Markers + reference

Commiphora

5 species · Burseraceae · Sapindales

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Species 5
Genome length 159–160 kb
Candidate markers 275
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 13 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 419 0.0311 0.98 70.6 yes View details
rpoB LSC 3213 0.0105 1.00 50.2 yes View details
petN-psbM LSC 600 0.0312 1.00 67.8 yes View details
psbC LSC 1422 0.0110 1.00 46.0 yes View details
trnN-GUU-ndhF IRb 1456 0.0193 1.00 62.0 yes View details
ccsA SSC 969 0.0083 1.00 53.2 yes View details
ndhH SSC 1182 0.0188 1.00 64.3 yes View details
ycf1 SSC 4155 0.0111 1.00 52.5 yes View details
ndhD-psaC SSC 149 0.0517 1.00 72.8 yes View details
ndhK-ndhC LSC 61 0.0377 1.00 71.1 yes View details
atpF-atpH LSC 536 0.0087 0.99 69.4 yes View details
trnD-GUC-trnY-GUA LSC 494 0.0092 0.99 68.2 yes View details
petA-psbJ LSC 1120 0.0071 1.00 66.5 yes View details
ndhC-trnV-UAC LSC 942 0.0074 1.00 66.4 yes View details
trnK-UUU-rps16 LSC 1060 0.0072 0.99 64.5 yes View details
trnT-UGU-trnL-UAA LSC 902 0.0077 1.00 63.2 yes View details
rrn16S IRa 1500 0.0048 1.00 62.6 yes View details
ccsA-ndhD SSC 316 0.0234 1.00 61.8 yes View details
rrn16S IRb 1500 0.0032 1.00 61.2 no View details
rrn16S IRb 1491 0.0000 1.00 28.5 no View details
rrn16S IRa 1491 0.0000 1.00 28.5 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 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 GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 479–487 1.000 83.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 493–501 1.000 83.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 492–500 1.000 83.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 494–502 1.000 83.3
trnH-GUG-psbA_p5 trnH-GUG-psbA ATGGTAGTTATGGGCGAACG TTCCCTCTAGACCTAGCTGC 544–552 1.000 82.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCGATGGTATGGACGAATC ATCTTTCCTTGAAAGGGGCG 1257–1336 1.000 79.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC ATCTTTCCTTGAAAGGGGCG 1256–1335 1.000 79.5
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATCTTTCCTTGAAAGGGGCG 1195–1274 1.000 78.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATCTTTCCTTGAAAGGGGCG 1194–1273 1.000 78.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA ATCTTTCCTTGAAAGGGGCG 1204–1283 1.000 78.0
atpF-atpH_p1 atpF-atpH CCAGTGAACCAAGGAAACGA CCGAGGCAGAGGGAAAAATA 677–704 1.000 78.3
atpF-atpH_p2 atpF-atpH CCAGTGAACCAAGGAAACGA TGGACTGGTTGTAGCATTAGC 607–634 1.000 76.3
atpF-atpH_p3 atpF-atpH CCAGTGAACCAAGGAAACGA GCAGAGGGAAAAATACGAGGT 672–699 1.000 75.9
atpF-atpH_p4 atpF-atpH CAAATGGCCAGTGAACCAAG CCGAGGCAGAGGGAAAAATA 684–711 1.000 75.0
atpF-atpH_p5 atpF-atpH CCAGTGAACCAAGGAAACGA GAGGCAGAGGGAAAAATACGA 675–702 1.000 73.9
rpoB_p1 rpoB GATACCGGGGCTTTGCAATA TCACTCACGTATTCTTCCGA 180 1.000 69.0
rpoB_p2 rpoB CGAAAGCCCATTATGGTCCA TCACTCACGTATTCTTCCGA 216 1.000 67.9
rpoB_p3 rpoB ACCGAAAGCCCATTATGGTC TCACTCACGTATTCTTCCGA 218 1.000 67.9
rpoB_p4 rpoB GATACCGGGGCTTTGCAATA TCACTCACGTATTCTTCCGAA 180 1.000 67.1
rpoB_p5 rpoB AATAGATACCGGGGCTTTGC TCACTCACGTATTCTTCCGA 184 1.000 66.9
petN-psbM_p1 petN-psbM GCAAAGGTCTTGGGTCAGAA ATGGTTGTACAAGGAAGGCG 1260–1567 1.000 81.4
petN-psbM_p2 petN-psbM TTCAGCAAAGGTCTTGGGTC ATGGTTGTACAAGGAAGGCG 1264–1571 1.000 81.4
petN-psbM_p3 petN-psbM GACGTGACTGCGTATCTTGT ATGGTTGTACAAGGAAGGCG 1349–1656 1.000 81.2
petN-psbM_p4 petN-psbM TAGTAAGTCTCGCTTGGGCT ATGGTTGTACAAGGAAGGCG 1138–1444 1.000 80.6
petN-psbM_p5 petN-psbM TGAAAGTCTCTGAGTGCACG ATGGTTGTACAAGGAAGGCG 1522–1830 1.000 80.0
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TTTTCTTCCTGGGTCGATGC 574–618 1.000 79.9
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 520–564 1.000 79.6
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 519–563 1.000 79.6
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 541–585 1.000 78.6
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 540–584 1.000 78.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Commiphora edulis subsp. holosericea OQ740737.1 159232 View on NCBI ↗
Commiphora foliacea NC_041103.1 160249 View on NCBI ↗
Commiphora gileadensis NC_041104.1 160268 View on NCBI ↗
Commiphora madagascariensis PP833220.1 159552 View on NCBI ↗
Commiphora tetramera OQ740738.1 159740 View on NCBI ↗