Markers + reference

Physochlaina

3 species · Solanaceae · Solanales

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Species 3
Genome length 156–156 kb
Candidate markers 270
Primer pairs 105

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 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 426 0.0230 0.99 66.8 yes View details
trnK-UUU-rps16 LSC 692 0.0077 1.00 64.0 yes View details
rps16 LSC 1088 0.0043 1.00 46.8 yes View details
rps16-trnQ-UUG LSC 1200 0.0089 1.00 64.5 yes View details
ycf3-trnS-GGA LSC 837 0.0096 1.00 65.1 yes View details
ndhC-trnV-UAC LSC 1094 0.0067 1.00 52.1 yes View details
petA-psbJ LSC 1074 0.0109 1.00 52.9 yes View details
rpl36-rps8 LSC 450 0.0207 1.00 59.0 yes View details
ndhF-rpl32 SSC 763 0.0061 1.00 52.5 yes View details
ccsA SSC 942 0.0042 1.00 47.6 yes View details
ycf1 SSC 5700 0.0029 0.99 52.8 yes View details
psaA-ycf3 LSC 789 0.0026 0.99 62.2 yes View details
trnL-UAA-trnF-GAA LSC 362 0.0074 1.00 62.0 yes View details
trnE-UUC-trnT-GGU LSC 846 0.0047 1.00 61.8 yes View details
atpB-rbcL LSC 773 0.0043 1.00 61.6 yes View details
atpH-atpI LSC 1142 0.0029 1.00 60.9 yes View details
trnT-UGU-trnL-UAA LSC 708 0.0028 1.00 60.6 yes View details
rrn16 IRa 1500 0.0027 1.00 60.5 yes View details
accD LSC 1515 0.0026 1.00 60.4 yes View details
rrn16 IRb 1500 0.0027 1.00 60.4 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 105 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 474–495 1.000 84.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA TTCCCTCTAGACCTAGCTGC 488–509 1.000 84.1
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC TTCCCTCTAGACCTAGCTGC 487–508 1.000 84.1
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC TTCCCTCTAGACCTAGCTGC 489–510 1.000 84.1
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCGTGCTAACCTTGGTATGG 523–544 1.000 81.6
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT TTGAAAAAGGGGCTCAACCT 822–825 1.000 75.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTGAAAAAGGGGCTCAACCT 821–824 1.000 75.9
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGTCGTGGTCTTCCAAAC TTGAAAAAGGGGCTCAACCT 907–910 1.000 75.2
trnK-UUU-rps16_p4 trnK-UUU-rps16 CAGTCGTGGTCTTCCAAACT TTGAAAAAGGGGCTCAACCT 906–909 1.000 75.2
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAAAGACACTAGCCGCACTT TTGAAAAAGGGGCTCAACCT 843–846 1.000 75.1
rps16_p1 rps16 ACTTGTGTTGGATTGGCACT TGGGAAGGCGTTCATTTCAA 2211–2225 1.000 80.2
rps16_p2 rps16 ACTTGTGTTGGATTGGCACT AACGGTGACAATTGCTCAGT 2183–2197 1.000 80.1
rps16_p3 rps16 ACTTGTGTTGGATTGGCACT TGAGTCACGTGAAGATGCAG 1766–1779 1.000 79.6
rps16_p4 rps16 ACTTGTGTTGGATTGGCACT CAGTAATGGGAAGGCGTTCA 2217–2231 1.000 79.5
rps16_p5 rps16 AAGCCGAGTACTCTACCGTT TGGGAAGGCGTTCATTTCAA 2524–2536 1.000 79.5
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AACGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1290–1312 1.000 79.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1273–1295 1.000 79.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CAACGGATCGTGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1291–1313 1.000 78.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1288–1310 1.000 77.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1287–1309 1.000 77.5
trnG-UCC_p1 trnG-UCC CCAATTCCCCTGTTCGACAA TGGATGTGAAAGAATTTTTGGA 922–924 1.000 40.4
trnG-UCC_p2 trnG-UCC CCCTGTTCGACAAAAGTTGC TGGATGTGAAAGAATTTTTGGA 915–917 1.000 40.4
trnG-UCC_p3 trnG-UCC CCAATTCCCCTGTTCGACAA TGGATGTGAAAGAATTTTTGGAA 922–924 1.000 40.4
trnG-UCC_p4 trnG-UCC CCAATTCCCCTGTTCGACAA TTGGATGTGAAAGAATTTTTGGA 923–925 1.000 40.4
trnG-UCC_p5 trnG-UCC CCCTGTTCGACAAAAGTTGC TGGATGTGAAAGAATTTTTGGAA 915–917 1.000 40.4
atpH-atpI_p1 atpH-atpI GGCAGAAACCAGTGGATTCA TACCTGTCATGCTCCTTGGA 1264–1272 1.000 79.4
atpH-atpI_p2 atpH-atpI TACCCTCTACAGCTTGACCC TACCTGTCATGCTCCTTGGA 1358–1366 1.000 79.0
atpH-atpI_p3 atpH-atpI GCGATACCCTCTACAGCTTG TACCTGTCATGCTCCTTGGA 1362–1370 1.000 78.9
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA TACCTGTCATGCTCCTTGGA 1276–1284 1.000 78.6
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC TACCTGTCATGCTCCTTGGA 1290–1298 1.000 78.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Physochlaina infundibularis PP056243.1 156340 View on NCBI ↗
Physochlaina orientalis NC_044154.1 156321 View on NCBI ↗
Physochlaina physaloides MN262642.1 156413 View on NCBI ↗