Markers + reference

Pternopetalum

2 species · Apiaceae · Apiales

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Species 2
Genome length 155–156 kb
Candidate markers 271
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1405 0.0214 1.00 61.3 yes View details
psbK-psbI LSC 424 0.0251 0.94 63.6 yes View details
rpoB-trnC-GCA LSC 1208 0.0182 1.00 64.2 yes View details
petN-psbM LSC 1097 0.0202 0.99 60.5 yes View details
psaA-ycf3 LSC 700 0.0186 1.00 60.4 yes View details
ndhC-trnV-UAC LSC 1094 0.0220 1.00 59.5 yes View details
petB LSC 1397 0.0122 1.00 61.1 yes View details
ycf1 IRb 2553 0.0038 0.73 44.7 no View details
ndhF-rpl32 SSC 1085 0.0213 1.00 67.4 yes View details
ccsA SSC 975 0.0072 1.00 48.3 yes View details
ndhG-ndhI SSC 349 0.0264 0.98 57.9 yes View details
ycf1 SSC 5406 0.0118 1.00 46.9 yes View details
trnL-UAG-ccsA SSC 102 0.0588 1.00 75.9 yes View details
trnS-GGA-rps4 LSC 312 0.0233 0.96 69.8 yes View details
trnD-GUC-trnY-GUA LSC 121 0.0354 0.93 69.1 yes View details
ycf4-cemA LSC 686 0.0148 0.99 68.5 yes View details
ndhK-ndhC LSC 49 0.0408 1.00 65.7 yes View details
trnE-UUC-trnT-GGU LSC 735 0.0195 0.98 63.4 yes View details
clpP-psbB LSC 460 0.0110 0.99 63.4 yes View details
trnT-UGU-trnL-UAA LSC 746 0.0111 0.97 63.1 yes View details
rps7-rps12 IRb 55 0.0182 1.00 63.0 yes View details
rps12-rps7 IRa 55 0.0182 1.00 63.0 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT AAATATAGATGGGGCGTGGC 1524–1547 1.000 79.7
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT AAATATAGATGGGGCGTGGC 1525–1548 1.000 79.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA AAATATAGATGGGGCGTGGC 1535–1558 1.000 78.8
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC AAATATAGATGGGGCGTGGC 1550–1573 1.000 77.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG AAATATAGATGGGGCGTGGC 1549–1572 1.000 77.0
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGAAAAGTTTGAGAGTAAGCA 452–477 1.000 55.2
psbK-psbI_p2 psbK-psbI TGGCAAGCTGCTGTAAGTTT ACGAAAAGTTTGAGAGTAAGCA 449–474 1.000 53.2
psbK-psbI_p3 psbK-psbI TTGGCAAGCTGCTGTAAGTT ACGAAAAGTTTGAGAGTAAGCA 450–475 1.000 53.2
psbK-psbI_p4 psbK-psbI TTTGGCAAGCTGCTGTAAGT ACGAAAAGTTTGAGAGTAAGCA 451–476 1.000 53.2
psbK-psbI_p5 psbK-psbI GTTTGGCAAGCTGCTGTAAG AACGAAAAGTTTGAGAGTAAGCA 453–478 1.000 52.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA CTTACCACTCGGCCATATCG 1254–1266 1.000 79.5
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TCCCTCATTTCCATCTCGGA CCGGATTTGAACTGGGGAAA 1294–1306 1.000 79.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA AGCCCTGATCCATGAACCTA CTTACCACTCGGCCATATCG 1321–1333 1.000 79.2
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AGCCCTGATCCATGAACCTA CCGGATTTGAACTGGGGAAA 1361–1373 1.000 79.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCCCTGATCCATGAACCTAC CTTACCACTCGGCCATATCG 1320–1332 1.000 78.7
petN-psbM_p1 petN-psbM ATGGGGAAGAAGTGGACTCT GCTTTTCTGCTTATCATTTATGT 1179–1189 1.000 42.0
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT GCTTTTCTGCTTATCATTTATGT 1240–1250 1.000 41.9
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC GCTTTTCTGCTTATCATTTATGT 1241–1251 1.000 41.9
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT GCTTTTCTGCTTATCATTTATGT 1232–1242 1.000 41.9
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC GCTTTTCTGCTTATCATTTATGT 1226–1236 1.000 41.9
trnD-GUC-trnY-GUA_p1 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA TGGCAATATGTCTACGCTGG 183–191 1.000 79.4
trnD-GUC-trnY-GUA_p2 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGCAATATGTCTACGCTGGT 182–190 1.000 79.4
trnD-GUC-trnY-GUA_p3 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGGACGGACTGTAAATTCG 204–212 1.000 78.0
trnD-GUC-trnY-GUA_p4 trnD-GUC-trnY-GUA CGGTGCTCTGACCAATTGAA GGGACGGACTGTAAATTCGT 203–211 1.000 77.8
trnD-GUC-trnY-GUA_p5 trnD-GUC-trnY-GUA TTGAATCTGTCGGGACTGAC TGGCAATATGTCTACGCTGG 237–245 1.000 76.1
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 822–839 1.000 81.6
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TACCGCTGAGTTAAAAGGGC 787–804 1.000 80.9
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 819–836 1.000 80.4
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA AGCTAAAGCCCCTTATCGGA 845–862 1.000 80.0
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TTGAACCGATGACTTACGCC 824–841 1.000 79.4

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
Pternopetalum davidii NC_057228.1 155533 View on NCBI ↗
Pternopetalum vulgare MT561032.1 154730 View on NCBI ↗