Markers + reference

Schweinfurthia

2 species · Plantaginaceae · Lamiales

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Species 2
Genome length 153–153 kb
Candidate markers 267
Primer pairs 80

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 7 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1168 0.0009 1.00 59.2 yes View details
rps16-trnQ-UUG LSC 738 0.0014 1.00 58.3 yes View details
petA-psbJ LSC 1023 0.0010 1.00 59.3 yes View details
rps19 LSC 279 0.0108 1.00 58.7 yes View details
ycf2 IRb 6846 0.0001 1.00 52.6 yes View details
ycf1 IRb 1068 0.0000 1.00 40.0 no View details
ccsA-ndhD SSC 245 0.0000 1.00 19.3 yes View details
ndhD SSC 1530 0.0007 1.00 59.1 yes View details
ycf1 SSC 5535 0.0002 1.00 52.6 yes View details
ycf2 IRa 6846 0.0001 1.00 52.6 yes View details
atpF LSC 1251 0.0000 1.00 58.9 yes View details
ycf3 LSC 1954 0.0000 1.00 57.9 yes View details
clpP1 LSC 1981 0.0000 1.00 57.8 yes View details
psbI-trnS-GCU LSC 122 0.0000 0.99 53.3 yes View details
rps18-rpl20 LSC 240 0.0000 1.00 52.9 yes View details
rpl22-rps19 LSC 62 0.0000 0.98 40.1 yes View details
psbA LSC 1059 0.0000 1.00 40.0 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbA_p1 psbA GGAGCAATAACCCCTCTTGA AAATTCGTGTGCTTGGGAGT 1207 1.000 71.0
psbA_p2 psbA AGGAGCAATAACCCCTCTTG AAATTCGTGTGCTTGGGAGT 1208 1.000 71.0
psbA_p3 psbA AAGGAGCAATAACCCCTCTTG AAATTCGTGTGCTTGGGAGT 1209 1.000 68.9
psbA_p4 psbA AGGAGCAATAACCCCTCTTGA AAATTCGTGTGCTTGGGAGT 1208 1.000 68.3
psbA_p5 psbA GGAGCAATAACCCCTCTTGA AATTCGTGTGCTTGGGAGTC 1206 1.000 67.4
rps16_p1 rps16 TCTATACAAGTTGCTACCCCC TGTACAACCGAACCAATGACT 1279 1.000 48.3
rps16_p2 rps16 TTCTATACAAGTTGCTACCCCC TGTACAACCGAACCAATGACT 1280 1.000 46.1
rps16_p3 rps16 TCTATACAAGTTGCTACCCCC TGTACAACCGAACCAATGAC 1279 1.000 44.1
rps16_p4 rps16 TCTATACAAGTTGCTACCCCC ATGTACAACCGAACCAATGACT 1280 1.000 44.0
rps16_p5 rps16 CTATACAAGTTGCTACCCCC TGTACAACCGAACCAATGACT 1278 1.000 43.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CCACAACGGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 832 1.000 78.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG CCACAACGGATCATGTCCTT CGAAATTGAAATGGGGCGTC 891 1.000 78.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAACGGATCATGTCCTT GAAATTGAAATGGGGCGTCG 890 1.000 78.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 811 1.000 78.4
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAAATTGAAATGGGGCGTCG 869 1.000 78.2
psbI-trnS-GCU_p1 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA TGGACTAAAGCGTCGGATTG 234–235 1.000 79.8
psbI-trnS-GCU_p2 psbI-trnS-GCU TATCTAATGATCCGGGGCGT TGGACTAAAGCGTCGGATTG 235–236 1.000 79.8
psbI-trnS-GCU_p3 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA GTGGACTAAAGCGTCGGATT 235–236 1.000 79.8
psbI-trnS-GCU_p4 psbI-trnS-GCU TATCTAATGATCCGGGGCGT GTGGACTAAAGCGTCGGATT 236–237 1.000 79.8
psbI-trnS-GCU_p5 psbI-trnS-GCU ATCTAATGATCCGGGGCGTA ATTGGGAGAGATGGCTGAGT 253–254 1.000 78.9
atpF_p1 atpF GGCTCGAATGGTTACCATGA AAGAGGGGCAAAGTAATAGA 1397–1399 1.000 40.1
atpF_p2 atpF GGCTCGAATGGTTACCATGA AGAGGGGCAAAGTAATAGAA 1396–1398 1.000 40.1
atpF_p3 atpF GGCTCGAATGGTTACCATGA AAAGAGGGGCAAAGTAATAGA 1398–1400 1.000 40.1
atpF_p4 atpF GGCTCGAATGGTTACCATGA AAGAGGGGCAAAGTAATAGAA 1397–1399 1.000 40.1
atpF_p5 atpF GGCTCGAATGGTTACCATGA AGAGGGGCAAAGTAATAGAAA 1396–1398 1.000 40.1
ycf3_p1 ycf3 ACAAAGAGACCTGCCAACAG TCGGAATAGTTGCCTTCGTT 2915–2943 1.000 73.8
ycf3_p2 ycf3 CAAAGAGACCTGCCAACAGT TCGGAATAGTTGCCTTCGTT 2914–2942 1.000 73.8
ycf3_p3 ycf3 AATTAAAAATCACGCGCGCA TCGGAATAGTTGCCTTCGTT 2626–2654 1.000 73.8
ycf3_p4 ycf3 TTAAAAATCACGCGCGCATT TCGGAATAGTTGCCTTCGTT 2624–2652 1.000 73.8
ycf3_p5 ycf3 GAGACCTGCCAACAGTCAAA TCGGAATAGTTGCCTTCGTT 2910–2938 1.000 73.7

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
Schweinfurthia imbricata PV137603.1 153206 View on NCBI ↗
Schweinfurthia papilionacea PV097193.1 153238 View on NCBI ↗