Markers + reference

Pterocyclus

4 species · Apiaceae · Apiales

Back to catalogue

Species 4
Genome length 156–158 kb
Candidate markers 267
Primer pairs 95

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

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 375 0.0124 1.00 54.6 yes View details
trnK-UUU-rps16 LSC 883 0.0408 0.99 78.7 yes View details
rpoC1 LSC 2803 0.0049 1.00 46.6 yes View details
petN-psbM LSC 1384 0.0207 0.69 53.8 yes View details
psbM-trnD-GUC LSC 707 0.0116 1.00 60.2 yes View details
petB LSC 1398 0.0079 1.00 51.0 yes View details
ndhF SSC 2247 0.0037 1.00 45.2 yes View details
rpl32-trnL-UAG SSC 986 0.0137 0.97 67.8 yes View details
ndhG-ndhI SSC 452 0.0281 0.98 63.7 yes View details
ycf1 SSC 5475 0.0068 1.00 44.3 yes View details
rpl2-trnH-GUG LSC 202 0.3020 0.25 73.1 no View details
ndhF-rpl32 SSC 1205 0.0082 1.00 68.2 yes View details
psbT-psbN LSC 86 0.0291 1.00 66.2 yes View details
trnE-UUC-trnT-GGU LSC 855 0.0058 0.99 65.4 yes View details
psbA-trnK-UUU LSC 214 0.0142 0.99 61.7 yes View details
trnF-GAA-ndhJ LSC 370 0.0099 1.00 61.1 yes View details
ndhC-trnV-UAC LSC 1169 0.0067 1.00 60.7 yes View details
rps12-clpP LSC 155 0.0162 0.99 60.5 yes View details
trnG-UCC-trnR-UCU LSC 215 0.0124 0.96 60.4 yes View details
ndhH SSC 1182 0.0021 1.00 60.2 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
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGCGCTAATCTTGGTATG 496–503 1.000 79.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA ACCGCGCTAATCTTGGTATG 510–517 1.000 79.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC ACCGCGCTAATCTTGGTATG 509–516 1.000 79.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC ACCGCGCTAATCTTGGTATG 511–518 1.000 79.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CGCGCTAATCTTGGTATGGA 494–501 1.000 79.2
psbA-trnK-UUU_p1 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT CTTGGGGAGGGGTTTTTACC 380–385 1.000 79.4
psbA-trnK-UUU_p2 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC CTTGGGGAGGGGTTTTTACC 381–386 1.000 78.9
psbA-trnK-UUU_p3 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT GAAAGCCGTGTGCAATGAAA 413–418 1.000 78.7
psbA-trnK-UUU_p4 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT CTAGTTCCGGGTTCGAATCC 328–333 1.000 78.5
psbA-trnK-UUU_p5 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC GAAAGCCGTGTGCAATGAAA 414–419 1.000 78.2
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 859–1280 1.000 88.2
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GGGGAATCGAGCGTTTGTAT 859–1748 1.000 87.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG AAAGTGTATCGCGGGGAATC 809–1709 1.000 87.1
trnK-UUU-rps16_p4 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG GGGGAATCGAGCGTTTGTAT 808–1697 1.000 87.1
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAGTGTATCGCGGGGAATC 860–1760 1.000 87.0
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 280–288 1.000 67.0
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 283–291 1.000 66.7
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 286–294 1.000 66.3
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 289–297 1.000 66.0
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 284–292 1.000 64.5
rpoC1_p1 rpoC1 AGAATTACTTAGCTTACGGACCA TTGCTCGTTCGAGAACTACG 2946–2950 1.000 49.2
rpoC1_p2 rpoC1 AGAATTACTTAGCTTACGGACCA ACGATCTTTGGCTCTGGAAC 2929–2933 1.000 48.7
rpoC1_p3 rpoC1 AGAATTACTTAGCTTACGGACCA AGGAGGGAAGCTTAATCGGA 2868–2872 1.000 48.1
rpoC1_p4 rpoC1 AGAATTACTTAGCTTACGGACCA CGATCTTTGGCTCTGGAACT 2928–2932 1.000 46.3
rpoC1_p5 rpoC1 AGAATTACTTAGCTTACGGACCA GCTCGTTCGAGAACTACGAT 2944–2948 1.000 45.8
petN-psbM_p1 petN-psbM AGTCCCTTTTTGACTCTGCG TTTTCGTTTCGCCCTTCTCA 885–2292 1.000 84.8
petN-psbM_p2 petN-psbM TGGCTGAGTCTTGAATTCCG TTTTCGTTTCGCCCTTCTCA 1260–2677 1.000 84.7
petN-psbM_p3 petN-psbM GGCTGAGTCTTGAATTCCGT TTTTCGTTTCGCCCTTCTCA 1259–2676 1.000 84.7
petN-psbM_p4 petN-psbM TGGCTGAGTCTTGAATTCCG CTTTCCCTTTTCGTTTCGCC 1260–2684 1.000 84.6
petN-psbM_p5 petN-psbM GGCTGAGTCTTGAATTCCGT CTTTCCCTTTTCGTTTCGCC 1259–2683 1.000 84.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Pterocyclus angelicoides NC_060754.1 157196 View on NCBI ↗
Pterocyclus forrestii NC_060752.1 156405 View on NCBI ↗
Pterocyclus rotundatus NC_060756.1 156476 View on NCBI ↗
Pterocyclus wolffianus NC_060755.1 157693 View on NCBI ↗