Markers + reference

Acronema

17 species · Apiaceae · Apiales

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Species 17
Genome length 153–161 kb
Candidate markers 267
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 752 0.0492 0.68 71.4 yes View details
rps16-trnQ-UUG LSC 1409 0.0436 0.99 76.8 yes View details
trnE-UUC-trnT-GGU LSC 725 0.0473 0.96 80.1 yes View details
ycf2-trnL-CAA IRb 666 0.0925 1.00 83.2 yes View details
ndhF-rpl32 SSC 1125 0.0544 0.98 75.8 yes View details
rpl32-trnL-UAG SSC 932 0.0592 0.95 80.2 yes View details
ycf1 SSC 5463 0.0271 1.00 68.0 yes View details
trnL-CAA-ycf2 IRa 666 0.0957 1.00 83.2 yes View details
rpl2-trnH-GUG IRa 2568 0.0532 0.05 58.3 no View details
trnC-GCA-petN LSC 636 0.0377 0.98 81.0 yes View details
ycf3-trnS-GGA LSC 877 0.0372 0.98 77.3 yes View details
petA-psbJ LSC 971 0.0422 0.98 77.3 yes View details
rbcL-accD LSC 607 0.0291 0.99 76.7 yes View details
atpH-atpI LSC 1137 0.0417 0.97 75.8 yes View details
psbM-trnD-GUC LSC 621 0.0372 0.99 75.7 yes View details
trnF-GAA-ndhJ LSC 386 0.0383 0.99 75.7 yes View details
trnH-GUG-psbA LSC 173 0.0574 1.00 75.6 yes View details
rps2-rpoC2 LSC 231 0.0453 0.99 75.5 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA CAATCCACTGCCTTGATCCA AGCTCCATCTACAAATGGGT 220–449 1.000 76.5
trnH-GUG-psbA_p2 trnH-GUG-psbA AATCCACTGCCTTGATCCAC AGCTCCATCTACAAATGGGT 219–448 1.000 76.5
trnH-GUG-psbA_p3 trnH-GUG-psbA ACAATCCACTGCCTTGATCC AGCTCCATCTACAAATGGGT 221–450 1.000 76.5
trnH-GUG-psbA_p4 trnH-GUG-psbA GATCCACTTGGCTACATCCG AGCTCCATCTACAAATGGGT 206–435 0.941 74.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG AAGCTCCATCTACAAATGGGT 207–436 0.941 72.4
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGCGGAGGTTTTTAAGTAG 566–951 1.000 52.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGCGGAGGTTTTTAAGTAG 565–950 1.000 52.0
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCCTAGCCGCACTTAAAAGC GGCGGAGGTTTTTAAGTAG 581–966 1.000 52.0
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGCGGAGGTTTTTAAGTAG 575–960 1.000 52.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GGCGGAGGTTTTTAAGTAG 552–937 1.000 52.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGCGCGATACACTTTGAATC TACAGCAGCTTGCCAAATGA 2385 0.118 43.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCGCGATACACTTTGAATCG TACAGCAGCTTGCCAAATGA 2384 0.118 43.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT TACAGCAGCTTGCCAAATGA 2044 0.118 43.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT TACAGCAGCTTGCCAAATGA 2045 0.118 43.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTTTTCTCCTCGTACGGC TACAGCAGCTTGCCAAATGA 2745 0.118 43.4
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTCTAATTGGTCAGGAGCGC 1279–1631 1.000 91.5
atpH-atpI_p2 atpH-atpI ATAACGGAAGCGGCAGAAAT CTAATTGGTCAGGAGCGCTT 1277–1629 1.000 91.5
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT TGCTTTGGCTTTACTCACGT 1186–1538 1.000 91.4
atpH-atpI_p4 atpH-atpI CTCGCGATACCTTCTACAGC TTCTAATTGGTCAGGAGCGC 1369–1721 0.941 89.1
atpH-atpI_p5 atpH-atpI CTCGCGATACCTTCTACAGC CTAATTGGTCAGGAGCGCTT 1367–1719 0.941 89.1
rps2-rpoC2_p1 rps2-rpoC2 AATGAACTCCGGCCTTCATC TTGGGGGTTCTTGATTGGTG 889–922 1.000 89.8
rps2-rpoC2_p2 rps2-rpoC2 AACATAATGACACCGAGCCC TTGGGGGTTCTTGATTGGTG 1119–1152 1.000 89.2
rps2-rpoC2_p3 rps2-rpoC2 CCGCATCTCTTTTCGGAAGA TTGGGGGTTCTTGATTGGTG 1246–1279 0.882 81.6
rps2-rpoC2_p4 rps2-rpoC2 CCGCATCTCTTTTCGGAAGA GAGGGTTGGCACGAATGTAT 1287–1320 0.882 81.3
rps2-rpoC2_p5 rps2-rpoC2 CCGCATCTCTTTTCGGAAGA GATTCGAGGGATTGGTGCAT 828–834 0.176 47.7
trnC-GCA-petN_p1 trnC-GCA-petN CGATATGGCCGAGTGGTAAG AGCCCAAGCGAGACTTACTA 455–813 1.000 90.3
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 415–773 1.000 90.1
trnC-GCA-petN_p3 trnC-GCA-petN CGATATGGCCGAGTGGTAAG AGAGTCCACTTCTTCCCCAT 516–874 1.000 88.7
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 476–834 1.000 88.5
trnC-GCA-petN_p5 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 433–791 1.000 87.9

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
Acronema astrantiifolium PP531564.1 156869 View on NCBI ↗
Acronema chienii PP531566.1 160762 View on NCBI ↗
Acronema chinense PP531559.1 153931 View on NCBI ↗
Acronema chinense var. humile PP531560.1 153065 View on NCBI ↗
Acronema commutatum PP531549.1 157434 View on NCBI ↗
Acronema crassifolium PP531565.1 156191 View on NCBI ↗
Acronema forrestii PP531563.1 156016 View on NCBI ↗
Acronema gracile PP531546.1 159450 View on NCBI ↗
Acronema graminifolium PP531551.1 157285 View on NCBI ↗
Acronema handelii PP531547.1 158492 View on NCBI ↗
Acronema hookeri PP531550.1 157324 View on NCBI ↗
Acronema minus PP531558.1 155763 View on NCBI ↗
Acronema muscicola PP531561.1 154713 View on NCBI ↗
Acronema nervosum PX091988.1 154471 View on NCBI ↗
Acronema paniculatum PP531548.1 157255 View on NCBI ↗
Acronema schneideri NC_064352.1 156845 View on NCBI ↗
Acronema tenerum PP531545.1 161107 View on NCBI ↗