Markers + reference

Hydrolithon

2 species · Hydrolithaceae · Corallinales

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Species 2
Genome length 173–173 kb
Candidate markers 438
Primer pairs 105

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 438 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ccs1-trnN-GUU Genome 523 0.0363 1.00 67.5 yes View details
rpl21-rpl32 Genome 856 0.0245 1.00 58.1 yes View details
rps16-groEL Genome 863 0.0220 1.00 60.9 yes View details
ntcA Genome 558 0.0287 1.00 59.4 yes View details
rpl11-trnW-CCA Genome 614 0.0312 0.89 67.8 yes View details
trnS-GCU-trnD-GUC Genome 472 0.2215 0.95 88.8 yes View details
tatC-apcE Genome 1242 0.0306 1.00 62.0 yes View details
infB Genome 2118 0.0151 1.00 51.4 yes View details
orf136 Genome 699 0.0229 1.00 57.1 yes View details
ycf4 Genome 546 0.0220 1.00 56.1 yes View details
ycf22-psaC Genome 534 0.0356 1.00 65.5 yes View details
apcB-atpE Genome 52 0.0962 1.00 85.1 yes View details
psbA-rne Genome 87 0.1279 0.99 81.5 yes View details
psaJ-psaF Genome 34 0.1765 1.00 78.6 yes View details
cpcA-pgmA Genome 141 0.0993 1.00 78.0 yes View details
psaD-chlB Genome 178 0.0506 1.00 76.8 yes View details
rps6-ycf60 Genome 30 0.1000 1.00 76.5 yes View details
dnaB-trnF-GAA Genome 53 0.0755 1.00 75.7 yes View details
rpl19-trnV-GAC Genome 14 0.0714 1.00 75.7 yes View details
rpl13-rpoA Genome 60 0.0500 1.00 75.2 yes View details
trnN-GUU-trnL-UAG Genome 117 0.0598 1.00 74.4 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rps6-ycf60_p1 rps6-ycf60 ACTTCAGTTATATCAGGTTTTACA TCCCGTAATTTCACAAGCTGT 135 1.000 41.8
rps6-ycf60_p2 rps6-ycf60 ACTTCAGTTATATCAGGTTTTACAA TCCCGTAATTTCACAAGCTGT 135 1.000 41.8
rps6-ycf60_p3 rps6-ycf60 ACTTCAGTTATATCAGGTTTTACA CCCGTAATTTCACAAGCTGTC 134 1.000 41.8
rps6-ycf60_p4 rps6-ycf60 GAGTATCTACTTCAGTTATATCAGGT TCCCGTAATTTCACAAGCTGT 143 1.000 41.7
rps6-ycf60_p5 rps6-ycf60 TCTACTTCAGTTATATCAGGTTT TCCCGTAATTTCACAAGCTGT 138 1.000 41.7
ccs1-trnN-GUU_p1 ccs1-trnN-GUU GCAAACCGTAAGCTACTAATCC GGTTCAAATCCTTCCTGGGG 604–611 1.000 59.0
ccs1-trnN-GUU_p2 ccs1-trnN-GUU GCAAACCGTAAGCTACTAATCC CTCAGTGGTAGAGCAATCGG 644–651 1.000 58.3
ccs1-trnN-GUU_p3 ccs1-trnN-GUU GCAAACCGTAAGCTACTAATCC TTCCTCAGTAGCTCAGTGGT 655–662 1.000 57.5
ccs1-trnN-GUU_p4 ccs1-trnN-GUU GCAAACCGTAAGCTACTAATCC CCGATTGGTCGTAGGTTCAA 617–624 1.000 57.1
ccs1-trnN-GUU_p5 ccs1-trnN-GUU ACCGTAAGCTACTAATCCACT GGTTCAAATCCTTCCTGGGG 600–607 1.000 56.5
trnN-GUU-trnL-UAG_p1 trnN-GUU-trnL-UAG ACTCCCCAGGAAGGATTTGA TACCAATTTCACCACGTCCG 211 1.000 80.6
trnN-GUU-trnL-UAG_p2 trnN-GUU-trnL-UAG CCGATTGCTCTACCACTGAG TACCAATTTCACCACGTCCG 168 1.000 80.0
trnN-GUU-trnL-UAG_p3 trnN-GUU-trnL-UAG CCCCAGGAAGGATTTGAACC TACCAATTTCACCACGTCCG 208 1.000 79.9
trnN-GUU-trnL-UAG_p4 trnN-GUU-trnL-UAG ACTCCCCAGGAAGGATTTGA AATGCGGACAGAGAGATTCG 275 1.000 79.8
trnN-GUU-trnL-UAG_p5 trnN-GUU-trnL-UAG CCCCAGGAAGGATTTGAACC AATGCGGACAGAGAGATTCG 272 1.000 79.2
psbA-rne_p1 psbA-rne AATGCACACAACTTCCCACT CCCATTCATTGTACCGCTGA 231–232 1.000 83.3
psbA-rne_p2 psbA-rne TGCACACAACTTCCCACTAG CCCATTCATTGTACCGCTGA 229–230 1.000 81.9
psbA-rne_p3 psbA-rne AATGCACACAACTTCCCACT ACCCATTCATTGTACCGCTG 232–233 1.000 81.6
psbA-rne_p4 psbA-rne AATGCACACAACTTCCCACT CACCCATTCATTGTACCGCT 233–234 1.000 81.5
psbA-rne_p5 psbA-rne AATGCACACAACTTCCCACT TCACCCATTCATTGTACCGC 234–235 1.000 81.5
rpl21-rpl32_p1 rpl21-rpl32 GACCTCTTTTGGATCGTGCA CAGCAGCTTCTTGGGCTATT 1455 0.500 56.5
rpl21-rpl32_p2 rpl21-rpl32 TGACCTCTTTTGGATCGTGC CAGCAGCTTCTTGGGCTATT 1456 0.500 56.5
rpl21-rpl32_p3 rpl21-rpl32 GACCTCTTTTGGATCGTGCA TGATTCCTGTTTTGGCAGCA 1470 0.500 56.1
rpl21-rpl32_p4 rpl21-rpl32 TGACCTCTTTTGGATCGTGC TGATTCCTGTTTTGGCAGCA 1471 0.500 56.1
rpl21-rpl32_p5 rpl21-rpl32 GACCTCTTTTGGATCGTGCA GATTCCTGTTTTGGCAGCAG 1469 0.500 55.6
psaJ-psaF_p1 psaJ-psaF ACCAGCTGTAAAAGTTAGCCA CCATTAGCAGCTTGGCAAGA 187 1.000 66.3
psaJ-psaF_p2 psaJ-psaF AACCAGCTGTAAAAGTTAGCCA CCATTAGCAGCTTGGCAAGA 188 1.000 60.9
psaJ-psaF_p3 psaJ-psaF ACCAGCTGTAAAAGTTAGCCAA CCATTAGCAGCTTGGCAAGA 187 1.000 60.9
psaJ-psaF_p4 psaJ-psaF ACCAGCTGTAAAAGTTAGCCA CATTAGCAGCTTGGCAAGAA 186 1.000 60.1
psaJ-psaF_p5 psaJ-psaF ACCAGCTGTAAAAGTTAGCCA TGGCAAGAATTTACTAGCGGT 175 1.000 60.0

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
Hydrolithon boergesenii OR992045.1 173224 View on NCBI ↗
Hydrolithon reinboldii OR992047.1 173063 View on NCBI ↗