Markers + reference

Synotis

4 species · Asteraceae · Asterales

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Species 4
Genome length 151–151 kb
Candidate markers 275
Primer pairs 105

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 10 remaining regions by MarkerSeek score (out of 275 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 412 0.0320 1.00 70.8 yes View details
psbM-trnD-GUC LSC 626 0.0043 1.00 52.3 yes View details
rpoC1 LSC 2808 0.0012 1.00 42.6 yes View details
rps14-psaB LSC 967 0.0060 0.94 57.7 yes View details
ndhC-trnV-UAC LSC 766 0.0044 0.99 53.3 yes View details
accD-psaI LSC 667 0.0067 1.00 56.8 yes View details
ycf4 LSC 555 0.0036 1.00 32.8 yes View details
petA-psbJ LSC 773 0.0075 0.99 51.8 yes View details
ycf1 IRb 576 0.0000 1.00 39.5 no View details
ndhF-rpl32 SSC 1066 0.0036 1.00 38.2 yes View details
rpl32-trnL-UAG SSC 796 0.0136 1.00 68.2 yes View details
ycf1 SSC 5073 0.0023 1.00 40.9 yes View details
trnE-UUC-rpoB LSC 950 0.0030 1.00 61.2 yes View details
psbE-petL LSC 1235 0.0015 1.00 60.0 yes View details
matK LSC 1512 0.0014 1.00 59.7 yes View details
petN-psbM LSC 500 0.0040 1.00 59.2 yes View details
ndhF SSC 2226 0.0028 1.00 58.6 yes View details
trnS-GCU-trnC-GCA LSC 739 0.0032 1.00 56.5 yes View details
rps16-trnQ-UUG LSC 953 0.0017 1.00 56.0 yes View details
trnR-UCU-trnG-UCC LSC 244 0.0041 0.99 55.9 yes View details
trnF-GAA-ndhJ LSC 743 0.0013 0.98 55.4 yes View details
rps15-ycf1 SSC 212 0.0102 1.00 55.1 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 105 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 461–531 1.000 83.4
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCGTGCTAACCTTGGTATGG 475–545 1.000 83.3
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCGTGCTAACCTTGGTATGG 474–544 1.000 83.3
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCGTGCTAACCTTGGTATGG 476–546 1.000 83.3
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG ACCGTGCTAACCTTGGTATG 462–532 1.000 82.9
matK_p1 matK TCCTTACTACCTCAACATTTCAGA CCTTGTTTTGACTGTATCGCA 1694–1695 1.000 40.2
matK_p2 matK TCCTTACTACCTCAACATTTCAGA ACCTTGTTTTGACTGTATCGC 1695–1696 1.000 40.2
matK_p3 matK TCCTTACTACCTCAACATTTCAGA CCTTGTTTTGACTGTATCGCAC 1694–1695 1.000 40.2
matK_p4 matK TCCTTACTACCTCAACATTTCAGA ACCTTGTTTTGACTGTATCGCA 1695–1696 1.000 40.2
matK_p5 matK CCTTACTACCTCAACATTTCAGA CCTTGTTTTGACTGTATCGCA 1693–1694 1.000 40.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1026–1048 1.000 78.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG AGAATAAGAATCCACGCCGG GAGGTTCGAATCCTTCCGTC 1058–1080 1.000 77.7
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1041–1063 1.000 76.7
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1040–1062 1.000 76.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 1030–1052 1.000 73.8
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 890 1.000 78.5
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 872 1.000 76.3
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 826 1.000 74.6
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA AACGGAAAGAGAGGGATTCG CCGGATTTGAACTGGGGAAA 891 1.000 74.3
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 808 1.000 72.5
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 662 1.000 59.8
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 662 1.000 58.1
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 663 1.000 53.8
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 654 1.000 53.8
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 648 1.000 53.0
psbM-trnD-GUC_p1 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT TTCAATAGGCTAGAGCACCG 742–743 1.000 45.9
psbM-trnD-GUC_p2 psbM-trnD-GUC AAAATGAACAGTGCAGTAGC TTCAATAGGCTAGAGCACCG 736–737 1.000 45.5
psbM-trnD-GUC_p3 psbM-trnD-GUC ACTAAAATGAACAGTGCAGTAGC TTCAATAGGCTAGAGCACCG 739–740 1.000 44.5
psbM-trnD-GUC_p4 psbM-trnD-GUC GGAACTAAAATGAACAGTGCAGT CAATAGGCTAGAGCACCGC 740–741 1.000 44.3
psbM-trnD-GUC_p5 psbM-trnD-GUC AGGAACTAAAATGAACAGTGCAG TTCAATAGGCTAGAGCACCG 743–744 1.000 43.8

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
Synotis cavaleriei NC_069228.1 151341 View on NCBI ↗
Synotis duclouxii NC_069229.1 151305 View on NCBI ↗
Synotis erythropappa NC_080520.1 151228 View on NCBI ↗
Synotis nagensium NC_069230.1 151298 View on NCBI ↗