Markers + reference

Syntrichia

2 species · Pottiaceae · Pottiales

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Species 2
Genome length 123–136 kb
Candidate markers 267
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl23 Genome 276 0.0254 1.00 52.2 yes View details
psaJ-trnP-UGG Genome 398 0.0328 0.99 66.9 yes View details
orf40 Genome 684 0.0336 1.00 65.6 yes View details
ycf4-psaI Genome 353 0.0516 0.99 70.3 yes View details
trnfM-CAU-trnG-GCC Genome 174 0.0471 0.98 70.9 yes View details
psbD-trnT-GGU Genome 430 0.0372 1.00 65.9 yes View details
ycf2 Genome 6750 0.0236 0.89 54.7 yes View details
trnS-GCU-psaM Genome 273 0.0590 0.99 71.2 yes View details
ycf66 Genome 953 0.0307 0.99 62.9 yes View details
ndhB Genome 2142 0.0206 1.00 57.3 yes View details
ycf1 Genome 4677 0.0269 1.00 54.7 yes View details
trnE-UUC-trnY-GUA Genome 93 0.1111 0.97 85.1 yes View details
psbN-psbT Genome 98 0.1531 1.00 84.9 yes View details
ndhE-psaC Genome 184 0.0652 1.00 83.2 yes View details
ndhG-ndhE Genome 40 0.0500 1.00 80.2 yes View details
trnG-GCC-trnR-UCU Genome 74 0.1250 0.76 76.8 yes View details
psbI-trnS-GCU Genome 101 0.0714 0.97 74.8 yes View details
clpP-rps12 Genome 142 0.0725 0.97 73.3 yes View details
psbJ-orf40 Genome 270 0.0448 0.99 73.1 yes View details
cemA-ycf4 Genome 108 0.0926 1.00 73.1 yes View details
trnI-CAU-rpl23 Genome 222 0.0676 1.00 72.0 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 110 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 ACGGGGTATTTTACTTCATCCA 308–309 1.000 60.7
trnI-CAU-rpl23_p2 trnI-CAU-rpl23 AAGCATCCATAGCTGAACGG ACGGGGTATTTTACTTCATCCA 321–322 1.000 60.6
trnI-CAU-rpl23_p3 trnI-CAU-rpl23 AACGGTTAAAGCACCCAACT ACGGGGTATTTTACTTCATCCA 306–307 1.000 60.6
trnI-CAU-rpl23_p4 trnI-CAU-rpl23 GCATCCATAGCTGAACGGTT ACGGGGTATTTTACTTCATCCA 319–320 1.000 58.3
trnI-CAU-rpl23_p5 trnI-CAU-rpl23 ACGGTTAAAGCACCCAACTC ACGGGGTATTTTACTTCATCCA 305–306 1.000 58.0
rpl23_p1 rpl23 AAGCATCCATAGCTGAACGG ACCTCCTCCTCTATAACGGC 773–775 1.000 82.2
rpl23_p2 rpl23 TGAACGGTTAAAGCACCCAA ACCTCCTCCTCTATAACGGC 760–762 1.000 82.2
rpl23_p3 rpl23 AACGGTTAAAGCACCCAACT ACCTCCTCCTCTATAACGGC 758–760 1.000 82.1
rpl23_p4 rpl23 AAGCATCCATAGCTGAACGG AAACGTTTGTGACCTCCTCC 784–786 1.000 81.9
rpl23_p5 rpl23 TGAACGGTTAAAGCACCCAA AAACGTTTGTGACCTCCTCC 771–773 1.000 81.9
psbN-psbT_p1 psbN-psbT CAGCTTTTGGACAACCCTCT TTTTCGTGAACCGCCTACAA 200–202 1.000 85.5
psbN-psbT_p2 psbN-psbT CAGCTTTTGGACAACCCTCT TTTTTCGTGAACCGCCTACA 201–203 1.000 85.4
psbN-psbT_p3 psbN-psbT CAGCTTTTGGACAACCCTCT TTCGTGAACCGCCTACAATT 198–200 1.000 84.5
psbN-psbT_p4 psbN-psbT CAGCTTTTGGACAACCCTCT TTTCGTGAACCGCCTACAAT 199–201 1.000 84.5
psbN-psbT_p5 psbN-psbT CAGCTTTTGGACAACCCTCT TCGTGAACCGCCTACAATTC 197–199 1.000 83.7
clpP-rps12_p1 clpP-rps12 GCTGTTGCTATAGAAAACACCT TCAATTGTTGAATAGTAGGCA 184–188 1.000 46.0
clpP-rps12_p2 clpP-rps12 GCTGTTGCTATAGAAAACACCT ATCAATTGTTGAATAGTAGGCA 185–189 1.000 46.0
clpP-rps12_p3 clpP-rps12 GCTGTTGCTATAGAAAACACCT TCAATTGTTGAATAGTAGGCAT 184–188 1.000 46.0
clpP-rps12_p4 clpP-rps12 GCTGTTGCTATAGAAAACACC TCAATTGTTGAATAGTAGGCA 184–188 1.000 46.0
clpP-rps12_p5 clpP-rps12 GCTGTTGCTATAGAAAACACCT AATCAATTGTTGAATAGTAGGCA 186–190 1.000 46.0
psaJ-trnP-UGG_p1 psaJ-trnP-UGG GTAGCTAATACGGGTGCTGT TACCAAACTGCGCTACATCC 467 1.000 75.3
psaJ-trnP-UGG_p2 psaJ-trnP-UGG GTAGCTAATACGGGTGCTGT GAACCTGCGGCATTTTGTAC 502 1.000 75.1
psaJ-trnP-UGG_p3 psaJ-trnP-UGG GTAGCTAATACGGGTGCTGT GGGATGACAGGATTCGAACC 517 1.000 74.9
psaJ-trnP-UGG_p4 psaJ-trnP-UGG GTAGCTAATACGGGTGCTGT AAACAAACGCGCTACCAAAC 479 1.000 74.1
psaJ-trnP-UGG_p5 psaJ-trnP-UGG GTAGCTAATACGGGTGCTGT CAAAACAAACGCGCTACCAA 481 1.000 74.0
psbJ-orf40_p1 psbJ-orf40 AGGTACTGTAGCCGGTATTCT TGCACTTTTTAAAATGGCTCGT 422–424 1.000 53.5
psbJ-orf40_p2 psbJ-orf40 GGCTCCTATTCTGGATTAGGC TGCACTTTTTAAAATGGCTCGT 370–372 1.000 53.5
psbJ-orf40_p3 psbJ-orf40 GCCGGTATTCTTGTAATTGGC TGCACTTTTTAAAATGGCTCGT 412–414 1.000 53.2
psbJ-orf40_p4 psbJ-orf40 ACTGTAGCCGGTATTCTTGT TGCACTTTTTAAAATGGCTCGT 418–420 1.000 50.1
psbJ-orf40_p5 psbJ-orf40 GGTACTGTAGCCGGTATTCT TGCACTTTTTAAAATGGCTCGT 421–423 1.000 49.1

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
Syntrichia filaris NC_050352.1 136227 View on NCBI ↗
Syntrichia ruralis NC_012052.1 122630 View on NCBI ↗