0.0037 0.98 29.9 yes View details
rrn23 IRb 2810 0.0017 1.00 41.5 yes View details
ndhF-rpl32 SSC 984 0.0083 1.00 44.0 yes View details
rrn23 IRa 2810 0.0002 1.00 40.1 no View details
rps18-rpl20 LSC 258 0.0157 1.00 53.4 yes View details
petN-psbM LSC 1125 0.0028 0.98 53.0 yes View details
trnT-GGU-atpE LSC 259 0.0051 1.00 53.0 yes View details
ccsA-ndhD SSC 310 0.0120 1.00 52.4 yes View details
petB LSC 1462 0.0011 1.00 52.3 yes View details
clpP LSC 2102 0.0017 1.00 52.0 yes View details
trnL-CAA-ycf2 IRa 968 0.0025 1.00 51.6 yes View details
ndhB IRa 2214 0.0006 1.00 51.4 yes View details
ndhA SSC 2190 0.0020 1.00 51.1 yes View details
ndhB IRb 2214 0.0005 1.00 44.3 no 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 512–532 1.000 88.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 526–546 1.000 88.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 525–545 1.000 88.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 527–547 1.000 88.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 561–581 1.000 86.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG TCAAAGAAGGCAGGGGTTTT 864–1086 1.000 83.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG TTCAAAGAAGGCAGGGGTTT 865–1087 1.000 83.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG TTTCAAAGAAGGCAGGGGTT 866–1088 1.000 83.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG CAACCTACAGGAACCGTTCA 891–1113 1.000 82.4
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG ATTTCAAAGAAGGCAGGGGT 867–1089 1.000 81.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC TAAGCCACTCAGCCATCTCT AACTGAAGGACCCCTTAACT 695–885 1.000 66.1
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AACTGAAGGACCCCTTAACT 762–952 1.000 65.8
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC AAGATACCAAGCCATCGACG AACTGAAGGACCCCTTAACT 785–975 1.000 65.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC TAAGCCACTCAGCCATCTCT AAACTGAAGGACCCCTTAACT 696–886 1.000 64.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA AAACTGAAGGACCCCTTAACT 763–953 1.000 64.3
petN-psbM_p1 petN-psbM CTTGGGCCGCTTTAATGGTA TGCTACTGCACTGTTCATTCT 1168–1275 1.000 71.4
petN-psbM_p2 petN-psbM TTGGGCCGCTTTAATGGTAG TGCTACTGCACTGTTCATTCT 1167–1274 1.000 71.4
petN-psbM_p3 petN-psbM GGCCGCTTTAATGGTAGTCT TGCTACTGCACTGTTCATTCT 1164–1271 1.000 70.7
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT TGCTACTGCACTGTTCATTCT 1119–1226 1.000 70.5
petN-psbM_p5 petN-psbM GGGCCGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTCT 1165–1272 1.000 67.8
psbC-trnS-UGA_p1 psbC-trnS-UGA TCCATGACTCCTCTTAACTGA GGTTGATAGCTCCGGTCTTG 335 1.000 53.4
psbC-trnS-UGA_p2 psbC-trnS-UGA GTTCTTTCCATGACTCCTCT GGTTGATAGCTCCGGTCTTG 341 1.000 52.9
psbC-trnS-UGA_p3 psbC-trnS-UGA TCCATGACTCCTCTTAACTGA GATGGCCGAGTGGTTGATAG 346 1.000 52.7
psbC-trnS-UGA_p4 psbC-trnS-UGA TCCATGACTCCTCTTAACTGA GGGTTCGAATCCCTCTCTCT 281 1.000 52.6
psbC-trnS-UGA_p5 psbC-trnS-UGA GTTCTTTCCATGACTCCTCT GATGGCCGAGTGGTTGATAG 352 1.000 52.2
trnT-GGU-atpE_p1 trnT-GGU-atpE CATGTGATGTGATGGGTCCC CTCTCAGACGAGCTAGGACA 404–428 1.000 82.0
trnT-GGU-atpE_p2 trnT-GGU-atpE CCATGTGATGTGATGGGTCC CTCTCAGACGAGCTAGGACA 405–429 1.000 82.0
trnT-GGU-atpE_p3 trnT-GGU-atpE CATGTGATGTGATGGGTCCC GCTAGGACACGAGTAGAGGT 393–417 1.000 81.9
trnT-GGU-atpE_p4 trnT-GGU-atpE CCATGTGATGTGATGGGTCC GCTAGGACACGAGTAGAGGT 394–418 1.000 81.9
trnT-GGU-atpE_p5 trnT-GGU-atpE CATGTGATGTGATGGGTCCC CGAGCTAGGACACGAGTAGA 396–420 1.000 81.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Toona ciliata NC_039592.1 159502 View on NCBI ↗
Toona ciliata var. ciliata OP373439.1 159617 View on NCBI ↗
Toona ciliata var. henryi OP373441.1 159616 View on NCBI ↗
Toona ciliata var. pubescens OP373443.1 159615 View on NCBI ↗
Toona ciliata var. yunnanensis OP373445.1 159546 View on NCBI ↗
Toona fargesii NC_069639.1 159583 View on NCBI ↗
Toona sinensis NC_059806.1 157228 View on NCBI ↗