Markers + reference

Calyptothecium

2 species · Pterobryaceae · Hypnales

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Species 2
Genome length 124–125 kb
Candidate markers 259
Primer pairs 75

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 259 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf2 Genome 6945 0.0029 1.00 54.2 yes View details
rbcL Genome 1428 0.0042 1.00 49.2 yes View details
psaI-ycf4 Genome 352 0.0341 1.00 60.5 yes View details
petD-rps11 Genome 320 0.0219 1.00 65.8 yes View details
rpl23-trnI-CAU Genome 203 0.0050 1.00 44.9 yes View details
ndhE Genome 303 0.0033 1.00 42.8 yes View details
atpE-atpB Genome 6 0.1667 1.00 87.5 yes View details
ndhG Genome 603 0.0050 1.00 61.6 yes View details
trnF-GAA Genome 73 0.0137 1.00 60.4 yes View details
trnV-GAC-rps12 Genome 1278 0.0024 1.00 60.4 no View details
chlB-trnK-UUU Genome 738 0.0027 1.00 60.3 yes View details
chlL Genome 876 0.0023 1.00 60.1 yes View details
cemA Genome 1518 0.0020 1.00 59.8 yes View details
rpl16 Genome 1263 0.0032 1.00 59.8 yes View details
trnT-GGU-psbD Genome 664 0.0015 1.00 59.6 yes View details
ndhA Genome 1847 0.0027 1.00 59.6 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
chlB-trnK-UUU_p1 chlB-trnK-UUU TGAAAAATTCGCGCGTCAAA AGTCGCACTTAAAAGCCGAG 865–866 1.000 74.8
chlB-trnK-UUU_p2 chlB-trnK-UUU TGAAAAATTCGCGCGTCAAA TAGTCGCACTTAAAAGCCGA 866–867 1.000 73.5
chlB-trnK-UUU_p3 chlB-trnK-UUU TGAAAAATTCGCGCGTCAAA TCGCACTTAAAAGCCGAGTA 863–864 1.000 73.5
chlB-trnK-UUU_p4 chlB-trnK-UUU TGAAAAATTCGCGCGTCAAA CGCACTTAAAAGCCGAGTAC 862–863 1.000 73.1
chlB-trnK-UUU_p5 chlB-trnK-UUU CTGAAAAATTCGCGCGTCAA AGTCGCACTTAAAAGCCGAG 866–867 1.000 73.0
ycf2_p1 ycf2 TAATAGATTCTTCACGTGGAA TGCTGAATGCTTTTGTCAGT 250 1.000 41.0
ycf2_p2 ycf2 TTAATAGATTCTTCACGTGGA TGCTGAATGCTTTTGTCAGT 251 1.000 41.0
ycf2_p3 ycf2 TTCACGTGGAAGATATTTAGA TGCTGAATGCTTTTGTCAGT 240 1.000 41.0
ycf2_p4 ycf2 TTAATAGATTCTTCACGTGGAA TGCTGAATGCTTTTGTCAGT 251 1.000 41.0
ycf2_p5 ycf2 TTTAATAGATTCTTCACGTGGA TGCTGAATGCTTTTGTCAGT 252 1.000 41.0
trnT-GGU-psbD_p1 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG TCTTCGTAGCCAGTCATCCA 797–806 1.000 78.4
trnT-GGU-psbD_p2 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA TCTTCGTAGCCAGTCATCCA 800–809 1.000 78.2
trnT-GGU-psbD_p3 trnT-GGU-psbD GGCGTAAGTCATCGGTTCAA TCTTCGTAGCCAGTCATCCA 774–783 1.000 76.6
trnT-GGU-psbD_p4 trnT-GGU-psbD GTGGTAGAGTAACGCCATGG CGATCTCTTCGTAGCCAGTC 802–811 1.000 76.4
trnT-GGU-psbD_p5 trnT-GGU-psbD TCAGTGGTAGAGTAACGCCA CGATCTCTTCGTAGCCAGTC 805–814 1.000 76.3
trnF-GAA_p1 trnF-GAA TGCAGAGACTCAATGGAAGC GGGCGATTATCTGGTTGGTT 978 1.000 78.8
trnF-GAA_p2 trnF-GAA GGGTATGGCGGAATTGGTAG GGGCGATTATCTGGTTGGTT 1134 1.000 78.8
trnF-GAA_p3 trnF-GAA AAGTCCCTCTACCCCCAAAA GGGCGATTATCTGGTTGGTT 803 1.000 78.5
trnF-GAA_p4 trnF-GAA TGCAGAGACTCAATGGAAGC AGTTGGATTGGTTGGCCTTT 579 1.000 78.5
trnF-GAA_p5 trnF-GAA GGAATTGGTAGACGCTACGG GGGCGATTATCTGGTTGGTT 1125 1.000 78.4
atpE-atpB_p1 atpE-atpB CGGCCACTGTTTGTAGATGA AGGCTGCAACCTTACAAGTG 124 1.000 76.8
atpE-atpB_p2 atpE-atpB TCGGCCACTGTTTGTAGATG AGGCTGCAACCTTACAAGTG 125 1.000 76.8
atpE-atpB_p3 atpE-atpB CGGCCACTGTTTGTAGATGA GCTGCAACCTTACAAGTGGA 122 1.000 76.7
atpE-atpB_p4 atpE-atpB TCGGCCACTGTTTGTAGATG GCTGCAACCTTACAAGTGGA 123 1.000 76.7
atpE-atpB_p5 atpE-atpB CGGCCACTGTTTGTAGATGA TGAAGCTACTGCAAAGGCTG 138 1.000 76.0
rbcL_p1 rbcL TCATAGCAACAGCTCGAACC CTTCATCCATAGGCTGCCAG 2887–2888 1.000 79.4
rbcL_p2 rbcL CATAGCAACAGCTCGAACCT CTTCATCCATAGGCTGCCAG 2886–2887 1.000 79.4
rbcL_p3 rbcL CACTCATAGCAACAGCTCGA CTTCATCCATAGGCTGCCAG 2890–2891 1.000 77.2
rbcL_p4 rbcL CCCACTCATAGCAACAGCTC CTTCATCCATAGGCTGCCAG 2892–2893 1.000 76.8
rbcL_p5 rbcL TTGAGTTGTAGGGAGGGACC CTTCATCCATAGGCTGCCAG 2182–2183 1.000 76.8

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
Calyptothecium hookeri OL405127.1 124401 View on NCBI ↗
Calyptothecium philippinense OL415138.1 124513 View on NCBI ↗