Markers + reference

Pellia

2 species · Pelliaceae · Pelliales

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Species 2
Genome length 116–116 kb
Candidate markers 271
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 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoB Genome 3198 0.0003 1.00 55.5 yes View details
trnD-GUC-trnY-GUA Genome 157 0.0064 1.00 56.2 yes View details
psbZ Genome 189 0.0053 1.00 55.5 yes View details
rps18 Genome 228 0.0044 1.00 55.0 yes View details
clpP-psbB Genome 360 0.0000 1.00 25.2 yes View details
ndhF-rpl21 Genome 418 0.0217 0.99 67.2 yes View details
trnV-GAC-rps12 Genome 693 0.0000 0.99 60.1 no View details
psbB Genome 1518 0.0007 1.00 59.1 yes View details
ycf66 Genome 910 0.0000 1.00 58.9 yes View details
rps3-rpl22 Genome 74 0.0000 0.92 56.5 yes View details
trnV-UAC-trnM-CAU Genome 188 0.0000 0.97 55.6 yes View details
psaM-trnS-GCU Genome 213 0.0000 0.98 54.3 yes View details
trnR-CCG-accD Genome 208 0.0000 1.00 52.3 yes View details
rps12 Genome 731 0.0000 1.00 40.0 yes View details
rps2 Genome 711 0.0000 1.00 40.0 yes View details
atpI Genome 747 0.0000 1.00 40.0 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
rps12_p1 rps12 TACGGTTCCGTAGAGTGACA TCTGCGATACTTTTACGTGACA 834 1.000 61.2
rps12_p2 rps12 TACGGTTCCGTAGAGTGACA TGGATCAGGCTTTCCTACTT 859 1.000 61.1
rps12_p3 rps12 TACGGTTCCGTAGAGTGACA TTGGATCAGGCTTTCCTACT 860 1.000 61.1
rps12_p4 rps12 ACGAGGAGCCGTATGAAATG TCTGCGATACTTTTACGTGACA 865 1.000 60.9
rps12_p5 rps12 ATTGAACGAGGAGCCGTATG TCTGCGATACTTTTACGTGACA 870 1.000 60.9
ycf66_p1 ycf66 TTTTTCAGCAGATGCAACGG AAACAAACCCCAGTCGATCC 1086–1087 1.000 76.0
ycf66_p2 ycf66 TTTTTCAGCAGATGCAACGG GGAAATTGAATCCCGTGACG 1008–1009 1.000 70.1
ycf66_p3 ycf66 TTTTTCAGCAGATGCAACGG TGCCTACCAGTATTTTTGCGA 1044–1045 1.000 68.2
ycf66_p4 ycf66 TTTTTCAGCAGATGCAACGG TAAACAAACCCCAGTCGATCC 1087–1088 1.000 68.2
ycf66_p5 ycf66 TTTTCAGCAGATGCAACGGG AAACAAACCCCAGTCGATCC 1085–1086 1.000 68.1
rpoB_p1 rpoB CAGCATCGAATGAGAGGGAG TGATTGGGATAGCGTCTTCG 234 1.000 75.1
rpoB_p2 rpoB CTCCAGCATCGAATGAGAGG TGATTGGGATAGCGTCTTCG 237 1.000 75.1
rpoB_p3 rpoB ACGCACGGATTTTATCACGT TGATTGGGATAGCGTCTTCG 212 1.000 74.0
rpoB_p4 rpoB GGAGGTACGCACGGATTTTA TGATTGGGATAGCGTCTTCG 218 1.000 73.9
rpoB_p5 rpoB TCGAATGAGAGGGAGGTACG TGATTGGGATAGCGTCTTCG 229 1.000 73.7
rps2_p1 rps2 TCCCATGCATATGCGTATGT CACCACCACTACCATTACCG 854 1.000 73.0
rps2_p2 rps2 TCCCATGCATATGCGTATGT ATCACTCACCACCACTACCA 860 1.000 72.9
rps2_p3 rps2 TCCCATGCATATGCGTATGT TCACTCACCACCACTACCAT 859 1.000 72.9
rps2_p4 rps2 CCCATGCATATGCGTATGTG CACCACCACTACCATTACCG 853 1.000 72.6
rps2_p5 rps2 CCCATGCATATGCGTATGTG TCACTCACCACCACTACCAT 858 1.000 72.6
atpI_p1 atpI ACATTTCCGGAGAGAGCAAC GCCATCGTCGACCCAATAAT 797 1.000 78.2
atpI_p2 atpI ACATTTCCGGAGAGAGCAAC CAATGAAAGCCATCGTCGAC 805 1.000 75.7
atpI_p3 atpI ACATTTCCGGAGAGAGCAAC TGTGAATCGATTCGACGACG 832 1.000 75.4
atpI_p4 atpI AAGGAATGTTGGCGAGGAAT GCCATCGTCGACCCAATAAT 838 1.000 74.9
atpI_p5 atpI AGGAATGTTGGCGAGGAATT GCCATCGTCGACCCAATAAT 837 1.000 74.9
psaM-trnS-GCU_p1 psaM-trnS-GCU ACTCCAATCTCGGATAGCCA TAGTTGCCAGGAGAGAGAGG 401–405 1.000 78.9
psaM-trnS-GCU_p2 psaM-trnS-GCU CGTTTTCGCAACAGGTGTTT TAGTTGCCAGGAGAGAGAGG 360–364 1.000 78.9
psaM-trnS-GCU_p3 psaM-trnS-GCU ACTCCAATCTCGGATAGCCA GTGCTTTAGTTGCCAGGAGA 407–411 1.000 78.6
psaM-trnS-GCU_p4 psaM-trnS-GCU CGTTTTCGCAACAGGTGTTT GTGCTTTAGTTGCCAGGAGA 366–370 1.000 78.6
psaM-trnS-GCU_p5 psaM-trnS-GCU TTTCGCAACAGGTGTTTTCG TAGTTGCCAGGAGAGAGAGG 357–361 1.000 78.2

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
Pellia epiphylla NC_080367.1 116459 View on NCBI ↗
Pellia epiphylla var. borealis OQ280815.1 116432 View on NCBI ↗