Markers + reference

Plagiomnium

2 species · Mniaceae · Bryales

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Species 2
Genome length 125–125 kb
Candidate markers 253
Primer pairs 80

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 9 remaining regions by MarkerSeek score (out of 253 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl14-rps8 Genome 337 0.0000 1.00 23.6 yes View details
petD Genome 1121 0.0009 1.00 59.3 yes View details
trnW-CCA-petG Genome 132 0.0000 1.00 33.8 yes View details
psbE Genome 252 0.0000 1.00 25.4 yes View details
psaI-accD Genome 277 0.0000 1.00 26.7 yes View details
accD Genome 930 0.0011 1.00 59.4 yes View details
rbcL-atpB Genome 559 0.0018 1.00 58.9 yes View details
ycf1 Genome 4809 0.0004 1.00 53.0 yes View details
rrn16-trnI-CAU Genome 1690 0.0000 0.94 63.0 no View details
atpI Genome 747 0.0013 1.00 59.5 yes View details
ycf66 Genome 985 0.0010 1.00 59.3 yes View details
psbC Genome 1422 0.0007 1.00 59.2 yes View details
atpF Genome 1232 0.0000 1.00 58.9 yes View details
petL Genome 96 0.0104 1.00 58.5 yes View details
ycf3 Genome 1857 0.0000 1.00 58.1 yes View details
ndhF Genome 2151 0.0005 1.00 57.7 yes View details
psaA Genome 2253 0.0004 1.00 57.4 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
rpl14-rps8_p1 rpl14-rps8 CCCTGTCGCACGAGAATTAA CAAGTTCGCGTTCCTTATAT 461 1.000 44.3
rpl14-rps8_p2 rpl14-rps8 AAGGAACACGTGTTTTTGGC CAAGTTCGCGTTCCTTATAT 480 1.000 42.1
rpl14-rps8_p3 rpl14-rps8 CCCTGTCGCACGAGAATTAA CAAGTTCGCGTTCCTTATATATGT 461 1.000 41.8
rpl14-rps8_p4 rpl14-rps8 CCCTGTCGCACGAGAATTAA AGTTCGCGTTCCTTATATATGT 459 1.000 41.4
rpl14-rps8_p5 rpl14-rps8 AAGGAACACGTGTTTTTGGC CAAGTTCGCGTTCCTTATATATGT 480 1.000 40.0
petD_p1 petD AGTTTGCGCAAAGGTAAACG GGTCGGCAAGTATGATGGTT 2322 1.000 78.8
petD_p2 petD GCGGACAAGTTGTTTCTTGG GGTCGGCAAGTATGATGGTT 2231 1.000 78.8
petD_p3 petD TCCAGGACGAGATACAGCTT GGTCGGCAAGTATGATGGTT 2074 1.000 78.6
petD_p4 petD AGTTTGCGCAAAGGTAAACG ACCTCTCTTAACTGCGGTCT 2012 1.000 78.5
petD_p5 petD TGCGCAAAGGTAAACGTAGA GGTCGGCAAGTATGATGGTT 2318 1.000 78.5
trnW-CCA-petG_p1 trnW-CCA-petG AAGCGCTCTTAGTTCAGTCC GCTGGATCATTTGTAACCGC 268 1.000 73.2
trnW-CCA-petG_p2 trnW-CCA-petG AGAACGCAGGTCTCCAAAAC GCTGGATCATTTGTAACCGC 245 1.000 73.0
trnW-CCA-petG_p3 trnW-CCA-petG GTAGAACGCAGGTCTCCAAA GCTGGATCATTTGTAACCGC 247 1.000 72.6
trnW-CCA-petG_p4 trnW-CCA-petG AAGCGCTCTTAGTTCAGTCC TGGATCATTTGTAACCGCCT 266 1.000 70.6
trnW-CCA-petG_p5 trnW-CCA-petG AGAACGCAGGTCTCCAAAAC TGGATCATTTGTAACCGCCT 243 1.000 70.4
petL_p1 petL TCGAGAAATACAATGAAATTAATCTGA AGGTAATTGTTTTAGAAAAGATGT 212 1.000 40.4
petL_p2 petL CGAGAAATACAATGAAATTAATCTGAC AGGTAATTGTTTTAGAAAAGATGT 211 1.000 40.4
petL_p3 petL ACAATGAAATTAATCTGACCTTAA AGGTAATTGTTTTAGAAAAGATGT 203 1.000 40.4
petL_p4 petL AGAAATACAATGAAATTAATCTGACCT AGGTAATTGTTTTAGAAAAGATGT 209 1.000 40.4
petL_p5 petL TGAAATTAATCTGACCTTAAAAGT AGGTAATTGTTTTAGAAAAGATGT 199 1.000 40.4
psbE_p1 psbE AGCCTCTACAAATATATATGGAGCT GGCCAACCACCTAACTGTAA 338 1.000 40.0
psbE_p2 psbE AGCCTCTACAAATATATATGGAGCT TAGGTACAGCTAGTCCGTGC 360 1.000 40.0
psbE_p3 psbE ACACTGATAATCTAACTAGGCT GGCCAACCACCTAACTGTAA 425–426 1.000 40.0
psbE_p4 psbE AGCCTCTACAAATATATATGGAGCT TGTAGGTACAGCTAGTCCGT 362 1.000 40.0
psbE_p5 psbE ACACTGATAATCTAACTAGGCT TAGGTACAGCTAGTCCGTGC 447–448 1.000 40.0
psaI-accD_p1 psaI-accD AAGCCATTGTAATCGCTGGA ACTTGATTTAATTGTCCCACGT 456 1.000 46.8
psaI-accD_p2 psaI-accD AGCCATTGTAATCGCTGGAA ACTTGATTTAATTGTCCCACGT 455 1.000 46.8
psaI-accD_p3 psaI-accD GAAGCCATTGTAATCGCTGG ACTTGATTTAATTGTCCCACGT 457 1.000 44.0
psaI-accD_p4 psaI-accD AGCCATTGTAATCGCTGGAA ACTTGATTTAATTGTCCCACG 455 1.000 40.5
psaI-accD_p5 psaI-accD AGCCATTGTAATCGCTGGAA CTTGATTTAATTGTCCCACGT 454 1.000 40.5

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
Plagiomnium cuspidatum OR113698.1 125199 View on NCBI ↗
Plagiomnium rostratum PP580048.1 125196 View on NCBI ↗