Markers + reference

Crepis

8 species · Asteraceae · Asterales

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Species 8
Genome length 148–152 kb
Candidate markers 275
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

8 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
trnC-GCA-petN LSC 787 0.0575 0.97 84.6 yes View details
trnT-GGU-psbD LSC 1006 0.0452 0.98 82.0 yes View details
trnT-UGU-trnL-UAA LSC 567 0.0705 0.99 88.6 yes View details
rbcL-accD LSC 509 0.0593 0.99 82.0 yes View details
ycf1 IRb 474 0.0174 1.00 54.8 no View details
ndhF-rpl32 SSC 1106 0.0607 0.95 85.6 yes View details
rpl32-trnL-UAG SSC 849 0.0684 0.97 80.7 yes View details
ycf1 SSC 5079 0.0590 0.98 78.0 yes View details
trnF-GAA-ndhJ LSC 626 0.0571 0.99 85.6 yes View details
rps16-trnQ-UUG LSC 945 0.0568 0.99 85.0 yes View details
psbM-trnD-GUC LSC 601 0.0462 0.95 84.4 yes View details
trnK-UUU-rps16 LSC 780 0.0468 0.99 83.9 yes View details
ycf3-trnS-GGA LSC 916 0.0498 0.99 83.7 yes View details
trnS-GCU-trnC-GCA LSC 751 0.0432 1.00 82.9 yes View details
petN-psbM LSC 496 0.0531 0.97 82.7 yes View details
ndhC-trnV-UAC LSC 967 0.0525 0.97 82.3 yes View details
psbE-petL LSC 1154 0.0414 1.00 82.3 yes View details
petA-psbJ LSC 777 0.0453 0.98 81.8 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG GCCGTACGAGGAGAAAACTT 1190–1233 1.000 91.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GCCGTACGAGGAGAAAACTT 1189–1232 1.000 91.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG ACGAATCAACCGTCGGTATG 1627–1675 1.000 90.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AGAACAAGGAAACACCGCTT 1494–1542 0.875 84.6
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AGAACAAGGAAACACCGCTT 1493–1541 0.875 84.6
rps16-trnQ-UUG_p1 rps16-trnQ-UUG GATCGTTGCCCCTGAGAAAT CTTACAGCAGCTTGCCAAAC 1747–1832 1.000 91.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GATCGTTGCCCCTGAGAAAT GAGGTTCGAATCCTTCCGTC 1163–1247 1.000 91.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG ATACCGACGGTTGATTCGTG CTTACAGCAGCTTGCCAAAC 1911–1996 1.000 90.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGCGGTGTTTCCTTGTTCT GAGGTTCGAATCCTTCCGTC 1511–1546 0.875 83.8
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGCGGTGTTTCCTTGTTCT CTTACAGCAGCTTGCCAAAC 2093–2131 0.875 83.1
trnS-GCU-trnC-GCA_p1 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC CCGGATTTGAACTGGGGAAA 831–849 1.000 84.2
trnS-GCU-trnC-GCA_p2 trnS-GCU-trnC-GCA CTTTCGTCCACTCAGCCATC AAAAGGATTTGCAGTCCCCC 813–831 1.000 82.0
trnS-GCU-trnC-GCA_p3 trnS-GCU-trnC-GCA TTTCGTCCACTCAGCCATCT CCGGATTTGAACTGGGGAAA 830–848 1.000 81.1
trnS-GCU-trnC-GCA_p4 trnS-GCU-trnC-GCA TCCACTCAGCCATCTCTCC CCGGATTTGAACTGGGGAAA 825–843 1.000 80.5
trnS-GCU-trnC-GCA_p5 trnS-GCU-trnC-GCA ATTAGCAATCCGCCGCTTT CCGGATTTGAACTGGGGAAA 846–864 1.000 79.6
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGCCCAAGCGAGACTTACTA 853–915 0.875 84.8
trnC-GCA-petN_p2 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGCCCAAGCGAGACTTACTA 871–933 0.875 82.5
trnC-GCA-petN_p3 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG ATCAACGGGCTATAATGGGC 1309–1379 0.500 63.1
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT ATCAACGGGCTATAATGGGC 1327–1397 0.500 60.9
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG GGCTATAATGGGCGGTAGTC 1302–1372 0.375 55.5
petN-psbM_p1 petN-psbM GCGGCTAACTAGTTGTGGAA TTTGATTGGTCCGGGAATCC 1460–1516 0.625 71.1
petN-psbM_p2 petN-psbM TCCGTTCTAGCGTCATTGTG GTCCCGACGGATCCAATAAC 1502–1519 0.375 58.5
petN-psbM_p3 petN-psbM TCCGTTCTAGCGTCATTGTG TTTGATTGGTCCGGGAATCC 1138–1152 0.375 57.9
petN-psbM_p4 petN-psbM TCCGTTCTAGCGTCATTGTG AGTCCCGACGGATCCAATAA 1503–1520 0.375 57.9
petN-psbM_p5 petN-psbM TCCGTTCTAGCGTCATTGTG CCGCGACTCATCTTTCTCAT 1356–1370 0.250 50.1
psbM-trnD-GUC_p1 psbM-trnD-GUC AAATGCAAGAATATTTACTTCCA CTGTCAAGGCGGACGTTG 654–750 1.000 52.0
psbM-trnD-GUC_p2 psbM-trnD-GUC AATGCAAGAATATTTACTTCCAT CTGTCAAGGCGGACGTTG 653–749 1.000 52.0
psbM-trnD-GUC_p3 psbM-trnD-GUC AAATGCAAGAATATTTACTTCCAT CTGTCAAGGCGGACGTTG 654–750 1.000 52.0
psbM-trnD-GUC_p4 psbM-trnD-GUC TAAATGCAAGAATATTTACTTCCA CTGTCAAGGCGGACGTTG 655–751 1.000 52.0
psbM-trnD-GUC_p5 psbM-trnD-GUC AAATGCAAGAATATTTACTTCCA CCTGTCAAGGCGGACGTT 655–751 1.000 52.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (8)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Crepis biennis PP693368.1 148458 View on NCBI ↗
Crepis capillaris PP693369.1 150652 View on NCBI ↗
Crepis froelichiana subsp. froelichiana PP693370.1 151592 View on NCBI ↗
Crepis paludosa PP693371.1 151652 View on NCBI ↗
Crepis pulchra subsp. pulchra PP693372.1 148908 View on NCBI ↗
Crepis purpurea PZ258326.1 149980 View on NCBI ↗
Crepis rigescens NC_061360.1 151330 View on NCBI ↗
Crepis vesicaria subsp. taraxacifolia PP693373.1 150614 View on NCBI ↗