Markers + reference

Vepris

13 species · Rutaceae · Sapindales

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Species 13
Genome length 115–159 kb
Candidate markers 275
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 11 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 407 0.0688 0.99 75.1 yes View details
trnK-UUU-rps16 LSC 574 0.0223 0.99 76.8 yes View details
trnR-UCU-atpA LSC 224 0.0246 0.92 57.5 yes View details
atpF LSC 1379 0.0077 1.00 50.2 yes View details
rpoB-trnC-GCA LSC 1277 0.0164 0.99 65.7 yes View details
petN-psbM LSC 1327 0.0163 0.97 67.7 yes View details
accD-psaI LSC 755 0.0169 1.00 69.4 yes View details
ndhF SSC 2226 0.0071 1.00 44.1 yes View details
rpl32-trnL-UAG SSC 1046 0.0153 0.99 58.0 yes View details
rps15-ycf1 SSC 4779 0.0122 1.00 51.3 yes View details
atpF-atpH LSC 462 0.0159 1.00 68.8 yes View details
psaI-ycf4 LSC 440 0.0124 1.00 68.2 yes View details
atpA-atpF LSC 62 0.0516 1.00 68.1 yes View details
trnT-CGU-trnR-UCU LSC 174 0.0317 1.00 65.5 yes View details
psbB-psbT LSC 215 0.0283 1.00 64.8 yes View details
ycf1 IRb 1209 0.0080 0.99 63.9 yes View details
trnS-GCU-trnT-CGU LSC 984 0.0127 0.99 63.6 yes View details
petA-psbJ LSC 1088 0.0112 0.99 62.9 yes View details
trnD-GUC-trnY-GUA LSC 485 0.0167 0.99 62.4 yes View details
ndhG-ndhI SSC 386 0.0090 1.00 61.8 yes View details
ycf1 IRa 1107 0.0069 0.99 46.0 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 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 CAATCCACTGCCTTGATCCA AGCTGCTATTGAAGTTCCATCT 457–508 0.923 67.9
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGCTGCTATTGAAGTTCCATCT 456–507 0.923 67.8
trnH-GUG-psbA_p3 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGCTGCTATTGAAGTTCCATCT 458–509 0.923 67.8
trnH-GUG-psbA_p4 trnH-GUG-psbA CGCATGGTGGATTCACAATC AGCTGCTATTGAAGTTCCATCT 472–523 0.923 65.1
trnH-GUG-psbA_p5 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCTGCTATTGAAGTTCCATCT 456–507 0.923 64.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG ATTTCAAAGAAAGCGGGGGT 664–692 0.923 85.8
trnK-UUU-rps16_p2 trnK-UUU-rps16 CTCTCCCGAAGATTTGGACG ATTTCAAAGAAAGCGGGGGT 719–747 0.923 84.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATTTCAAAGAAAGCGGGGGT 653–681 0.923 84.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTCAAAGAAAGCGGGGGT 652–680 0.923 84.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 AGCCGTACTTAAAAGCCGAG CCAACCTACAGGAACCGTTC 689–717 0.923 84.0
trnS-GCU-trnT-CGU_p1 trnS-GCU-trnT-CGU CCGACGCTTTAATCCACTCA ACGAATCGCACTTTTACCACT 1049–1093 0.923 72.5
