Markers + reference

Calypogeia

2 species · Calypogeiaceae · Jungermanniales

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Species 2
Genome length 120–120 kb
Candidate markers 270
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petN-trnC-GCA Genome 353 0.0482 1.00 68.6 yes View details
rpoC2 Genome 4206 0.0207 1.00 50.8 yes View details
trnH-GUG-ycf2 Genome 854 0.0328 0.96 67.7 yes View details
trnT-UGU-trnL-UAA Genome 270 0.0407 1.00 64.2 yes View details
trnR-CCG-accD Genome 267 0.0262 1.00 57.2 yes View details
petB Genome 1210 0.0273 1.00 61.1 yes View details
trnI-CAU-trnV-GAC Genome 485 0.0507 0.77 70.0 yes View details
rps15-ycf1 Genome 1696 0.0266 1.00 61.0 yes View details
ycf1 Genome 3147 0.0203 1.00 52.8 yes View details
trnV-GAC-rps12 Genome 684 0.0374 0.82 70.7 no View details
trnV-UAC-trnM-CAU Genome 171 0.0819 1.00 80.2 yes View details
ndhH-rps15 Genome 29 0.1034 1.00 77.6 yes View details
petA-psbJ Genome 134 0.0703 0.96 73.4 yes View details
rps11-rpl36 Genome 49 0.1224 1.00 73.4 yes View details
rbcL-trnR-CCG Genome 70 0.1143 1.00 72.8 yes View details
trnI-GAU-trnA-UGC Genome 78 0.0385 1.00 70.9 yes View details
trnA-UGC-trnI-GAU Genome 78 0.0385 1.00 70.9 yes View details
ndhl-ndhA Genome 105 0.0505 0.94 70.7 yes View details
psbA-trnH-GUG Genome 129 0.0465 1.00 70.4 yes View details
rps7-ndhB Genome 135 0.0519 1.00 70.1 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps7-ndhB_p1 rps7-ndhB GCTTTTGCGCATTTTCGTTA TGGAATACATTCGGGTAAAATTGT 219–220 1.000 42.6
rps7-ndhB_p2 rps7-ndhB GCTTTTGCGCATTTTCGTTA CAAAAATTGGAATACATTCGGGT 226–227 1.000 42.5
rps7-ndhB_p3 rps7-ndhB GCTTTTGCGCATTTTCGTTA AAATTGGAATACATTCGGGT 223–224 1.000 42.5
rps7-ndhB_p4 rps7-ndhB GCTTTTGCGCATTTTCGTTAA CAAAAATTGGAATACATTCGGGT 226–227 1.000 42.5
rps7-ndhB_p5 rps7-ndhB GCTTTTGCGCATTTTCGTTA AAAATTGGAATACATTCGGGT 224–225 1.000 42.5
petN-trnC-GCA_p1 petN-trnC-GCA AGCACCCCAAGCTATATTAGT CTGCAAATCCTTCATCCCCA 422–424 1.000 59.5
petN-trnC-GCA_p2 petN-trnC-GCA AGCACCCCAAGCTATATTAGT TGCAAATCCTTCATCCCCAG 421–423 1.000 59.5
petN-trnC-GCA_p3 petN-trnC-GCA AGCACCCCAAGCTATATTAGT ACTGCAAATCCTTCATCCCC 423–425 1.000 59.5
petN-trnC-GCA_p4 petN-trnC-GCA AGCACCCCAAGCTATATTAGT GCAAATCCTTCATCCCCAGT 420–422 1.000 59.5
petN-trnC-GCA_p5 petN-trnC-GCA AGCACCCCAAGCTATATTAGT GTAAGGCAAGGGACTGCAAA 435–437 1.000 57.5
rpoC2_p1 rpoC2 TGAAGGACGAACCAGCAAAA GGTCCCTCCTCCAAAGTAGT 1138 1.000 81.4
rpoC2_p2 rpoC2 TTGAAGGACGAACCAGCAAA GGTCCCTCCTCCAAAGTAGT 1139 1.000 81.4
rpoC2_p3 rpoC2 TGAAGGACGAACCAGCAAAA TTGCTTCCTCCAAAACACGA 1215 1.000 81.2
rpoC2_p4 rpoC2 TTGAAGGACGAACCAGCAAA TTGCTTCCTCCAAAACACGA 1216 1.000 81.2
rpoC2_p5 rpoC2 AGGACGAACCAGCAAAAACT TTGCTTCCTCCAAAACACGA 1212 1.000 81.2
psbA-trnH-GUG_p1 psbA-trnH-GUG CAACCGTGCTAACCTTGGTA CTGCCTTAATCCACTTGGCT 256 1.000 79.4
psbA-trnH-GUG_p2 psbA-trnH-GUG ATCAACCGTGCTAACCTTGG CTGCCTTAATCCACTTGGCT 258 1.000 79.4
psbA-trnH-GUG_p3 psbA-trnH-GUG CAACCGTGCTAACCTTGGTA GATCCACAATCCACTGCCTT 269 1.000 79.3
psbA-trnH-GUG_p4 psbA-trnH-GUG ATCAACCGTGCTAACCTTGG GATCCACAATCCACTGCCTT 271 1.000 79.3
psbA-trnH-GUG_p5 psbA-trnH-GUG CAACCGTGCTAACCTTGGTA ACTGCCTTAATCCACTTGGC 257 1.000 79.2
trnH-GUG-ycf2_p1 trnH-GUG-ycf2 TTGGGTATTAGCACCATGGC AACTTTCTGGAGATTCGCCC 1908–1927 1.000 82.5
trnH-GUG-ycf2_p2 trnH-GUG-ycf2 CCTTATGCATCCGTTCCACA AACTTTCTGGAGATTCGCCC 2194–2213 1.000 82.4
trnH-GUG-ycf2_p3 trnH-GUG-ycf2 AAGGCAGTGGATTGTGGATC AACTTTCTGGAGATTCGCCC 1558–1577 1.000 82.4
trnH-GUG-ycf2_p4 trnH-GUG-ycf2 ATCTGGTTCACTGCTTTGGG AACTTTCTGGAGATTCGCCC 1923–1942 1.000 82.3
trnH-GUG-ycf2_p5 trnH-GUG-ycf2 GCCAAGTGGATTAAGGCAGT AACTTTCTGGAGATTCGCCC 1570–1589 1.000 82.2
trnT-UGU-trnL-UAA_p1 trnT-UGU-trnL-UAA GACCTCTGAGCTAAACAGGC ACCAATTTCGCCATACTCCC 310 1.000 82.3
trnT-UGU-trnL-UAA_p2 trnT-UGU-trnL-UAA TACAAGTGCGATGCTCTGAC ACCAATTTCGCCATACTCCC 327 1.000 82.2
trnT-UGU-trnL-UAA_p3 trnT-UGU-trnL-UAA GACCTCTGAGCTAAACAGGC TAGCGTCTACCAATTTCGCC 318 1.000 82.1
trnT-UGU-trnL-UAA_p4 trnT-UGU-trnL-UAA TACAAGTGCGATGCTCTGAC TAGCGTCTACCAATTTCGCC 335 1.000 82.0
trnT-UGU-trnL-UAA_p5 trnT-UGU-trnL-UAA GCATTACAAGTGCGATGCTC ACCAATTTCGCCATACTCCC 331 1.000 81.5

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
Calypogeia fissa NC_043787.1 120500 View on NCBI ↗
Calypogeia suecica NC_071973.1 120116 View on NCBI ↗