Markers + reference

Chiharaea

2 species · Corallinaceae · Corallinales

Back to catalogue

Species 2
Genome length 181–181 kb
Candidate markers 449
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 449 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rns-ompR Genome 2031 0.0246 1.00 60.8 yes View details
syfB Genome 2013 0.0094 1.00 59.8 yes View details
argB-trnM(cat) Genome 1130 0.0177 1.00 62.3 yes View details
rps14 Genome 303 0.0099 1.00 45.0 yes View details
chlB Genome 3488 0.0080 1.00 46.4 yes View details
acsF-petN Genome 442 0.0113 1.00 56.3 yes View details
sufB Genome 1464 0.0102 1.00 50.2 yes View details
orf702 Genome 2109 0.0133 1.00 51.7 yes View details
orf395 Genome 1188 0.0118 1.00 62.0 yes View details
orf448 Genome 1347 0.0119 1.00 51.0 yes View details
pgmA-ycf21 Genome 917 0.0144 0.76 53.1 yes View details
rpl1-rpl11 Genome 23 0.0435 1.00 77.5 yes View details
rps19-rpl2 Genome 8 0.1250 1.00 74.5 yes View details
rpl29-rpl16 Genome 4 0.2500 1.00 73.9 yes View details
rps4-orf448 Genome 40 0.0500 1.00 72.1 yes View details
atpE-atpB Genome 12 0.0833 1.00 71.5 yes View details
rpl35-rpl20 Genome 31 0.0323 1.00 71.0 yes View details
trnF(gaa)-clpC Genome 72 0.0556 1.00 69.9 yes View details
trnY(gta)-trnT(ggt) Genome 25 0.0400 1.00 67.8 yes View details
trnS(gct)-trnD(gtc) Genome 61 0.0328 1.00 67.5 yes View details
rpl6-rps8 Genome 23 0.0435 1.00 66.8 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
rns-ompR_p1 rns-ompR GAGCCAGGATCAAACTCTCC CGAATACTTGTTTCGTCATCAACA 2106 1.000 46.6
rns-ompR_p2 rns-ompR TGCATGTGTTAGGCATACCG CGAATACTTGTTTCGTCATCAACA 2140 1.000 46.5
rns-ompR_p3 rns-ompR AGCCAGGATCAAACTCTCCA CGAATACTTGTTTCGTCATCAACA 2105 1.000 46.5
rns-ompR_p4 rns-ompR TATTACTCACCCGTCCGCTA CGAATACTTGTTTCGTCATCAACA 2185 1.000 46.3
rns-ompR_p5 rns-ompR GAGCCAGGATCAAACTCTCC ACTTGTTTCGTCATCAACAA 2101 1.000 44.8
syfB_p1 syfB ACAAAAGCCTCTTCTTAGTT AACAGAACCCGGCTTATGTC 2113 1.000 40.7
syfB_p2 syfB ACAAAAGCCTCTTCTTAGTT GAACAGAACCCGGCTTATGT 2114 1.000 40.7
syfB_p3 syfB TGGAACGTTATTCAAAAGAGA AACAGAACCCGGCTTATGTC 2148 1.000 40.7
syfB_p4 syfB TGGAACGTTATTCAAAAGAGA GAACAGAACCCGGCTTATGT 2149 1.000 40.7
syfB_p5 syfB ACAAAAGCCTCTTCTTAGTT CAGAACCCGGCTTATGTCTT 2111 1.000 40.7
rpl1-rpl11_p1 rpl1-rpl11 GCTTGTAACGACGAGAAGACT AGCAGCCACAAAAATACCAGA 154 1.000 63.0
rpl1-rpl11_p2 rpl1-rpl11 TGCTTGTAACGACGAGAAGA AGCAGCCACAAAAATACCAGA 155 1.000 62.9
rpl1-rpl11_p3 rpl1-rpl11 GCTTGTAACGACGAGAAGACT GCAGCCACAAAAATACCAGA 153 1.000 60.8
rpl1-rpl11_p4 rpl1-rpl11 TGCTTGTAACGACGAGAAGA GCAGCCACAAAAATACCAGA 154 1.000 60.8
rpl1-rpl11_p5 rpl1-rpl11 TGCTTGTAACGACGAGAAGAC AGCAGCCACAAAAATACCAGA 155 1.000 60.8
trnF(gaa)-clpC_p1 trnF(gaa)-clpC TGGTAGAGCAGTGGACTGAA AGGCGAAAAATTGGAATTACT 160 1.000 42.3
trnF(gaa)-clpC_p2 trnF(gaa)-clpC TTGGTAGAGCAGTGGACTGA AGGCGAAAAATTGGAATTACT 161 1.000 42.3
trnF(gaa)-clpC_p3 trnF(gaa)-clpC TCAGTTGGTAGAGCAGTGGA AGGCGAAAAATTGGAATTACT 165 1.000 42.2
trnF(gaa)-clpC_p4 trnF(gaa)-clpC AGTTGGTAGAGCAGTGGACT AGGCGAAAAATTGGAATTACT 163 1.000 42.2
trnF(gaa)-clpC_p5 trnF(gaa)-clpC ATCATAAGGCCGGGATAGCT AGGCGAAAAATTGGAATTACT 184 1.000 41.8
trnY(gta)-trnT(ggt)_p1 trnY(gta)-trnT(ggt) ACTGTAAATCCGCTGGCAAT TCTGCCATTGAGCTACAAGG 98 1.000 76.5
trnY(gta)-trnT(ggt)_p2 trnY(gta)-trnT(ggt) CTGTAAATCCGCTGGCAATG TCTGCCATTGAGCTACAAGG 97 1.000 73.7
trnY(gta)-trnT(ggt)_p3 trnY(gta)-trnT(ggt) GACTGTAAATCCGCTGGCAA TCTGCCATTGAGCTACAAGG 99 1.000 73.1
trnY(gta)-trnT(ggt)_p4 trnY(gta)-trnT(ggt) ATTCTTGATAGGGTCGGTGC TCTGCCATTGAGCTACAAGG 139 1.000 72.3
trnY(gta)-trnT(ggt)_p5 trnY(gta)-trnT(ggt) TAATGGGGGCGGACTGTAAA TCTGCCATTGAGCTACAAGG 110 1.000 71.8
argB-trnM(cat)_p1 argB-trnM(cat) TTAGTCAAGGCGTGCAATCA CGACCTTGGGCTTATGAGTC 1284 1.000 79.4
argB-trnM(cat)_p2 argB-trnM(cat) TGATGGCAGAGTTGAGCATG CGACCTTGGGCTTATGAGTC 1253 1.000 78.8
argB-trnM(cat)_p3 argB-trnM(cat) TAGTCAAGGCGTGCAATCAG CGACCTTGGGCTTATGAGTC 1283 1.000 78.6
argB-trnM(cat)_p4 argB-trnM(cat) TTAGTCAAGGCGTGCAATCA CTCAAGCGGGATTTGAACCT 1305 1.000 78.5
argB-trnM(cat)_p5 argB-trnM(cat) TGATGGCAGAGTTGAGCATG CTCAAGCGGGATTTGAACCT 1274 1.000 77.9

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
Chiharaea americana f. americana PZ226321.1 180947 View on NCBI ↗
Chiharaea bodegensis f. bodegensis PZ226319.1 180756 View on NCBI ↗