Markers + reference

Tephroseris

2 species · Asteraceae · Asterales

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Species 2
Genome length 151–151 kb
Candidate markers 272
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 8 remaining regions by MarkerSeek score (out of 272 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnC-GCA LSC 735 0.0014 1.00 54.4 yes View details
trnC-GCA-petN LSC 803 0.0025 1.00 60.2 yes View details
petN-psbM LSC 492 0.0041 1.00 58.8 yes View details
rps2 LSC 711 0.0028 1.00 60.4 yes View details
atpH-atpF LSC 391 0.0153 1.00 63.2 yes View details
trnR-UCU-trnG-UCC LSC 213 0.0000 1.00 26.9 yes View details
accD-psaI LSC 678 0.0044 1.00 61.3 yes View details
psbE-petL LSC 1226 0.0025 0.99 54.4 yes View details
rpl20-rps12 LSC 742 0.0040 1.00 61.1 yes View details
ndhF-rpl32 SSC 1022 0.0029 1.00 60.8 yes View details
rpl32-trnL-UAG SSC 811 0.0038 0.98 62.8 yes View details
rps15 SSC 279 0.0036 1.00 40.8 yes View details
atpA-trnR-UCU LSC 110 0.0182 1.00 63.0 yes View details
trnT-GGU-psbD LSC 1220 0.0017 0.98 61.2 yes View details
trnT-UGU-trnL-UAA LSC 613 0.0000 0.98 61.0 yes View details
rpl16 LSC 1442 0.0007 0.99 60.6 yes View details
rps16-trnQ-UUG LSC 963 0.0010 0.99 60.4 yes View details
psaA-pafI LSC 713 0.0028 1.00 60.4 yes View details
matK-trnK-UUU LSC 759 0.0000 0.99 60.2 yes View details
petL-petG LSC 153 0.0131 1.00 60.0 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
trnK-UUU_p1 trnK-UUU GGGGTTTGCAAAAATGAAAAAGG TTCGTAGATTAATGCTTTGATTT 2761–2774 1.000 40.8
trnK-UUU_p2 trnK-UUU GGGGTTTGCAAAAATGAAAAAGG TTTCGTAGATTAATGCTTTGATT 2762–2775 1.000 40.8
trnK-UUU_p3 trnK-UUU GGGGTTTGCAAAAATGAAAAAGG TTTCGTAGATTAATGCTTTGATTT 2762–2775 1.000 40.8
trnK-UUU_p4 trnK-UUU GGGGTTTGCAAAAATGAAAAAGG ATTTCGTAGATTAATGCTTTGAT 2763–2776 1.000 40.8
trnK-UUU_p5 trnK-UUU GGGGTTTGCAAAAATGAAAAAGG ATTTCGTAGATTAATGCTTTGATT 2763–2776 1.000 40.8
matK-trnK-UUU_p1 matK-trnK-UUU ACCATGATCATGAGCAAGTACA AACGGTAGAGTACTCGGCTT 881–891 1.000 59.7
matK-trnK-UUU_p2 matK-trnK-UUU ACCATGATCATGAGCAAGTACA ACGGTAGAGTACTCGGCTTT 880–890 1.000 59.7
matK-trnK-UUU_p3 matK-trnK-UUU ACCATGATCATGAGCAAGTACA TTGGGTTGCTAACTCAACGG 896–906 1.000 57.8
matK-trnK-UUU_p4 matK-trnK-UUU ACCATGATCATGAGCAAGTACA GGGTTGCTAACTCAACGGTA 894–904 1.000 57.4
matK-trnK-UUU_p5 matK-trnK-UUU AACCATGATCATGAGCAAGT ACGGTAGAGTACTCGGCTTT 881–891 1.000 55.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1036–1053 1.000 79.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GTGGTAAGAATCCACGTCGG GAGGTTCGAATCCTTCCGTC 1068–1085 1.000 77.3
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGGATCGTGTCCTTCAAGTC GAGGTTCGAATCCTTCCGTC 1051–1068 1.000 77.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATCGTGTCCTTCAAGTCG GAGGTTCGAATCCTTCCGTC 1050–1067 1.000 77.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GTCGGATCGTGTCCTTCAAG GAGGTTCGAATCCTTCCGTC 1053–1070 1.000 77.3
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA CCGGATTTGAACTGGGGAAA 886–887 1.000 78.2
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA ACGGAAAGAGAGGGATTCGA AAAAGGATTTGCAGTCCCCC 868–869 1.000 76.0
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 822–823 1.000 74.4
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA AACGGAAAGAGAGGGATTCG CCGGATTTGAACTGGGGAAA 887–888 1.000 74.0
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 804–805 1.000 72.2
trnC-GCA-petN_p1 trnC-GCA-petN GTTGTGTATCGTTTTGGCGG AGCCCAAGCGAGACTTACTA 916 1.000 78.6
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 859 1.000 78.3
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 877 1.000 76.1
trnC-GCA-petN_p4 trnC-GCA-petN TGTTGTGTATCGTTTTGGCG AGCCCAAGCGAGACTTACTA 917 1.000 73.6
trnC-GCA-petN_p5 trnC-GCA-petN GTTGTGTATCGTTTTGGCGG GCCCAAGCGAGACTTACTAT 915 1.000 72.7
petN-psbM_p1 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTT 654 1.000 59.7
petN-psbM_p2 petN-psbM TAGTAAGTCTCGCTTGGGCT TGCTACTGCACTGTTCATTTT 654 1.000 58.0
petN-psbM_p3 petN-psbM ATAGTAAGTCTCGCTTGGGC TGCTACTGCACTGTTCATTT 655 1.000 53.7
petN-psbM_p4 petN-psbM CTCGCTTGGGCTGCTTTAAT TGCTACTGCACTGTTCATTT 646 1.000 53.7
petN-psbM_p5 petN-psbM TGGGCTGCTTTAATGGTAGTC TGCTACTGCACTGTTCATTT 640 1.000 52.9

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
Tephroseris kirilowii PV955039.1 150601 View on NCBI ↗
Tephroseris longifolia subsp. gaudinii OR990551.1 150540 View on NCBI ↗