Markers + reference

Paragynoxys

2 species · Asteraceae · Asterales

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Species 2
Genome length 151–151 kb
Candidate markers 272
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 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
petN-psbM LSC 500 0.0040 0.99 47.6 yes View details
psaB LSC 2205 0.0023 1.00 58.6 yes View details
trnT-TGT-trnL-TAA LSC 622 0.0067 0.97 59.7 yes View details
psbE-petL LSC 1231 0.0051 0.96 65.1 yes View details
rpl14 LSC 369 0.0000 1.00 26.3 yes View details
trnL-CAA-ndhB IRb 574 0.0139 1.00 53.8 yes View details
ndhB IRb 2204 0.0009 1.00 43.6 no View details
ndhH SSC 1179 0.0076 1.00 53.7 yes View details
ndhD SSC 1503 0.0060 1.00 62.2 yes View details
trnL-TAG-rpl32 SSC 804 0.0062 1.00 62.3 yes View details
ndhB IRa 2204 0.0009 1.00 43.6 yes View details
rpl36-infA LSC 115 0.0174 1.00 62.5 yes View details
rpl14-rpl16 LSC 119 0.0360 0.93 62.4 yes View details
ndhC-trnV-TAC LSC 757 0.0040 1.00 61.0 yes View details
trnE-TTC-rpoB LSC 747 0.0027 0.99 60.9 yes View details
psbM-trnD-GTC LSC 643 0.0031 1.00 60.5 yes View details
atpB-rbcL LSC 736 0.0027 1.00 60.3 yes View details
rpl20-rps12 LSC 742 0.0027 1.00 60.3 yes View details
rpl32-ndhF SSC 1062 0.0028 1.00 60.3 yes View details
petB LSC 1410 0.0021 1.00 60.0 yes View details
accD LSC 1497 0.0020 1.00 59.9 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
petN-psbM_p1 petN-psbM AGTATGGGGAAGAAGTGGACT TGCTACTGCACTGTTCATTT 604 1.000 51.2
petN-psbM_p2 petN-psbM AGTATGGGGAAGAAGTGGACT TGCTACTGCACTGTTCATTTT 604 1.000 49.5
petN-psbM_p3 petN-psbM CCCTTTCACTCGTAGTATGGG TGCTACTGCACTGTTCATTT 617 1.000 49.2
petN-psbM_p4 petN-psbM CCTTTCACTCGTAGTATGGGG TGCTACTGCACTGTTCATTT 616 1.000 49.2
petN-psbM_p5 petN-psbM CGTAGTATGGGGAAGAAGTGG TGCTACTGCACTGTTCATTT 607 1.000 49.2
psbM-trnD-GTC_p1 psbM-trnD-GTC GGAACTAAAATGAACAGTGCAGT TTCAATAGGCTAGAGCACCG 760–766 1.000 45.6
psbM-trnD-GTC_p2 psbM-trnD-GTC AAAATGAACAGTGCAGTAGC TTCAATAGGCTAGAGCACCG 754–760 1.000 45.1
psbM-trnD-GTC_p3 psbM-trnD-GTC ACTAAAATGAACAGTGCAGTAGC TTCAATAGGCTAGAGCACCG 757–763 1.000 44.2
psbM-trnD-GTC_p4 psbM-trnD-GTC GGAACTAAAATGAACAGTGCAGT CAATAGGCTAGAGCACCGC 758–764 1.000 43.9
psbM-trnD-GTC_p5 psbM-trnD-GTC AGGAACTAAAATGAACAGTGCAG TTCAATAGGCTAGAGCACCG 761–767 1.000 43.5
trnE-TTC-rpoB_p1 trnE-TTC-rpoB GGGAGTTGAACCCTCGTTTT GTTCTTCTGTCAAACCCCGA 884–888 1.000 78.4
trnE-TTC-rpoB_p2 trnE-TTC-rpoB GGGAGTTGAACCCTCGTTTT AGTTCTTCTGTCAAACCCCG 885–889 1.000 78.4
trnE-TTC-rpoB_p3 trnE-TTC-rpoB TAACCACTGGACCATAGGGG GTTCTTCTGTCAAACCCCGA 843–847 1.000 77.8
trnE-TTC-rpoB_p4 trnE-TTC-rpoB TAACCACTGGACCATAGGGG AGTTCTTCTGTCAAACCCCG 844–848 1.000 77.7
trnE-TTC-rpoB_p5 trnE-TTC-rpoB CCCTCGTTTTCTCCGTGAAA GTTCTTCTGTCAAACCCCGA 874–878 1.000 77.6
psaB_p1 psaB GGCGGATCTCTTCTTCATCG ACAACATGGGCGTTCTTCTT 2340 1.000 78.2
psaB_p2 psaB GGCGGATCTCTTCTTCATCG TACAAGGACGTGCTGTAGGA 2390 1.000 77.7
psaB_p3 psaB GGCGGATCTCTTCTTCATCG GGGCGTTCTTCTTAGCAAGA 2333 1.000 77.6
psaB_p4 psaB GGCGGATCTCTTCTTCATCG TGGGCGTTCTTCTTAGCAAG 2334 1.000 76.9
psaB_p5 psaB GGCGGATCTCTTCTTCATCG AGGACGTGCTGTAGGAGTAA 2386 1.000 76.7
trnT-TGT-trnL-TAA_p1 trnT-TGT-trnL-TAA GCGATGCTCTAACCTCTGAG CCGTAGCGTCTACCGATTTC 662–683 1.000 79.9
trnT-TGT-trnL-TAA_p2 trnT-TGT-trnL-TAA GGAATCGAACCGATGACCAT CCGTAGCGTCTACCGATTTC 694–715 1.000 78.9
trnT-TGT-trnL-TAA_p3 trnT-TGT-trnL-TAA GCGATGCTCTAACCTCTGAG CGTCTACCGATTTCGCCATA 656–677 1.000 78.7
trnT-TGT-trnL-TAA_p4 trnT-TGT-trnL-TAA GGAATCGAACCGATGACCAT CGTCTACCGATTTCGCCATA 688–709 1.000 77.7
trnT-TGT-trnL-TAA_p5 trnT-TGT-trnL-TAA GCGATGCTCTAACCTCTGAG CGTAGCGTCTACCGATTTCG 661–682 1.000 77.0
ndhC-trnV-TAC_p1 ndhC-trnV-TAC CCCTTTGCTAATCGGAGCTA AGAAGGTCTACGGTTCGAGT 901 1.000 71.4
ndhC-trnV-TAC_p2 ndhC-trnV-TAC TCGGAGCTAAAAATCCCGAA AGAAGGTCTACGGTTCGAGT 890 1.000 70.2
ndhC-trnV-TAC_p3 ndhC-trnV-TAC CCCTTTGCTAATCGGAGCTAA AGAAGGTCTACGGTTCGAGT 901 1.000 69.1
ndhC-trnV-TAC_p4 ndhC-trnV-TAC CCCTTTGCTAATCGGAGCTA GAAGGTCTACGGTTCGAGTC 900 1.000 68.7
ndhC-trnV-TAC_p5 ndhC-trnV-TAC GGCCCTTTGCTAATCGGAG AGAAGGTCTACGGTTCGAGT 903 1.000 68.4

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
Paragynoxys martingrantii NC_062448.1 150996 View on NCBI ↗
Paragynoxys venezuelae NC_062444.1 150927 View on NCBI ↗