Markers + reference

Dicranostigma

2 species · Papaveraceae · Ranunculales

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Species 2
Genome length 163–167 kb
Candidate markers 270
Primer pairs 70

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 7 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhC-atpB LSC 2131 0.1111 0.98 79.5 yes View details
atpB LSC 1488 0.4813 0.88 81.6 yes View details
atpE LSC 402 0.5101 0.86 77.0 yes View details
trnM-CAU-rbcL LSC 1120 0.3553 0.80 79.3 yes View details
rbcL-psaI LSC 3035 0.3181 0.72 78.2 yes View details
rpl14 IRb 369 0.0244 1.00 53.6 no View details
rpl16-rps3 IRb 772 0.4250 0.77 80.1 yes View details
rpl14 IRa 369 0.4375 0.17 62.9 yes View details
petA-psbJ LSC 1109 0.0550 0.97 86.3 yes View details
trnN-GUU-ndhF IRb 570 0.1578 0.96 82.4 yes View details
ccsA-ndhD SSC 204 0.0792 0.99 80.6 yes View details
trnT-UGU-trnL-UAA LSC 646 0.0339 0.96 80.1 yes View details
rps12-psbB LSC 3075 0.0909 0.94 78.7 yes View details
trnF-GAA-ndhJ LSC 674 0.0426 0.97 78.4 yes View details
rps15-trnN-GUU SSC 5911 0.1186 0.93 77.7 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG ATCCAATCAAGTCCGTAGCG 713–719 1.000 82.5
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CCGTAGCGTCTACCGATTTC 701–707 1.000 82.4
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GCGATGCTCTAACCTCTGAG CAATCAAGTCCGTAGCGTCT 710–716 1.000 82.1
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT ATCCAATCAAGTCCGTAGCG 745–751 1.000 81.4
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GGAATCGAACCGATGACCAT CCGTAGCGTCTACCGATTTC 733–739 1.000 81.3
trnF-GAA-ndhJ_p1 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA GTTGGATAGGATGGCCCTTG 779–806 1.000 84.0
trnF-GAA-ndhJ_p2 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA AGTTGGATAGGATGGCCCTT 780–807 1.000 83.4
trnF-GAA-ndhJ_p3 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA TCCACGCCTGAAACGTATTT 811–838 1.000 82.6
trnF-GAA-ndhJ_p4 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA CATCCACGCCTGAAACGTAT 813–840 1.000 81.2
trnF-GAA-ndhJ_p5 trnF-GAA-ndhJ CCTCGTGTCACCAGTTCAAA ATCCACGCCTGAAACGTATT 812–839 1.000 80.8
ndhC-atpB_p1 ndhC-atpB AGTACCGGAAACTCAGTGGA TGAATAGGGGATGTTGTGCG 2968 0.500 59.7
ndhC-atpB_p2 ndhC-atpB AGTACCGGAAACTCAGTGGA CATCCAGTACCGGACCAATG 2667 0.500 59.6
ndhC-atpB_p3 ndhC-atpB AGTACCGGAAACTCAGTGGA ATTGTATAAAGGCAGGCGCA 2994 0.500 59.5
ndhC-atpB_p4 ndhC-atpB GAAACTCATCGCCCATGGAT TGAATAGGGGATGTTGTGCG 2778 0.500 59.5
ndhC-atpB_p5 ndhC-atpB GAAACTCATCGCCCATGGAT CATCCAGTACCGGACCAATG 2477 0.500 59.4
atpB_p1 atpB TATGGCATTCACCCACGAAG TATTATTTGGACGCACCGCA 2493 0.500 59.5
atpB_p2 atpB TATGGCATTCACCCACGAAG CCGCCCATCAGAGCTATTTT 2257 0.500 59.5
atpB_p3 atpB ACCAATCAGCTTGCTATCGG TATTATTTGGACGCACCGCA 1984 0.500 59.5
atpB_p4 atpB ACCAATCAGCTTGCTATCGG CCGCCCATCAGAGCTATTTT 1748 0.500 59.5
atpB_p5 atpB TATGGCATTCACCCACGAAG TACGATGGGTCCCTTTTCCT 2778 0.500 59.4
atpE_p1 atpE TTGGTTTGACTGCCCTAACC TGGGTTCTATTTGGGGCCTA 1803 0.500 59.8
atpE_p2 atpE GCAGTTTATGTACCTGCGGA TGGGTTCTATTTGGGGCCTA 1573 0.500 59.8
atpE_p3 atpE TTGGTTTGACTGCCCTAACC TATTATTTGGACGCACCGCA 1178 0.500 59.7
atpE_p4 atpE TTGGTTTGACTGCCCTAACC TGGGCTGGGTATTCACCTTA 1842 0.500 59.7
atpE_p5 atpE GCAGTTTATGTACCTGCGGA TATTATTTGGACGCACCGCA 948 0.500 59.6
trnM-CAU-rbcL_p1 trnM-CAU-rbcL TGCGGTGCGTCCAAATAATA CGGTCTCTCCAACGCATAAA 2035 0.500 59.8
trnM-CAU-rbcL_p2 trnM-CAU-rbcL TGCGGTGCGTCCAAATAATA GTAAGTCCATCGGTCCACAC 1609 0.500 59.7
trnM-CAU-rbcL_p3 trnM-CAU-rbcL AAAATAGCTCTGATGGGCGG CGGTCTCTCCAACGCATAAA 2271 0.500 59.7
trnM-CAU-rbcL_p4 trnM-CAU-rbcL AAAATAGCTCTGATGGGCGG GTAAGTCCATCGGTCCACAC 1845 0.500 59.7
trnM-CAU-rbcL_p5 trnM-CAU-rbcL TATTGGGGTTCTGCCGATTG CGGTCTCTCCAACGCATAAA 1989 0.500 59.6

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
Dicranostigma lactucoides NC_081064.1 166819 View on NCBI ↗
Dicranostigma leptopodum NC_065057.1 162942 View on NCBI ↗