Markers + reference

Porphyra

2 species · Bangiaceae · Bangiales

Back to catalogue

Species 2
Genome length 190–191 kb
Candidate markers 496
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 496 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rne Genome 1536 0.0996 1.00 78.9 yes View details
ORF450 Genome 1353 0.1596 1.00 78.9 yes View details
ORF621 Genome 1866 0.1641 0.87 80.5 yes View details
infB Genome 2292 0.1082 1.00 77.1 yes View details
ftsH Genome 1887 0.0514 1.00 72.1 yes View details
dnaB Genome 1707 0.1347 1.00 79.0 yes View details
PopuC001 Genome 3598 0.1165 1.00 75.4 yes View details
trnR_3-groEL Genome 994 0.2381 0.30 68.7 yes View details
ccs1-ORF240 Genome 268 0.2644 0.97 75.1 yes View details
psbA-ycf35 Genome 314 0.1213 0.97 80.2 yes View details
ycf16 Genome 756 0.1071 1.00 79.7 yes View details
preA Genome 972 0.1104 1.00 79.6 yes View details
rps1 Genome 792 0.0997 1.00 79.5 yes View details
ORF263 Genome 792 0.1086 1.00 79.4 yes View details
ycf23 Genome 798 0.1178 1.00 79.3 yes View details
trnP-ORF174 Genome 57 0.1111 0.95 79.1 yes View details
ycf22 Genome 630 0.1143 1.00 79.0 yes View details
ORF287 Genome 864 0.1319 1.00 78.9 yes View details
syh Genome 1293 0.1098 1.00 78.9 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
trnP-ORF174_p1 trnP-ORF174 GCTACCAAGCTGCGCTATAT GGGATGTTTTGGTATCCTAGA 102–105 1.000 49.5
trnP-ORF174_p2 trnP-ORF174 GCTACCAAGCTGCGCTATAT GGGATGTTTTGGTATCCTAGAT 102–105 1.000 47.0
trnP-ORF174_p3 trnP-ORF174 TTTGAACCTGCGACATCCTG GGGATGTTTTGGTATCCTAGA 138–141 1.000 45.2
trnP-ORF174_p4 trnP-ORF174 ATTTGAACCTGCGACATCCT GGGATGTTTTGGTATCCTAGA 139–142 1.000 45.1
trnP-ORF174_p5 trnP-ORF174 CAGGATTTGAACCTGCGACA GGGATGTTTTGGTATCCTAGA 143–146 1.000 45.0
ORF263_p1 ORF263 ACCAGTTTTAGCAGCTGCAT CCGTTACTTGTTCACCACCA 1870 0.500 59.0
ORF263_p2 ORF263 ACCAGTTTTAGCAGCTGCAT GAATCTCGGCCATTCCTTGT 1820 0.500 59.0
ORF263_p3 ORF263 ACCAGTTTTAGCAGCTGCAT CGGCCATTCCTTGTACTACC 1814 0.500 58.9
ORF263_p4 ORF263 ACCAGTTTTAGCAGCTGCAT AATTGATTGCCCTGGCTCAA 1513 0.500 58.9
ORF263_p5 ORF263 ACCAGTTTTAGCAGCTGCAT CCTGGCTCAACGGGTATATG 1503 0.500 58.0
rne_p1 rne TGGTGGTGAACAAGTAACGG ATTCCAAGCTGAGCACAACA 2540 0.500 59.5
rne_p2 rne TGGTGGTGAACAAGTAACGG TTCCAAGCTGAGCACAACAT 2539 0.500 59.5
rne_p3 rne ACAAGGAATGGCCGAGATTC ATTCCAAGCTGAGCACAACA 2590 0.500 59.5
rne_p4 rne ACAAGGAATGGCCGAGATTC TTCCAAGCTGAGCACAACAT 2589 0.500 59.5
rne_p5 rne GGTAGTACAAGGAATGGCCG TTCCAAGCTGAGCACAACAT 2595 0.500 59.5
psbA-ycf35_p1 psbA-ycf35 TCCAAGAGCAGAAACGTTCC AGCCTAAATCTGTTAAAGCATGC 447–451 1.000 61.2
psbA-ycf35_p2 psbA-ycf35 TCCAAGAGCAGAAACGTTCC GCCTAAATCTGTTAAAGCATGCT 446–450 1.000 61.2
psbA-ycf35_p3 psbA-ycf35 AAGAGCAGAAACGTTCCCAC AGCCTAAATCTGTTAAAGCATGC 444–448 1.000 59.0
psbA-ycf35_p4 psbA-ycf35 AAGAGCAGAAACGTTCCCAC GCCTAAATCTGTTAAAGCATGCT 443–447 1.000 59.0
psbA-ycf35_p5 psbA-ycf35 CAAGAGCAGAAACGTTCCCA GCCTAAATCTGTTAAAGCATGCT 444–448 1.000 59.0
ORF450_p1 ORF450 AATGGACGTGGGTTCAAGTC ACCACGAGTACGCATTTCTC 2577–2586 1.000 87.4
ORF450_p2 ORF450 AAGCAAGGAGGTTGTTCAGG ACCACGAGTACGCATTTCTC 2386 0.500 59.8
ORF450_p3 ORF450 AAGCAAGGAGGTTGTTCAGG GACCACGAGTACGCATTTCT 2387 0.500 59.8
ORF450_p4 ORF450 GCAAGGAGGTTGTTCAGGAA ACCACGAGTACGCATTTCTC 2384 0.500 59.8
ORF450_p5 ORF450 GCAAGGAGGTTGTTCAGGAA GACCACGAGTACGCATTTCT 2385 0.500 59.8
ORF621_p1 ORF621 GATCTTGGGATGGGACCAAC TCCCCACCTCAATGAAGCTA 2606 0.500 59.3
ORF621_p2 ORF621 GATCTTGGGATGGGACCAAC GAGATCTCTCCCCACCTCAA 2614 0.500 58.2
ORF621_p3 ORF621 GATCTTGGGATGGGACCAAC TATGTTGTGCGTTGCGAGAT 2503 0.500 57.3
ORF621_p4 ORF621 CTTGGGATGGGACCAACTTT TCCCCACCTCAATGAAGCTA 2603 0.500 57.3
ORF621_p5 ORF621 ATCTTGGGATGGGACCAACT TCCCCACCTCAATGAAGCTA 2605 0.500 57.2

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
Porphyra purpurea NC_000925.1 191028 View on NCBI ↗
Porphyra umbilicalis NC_035573.1 190173 View on NCBI ↗