Markers + reference

Spuriopimpinella

2 species · Apiaceae · Apiales

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Species 2
Genome length 147–158 kb
Candidate markers 271
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

7 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
trnE-UUC-trnT-GGU LSC 751 0.0974 0.93 87.4 yes View details
trnT-GGU-psbD LSC 1404 0.0653 0.97 83.5 yes View details
psbE-petL LSC 4283 0.0798 0.23 58.0 yes View details
ycf2 IRb 6270 0.0186 0.98 51.8 no View details
ndhF-rpl32 SSC 1129 0.0660 0.81 75.2 yes View details
rpl32-trnL-UAG SSC 920 0.0950 0.96 83.0 yes View details
ycf2 IRa 6270 0.0303 0.09 43.0 yes View details
petA-psbJ LSC 969 0.0645 0.98 87.4 yes View details
ycf3-trnS-GGA LSC 889 0.0458 0.91 82.9 yes View details
trnT-UGU-trnL-UAA LSC 769 0.0561 0.97 82.7 yes View details
petN-psbM LSC 1130 0.0554 0.96 82.2 yes View details
atpH-atpI LSC 1176 0.0671 0.96 82.1 yes View details
psbA-trnK-UUU LSC 215 0.1150 0.93 82.0 yes View details
trnS-GGA-rps4 LSC 312 0.0567 0.96 79.8 yes View details
trnW-CCA-trnP-UGG LSC 133 0.0846 0.98 78.1 yes View details
trnH-GUG-psbA LSC 185 0.1381 0.98 78.0 yes View details
rps16-trnQ-UUG LSC 1238 0.0555 0.82 77.2 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 80 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 CCTCTAGACCTAGCTGCTGT 252–271 1.000 87.3
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 266–285 1.000 86.8
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 265–284 1.000 86.8
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 267–286 1.000 86.8
trnH-GUG-psbA_p5 trnH-GUG-psbA CGCATGGTGGATTCACAATC CCTCTAGACCTAGCTGCTGT 281–300 1.000 83.6
psbA-trnK-UUU_p1 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT CTAGTTCCGGGTTCGAATCC 317–332 1.000 85.7
psbA-trnK-UUU_p2 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC CTAGTTCCGGGTTCGAATCC 318–333 1.000 85.1
psbA-trnK-UUU_p3 psbA-trnK-UUU TACAGAAGCGACCCCATAGG CTAGTTCCGGGTTCGAATCC 286–301 1.000 83.8
psbA-trnK-UUU_p4 psbA-trnK-UUU TTTTCGGTGCTGGTTATCCA CTAGTTCCGGGTTCGAATCC 308–323 1.000 83.3
psbA-trnK-UUU_p5 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT ACTCCATCCGACTAGTTCCG 328–343 1.000 82.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT GGGTTTTGGTCCCGGTATTC 1321–1336 1.000 82.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT GGGTTTTGGTCCCGGTATTC 1322–1337 1.000 82.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 1332–1347 1.000 82.0
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT TCGGAGGTTCGAATCCTTTC 1303–1318 1.000 81.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT TCGGAGGTTCGAATCCTTTC 1304–1319 1.000 81.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 1199–1238 1.000 87.0
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 1255–1294 1.000 86.0
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA ATAGGGGAATCCATGGAGGG 1215–1254 1.000 86.0
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA ATAGGGGAATCCATGGAGGG 1200–1239 1.000 85.8
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC ATAGGGGAATCCATGGAGGG 1259–1298 1.000 85.4
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT AGTTCCTACTGCTTTTCTGCT 1272–1283 1.000 71.2
petN-psbM_p2 petN-psbM ATGGGGAAGAAGTGGACTCT AGTTCCTACTGCTTTTCTGCT 1211–1222 1.000 69.9
petN-psbM_p3 petN-psbM TAGTAAGTCTCGCTTGGGCT AGTTCCTACTGCTTTTCTGCTT 1272–1283 1.000 68.7
petN-psbM_p4 petN-psbM ATGGGGAAGAAGTGGACTCT AGTTCCTACTGCTTTTCTGCTT 1211–1222 1.000 67.4
petN-psbM_p5 petN-psbM TAGTAAGTCTCGCTTGGGCT GTTCCTACTGCTTTTCTGCT 1271–1282 1.000 66.8
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA GAACCGATGACTTACGCCTT 855 1.000 89.0
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TACCGCTGAGTTAAAAGGGC 820 1.000 88.4
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA CCGATGACTTACGCCTTACC 852 1.000 87.8
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU CGTTGCCTCCTTGAAAGAGA TTGAACCGATGACTTACGCC 857 1.000 86.7
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU TTGTAGTACCCTACCCCCAG GAACCGATGACTTACGCCTT 890 1.000 85.6

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
Spuriopimpinella brachycarpa PV794604.1 158110 View on NCBI ↗
Spuriopimpinella brachystyla PV794605.1 147181 View on NCBI ↗