Markers + reference

Hypnea

7 species · Hypneaceae · Gigartinales

Back to catalogue

Species 7
Genome length 173–176 kb
Candidate markers 456
Primer pairs 90

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 10 remaining regions by MarkerSeek score (out of 456 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
orf692 Genome 2079 0.2102 1.00 78.0 yes View details
trnL(caa)-sufB Genome 842 0.1939 1.00 83.6 yes View details
acpP-ycf45 Genome 291 0.2575 1.00 78.0 yes View details
dnaB Genome 1806 0.1596 1.00 79.5 yes View details
syfB Genome 2151 0.1798 1.00 77.7 yes View details
groEL-ycf65 Genome 542 0.2195 0.99 83.2 yes View details
psbD-ompR Genome 528 0.2430 0.98 79.4 yes View details
ompR-rns Genome 503 0.2932 1.00 82.9 no View details
orf244 Genome 735 0.2046 1.00 84.7 yes View details
orf244-trnMe(cat) Genome 562 0.1271 1.00 84.1 yes View details
ycf80 Genome 1455 0.1501 1.00 83.0 yes View details
apcF-trnR(ccg) Genome 476 0.1762 1.00 82.0 yes View details
rps1-syfB Genome 444 0.0764 0.99 81.2 yes View details
ssrA Genome 395 0.1391 1.00 80.5 yes View details
ycf21-pgmA Genome 481 0.1727 0.99 80.4 yes View details
orf193 Genome 582 0.1612 0.99 80.3 yes View details
ntcA Genome 663 0.1719 1.00 79.8 yes View details
trnR(acg)-groEL Genome 49 0.0807 1.00 79.8 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf21-pgmA_p1 ycf21-pgmA GCGCACGTCTAATAGCTTCT TACATCAGACCACGGCAATG 1028–1037 0.286 58.7
ycf21-pgmA_p2 ycf21-pgmA CACTGGTCATGGATTGCTGA CATTACATCAGACCACGGCA 1295 0.143 44.6
ycf21-pgmA_p3 ycf21-pgmA CACTGGTCATGGATTGCTGA TACATCAGACCACGGCAATG 1292 0.143 44.6
ycf21-pgmA_p4 ycf21-pgmA TCACTGGTCATGGATTGCTG CATTACATCAGACCACGGCA 1296 0.143 44.6
ycf21-pgmA_p5 ycf21-pgmA TCACTGGTCATGGATTGCTG TACATCAGACCACGGCAATG 1293 0.143 44.6
apcF-trnR(ccg)_p1 apcF-trnR(ccg) CTTGCTGCCGCTTCTTTAAC ATCCACTGAGTTACATGCCC 669 0.143 39.7
apcF-trnR(ccg)_p2 apcF-trnR(ccg) TGATTTTAGCGCAGGCGTAT ATCCACTGAGTTACATGCCC 949 0.143 39.6
apcF-trnR(ccg)_p3 apcF-trnR(ccg) TCTTGCTGCCGCTTCTTTAA ATCCACTGAGTTACATGCCC 670 0.143 39.1
apcF-trnR(ccg)_p4 apcF-trnR(ccg) ATCTTGCTGCCGCTTCTTTA ATCCACTGAGTTACATGCCC 671 0.143 39.1
apcF-trnR(ccg)_p5 apcF-trnR(ccg) TAATCTTGCTGCCGCTTCTT ATCCACTGAGTTACATGCCC 673 0.143 39.1
ssrA_p1 ssrA AGGGCATGTAACTCAGTGGA CACTGATACCTGACATGGCA 841 0.143 37.4
ssrA_p2 ssrA AAGGGCATGTAACTCAGTGG CACTGATACCTGACATGGCA 842 0.143 36.2
ssrA_p3 ssrA AGGGCATGTAACTCAGTGGA TCACTGATACCTGACATGGC 842 0.143 35.1
ssrA_p4 ssrA AGGGCATGTAACTCAGTGGA CACTGATACCTGACATGGCAA 841 0.143 34.9
ssrA_p5 ssrA GGGCATGTAACTCAGTGGAT CACTGATACCTGACATGGCA 840 0.143 34.4
ycf80_p1 ycf80 AGGGCATGTAACTCAGTGGA CGTTATCGAGGACCACGTTT 2741–2879 1.000 89.1
ycf80_p2 ycf80 AAGGGCATGTAACTCAGTGG CGTTATCGAGGACCACGTTT 2742–2842 0.857 82.2
ycf80_p3 ycf80 AGGGCATGTAACTCAGTGGA GCACCTACTATACCTGCAGC 2527–2582 0.571 69.1
ycf80_p4 ycf80 AGGGCATGTAACTCAGTGGA TGGCACCTACTATACCTGCA 2529–2584 0.571 69.0
ycf80_p5 ycf80 AGGGCATGTAACTCAGTGGA GTACAAGGTGCAACAGGTCT 2608–2660 0.571 68.3
trnMe(cat)_p1 trnMe(cat) TTCCAAGCTAATGATGCGGG CAGGAAGAACGAGCATTTGC 2122–2387 0.714 76.0
trnMe(cat)_p2 trnMe(cat) GCTAATGATGCGGGTTCGAT CAGGAAGAACGAGCATTTGC 2116–2381 0.714 74.6
trnMe(cat)_p3 trnMe(cat) CCAAGCTAATGATGCGGGTT CAGGAAGAACGAGCATTTGC 2120–2385 0.714 73.7
trnMe(cat)_p4 trnMe(cat) AATGATGCGGGTTCGATTCC CAGGAAGAACGAGCATTTGC 2113–2378 0.714 73.0
trnMe(cat)_p5 trnMe(cat) AAGCTAATGATGCGGGTTCG CAGGAAGAACGAGCATTTGC 2118–2383 0.714 72.9
orf244_p1 orf244 TATGCATCTGGCTGGATTCG AAAATGCAGACGTATTGCGC 955–1185 0.857 83.5
orf244_p2 orf244 TATGCATCTGGCTGGATTCG CTACTAAGCATCTGTGGCCG 1499–1627 0.286 56.9
orf244_p3 orf244 ACCAGCGACGTCCTTTTAAG AAAATGCAGACGTATTGCGC 934 0.143 43.2
orf244_p4 orf244 GAACCAGCGACGTCCTTTTA AAAATGCAGACGTATTGCGC 936 0.143 43.2
orf244_p5 orf244 AACCAGCGACGTCCTTTTAA AAAATGCAGACGTATTGCGC 935 0.143 42.9

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Hypnea cryptica NC_081597.1 173464 View on NCBI ↗
Hypnea flava NC_081594.1 174543 View on NCBI ↗
Hypnea musciformis NC_081599.1 173580 View on NCBI ↗
Hypnea nidifica NC_081592.1 173169 View on NCBI ↗
Hypnea nidulans NC_081593.1 173835 View on NCBI ↗
Hypnea pseudomusciformis NC_081595.1 173626 View on NCBI ↗
Hypnea wynnei NC_081598.1 175748 View on NCBI ↗