Markers + reference

Pertya

2 species · Asteraceae · Asterales

Back to catalogue

Species 2
Genome length 153–154 kb
Candidate markers 273
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 273 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 402 0.0315 0.95 77.3 yes View details
atpI-atpH LSC 1179 0.0087 0.98 66.0 yes View details
trnT-UGU-trnL-UAA LSC 547 0.0372 0.98 80.5 yes View details
trnF-GAA-ndhJ LSC 675 0.0136 0.87 68.9 yes View details
ndhC-trnV-UAC LSC 1155 0.0324 0.99 78.5 yes View details
accD-psaI LSC 536 0.0225 1.00 58.1 yes View details
ycf4-cemA LSC 301 0.0337 0.99 58.4 yes View details
ndhF-rpl32 SSC 1057 0.0132 1.00 66.4 yes View details
rpl32-trnL-UAG SSC 903 0.0182 0.98 69.5 yes View details
ccsA SSC 969 0.0041 1.00 47.0 yes View details
ndhG-ndhI SSC 371 0.0238 0.57 47.8 yes View details
rps19-trnH-GUG LSC 1207 0.0000 0.01 40.6 no View details
ccsA-ndhD SSC 223 0.0404 1.00 68.4 yes View details
rps15-ycf1 SSC 1600 0.0090 0.98 65.8 yes View details
trnC-GCA-petN LSC 596 0.0134 1.00 65.6 yes View details
rbcL-accD LSC 580 0.0061 0.85 63.8 yes View details
petN-psbM LSC 549 0.0040 0.91 63.7 yes View details
trnE-UUC-rpoB LSC 885 0.0113 1.00 62.7 yes View details
rpoA LSC 1008 0.0069 1.00 62.7 yes View details
rps16 LSC 1102 0.0064 1.00 62.4 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 95 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 CCGTGCTAACCTTGGTATGG 511–521 1.000 81.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 525–535 1.000 81.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 524–534 1.000 81.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 526–536 1.000 81.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 512–522 1.000 80.9
rps16_p1 rps16 AGAAATCACTATCCTACCCTTAGT TCTCTGTACCGACTGAACCA 1242–1266 1.000 40.4
rps16_p2 rps16 AGAAATCACTATCCTACCCT TCTCTGTACCGACTGAACCA 1242–1266 1.000 40.4
rps16_p3 rps16 AGAAATCACTATCCTACCCTT TCTCTGTACCGACTGAACCA 1242–1266 1.000 40.4
rps16_p4 rps16 AGAAATCACTATCCTACCCTTAGTT TCTCTGTACCGACTGAACCA 1242–1266 1.000 40.4
rps16_p5 rps16 AGAAATCACTATCCTACCCTTAGT GTCTCTGTACCGACTGAACC 1243–1267 1.000 40.4
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 662–896 1.000 79.0
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 680–914 1.000 76.7
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GCCCAAGCGAGACTTACTAT 661–895 1.000 73.0
trnC-GCA-petN_p4 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATTAAAGCAGCCCAAGCGAG 670–904 1.000 72.9
trnC-GCA-petN_p5 trnC-GCA-petN ATTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 719–953 1.000 72.3
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 663–711 1.000 63.6
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 663–711 1.000 61.9
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 664–712 1.000 57.7
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 655–703 1.000 57.6
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 649–697 1.000 56.9
trnE-UUC-rpoB_p1 trnE-UUC-rpoB GAAGTCGTAACCACTGGACC AGTTCTTCTGTCAAACCCTGA 993–1030 1.000 62.6
trnE-UUC-rpoB_p2 trnE-UUC-rpoB TAACCACTGGACCATAGGGG AGTTCTTCTGTCAAACCCTGA 986–1023 1.000 62.3
trnE-UUC-rpoB_p3 trnE-UUC-rpoB AACCCTCGTTATCTCCGTGA AGTTCTTCTGTCAAACCCTGA 1019–1056 1.000 62.0
trnE-UUC-rpoB_p4 trnE-UUC-rpoB ACCCTCGTTATCTCCGTGAA AGTTCTTCTGTCAAACCCTGA 1018–1055 1.000 62.0
trnE-UUC-rpoB_p5 trnE-UUC-rpoB TGAACCCTCGTTATCTCCGT AGTTCTTCTGTCAAACCCTGA 1021–1058 1.000 62.0
atpI-atpH_p1 atpI-atpH TCCCTGTCATGTTCCTTGGA ATAACGGAAGCGGCAGAAAT 1315–1348 1.000 79.9
atpI-atpH_p2 atpI-atpH TCCCTGTCATGTTCCTTGGA TACCTTGACCAACTCCAGGT 1371–1404 1.000 79.2
atpI-atpH_p3 atpI-atpH TCCCTGTCATGTTCCTTGGA AGCCAATCCAGCAGCAATAA 1331–1364 1.000 79.0
atpI-atpH_p4 atpI-atpH TCCCTGTCATGTTCCTTGGA AATAACGGAAGCGGCAGAAA 1316–1349 1.000 78.7
atpI-atpH_p5 atpI-atpH TCCCTGTCATGTTCCTTGGA GCAGTACCTTGACCAACTCC 1375–1408 1.000 78.6

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
Pertya dioica NC_058225.1 153793 View on NCBI ↗
Pertya phylicoides NC_057464.1 153379 View on NCBI ↗