Markers + reference

Acronychia

2 species · Rutaceae · Sapindales

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Species 2
Genome length 158–158 kb
Candidate markers 272
Primer pairs 100

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 8 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 353 0.0567 1.00 83.2 yes View details
trnS-GCU-trnG-UCC LSC 961 0.0063 0.99 49.9 yes View details
rpoC2 LSC 4206 0.0057 1.00 42.1 yes View details
petN-psbM LSC 1277 0.0104 0.97 66.9 yes View details
rps14 LSC 303 0.0033 1.00 43.0 yes View details
accD-psaI LSC 735 0.0150 1.00 67.8 yes View details
psbE-petL LSC 1380 0.0029 1.00 55.8 yes View details
petL-petG LSC 190 0.0526 1.00 71.0 yes View details
petD LSC 1195 0.0109 1.00 57.4 yes View details
rpl32-trnL-UAG SSC 992 0.0121 1.00 54.4 yes View details
ycf1 SSC 5478 0.0080 1.00 43.7 yes View details
trnfM-CAU-rps14 LSC 180 0.0303 0.92 66.8 yes View details
petA-psbJ LSC 1059 0.0076 1.00 63.1 yes View details
psaI-ycf4 LSC 468 0.0067 0.96 62.8 yes View details
petB LSC 1395 0.0057 1.00 62.0 yes View details
atpB-rbcL LSC 765 0.0052 1.00 61.8 yes View details
trnT-GGU-psbD LSC 1262 0.0048 1.00 61.6 yes View details
trnI-GAU-trnA-UGC IRb 64 0.0156 1.00 61.5 yes View details
trnA-UGC-trnI-GAU IRa 64 0.0156 1.00 61.5 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 100 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 CGTGCTAACCTTGGTATGGA 478–479 1.000 76.8
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TCGTGCTAACCTTGGTATGG 479–480 1.000 76.8
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC CGTGCTAACCTTGGTATGGA 479–480 1.000 76.6
trnH-GUG-psbA_p4 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TCGTGCTAACCTTGGTATGG 480–481 1.000 76.6
trnH-GUG-psbA_p5 trnH-GUG-psbA CAACCCACTGCCTTAATCCA CGTGCTAACCTTGGTATGGA 485–486 1.000 76.1
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA TACCACTAAACTATACCCGC 1006–1012 1.000 48.8
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA TTACCACTAAACTATACCCGC 1007–1013 1.000 47.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA TACCACTAAACTATACCCGC 1064–1070 1.000 47.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGCTTTAATCCACTCAGCC TACCACTAAACTATACCCGC 1003–1009 1.000 46.8
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGCTTTAATCCACTCAGCCA TACCACTAAACTATACCCGC 1002–1008 1.000 46.8
trnG-UCC_p1 trnG-UCC TCCGATTCTCTTGTTCGACA TGGCGATGCATTAAGGAAAC 940 1.000 60.1
trnG-UCC_p2 trnG-UCC TCCGATTCTCTTGTTCGACAA TGGCGATGCATTAAGGAAAC 940 1.000 58.0
trnG-UCC_p3 trnG-UCC TCCGATTCTCTTGTTCGACA TTGGCGATGCATTAAGGAAAC 941 1.000 57.9
trnG-UCC_p4 trnG-UCC ACATCCGATTCTCTTGTTCGA TGGCGATGCATTAAGGAAAC 943 1.000 56.3
trnG-UCC_p5 trnG-UCC ATCCGATTCTCTTGTTCGACA TGGCGATGCATTAAGGAAAC 941 1.000 56.3
rpoC2_p1 rpoC2 AGAATGGTGTTATGCTGCCT AGTTTTCAAGAAACCACGCG 161 1.000 72.2
rpoC2_p2 rpoC2 AAGAATGGTGTTATGCTGCCT AGTTTTCAAGAAACCACGCG 162 1.000 70.0
rpoC2_p3 rpoC2 AGAATGGTGTTATGCTGCCTT AGTTTTCAAGAAACCACGCG 161 1.000 70.0
rpoC2_p4 rpoC2 AGAATGGTGTTATGCTGCCT AAGTTTTCAAGAAACCACGCG 162 1.000 66.3
rpoC2_p5 rpoC2 GAATGGTGTTATGCTGCCTT AGTTTTCAAGAAACCACGCG 160 1.000 65.8
petN-psbM_p1 petN-psbM ACATTTTCCCTTTCGCTCGT TCGTTCTAGTTCCTACTGCCT 1356–1387 1.000 73.2
petN-psbM_p2 petN-psbM CTTTCGCTCGTAGTATGGGG TCGTTCTAGTTCCTACTGCCT 1347–1378 1.000 73.0
petN-psbM_p3 petN-psbM CCCTTTCGCTCGTAGTATGG TCGTTCTAGTTCCTACTGCCT 1349–1380 1.000 72.9
petN-psbM_p4 petN-psbM CCTTTCGCTCGTAGTATGGG TCGTTCTAGTTCCTACTGCCT 1348–1379 1.000 72.9
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT TCGTTCTAGTTCCTACTGCCT 1394–1425 1.000 72.7
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG AAAAACGAATCGGTCCCTCC 1410–1425 1.000 78.5
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA AAAAACGAATCGGTCCCTCC 1413–1428 1.000 78.3
trnT-GGU-psbD_p3 trnT-GGU-psbD TCCGTCTAGTGACTCCTTCC AAAAACGAATCGGTCCCTCC 1460–1475 1.000 78.0
trnT-GGU-psbD_p4 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG GACCGGACCAACCTACAAAA 1426–1441 1.000 77.9
trnT-GGU-psbD_p5 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG ACAAAAACGAATCGGTCCCT 1412–1427 1.000 77.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (2)

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

Species Accession Length (bp) Link
Acronychia laevis NC_081864.1 158267 View on NCBI ↗
Acronychia pedunculata MW542636.1 158058 View on NCBI ↗