Markers + reference

Rhodobryum

2 species · Bryaceae · Bryales

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Species 2
Genome length 124–125 kb
Candidate markers 266
Primer pairs 85

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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnI-CAU-rpl23 Genome 242 0.0996 1.00 73.4 yes View details
psbZ-trnS-UGA Genome 213 0.1005 0.98 75.9 yes View details
ycf2 Genome 6846 0.0391 1.00 61.2 yes View details
rpoC1 Genome 2768 0.0372 1.00 64.6 yes View details
trnC-GCA-ycf66 Genome 484 0.0707 0.99 74.6 yes View details
ndhB Genome 2155 0.0375 0.99 69.1 yes View details
trnK-UUU-chlB Genome 676 0.0643 0.99 82.2 yes View details
trnR-UCU-atpA Genome 148 0.1361 0.99 81.2 yes View details
ycf2-trnH-GUG Genome 373 0.0587 0.96 76.2 yes View details
psbI-trnS-GCU Genome 113 0.0826 0.96 75.9 yes View details
trnR-CCG-rbcL Genome 233 0.0826 0.94 75.4 yes View details
trnE-UUC-trnY-GUA Genome 116 0.0690 1.00 75.2 yes View details
trnF-GAA-trnL-UAA Genome 60 0.0667 1.00 75.0 yes View details
trnS-GCU-psaM Genome 280 0.0566 0.95 75.0 yes View details
infA-rpl36 Genome 110 0.0935 0.97 74.9 yes View details
rps12-rpl20 Genome 936 0.0460 1.00 74.8 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 85 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnI-CAU-rpl23_p1 trnI-CAU-rpl23 TGAACGGTTAAAGCACCCAA AAACGTTTGTGACCTCCTCC 791–797 1.000 83.8
trnI-CAU-rpl23_p2 trnI-CAU-rpl23 AACGGTTAAAGCACCCAACT AAACGTTTGTGACCTCCTCC 789–795 1.000 83.8
trnI-CAU-rpl23_p3 trnI-CAU-rpl23 CCCAACTCATAATTGGCGGA AAACGTTTGTGACCTCCTCC 776 0.500 59.3
trnI-CAU-rpl23_p4 trnI-CAU-rpl23 GATTCGCAGGTTCAACTCCT AAACGTTTGTGACCTCCTCC 758 0.500 58.9
trnI-CAU-rpl23_p5 trnI-CAU-rpl23 CCCAACTCATAATTGGCGGA TTTGTGACCTCCTCCTCTGT 771 0.500 58.8
infA-rpl36_p1 infA-rpl36 ATCGGGAAGCACGAGAAAAA CCTTGATCGATCAAAACGCG 1004–1006 1.000 80.9
infA-rpl36_p2 infA-rpl36 ATCGGGAAGCACGAGAAAAA AAGCTGTATCTCGTCCTGGA 1060–1062 1.000 80.3
infA-rpl36_p3 infA-rpl36 AAGACGGTTCAAGTACCAGC CCTTGATCGATCAAAACGCG 1286 0.500 58.1
infA-rpl36_p4 infA-rpl36 ACCGCCTTCGTAGTAAATCG CCTTGATCGATCAAAACGCG 630 0.500 57.8
infA-rpl36_p5 infA-rpl36 AAGACGGTTCAAGTACCAGC AAGCTGTATCTCGTCCTGGA 1342 0.500 57.5
rps12-rpl20_p1 rps12-rpl20 CGGATGTCCTCAACGAAGAG TGAGCTCCCTGAAATCCAGA 1059–1108 1.000 82.2
rps12-rpl20_p2 rps12-rpl20 ACAAAATCTCCAGCCCTTCG TGAGCTCCCTGAAATCCAGA 1079–1128 1.000 81.5
rps12-rpl20_p3 rps12-rpl20 CTCAACGAAGAGGGGTTTGT TGAGCTCCCTGAAATCCAGA 1051–1100 1.000 80.9
rps12-rpl20_p4 rps12-rpl20 CGGATGTCCTCAACGAAGAG GCTCCCTGAAATCCAGATGT 1056–1105 1.000 76.8
rps12-rpl20_p5 rps12-rpl20 ACAAAATCTCCAGCCCTTCG GCTCCCTGAAATCCAGATGT 1076–1125 1.000 76.0
trnR-CCG-rbcL_p1 trnR-CCG-rbcL ATCCACCAAATCGGCGTTTA CGCCGGTACTGTAGTAGGTA 962–964 1.000 83.3
trnR-CCG-rbcL_p2 trnR-CCG-rbcL TAATCCACCAAATCGGCGTT CGCCGGTACTGTAGTAGGTA 964–966 1.000 83.3
trnR-CCG-rbcL_p3 trnR-CCG-rbcL TCCACCAAATCGGCGTTTAT CGCCGGTACTGTAGTAGGTA 961–963 1.000 83.3
trnR-CCG-rbcL_p4 trnR-CCG-rbcL CTTCATCCATAGGCTGCCAG CGCCGGTACTGTAGTAGGTA 1205–1207 1.000 82.7
trnR-CCG-rbcL_p5 trnR-CCG-rbcL AGGTTCCGCGATCAATCAAA CGCCGGTACTGTAGTAGGTA 1187 0.500 58.8
trnF-GAA-trnL-UAA_p1 trnF-GAA-trnL-UAA TCCTCTGCTCTACCAACTGA CGTTGGCTTTATTGACCGTG 135 1.000 75.6
trnF-GAA-trnL-UAA_p2 trnF-GAA-trnL-UAA TCAGTCCTCTGCTCTACCAA CGTTGGCTTTATTGACCGTG 139 1.000 75.5
trnF-GAA-trnL-UAA_p3 trnF-GAA-trnL-UAA TTCAGTCCTCTGCTCTACCA CGTTGGCTTTATTGACCGTG 140 1.000 75.5
trnF-GAA-trnL-UAA_p4 trnF-GAA-trnL-UAA AGTCCTCTGCTCTACCAACT CGTTGGCTTTATTGACCGTG 137 1.000 75.5
trnF-GAA-trnL-UAA_p5 trnF-GAA-trnL-UAA GTCCTCTGCTCTACCAACTG CGTTGGCTTTATTGACCGTG 136 1.000 75.1
psbZ-trnS-UGA_p1 psbZ-trnS-UGA CCAACTGAAAGGCAATAGTCA CATAAACCACTCGGCCATCT 255–259 1.000 62.4
psbZ-trnS-UGA_p2 psbZ-trnS-UGA CCAACTGAAAGGCAATAGTCA TAAACCACTCGGCCATCTCT 253–257 1.000 61.6
psbZ-trnS-UGA_p3 psbZ-trnS-UGA CCAACTGAAAGGCAATAGTCA TCAAGACCGGAGCCATAAAC 268–272 1.000 61.5
psbZ-trnS-UGA_p4 psbZ-trnS-UGA CCAACTGAAAGGCAATAGTCA GTTTTCAAGACCGGAGCCAT 272–276 1.000 60.8
psbZ-trnS-UGA_p5 psbZ-trnS-UGA CCAACTGAAAGGCAATAGTCA CAAGACCGGAGCCATAAACC 267–271 1.000 59.7

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
Rhodobryum giganteum PP485722.1 124315 View on NCBI ↗
Rhodobryum laxelimbatum NC_056918.1 124632 View on NCBI ↗