Markers + reference

Ruta

2 species · Rutaceae · Sapindales

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Species 2
Genome length 157–158 kb
Candidate markers 274
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 274 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 333 0.0396 0.98 69.6 yes View details
rps16-trnQ-UUG LSC 710 0.0183 1.00 67.2 yes View details
trnS-GCU-trnG-UCC LSC 835 0.0192 1.00 58.9 yes View details
rpoB-trnC-GCA LSC 1254 0.0216 0.96 74.8 yes View details
trnE-UUC-trnT-GGU LSC 849 0.0212 1.00 70.9 yes View details
psbZ-trnG-GCC LSC 548 0.0172 0.95 62.5 yes View details
rpl32-trnL-UAG SSC 881 0.0328 0.97 72.2 yes View details
trnR-UCU-atpA LSC 218 0.0193 0.95 68.2 yes View details
atpI-rps2 LSC 233 0.0258 1.00 67.3 yes View details
petA-psbJ LSC 1075 0.0113 0.98 66.8 yes View details
ndhK-ndhC LSC 70 0.0351 0.81 65.3 yes View details
psbT-pbf1 LSC 72 0.0417 1.00 65.3 yes View details
rpl14-rpl16 LSC 128 0.0397 0.98 64.0 yes View details
petL-petG LSC 181 0.0223 0.99 63.9 yes View details
psbK-psbI LSC 414 0.0152 0.96 63.6 yes View details
trnD-GUC-trnY-GUA LSC 468 0.0171 1.00 63.4 yes View details
rps7-rps12 IRb 53 0.0189 1.00 63.3 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 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 403–409 1.000 81.9
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 417–423 1.000 81.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 416–422 1.000 81.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 418–424 1.000 81.7
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC TTCCCTCTAGACCTAGCTGC 432–438 1.000 78.9
trnK-UUU_p1 trnK-UUU TATCTCCGTGTCAACCGCTA TGATCAGGGCTAAATGGACC 2869 1.000 71.0
trnK-UUU_p2 trnK-UUU GGGACTCCCAAGCATACAAA TGATCAGGGCTAAATGGACC 2943 1.000 68.9
trnK-UUU_p3 trnK-UUU TATCTCCGTGTCAACCGCTA TTGATCAGGGCTAAATGGACC 2870 1.000 68.9
trnK-UUU_p4 trnK-UUU CCGTGTCAACCGCTAATGTA TGATCAGGGCTAAATGGACC 2864 0.500 51.8
trnK-UUU_p5 trnK-UUU CCGTGTCAACCGCTAATGTA TTGATCAGGGCTAAATGGACC 2865 0.500 49.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 801–804 1.000 80.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 799–802 1.000 80.6
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GAAATTGAAATGGGGCGTCG 859–862 1.000 80.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT GAAATTGAAATGGGGCGTCG 857–860 1.000 80.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 783–786 1.000 79.7
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG CGCCCTGGATCATTAGACAG 515–533 1.000 81.9
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT CGCCCTGGATCATTAGACAG 512–530 1.000 79.9
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT CGCCCTGGATCATTAGACAG 513–531 1.000 79.9
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT CGCCCTGGATCATTAGACAG 514–532 1.000 79.9
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGCCCTGGATCATTAGACA 516–534 1.000 79.2
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA TGAACGAATCACACTTTTACCAC 903–922 1.000 54.2
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA ACGAATCACACTTTTACCACT 900–919 1.000 53.3
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CCGACGCTTTAATCCACTCA GAACGAATCACACTTTTACCACT 902–921 1.000 52.2
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC ACGCTTTAATCCACTCAGCC TGAACGAATCACACTTTTACCAC 900–919 1.000 52.2
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC CGCTTTAATCCACTCAGCCA TGAACGAATCACACTTTTACCAC 899–918 1.000 52.2
trnG-UCC_p1 trnG-UCC GCACAAGGACTCCTGACAAA TGTCATTAATGCATCGCCGA 1011–1019 1.000 81.3
trnG-UCC_p2 trnG-UCC GGACTCCTGACAAAGACGTC TGTCATTAATGCATCGCCGA 1005–1013 1.000 81.0
trnG-UCC_p3 trnG-UCC GCACAAGGACTCCTGACAAA AATGGACGCCTTTGACCATT 1148–1156 1.000 80.9
trnG-UCC_p4 trnG-UCC GGACTCCTGACAAAGACGTC AATGGACGCCTTTGACCATT 1142–1150 1.000 80.6
trnG-UCC_p5 trnG-UCC CTCCTCCTTTCCGAATTGCA TGTCATTAATGCATCGCCGA 1028–1036 1.000 80.6

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
Ruta chalepensis NC_066007.1 158003 View on NCBI ↗
Ruta graveolens NC_045946.1 157434 View on NCBI ↗