Markers + reference

Vicatia

2 species · Apiaceae · Apiales

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Species 2
Genome length 145–155 kb
Candidate markers 272
Primer pairs 65

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl2 IRb 1476 0.0102 1.00 50.4 no View details
rpl23 IRb 282 0.0000 1.00 25.3 no View details
ycf2 IRb 6255 0.0120 0.99 45.6 no View details
ycf2 IRa 6255 0.2177 0.24 57.4 yes View details
rpl23 IRa 282 0.3889 0.26 63.1 yes View details
rpl2 IRa 1476 0.3580 0.12 70.6 yes View details
pafI-trnS-GGA LSC 719 0.0547 0.92 86.1 yes View details
rps4-trnT-UGU LSC 343 0.1287 0.97 83.8 yes View details
atpH-atpI LSC 1166 0.0543 0.95 81.7 yes View details
trnG-UCC-trnR-UCU LSC 123 0.0948 0.94 81.3 yes View details
rpl32-trnL-UAG SSC 921 0.0729 0.94 80.9 yes View details
trnT-UGU-trnL-UAA LSC 798 0.0479 0.97 80.3 yes View details
ccsA-ndhD SSC 217 0.1023 0.99 80.1 yes View details
trnH-GUG-psbA LSC 174 0.1914 0.93 79.4 yes View details
rbcL-accD LSC 621 0.0469 0.96 78.4 yes View details
psbA-trnK-UUU LSC 214 0.0909 0.93 77.5 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 65 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 AGCTCCATCTACAAATGGGT 217–218 1.000 76.5
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGCTCCATCTACAAATGGGT 231–232 1.000 76.5
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGCTCCATCTACAAATGGGT 230–231 1.000 76.5
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGCTCCATCTACAAATGGGT 232–233 1.000 76.5
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG AAGCTCCATCTACAAATGGGT 218–219 1.000 74.7
psbA-trnK-UUU_p1 psbA-trnK-UUU GCTTTCGCGTCTCTCTAAAA CTAGTTCCGGGTTCGAATCC 265–275 1.000 73.2
psbA-trnK-UUU_p2 psbA-trnK-UUU TCGCGTCTCTCTAAAATAGCAG CTAGTTCCGGGTTCGAATCC 261–271 1.000 71.3
psbA-trnK-UUU_p3 psbA-trnK-UUU TCGCGTCTCTCTAAAATAGCA CTAGTTCCGGGTTCGAATCC 261–271 1.000 71.3
psbA-trnK-UUU_p4 psbA-trnK-UUU GCTTTCGCGTCTCTCTAAAA ACTCCATCCGACTAGTTCCG 276–286 1.000 69.9
psbA-trnK-UUU_p5 psbA-trnK-UUU GCTTTCGCGTCTCTCTAAAAT CTAGTTCCGGGTTCGAATCC 265–275 1.000 69.4
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 203–215 1.000 70.2
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 206–218 1.000 69.9
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 209–221 1.000 69.4
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 212–224 1.000 69.1
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 207–219 1.000 67.7
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 1177–1228 1.000 87.2
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 1233–1284 1.000 86.3
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA ATAGGGGAATCCATGGAGGG 1193–1244 1.000 86.2
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA ATAGGGGAATCCATGGAGGG 1178–1229 1.000 86.0
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC ATAGGGGAATCCATGGAGGG 1237–1288 1.000 85.7
pafI-trnS-GGA_p1 pafI-trnS-GGA CATTTATCCGCGATCTAGGCA CCCTCGGTAAACAAAAGCCT 808–915 1.000 78.3
pafI-trnS-GGA_p2 pafI-trnS-GGA CATTTATCCGCGATCTAGGCA ACGGAAAGAGAGGGATTCGA 829–936 1.000 77.7
pafI-trnS-GGA_p3 pafI-trnS-GGA CATTTATCCGCGATCTAGGCA TTCCAATGCTACGCCTTCAA 779–886 1.000 77.6
pafI-trnS-GGA_p4 pafI-trnS-GGA CATTTATCCGCGATCTAGGCA AGTTCCAATGCTACGCCTTC 781–888 1.000 77.0
pafI-trnS-GGA_p5 pafI-trnS-GGA CATTTATCCGCGATCTAGGCA ACCCTCGGTAAACAAAAGCC 809–916 1.000 75.9
rps4-trnT-UGU_p1 rps4-trnT-UGU GTTAGTCCCGGTAAAGCTCC CTCAGAGGTTAGAGCATCGC 471–472 1.000 85.3
rps4-trnT-UGU_p2 rps4-trnT-UGU GTTAGTCCCGGTAAAGCTCC ATGGTCATCGGTTCGATTCC 439–440 1.000 85.1
rps4-trnT-UGU_p3 rps4-trnT-UGU AGATCACTTCCGGCTCTAGG CTCAGAGGTTAGAGCATCGC 501–502 1.000 84.8
rps4-trnT-UGU_p4 rps4-trnT-UGU AGATCACTTCCGGCTCTAGG ATGGTCATCGGTTCGATTCC 469–470 1.000 84.5
rps4-trnT-UGU_p5 rps4-trnT-UGU TTTTTGAAACGAGGTCCCCG CTCAGAGGTTAGAGCATCGC 438–439 1.000 82.9

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
Vicatia coniifolia NC_071816.1 155476 View on NCBI ↗
Vicatia thibetica NC_086813.1 145265 View on NCBI ↗