trnS-GCU-trnT-CGU_p2 trnS-GCU-trnT-CGU CCGACGCTTTAATCCACTCA ACGAATCGCACTTTTACCAC 1049–1093 0.923 72.4
trnS-GCU-trnT-CGU_p3 trnS-GCU-trnT-CGU ACGGAAAGAGAGGGATTCGA ACGAATCGCACTTTTACCACT 1107–1151 0.923 71.0
trnS-GCU-trnT-CGU_p4 trnS-GCU-trnT-CGU ACGGAAAGAGAGGGATTCGA ACGAATCGCACTTTTACCAC 1107–1151 0.923 71.0
trnS-GCU-trnT-CGU_p5 trnS-GCU-trnT-CGU ACGCTTTAATCCACTCAGCC ACGAATCGCACTTTTACCACT 1046–1090 0.923 70.5
trnT-CGU-trnR-UCU_p1 trnT-CGU-trnR-UCU AGCCTTCCAAGCTAACGATG TGGAAATCAATTGCGTCCAA 304–312 0.923 68.0
trnT-CGU-trnR-UCU_p2 trnT-CGU-trnR-UCU CCTAGCCTTCCAAGCTAACG TGGAAATCAATTGCGTCCAA 307–315 0.923 67.7
trnT-CGU-trnR-UCU_p3 trnT-CGU-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 257–265 0.923 66.8
trnT-CGU-trnR-UCU_p4 trnT-CGU-trnR-UCU AGCCTTCCAAGCTAACGATG ATGGAAATCAATTGCGTCCA 305–313 0.923 66.1
trnT-CGU-trnR-UCU_p5 trnT-CGU-trnR-UCU CCTAGCCTTCCAAGCTAACG ATGGAAATCAATTGCGTCCA 308–316 0.923 65.8
trnR-UCU-atpA_p1 trnR-UCU-atpA CTGAAAGGCGTCCATTGTCT TCAGGAACAAATGGAACGCT 317–394 0.923 81.1
trnR-UCU-atpA_p2 trnR-UCU-atpA ACTGAAAGGCGTCCATTGTC TCAGGAACAAATGGAACGCT 318–395 0.923 78.8
trnR-UCU-atpA_p3 trnR-UCU-atpA GACTGAAAGGCGTCCATTGT TCAGGAACAAATGGAACGCT 319–396 0.923 78.8
trnR-UCU-atpA_p4 trnR-UCU-atpA TTCGGAATGGGACTGAAAGG TCAGGAACAAATGGAACGCT 329–406 0.923 78.8
trnR-UCU-atpA_p5 trnR-UCU-atpA CTGAAAGGCGTCCATTGTCT TGGAACGCTTTCTACTTCAGG 306–383 0.923 75.1
atpA-atpF_p1 atpA-atpF AGCCTCGCTTACTGGTATCT CGGCCGCAAGATTCATTTTT 978–990 0.923 79.1
atpA-atpF_p2 atpA-atpF CCGTTTCGGCTACCACAATA CGGCCGCAAGATTCATTTTT 1354–1366 0.923 79.0
atpA-atpF_p3 atpA-atpF AGCCTCGCTTACTGGTATCT TGTTTGGGGCGATGAAAGAA 402–405 0.923 79.0
atpA-atpF_p4 atpA-atpF CCGTTTCGGCTACCACAATA TGTTTGGGGCGATGAAAGAA 778–781 0.923 78.5
atpA-atpF_p5 atpA-atpF CCGTTTCGGCTACCACAATA AGTCCTCCGAATATTCCGGT 1388–1400 0.923 78.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (13)

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

Species Accession Length (bp) Link
Vepris amaniensis PQ679356.1 159053 View on NCBI ↗
Vepris arushensis PV583365.1 158338 View on NCBI ↗
Vepris bachmannii PV583371.1 158954 View on NCBI ↗
Vepris eugeniifolia PV546309.1 158990 View on NCBI ↗
Vepris fadenii PV583366.1 159208 View on NCBI ↗
Vepris glomerata PV583367.1 158978 View on NCBI ↗
Vepris hanangensis PQ605431.1 158978 View on NCBI ↗
Vepris lanceolata PQ605430.1 159192 View on NCBI ↗
Vepris ngamensis PV583368.1 159067 View on NCBI ↗
Vepris nobilis PV583369.1 159184 View on NCBI ↗
Vepris robertsoniae PV693364.1 114584 View on NCBI ↗
Vepris simplicifolia PV555994.1 158814 View on NCBI ↗
Vepris uguenensis PV555993.1 159267 View on NCBI ↗