Markers + reference

Notoseris

2 species · Asteraceae · Asterales

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Species 2
Genome length 152–152 kb
Candidate markers 272
Primer pairs 95

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 10 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16 LSC 1126 0.0009 1.00 59.3 yes View details
ycf3-trnS LSC 919 0.0022 1.00 53.5 yes View details
atpB-rbcL LSC 768 0.0013 1.00 59.6 yes View details
accD LSC 1518 0.0013 1.00 59.5 yes View details
clpP LSC 2035 0.0000 1.00 43.9 yes View details
ycf1 IRb 472 0.0000 1.00 37.3 no View details
rpl32-trnL SSC 921 0.0022 1.00 60.0 yes View details
ndhA SSC 2147 0.0009 1.00 57.9 yes View details
ycf1 SSC 5007 0.0010 1.00 53.1 yes View details
trnF-ndhJ LSC 639 0.0000 0.98 60.3 yes View details
rps12-clpP LSC 161 0.0124 1.00 59.6 yes View details
psbM-trnD-GUC LSC 657 0.0000 0.99 59.5 yes View details
petA LSC 963 0.0010 1.00 59.3 yes View details
ndhF-rpl32 SSC 1059 0.0009 1.00 59.3 yes View details
atpF LSC 1272 0.0008 1.00 59.2 yes View details
rpl16 LSC 1424 0.0007 1.00 59.2 yes View details
ycf4 LSC 555 0.0018 1.00 58.8 yes View details
ndhD-psaC SSC 97 0.0103 1.00 58.4 yes View details
ndhG SSC 531 0.0019 1.00 58.4 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
trnK-UUU_p1 trnK-UUU GCCCGTGTCAACCAATATCT TCTGATTGTATCTACATACCCGT 2748 1.000 42.6
trnK-UUU_p2 trnK-UUU TGCCCGTGTCAACCAATATC TCTGATTGTATCTACATACCCGT 2749 1.000 40.9
trnK-UUU_p3 trnK-UUU GCCCGTGTCAACCAATATCT TCTGATTGTATCTACATACCCGTT 2748 1.000 40.0
trnK-UUU_p4 trnK-UUU GCCCGTGTCAACCAATATCT TTCTGATTGTATCTACATACCCGT 2749 1.000 40.0
trnK-UUU_p5 trnK-UUU GCCCGTGTCAACCAATATCT CTGATTGTATCTACATACCCGT 2747 1.000 40.0
rps16_p1 rps16 AGAGCAAGAAAAGAAGGAAA TCTCTGTACCGACTGAACCA 1321–1322 1.000 40.1
rps16_p2 rps16 AGAGCAAGAAAAGAAGGAAAT TCTCTGTACCGACTGAACCA 1321–1322 1.000 40.1
rps16_p3 rps16 AGAGCAAGAAAAGAAGGAAA GTCTCTGTACCGACTGAACC 1322–1323 1.000 40.1
rps16_p4 rps16 TCGAAATCACTATCCTATCCT TCTCTGTACCGACTGAACCA 1261–1262 1.000 40.1
rps16_p5 rps16 AGAGCAAGAAAAGAAGGAAAT GTCTCTGTACCGACTGAACC 1322–1323 1.000 40.1
psbM-trnD-GUC_p1 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TTCAATAGGCAAGAGCACCG 769–774 1.000 50.9
psbM-trnD-GUC_p2 psbM-trnD-GUC AAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 763–768 1.000 50.5
psbM-trnD-GUC_p3 psbM-trnD-GUC ACTAAAATGAACAGTGCAGTAGC TTCAATAGGCAAGAGCACCG 766–771 1.000 49.5
psbM-trnD-GUC_p4 psbM-trnD-GUC AGGAACTAAAATGAACAGTGCAG TTCAATAGGCAAGAGCACCG 770–775 1.000 48.9
psbM-trnD-GUC_p5 psbM-trnD-GUC AGGAACTAAAATGAACAGTGCA TTCAATAGGCAAGAGCACCG 770–775 1.000 48.0
atpF_p1 atpF ACAAAAAGAACTCTGTTCGA ATTTCGTCGGCTTGAATGGT 1412 1.000 40.1
atpF_p2 atpF ACAAAAAGAACTCTGTTCGA GTCGGCTTGAATGGTTACCA 1407 1.000 40.1
atpF_p3 atpF ACAAAAAGAACTCTGTTCGA TCGTCGGCTTGAATGGTTAC 1409 1.000 40.1
atpF_p4 atpF ACAAAAAGAACTCTGTTCGA TTTCGTCGGCTTGAATGGTT 1411 1.000 40.1
atpF_p5 atpF ACAAAAAGAACTCTGTTCGA TTCGTCGGCTTGAATGGTTA 1410 1.000 40.1
ycf3-trnS_p1 ycf3-trnS CATTTATCCGCGATCTAGGCA ACGGAAAGAGAGGGATTCGA 1029 1.000 70.6
ycf3-trnS_p2 ycf3-trnS CATTTATCCGCGATCTAGGCA TTCCAATGCTACGCCTTCAA 979 1.000 70.3
ycf3-trnS_p3 ycf3-trnS CATTTATCCGCGATCTAGGCA GGATTCGAACCCTCGGTAAG 1017 1.000 70.1
ycf3-trnS_p4 ycf3-trnS CATTTATCCGCGATCTAGGCA AGTTCCAATGCTACGCCTTC 981 1.000 69.8
ycf3-trnS_p5 ycf3-trnS CATTTATCCGCGATCTAGGCA CCTCGGTAAGCAAAAGCCTA 1007 1.000 68.7
trnF-ndhJ_p1 trnF-ndhJ CCTCGTGTCACCAGTTCAAA TGGATAGGATGGCCTTTACG 732–742 1.000 70.9
trnF-ndhJ_p2 trnF-ndhJ CCTCGTGTCACCAGTTCAAA GGATAGGATGGCCTTTACGT 731–741 1.000 70.9
trnF-ndhJ_p3 trnF-ndhJ CCTCGTGTCACCAGTTCAAA TGAAAGTTGGATAGGATGGCC 739–749 1.000 70.3
trnF-ndhJ_p4 trnF-ndhJ CCTCGTGTCACCAGTTCAAA TTGGATAGGATGGCCTTTACG 733–743 1.000 68.8
trnF-ndhJ_p5 trnF-ndhJ CCTCGTGTCACCAGTTCAAA TGGATAGGATGGCCTTTACGT 732–742 1.000 67.9

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
Notoseris macilenta NC_066766.1 152174 View on NCBI ↗
Notoseris triflora NC_066767.1 152225 View on NCBI ↗