Markers + reference

Chondracanthus

2 species · Gigartinaceae · Gigartinales

Back to catalogue

Species 2
Genome length 176–176 kb
Candidate markers 454
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 454 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf35 Genome 387 0.0904 1.00 73.3 yes View details
ycf37 Genome 513 0.1053 1.00 77.1 yes View details
cemA Genome 837 0.0430 1.00 69.5 yes View details
cemA-ycf58 Genome 2355 0.0956 0.99 78.5 yes View details
infB Genome 2322 0.0746 0.99 76.0 yes View details
ycf3-atpB Genome 350 0.1271 0.67 69.6 yes View details
petF Genome 297 0.0976 1.00 72.4 yes View details
moeB Genome 1101 0.0799 1.00 76.3 yes View details
syfB Genome 2166 0.0700 1.00 76.5 yes View details
psb28-trnQ(ttg) Genome 386 0.1157 0.94 81.2 yes View details
ompR-rns Genome 393 0.0662 1.00 86.0 no View details
trnL(taa)-trnC(gca) Genome 19 0.1053 1.00 78.6 yes View details
rpl2-rps19 Genome 13 0.1538 1.00 77.6 yes View details
trnN(gtt)-trnL(tag) Genome 137 0.1387 1.00 77.5 yes View details
trnG(tcc)-trnMe(cat) Genome 26 0.1923 1.00 77.5 yes View details
trnC(gca)-cbbX Genome 74 0.1351 1.00 77.0 yes View details
rpl32-psbY Genome 170 0.1267 0.88 76.8 yes View details
trnD(gtc)-trnS(gct) Genome 190 0.1088 0.77 76.8 yes View details
psbF-psbL Genome 9 0.1111 1.00 76.7 yes View details
trnL(caa)-sufB Genome 948 0.0728 1.00 76.7 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnN(gtt)-trnL(tag)_p1 trnN(gtt)-trnL(tag) CTACCACTGAGCTACTGAGGA AGCGTGTCTACCAATTCCAC 187 1.000 79.2
trnN(gtt)-trnL(tag)_p2 trnN(gtt)-trnL(tag) TCTACCACTGAGCTACTGAGG AGCGTGTCTACCAATTCCAC 188 1.000 79.2
trnN(gtt)-trnL(tag)_p3 trnN(gtt)-trnL(tag) CTACCACTGAGCTACTGAGGA CTACCAATTCCACCACGTCC 180 1.000 77.8
trnN(gtt)-trnL(tag)_p4 trnN(gtt)-trnL(tag) TCTACCACTGAGCTACTGAGG CTACCAATTCCACCACGTCC 181 1.000 77.8
trnN(gtt)-trnL(tag)_p5 trnN(gtt)-trnL(tag) ACCAATCGGTTAACAGCCG AGCGTGTCTACCAATTCCAC 212 1.000 77.2
ycf35_p1 ycf35 GTGGAATTGGTAGACACGCT AAGATGCAGCTTCCCAAACA 1037–1043 1.000 84.0
ycf35_p2 ycf35 CCCCAGGAAGGATTTGAACC AAGATGCAGCTTCCCAAACA 1253–1259 1.000 84.0
ycf35_p3 ycf35 CTTAACCTCCCCAGGAAGGA AAGATGCAGCTTCCCAAACA 1267 0.500 59.7
ycf35_p4 ycf35 CTTAACCTCCCCAGGAAGGA CTGCAACTGGTTCACGGATA 1168 0.500 59.0
ycf35_p5 ycf35 AACCTTAACCTCCCCAGGAA AAGATGCAGCTTCCCAAACA 1270 0.500 58.9
rpl32-psbY_p1 rpl32-psbY GCCTTTACGTTTCCATTGAGC TAGACTAATTGCTGGCTGCG 694–714 1.000 77.6
rpl32-psbY_p2 rpl32-psbY GCCTTTACGTTTCCATTGAGC CTAATTGCTGGCTGCGAAAC 690–710 1.000 77.3
rpl32-psbY_p3 rpl32-psbY GCCTTTACGTTTCCATTGAGC GCACGACATGTCTCTTCACA 834–854 1.000 75.6
rpl32-psbY_p4 rpl32-psbY GCCTTTACGTTTCCATTGAGC AACTCCTGTATTGGCAGCAG 321 0.500 50.0
rpl32-psbY_p5 rpl32-psbY CCTGAGGGGCAATAAATGTGT TAGACTAATTGCTGGCTGCG 1132 0.500 49.4
ycf37_p1 ycf37 GAGCTTACGGGATATAGCGC AAAATGGCGCGATGACAGTA 936–959 1.000 83.8
ycf37_p2 ycf37 GAGCTTACGGGATATAGCGC AAATGGCGCGATGACAGTAA 935–958 1.000 83.8
ycf37_p3 ycf37 GAGCTTACGGGATATAGCGC AATGGCGCGATGACAGTAAA 934–957 1.000 83.8
ycf37_p4 ycf37 GAGCTTACGGGATATAGCGC ATGGCGCGATGACAGTAAAA 933–956 1.000 83.8
ycf37_p5 ycf37 GCTTACGGGATATAGCGCAG ATGGCGCGATGACAGTAAAA 931–954 1.000 81.6
psbF-psbL_p1 psbF-psbL TCCATGGATTGGCTATTCCA ATTAGGATTAGGACCACTCA 101 1.000 40.8
psbF-psbL_p2 psbF-psbL TCCATGGATTGGCTATTCCA TTAGGATTAGGACCACTCAT 100 1.000 40.8
psbF-psbL_p3 psbF-psbL TCCATGGATTGGCTATTCCA ATTAGGATTAGGACCACTCAT 101 1.000 40.8
psbF-psbL_p4 psbF-psbL GTTAGCTATCCATGGATTGGCT ATTAGGATTAGGACCACTCA 109 1.000 40.7
psbF-psbL_p5 psbF-psbL GTTAGCTATCCATGGATTGGCT TTAGGATTAGGACCACTCAT 108 1.000 40.7
trnL(taa)-trnC(gca)_p1 trnL(taa)-trnC(gca) GTCTACCATTCCACCACACC AGGCGGTATAGCTAAGTGGT 117 1.000 79.8
trnL(taa)-trnC(gca)_p2 trnL(taa)-trnC(gca) GTCTACCATTCCACCACACC GGTAAGGCAGAGGATTGCAA 100 1.000 79.7
trnL(taa)-trnC(gca)_p3 trnL(taa)-trnC(gca) GTCTACCATTCCACCACACC AGGCAGAGGATTGCAAATCC 96 1.000 79.0
trnL(taa)-trnC(gca)_p4 trnL(taa)-trnC(gca) GTCTACCATTCCACCACACC GCTAAGTGGTAAGGCAGAGG 107 1.000 78.1
trnL(taa)-trnC(gca)_p5 trnL(taa)-trnC(gca) GGGATTTGAACCCTCACGAT AGGCGGTATAGCTAAGTGGT 169 1.000 76.9

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
Chondracanthus serratus OP171937.1 175591 View on NCBI ↗
Chondracanthus spinosus OP142701.1 175539 View on NCBI ↗