Markers + reference

Cyanophora

2 species · Cyanophoraceae · Cyanophorales

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Species 2
Genome length 131–150 kb
Candidate markers 378
Primer pairs 80

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 9 remaining regions by MarkerSeek score (out of 378 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ccsA SSC 960 0.4286 0.72 77.2 yes View details
ftsW SSC 1191 0.4376 0.71 76.7 yes View details
psaC SSC 246 0.5253 0.80 73.3 yes View details
mntB SSC 885 0.4258 0.87 81.3 yes View details
mntA SSC 735 0.4747 0.94 83.5 yes View details
chlL SSC 852 0.4718 0.87 81.5 yes View details
chlN SSC 1377 0.4554 0.93 83.1 yes View details
ycf27 SSC 720 0.4321 0.84 80.5 yes View details
crtE SSC 912 0.4350 0.95 83.3 yes View details
ycf21 SSC 609 0.4235 0.92 82.8 yes View details
ftsQ SSC 855 0.4249 0.92 82.7 yes View details
rbcL-atpB LSC 477 0.0897 0.97 82.3 no View details
rbcR SSC 975 0.4290 0.97 81.9 yes View details
trnM-trnF LSC 156 0.2467 0.96 81.7 yes View details
cpcB SSC 519 0.4061 0.95 81.5 yes View details
trnL-trnE LSC 130 0.1951 0.95 81.2 yes View details
apcF SSC 510 0.4030 0.92 81.1 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 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ccsA_p1 ccsA GGTTTTGGACGGCTTTTACG ACAGGTTTACCTTTGCCGTT 2064 0.500 59.2
ccsA_p2 ccsA AGGTGGTGGGGTTCGTAATA ACAGGTTTACCTTTGCCGTT 2044 0.500 59.2
ccsA_p3 ccsA GGTTTTGGACGGCTTTTACG GAATTTTCCCGACCACAGGT 2078 0.500 58.9
ccsA_p4 ccsA AGGTGGTGGGGTTCGTAATA GAATTTTCCCGACCACAGGT 2058 0.500 58.9
ccsA_p5 ccsA GCTTGGACAGAAGATGGGTT ACAGGTTTACCTTTGCCGTT 2325 0.500 57.9
ftsW_p1 ftsW AACCGGCTGTAATCCATCTA AGGACTTGAACCTACGACCA 2130 0.500 44.1
ftsW_p2 ftsW ACCGGCTGTAATCCATCTAA AGGACTTGAACCTACGACCA 2129 0.500 44.1
ftsW_p3 ftsW TAACCGGCTGTAATCCATCT AGGACTTGAACCTACGACCA 2131 0.500 44.1
ftsW_p4 ftsW AACCGGCTGTAATCCATCTA CTCCCCAGGTAGGACTTGAA 2140 0.500 43.7
ftsW_p5 ftsW ACCGGCTGTAATCCATCTAA CTCCCCAGGTAGGACTTGAA 2139 0.500 43.7
psaC_p1 psaC AGCCAACGCAATTGTATTGC TTCAATCAAATCGGCACCCA 1264 0.500 59.3
psaC_p2 psaC GCCAACGCAATTGTATTGCT TTCAATCAAATCGGCACCCA 1263 0.500 59.3
psaC_p3 psaC TGGTCGTAGGTTCAAGTCCT TTCAATCAAATCGGCACCCA 946 0.500 59.3
psaC_p4 psaC TTCAAGTCCTACCTGGGGAG TTCAATCAAATCGGCACCCA 936 0.500 59.0
psaC_p5 psaC GCCAACGCAATTGTATTGCT TCAATCAAATCGGCACCCAT 1262 0.500 58.8
mntB_p1 mntB TGGGTGCCGATTTGATTGAA CGTGAACTTTCTGGTGGACA 1842 0.500 58.9
mntB_p2 mntB TGGGTGCCGATTTGATTGAA GTTATGTTCCACAACGTGCG 2021 0.500 58.9
mntB_p3 mntB TGGGTGCCGATTTGATTGAA GGACCAAATGGAGCAGGAAA 2139 0.500 58.7
mntB_p4 mntB TGGGTGCCGATTTGATTGAA GCTCGTTTACTTGCTCAGGA 1803 0.500 58.7
mntB_p5 mntB TGGGTGCCGATTTGATTGAA AGCTCGTTTACTTGCTCAGG 1804 0.500 58.6
mntA_p1 mntA TGCAATTGCTAAACCCGGTA GGATGAGAATTATCGTTGGCC 1047 0.500 41.0
mntA_p2 mntA TGCAATTGCTAAACCCGGTA TGAGAATTATCGTTGGCCTTCA 1044 0.500 40.7
mntA_p3 mntA TGCAATTGCTAAACCCGGTA AGGATGAGAATTATCGTTGGCC 1048 0.500 40.3
mntA_p4 mntA TGCAATTGCTAAACCCGGTA GGATGAGAATTATCGTTGGCCT 1047 0.500 40.3
mntA_p5 mntA TAAACCAGTTGCACCAGGTG GGATGAGAATTATCGTTGGCC 1515 0.500 40.1
ftsQ_p1 ftsQ TGTCCACCAGAAAGTTCACG GCATCTGCGCGTATTGAATC 1885 0.500 59.1
ftsQ_p2 ftsQ TTTCCTGCTCCATTTGGTCC GCATCTGCGCGTATTGAATC 1588 0.500 58.9
ftsQ_p3 ftsQ TCCTGAGCAAGTAAACGAGC GCATCTGCGCGTATTGAATC 1924 0.500 58.9
ftsQ_p4 ftsQ CCTGAGCAAGTAAACGAGCT GCATCTGCGCGTATTGAATC 1923 0.500 58.9
ftsQ_p5 ftsQ CCTGCTCCATTTGGTCCAAT GCATCTGCGCGTATTGAATC 1585 0.500 58.4

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
Cyanophora biloba NC_038216.1 130509 View on NCBI ↗
Cyanophora sudae NC_038215.1 150128 View on NCBI ↗