Markers + reference

Gelidium

4 species · Gelidiaceae · Gelidiales

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Species 4
Genome length 175–177 kb
Candidate markers 451
Primer pairs 85

Genome-wide nucleotide diversity

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

Candidate markers

7 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 451 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-psaD Genome 2303 0.0829 0.66 63.5 yes View details
ORF614 Genome 1920 0.0523 1.00 68.4 yes View details
ORF12 Genome 1194 0.0565 1.00 79.7 yes View details
psaL-trnT Genome 478 0.1482 1.00 69.3 yes View details
ycf37 Genome 453 0.0618 1.00 75.8 yes View details
rps6-rrf Genome 462 0.0819 1.00 72.5 yes View details
ycf27-psbD Genome 960 0.0918 1.00 86.5 yes View details
ORF256 Genome 759 0.0523 1.00 79.2 yes View details
trpG-thiG Genome 111 0.0480 1.00 74.4 yes View details
trnV-trnY Genome 54 0.1019 1.00 73.6 yes View details
trnV-trnR Genome 23 0.0725 1.00 73.5 yes View details
trnI-rrs Genome 66 0.0581 1.00 72.8 yes View details
dnaB-trnF Genome 46 0.1304 1.00 72.7 yes View details
acsF-petN Genome 424 0.0460 1.00 72.2 yes View details
infB Genome 2202 0.0441 1.00 72.2 yes View details
trnY-trnT Genome 21 0.0476 1.00 72.1 yes View details
ccdA Genome 720 0.0407 1.00 71.1 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
trnS-psaD_p1 trnS-psaD ACCAACTCTACCACCTCTCC AGCAAGAAAAGAGCAGTGCT 343–2564 1.000 91.3
trnS-psaD_p2 trnS-psaD ACCAACTCTACCACCTCTCC GGTAGTACAGGGGGATGGTT 483–2704 1.000 90.6
trnS-psaD_p3 trnS-psaD ACCAACTCTACCACCTCTCC CCGATAGAATCAGCAAGCGT 719–2979 1.000 90.4
trnS-psaD_p4 trnS-psaD ATACCTTACGGAGAGGGTGG AGCAAGAAAAGAGCAGTGCT 1891–2638 0.750 81.2
trnS-psaD_p5 trnS-psaD ATACCTTACGGAGAGGGTGG GGTAGTACAGGGGGATGGTT 2031–2778 0.750 80.4
acsF-petN_p1 acsF-petN TTCGGCCATTACAGGATTGG ATCGGATTCCCCAGTACTGT 1185 0.500 58.3
acsF-petN_p2 acsF-petN CCTTGCTTCATCTCGTGACA ATCGGATTCCCCAGTACTGT 1218 0.500 58.0
acsF-petN_p3 acsF-petN GCATTCGGCCATTACAGGAT ATCGGATTCCCCAGTACTGT 1188 0.500 55.6
acsF-petN_p4 acsF-petN AAGCATTCGGCCATTACAGG ATCGGATTCCCCAGTACTGT 1190 0.500 53.9
acsF-petN_p5 acsF-petN ATGCCTTGCTTCATCTCGTG ATCGGATTCCCCAGTACTGT 1221 0.500 53.7
infB_p1 infB CATGCCATCCCGGTAGTAAC TATCACGTCGCTCTACTGGT 2638 1.000 84.6
infB_p2 infB CATGCCATCCCGGTAGTAAC ACGTCGCTCTACTGGTCTTA 2634 1.000 84.1
infB_p3 infB CATGCCATCCCGGTAGTAAC GGGAAAAACAAAGGAGCACG 2949 1.000 83.6
infB_p4 infB CATGCCATCCCGGTAGTAAC TGGGGAAAAACAAAGGAGCA 2951 1.000 83.3
infB_p5 infB CATGCCATCCCGGTAGTAAC GGAATACACCACAGCGCTTA 2834 0.500 58.9
ORF256_p1 ORF256 GGGCAATGAGTATCTGGTGG TGCGTATACCAATTTCGCCA 1563–1565 0.750 73.3
ORF256_p2 ORF256 GGGCAATGAGTATCTGGTGG ATCTGAGGGCCTAGCAGTAG 1868–1870 0.750 73.1
ORF256_p3 ORF256 GGGCAATGAGTATCTGGTGG ACCAATTTCGCCATCTACCC 1556–1558 0.750 73.1
ORF256_p4 ORF256 GGGCAATGAGTATCTGGTGG CCAATTTCGCCATCTACCCT 1555–1557 0.750 70.7
ORF256_p5 ORF256 GGGCAATGAGTATCTGGTGG AAATCTGAGGGCCTAGCAGT 1870–1872 0.750 69.9
ORF614_p1 ORF614 TGACCCATCAAGAAATCCTAACA ACAAGGGCCGAATAGTAAGC 2773–2788 0.750 42.8
ORF614_p2 ORF614 TGACCCATCAAGAAATCCTAACA CAAAACGTTGCAGTTCAGCA 2861 0.500 31.2
ORF614_p3 ORF614 TGACCCATCAAGAAATCCTAACA TCAAAACGTTGCAGTTCAGC 2862 0.500 30.4
ORF614_p4 ORF614 TCAGGAACATAAGGATGCTTACA CAAAACGTTGCAGTTCAGCA 2952 0.500 29.7
ORF614_p5 ORF614 ACCCATCAAGAAATCCTAACAGA CAAAACGTTGCAGTTCAGCA 2859 0.500 29.0
ORF12_p1 ORF12 TATAGCATCTGTGGCCGAGA CACGTGTGGGTCAACCTTTA 2136–2139 0.750 74.4
ORF12_p2 ORF12 TCTATAGCATCTGTGGCCGA CACGTGTGGGTCAACCTTTA 2138–2141 0.750 74.4
ORF12_p3 ORF12 TATAGCATCTGTGGCCGAGA ACTAACACGTGTGGGTCAAC 2141–2144 0.750 74.3
ORF12_p4 ORF12 TCTATAGCATCTGTGGCCGA ACTAACACGTGTGGGTCAAC 2143–2146 0.750 74.3
ORF12_p5 ORF12 TATAGCATCTGTGGCCGAGA CACTAACACGTGTGGGTCAA 2142–2145 0.750 74.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Gelidium coulteri NC_041173.1 177099 View on NCBI ↗
Gelidium gabrielsonii NC_040156.1 175499 View on NCBI ↗
Gelidium galapagense NC_041174.1 176601 View on NCBI ↗
Gelidium sinicola NC_041175.1 177095 View on NCBI ↗