Markers + reference

Seseli

17 species · Apiaceae · Apiales

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Species 17
Genome length 145–156 kb
Candidate markers 265
Primer pairs 90

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 265 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbA LSC 1062 0.0030 1.00 40.4 yes View details
trnT-GGU-psbD LSC 1464 0.0153 0.98 74.4 yes View details
petA-psbJ LSC 955 0.0184 0.99 67.7 yes View details
ycf2-trnL-CAA IRb 1244 0.0798 0.36 63.4 yes View details
ycf1 IRb 1939 0.0027 1.00 43.1 no View details
ndhF SSC 2247 0.0110 1.00 55.6 yes View details
ndhF-rpl32 SSC 1064 0.0225 1.00 68.1 yes View details
rpl32-trnL-UAG SSC 945 0.0216 1.00 83.1 yes View details
ycf1 SSC 5496 0.0086 1.00 48.7 yes View details
trnL-CAA-trnH-GUG IRa 1190 0.1645 0.77 77.3 no View details
trnH-GUG-psbA LSC 195 0.0683 1.00 82.8 yes View details
rps2-rpoC2 LSC 211 0.0252 1.00 79.3 yes View details
rps19-rpl2 LSC 57 0.0337 1.00 77.4 yes View details
trnC-GCA-petN LSC 694 0.0117 1.00 75.9 yes View details
petN-psbM LSC 1139 0.0123 1.00 73.2 yes View details
psbA-trnK-UUU LSC 201 0.0238 0.99 72.7 yes View details
psaA-ycf3 LSC 709 0.0082 0.99 71.0 yes View details
atpH-atpI LSC 1134 0.0115 1.00 69.7 yes View details
psbE-petL LSC 1005 0.0094 1.00 69.4 yes View details
rpoB-trnC-GCA LSC 1210 0.0150 1.00 69.0 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 90 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 GCGCTAACCTTGGTATGGAA 307–348 1.000 90.7
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 321–362 1.000 90.7
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 320–361 1.000 90.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 322–363 1.000 90.7
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 257–298 1.000 90.4
psbA_p1 psbA GATCCACTTGGCTACATCCG AAATTCGTGTGCTTGGGAGT 1325–1366 1.000 86.1
psbA_p2 psbA CAATCCACTGCCTTGATCCA AAATTCGTGTGCTTGGGAGT 1339–1380 1.000 85.9
psbA_p3 psbA AATCCACTGCCTTGATCCAC AAATTCGTGTGCTTGGGAGT 1338–1379 1.000 85.9
psbA_p4 psbA ACAATCCACTGCCTTGATCC AAATTCGTGTGCTTGGGAGT 1340–1381 1.000 85.9
psbA_p5 psbA GATCCACTTGGCTACATCCG AAAGCTTCTTCCACTTCGCA 1861–1904 0.765 76.4
psbA-trnK-UUU_p1 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT CTGAAAAATGCAAGCACGGT 383–403 1.000 84.8
psbA-trnK-UUU_p2 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT ACTGAAAAATGCAAGCACGG 384–404 1.000 84.7
psbA-trnK-UUU_p3 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC CTGAAAAATGCAAGCACGGT 384–404 1.000 84.2
psbA-trnK-UUU_p4 psbA-trnK-UUU TAAAGACGGTTTTCGGTGCT TTGGGGAGGGGTGTTTATCT 363–375 0.941 79.5
psbA-trnK-UUU_p5 psbA-trnK-UUU GTAAAGACGGTTTTCGGTGC TTGGGGAGGGGTGTTTATCT 364–376 0.941 79.0
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 1195–1260 1.000 86.2
atpH-atpI_p2 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 1251–1316 1.000 85.5
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA ATAGGGGAATCCATGGAGGG 1211–1276 1.000 85.3
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA ATAGGGGAATCCATGGAGGG 1196–1261 1.000 85.1
atpH-atpI_p5 atpH-atpI GCAGTACCTTGACCAACTCC ATAGGGGAATCCATGGAGGG 1255–1320 0.941 79.6
rps2-rpoC2_p1 rps2-rpoC2 AATGAACTCCGGCCTTCATC TGCCTTTCAAAGAATTTCCACG 335–359 0.941 66.3
rps2-rpoC2_p2 rps2-rpoC2 CGGCCTTCATCATCTCTTCC TGCCTTTCAAAGAATTTCCACG 326–350 0.941 65.8
rps2-rpoC2_p3 rps2-rpoC2 CCGGCCTTCATCATCTCTTC TGCCTTTCAAAGAATTTCCACG 327–351 0.941 65.7
rps2-rpoC2_p4 rps2-rpoC2 AATGAACTCCGGCCTTCATC GCCTTTCAAAGAATTTCCACGA 334–358 0.941 64.6
rps2-rpoC2_p5 rps2-rpoC2 AAAATGAACTCCGGCCTTCA TGCCTTTCAAAGAATTTCCACG 337–361 0.882 61.7
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TCCTTCATTTACATCTCGGAGC CCGGATTTGAACTGGGGAAA 1138–1384 0.941 68.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCTTCATTTACATCTCGGAGCA CCGGATTTGAACTGGGGAAA 1137–1383 0.941 67.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TCCTTCATTTACATCTCGGAGC TTATTGATCAGGCGACACCC 1156–1402 0.941 66.4
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TCCTTCATTTACATCTCGGAGC AAAAGGATTTGCAGTCCCCC 1120–1366 0.941 66.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCCAGGTATTGTAGACATTCCT CCGGATTTGAACTGGGGAAA 1156–1402 0.941 65.5

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (17)

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

Species Accession Length (bp) Link
Seseli aemulans OQ570473.1 147473 View on NCBI ↗
Seseli asperulum OQ570474.1 145374 View on NCBI ↗
Seseli buchtormense NC_058871.1 147036 View on NCBI ↗
Seseli coronatum NC_066698.1 145937 View on NCBI ↗
Seseli delavayi NC_066697.1 153859 View on NCBI ↗
Seseli eriocephalum NC_066696.1 155617 View on NCBI ↗
Seseli giganteum PV631426.1 147554 View on NCBI ↗
Seseli incisodentatum NC_066694.1 154590 View on NCBI ↗
Seseli intramongolicum NC_066693.1 151526 View on NCBI ↗
Seseli junatovii OQ570475.1 146848 View on NCBI ↗
Seseli mairei NC_066692.1 145859 View on NCBI ↗
Seseli mairei var. simplicifolia ON975060.1 144957 View on NCBI ↗
Seseli montanum NC_027451.1 147823 View on NCBI ↗
Seseli seseloides NC_087714.1 147950 View on NCBI ↗
Seseli squarrulosum NC_066691.1 154502 View on NCBI ↗
Seseli valentinae NC_066690.1 147460 View on NCBI ↗
Seseli yunnanense NC_066689.1 145975 View on NCBI ↗