Markers + reference

Dicranum

2 species · Dicranaceae · Dicranales

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Species 2
Genome length 124–124 kb
Candidate markers 254
Primer pairs 80

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 254 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petB Genome 1216 0.0049 1.00 54.0 yes View details
psbZ-trnS-UGA Genome 222 0.0225 1.00 56.0 yes View details
psbD-trnT-GGU Genome 518 0.0155 1.00 51.4 yes View details
trnC-GCA-psbM Genome 1486 0.0128 1.00 53.8 yes View details
psbM-trnL-CAA Genome 226 0.0000 1.00 24.1 yes View details
trnV-GAC-rpl23 Genome 1567 0.0045 1.00 47.0 no View details
psbN-psbT Genome 82 0.0732 1.00 84.1 yes View details
trnL-CAA-ndhB Genome 193 0.0213 0.97 67.2 yes View details
rbcL-atpB Genome 551 0.0038 0.97 63.2 yes View details
atpF-atpH Genome 307 0.0163 1.00 62.0 yes View details
psbJ-petA Genome 1104 0.0045 1.00 61.4 yes View details
rps3 Genome 657 0.0061 1.00 61.0 yes View details
rps12-rpl20 Genome 824 0.0036 1.00 61.0 yes View details
rps12-trnV-GAC Genome 1375 0.0036 1.00 60.9 yes View details
ndhH Genome 1176 0.0034 1.00 60.7 yes View details
trnK-UUU-chlB Genome 897 0.0100 1.00 60.6 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps3_p1 rps3 AGCCCAAGGACGAGGATATC GGTCGCACACTAAGCATAAC 890 1.000 66.4
rps3_p2 rps3 GAGCCCAAGGACGAGGATAT GGTCGCACACTAAGCATAAC 891 1.000 66.4
rps3_p3 rps3 GAGCCCAAGGACGAGGATA GGTCGCACACTAAGCATAAC 891 1.000 62.2
rps3_p4 rps3 AGCCCAAGGACGAGGATATC GGTCGCACACTAAGCATAACA 890 1.000 61.8
rps3_p5 rps3 GAGCCCAAGGACGAGGATAT GGTCGCACACTAAGCATAACA 891 1.000 61.8
petB_p1 petB TGTTAATACCTTCATTCAAATAGCT TGGTAGTTTAATCGTGTAAGCA 1286–1292 1.000 40.4
petB_p2 petB TGTTAATACCTTCATTCAAATAGCT TGGTAGTTTAATCGTGTAAGCAA 1286–1292 1.000 40.4
petB_p3 petB TTGTTAATACCTTCATTCAAATAGCT TGGTAGTTTAATCGTGTAAGCA 1287–1293 1.000 40.4
petB_p4 petB TGTTAATACCTTCATTCAAATAGC TGGTAGTTTAATCGTGTAAGCA 1286–1292 1.000 40.4
petB_p5 petB TGTTAATACCTTCATTCAAATAGCT ATGGTAGTTTAATCGTGTAAGCA 1287–1293 1.000 40.4
psbN-psbT_p1 psbN-psbT CAGCTTTTGGACAACCCTCT TCGTGAACCTCCCAAAATTCA 181 1.000 72.8
psbN-psbT_p2 psbN-psbT ACAGCTTTTGGACAACCCTC TCGTGAACCTCCCAAAATTCA 182 1.000 70.4
psbN-psbT_p3 psbN-psbT CAGCTTTTGGACAACCCTCT CGTGAACCTCCCAAAATTCA 180 1.000 68.5
psbN-psbT_p4 psbN-psbT CAGCTTTTGGACAACCCTCT CGTGAACCTCCCAAAATTCAA 180 1.000 66.6
psbN-psbT_p5 psbN-psbT CAGCTTTTGGACAACCCTCT TCGTGAACCTCCCAAAATTC 181 1.000 66.2
rps12-rpl20_p1 rps12-rpl20 CTCAACGACGAGGAGTTTGT CCTCGAAACCCCGATGTAAG 932–933 1.000 78.7
rps12-rpl20_p2 rps12-rpl20 CTCAACGACGAGGAGTTTGT CTCGAAACCCCGATGTAAGG 931–932 1.000 78.7
rps12-rpl20_p3 rps12-rpl20 ACAAAATCTCCAGCCCTTCG CCTCGAAACCCCGATGTAAG 960–961 1.000 78.4
rps12-rpl20_p4 rps12-rpl20 ACAAAATCTCCAGCCCTTCG CTCGAAACCCCGATGTAAGG 959–960 1.000 78.4
rps12-rpl20_p5 rps12-rpl20 CTCAACGACGAGGAGTTTGT AATTTCGAATGAGCCCCTCG 947–948 1.000 76.6
psbJ-petA_p1 psbJ-petA GCAAATACCACCGGAAGAAT GCACAAATATTTTCGGTACCCA 1293–1300 1.000 43.4
psbJ-petA_p2 psbJ-petA GGCTCATACTCTGGATTAGGG GCACAAATATTTTCGGTACCCA 1206–1213 1.000 42.9
psbJ-petA_p3 psbJ-petA GCAAATACCACCGGAAGAATTC GCACAAATATTTTCGGTACCCA 1293–1300 1.000 42.4
psbJ-petA_p4 psbJ-petA GCAAATACCACCGGAAGAAT TCGGTACCCAAAAAGAAACA 1281–1288 1.000 41.9
psbJ-petA_p5 psbJ-petA GCAAATACCACCGGAAGAATT GCACAAATATTTTCGGTACCCA 1293–1300 1.000 41.5
rbcL-atpB_p1 rbcL-atpB GTCTCCGTTTGTGGTGACAT AGCAATGAGTGTGGAAGTCC 598–616 1.000 80.3
rbcL-atpB_p2 rbcL-atpB GTCTCCGTTTGTGGTGACAT AGGCATTTTACCTGGGGAGA 670–688 1.000 79.0
rbcL-atpB_p3 rbcL-atpB AACACCTGCTTTAGTCTCCG AGCAATGAGTGTGGAAGTCC 611–629 1.000 77.5
rbcL-atpB_p4 rbcL-atpB CACCTGCTTTAGTCTCCGTT AGCAATGAGTGTGGAAGTCC 609–627 1.000 77.5
rbcL-atpB_p5 rbcL-atpB GTCTCCGTTTGTGGTGACAT GGCATTTTACCTGGGGAGAA 669–687 1.000 77.3

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
Dicranum hengduanensis NC_080897.1 123908 View on NCBI ↗
Dicranum motuoense PQ821713.1 123936 View on NCBI ↗