Markers + reference

Archiphysalis

2 species · Solanaceae · Solanales

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Species 2
Genome length 156–156 kb
Candidate markers 265
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 8 remaining regions by MarkerSeek score (out of 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1122 0.0018 1.00 59.8 yes View details
petN-psbM LSC 1114 0.0090 1.00 63.9 yes View details
psbM-trnD-GUC LSC 1080 0.0028 1.00 60.3 yes View details
trnE-UUC-trnT-GGU LSC 867 0.0023 1.00 60.1 yes View details
trnL-UAA-trnF-GAA LSC 571 0.0053 1.00 61.2 yes View details
petD LSC 1232 0.0016 1.00 59.7 yes View details
rpl16 LSC 1429 0.0014 1.00 59.6 yes View details
ycf1 IRb 1149 0.0009 1.00 59.3 yes View details
ndhF SSC 2223 0.0014 1.00 43.3 yes View details
ndhA SSC 2259 0.0022 1.00 58.4 yes View details
ycf1 SSC 5670 0.0014 1.00 53.3 no View details
petA-psbJ LSC 1079 0.0009 0.99 60.0 yes View details
rps16-trnQ-UUG LSC 1227 0.0008 0.99 59.9 yes View details
trnS-GCU-trnG-GCC LSC 614 0.0016 1.00 59.7 yes View details
ycf4-cemA LSC 755 0.0000 0.99 59.5 yes View details
ccsA SSC 951 0.0011 1.00 59.4 yes View details
ndhC-trnV-UAC LSC 1145 0.0009 1.00 59.3 yes View details
atpH-atpI LSC 1220 0.0008 1.00 59.2 yes View details
rbcL LSC 1434 0.0007 1.00 59.2 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
rps16_p1 rps16 ACAAATCACTACCCCCTTTT CATCAGCCCAACCAATGACT 1237 1.000 50.1
rps16_p2 rps16 ACAAATCACTACCCCCTTTTT CATCAGCCCAACCAATGACT 1237 1.000 49.0
rps16_p3 rps16 ACAAATCACTACCCCCTTTT ACATCAGCCCAACCAATGAC 1238 1.000 47.7
rps16_p4 rps16 AGAAAAGGAAAGGGAGGAAA CATCAGCCCAACCAATGACT 1296 1.000 46.9
rps16_p5 rps16 ACAAATCACTACCCCCTTTTT ACATCAGCCCAACCAATGAC 1238 1.000 46.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1308–1317 1.000 79.4
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1291–1300 1.000 78.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1309–1318 1.000 78.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1306–1315 1.000 77.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1305–1314 1.000 77.0
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA ACGAATCACACTTTTACCACT 688 1.000 51.5
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 737 1.000 50.6
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AGAACGAATCACACTTTTACCAC 691 1.000 50.5
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA GAACGAATCACACTTTTACCACT 690 1.000 50.5
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC ATTAGCAATCCGCCGCTTTA AACGAATCACACTTTTACCACT 689 1.000 49.6
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TACCTGTCATGCTCCTTGGA 1356–1363 1.000 79.4
atpH-atpI_p2 atpH-atpI TACCCTCTACAGCTTGACCC TACCTGTCATGCTCCTTGGA 1439–1446 1.000 78.6
atpH-atpI_p3 atpH-atpI GCGATACCCTCTACAGCTTG TACCTGTCATGCTCCTTGGA 1443–1450 1.000 78.5
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TACCTGTCATGCTCCTTGGA 1357–1364 1.000 78.2
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TACCTGTCATGCTCCTTGGA 1371–1378 1.000 78.0
petN-psbM_p1 petN-psbM TCTTGCTTGGGCTGCTTTAA AGTTCCTACCGCTTTTCTACT 1248 1.000 59.7
petN-psbM_p2 petN-psbM AGTAAGTCTTGCTTGGGCTG AGTTCCTACCGCTTTTCTACT 1254 1.000 58.2
petN-psbM_p3 petN-psbM GGGGAAGGAGTGGACTCTAG AGTTCCTACCGCTTTTCTACT 1192 1.000 58.0
petN-psbM_p4 petN-psbM TCTTGCTTGGGCTGCTTTAA AGTTCCTACCGCTTTTCTACTT 1248 1.000 57.5
petN-psbM_p5 petN-psbM TCTTGCTTGGGCTGCTTTAA TCTAGTTCCTACCGCTTTTCT 1251 1.000 57.5
psbM-trnD-GUC_p1 psbM-trnD-GUC AGTAGAAAAGCGGTAGGAACT CCCGTATTTCCCTGGGATTG 1235–1236 1.000 59.2
psbM-trnD-GUC_p2 psbM-trnD-GUC AGTAGAAAAGCGGTAGGAACT TCCCGTATTTCCCTGGGATT 1236–1237 1.000 58.5
psbM-trnD-GUC_p3 psbM-trnD-GUC AAGTAGAAAAGCGGTAGGAACT CCCGTATTTCCCTGGGATTG 1236–1237 1.000 57.0
psbM-trnD-GUC_p4 psbM-trnD-GUC AGAAAAGCGGTAGGAACTAGA CCCGTATTTCCCTGGGATTG 1232–1233 1.000 56.9
psbM-trnD-GUC_p5 psbM-trnD-GUC AAGTAGAAAAGCGGTAGGAACT TCCCGTATTTCCCTGGGATT 1237–1238 1.000 56.3

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
Archiphysalis chamaesarachoides PV472655.1 156345 View on NCBI ↗
Archiphysalis sinensis PV472654.1 156352 View on NCBI ↗