Markers + reference

Anethum

4 species · Apiaceae · Apiales

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Species 4
Genome length 153–154 kb
Candidate markers 269
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 746 0.0069 1.00 59.4 yes View details
rps16-trnQ-UUG LSC 1229 0.0045 1.00 46.9 yes View details
atpH-atpI LSC 1151 0.0080 1.00 65.3 yes View details
rpoB-trnC-GCA LSC 1217 0.0041 1.00 42.1 yes View details
trnC-GCA-petN LSC 681 0.0044 1.00 58.4 yes View details
petN-psbM LSC 1109 0.0036 1.00 48.2 yes View details
trnE-UUC-trnT-GGU LSC 671 0.0057 1.00 57.9 yes View details
ycf3-trnS-GGA LSC 813 0.0059 1.00 52.2 yes View details
trnF-GAA-ndhJ LSC 401 0.0079 1.00 41.6 yes View details
petA-psbJ LSC 916 0.0120 1.00 55.5 yes View details
ycf1 SSC 1908 0.0013 1.00 49.9 no View details
ndhF-rpl32 SSC 971 0.0096 1.00 55.5 yes View details
ycf1 SSC 5454 0.0034 1.00 53.0 yes View details
rpl20-rps12 LSC 762 0.0046 1.00 62.0 yes View details
atpB-rbcL LSC 781 0.0026 1.00 55.4 yes View details
rpl14-rpl16 LSC 147 0.0034 0.98 55.1 yes View details
ycf2 IRb 6360 0.0010 1.00 54.9 yes View details
ycf2 IRa 6360 0.0010 1.00 54.9 yes View details
trnH-GUG-psbA LSC 191 0.0131 1.00 53.4 yes View details
rpl32-trnL-UAG SSC 882 0.0047 1.00 52.8 yes View details
rpoC1 LSC 2792 0.0011 1.00 52.1 yes View details
trnT-GGU-psbD LSC 1232 0.0032 1.00 52.1 yes View details
psbE-petL LSC 910 0.0022 1.00 51.6 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 110 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA TTTACTTGGTTGGCAGGGTC CCTCTAGACCTAGCTGCTGT 336–347 1.000 83.3
trnH-GUG-psbA_p2 trnH-GUG-psbA TTTACTTGGTTGGCAGGGTC TTCCCTCTAGACCTAGCTGC 339–350 1.000 83.2
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 297–308 1.000 83.2
trnH-GUG-psbA_p4 trnH-GUG-psbA TTTACTTGGTTGGCAGGGTC GCGCTAACCTTGGTATGGAA 386–397 1.000 83.1
trnH-GUG-psbA_p5 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 311–322 1.000 82.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCCCTCGCTTCATCCAAATG AGGAACTGTTCGGGATCTTT 868–875 1.000 68.9
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCGATGGTATGGACGAATCC AGGAACTGTTCGGGATCTTT 885–892 1.000 68.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 CGATGGTATGGACGAATCCC AGGAACTGTTCGGGATCTTT 884–891 1.000 68.6
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT AGGAACTGTTCGGGATCTTT 824–831 1.000 68.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT AGGAACTGTTCGGGATCTTT 823–830 1.000 68.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT GGGTTTTGGTCCCGGTATTC 1310–1312 1.000 76.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT GGGTTTTGGTCCCGGTATTC 1311–1313 1.000 76.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GGGTTTTGGTCCCGGTATTC 1321–1323 1.000 75.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGCTTTCTACCACAGCGTTT TCGGAGGTTCGAATCCTTTC 1292–1294 1.000 75.5
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TTGCTTTCTACCACAGCGTT TCGGAGGTTCGAATCCTTTC 1293–1295 1.000 75.5
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT ATAGGGGAATCCATGGAGGG 1213–1225 1.000 81.0
atpH-atpI_p2 atpH-atpI AGCGGCAGAAATCAATGGAT ATAGGGGAATCCATGGAGGG 1205–1217 1.000 80.8
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT ATAGGGGAATCCATGGAGGG 1269–1281 1.000 80.3
atpH-atpI_p4 atpH-atpI AGCCAATCCAGCAGCAATAA ATAGGGGAATCCATGGAGGG 1229–1241 1.000 80.1
atpH-atpI_p5 atpH-atpI AAGCGGCAGAAATCAATGGA ATAGGGGAATCCATGGAGGG 1206–1218 1.000 80.0
rpoC1_p1 rpoC1 CCGTCCTAGTTGAATCGGAG TTGCTCGTTCGAGAACTACG 2978–2983 1.000 76.2
rpoC1_p2 rpoC1 CCGTCCTAGTTGAATCGGAG ACGATCTTTGGCTCTGGAAC 2961–2966 1.000 75.7
rpoC1_p3 rpoC1 CCGTCCTAGTTGAATCGGAG CGATCTTTGGCTCTGGAACT 2960–2965 1.000 73.3
rpoC1_p4 rpoC1 CCCGTCCTAGTTGAATCGGA TTGCTCGTTCGAGAACTACG 2979–2984 1.000 73.0
rpoC1_p5 rpoC1 TCCCGTCCTAGTTGAATCGG TTGCTCGTTCGAGAACTACG 2980–2985 1.000 73.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCCTCATTTACATCTCGGAGC CTTACCACTCGGCCATATCG 1262–1272 1.000 70.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCCTCATTTACATCTCGGAGC CCGGATTTGAACTGGGGAAA 1302–1312 1.000 70.2
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCTCATTTACATCTCGGAGCA CTTACCACTCGGCCATATCG 1261–1271 1.000 68.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCTCATTTACATCTCGGAGCA CCGGATTTGAACTGGGGAAA 1301–1311 1.000 68.4
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCCTCATTTACATCTCGGAGC TTATTGATCAGGCGACACCC 1320–1330 1.000 68.2

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
Anethum foeniculum NC_029469.1 153628 View on NCBI ↗
Anethum foeniculum subsp. foeniculum ON641350.1 153618 View on NCBI ↗
Anethum graveolens NC_029470.1 153356 View on NCBI ↗
Anethum piperitum ON641289.1 153665 View on NCBI ↗