Markers + reference

Corallina

3 species · Corallinaceae · Corallinales

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Species 3
Genome length 177–178 kb
Candidate markers 452
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 452 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
upp Genome 588 0.0567 1.00 76.6 yes View details
ORF172 Genome 552 0.0543 1.00 75.7 yes View details
groEL-trnR1(acg) Genome 639 0.0777 1.00 86.2 yes View details
moeB Genome 1095 0.0475 1.00 73.9 yes View details
dnaB-trnF(gaa) Genome 844 0.0434 1.00 71.7 yes View details
clpC-rpl19 Genome 524 0.0770 1.00 83.3 yes View details
argB Genome 852 0.0246 1.00 60.5 yes View details
argB-trnM1(cat) Genome 346 0.0922 0.98 79.5 yes View details
chlB Genome 3475 0.0350 1.00 62.7 yes View details
ORF700 Genome 2103 0.0428 1.00 71.6 yes View details
trnG2(tcc)-ycf4 Genome 1499 0.1075 0.10 56.9 yes View details
ycf80 Genome 1356 0.0450 1.00 69.7 yes View details
nblA-cpeB Genome 923 0.1030 1.00 81.9 yes View details
trnM1(cat)-trnS(gct) Genome 51 0.0850 1.00 84.8 yes View details
rrl-trnA(tgc) Genome 50 0.0533 1.00 79.4 yes View details
trnV(tac)-trnR3(tct) Genome 23 0.1739 1.00 78.4 yes View details
trnS(gct)-trnD(gtc) Genome 58 0.0805 1.00 78.3 yes View details
trnN(gtt)-trnL(tag) Genome 106 0.0692 1.00 78.2 yes View details
moeB-trnS(gga) Genome 12 0.1667 1.00 77.5 yes View details
trnL(tag)-psbA Genome 147 0.0499 1.00 76.2 yes View details
ORF456 Genome 1368 0.0482 1.00 76.2 yes View details
rps5-rpl18 Genome 18 0.1481 1.00 76.0 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 110 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) CCGATTGCTCTACCACTGAG TACCAATTTCACCACGTCCG 157 1.000 82.3
trnN(gtt)-trnL(tag)_p2 trnN(gtt)-trnL(tag) CCCCAGGAAGGATTTGAACC TACCAATTTCACCACGTCCG 197 1.000 81.7
trnN(gtt)-trnL(tag)_p3 trnN(gtt)-trnL(tag) CCGATTGCTCTACCACTGAG GACGGAGAGACTCGAACTCT 215 1.000 80.2
trnN(gtt)-trnL(tag)_p4 trnN(gtt)-trnL(tag) CCCCAGGAAGGATTTGAACC GACGGAGAGACTCGAACTCT 255 1.000 80.1
trnN(gtt)-trnL(tag)_p5 trnN(gtt)-trnL(tag) TCTCCCCAGGAAGGATTTGA TACCAATTTCACCACGTCCG 200 1.000 79.9
trnL(tag)-psbA_p1 trnL(tag)-psbA AGAGTTCGAGTCTCTCCGTC TACAGAAACGTTCCCACAGG 224–226 1.000 78.2
trnL(tag)-psbA_p2 trnL(tag)-psbA GAGAGTTCGAGTCTCTCCGT TACAGAAACGTTCCCACAGG 225–227 1.000 78.1
trnL(tag)-psbA_p3 trnL(tag)-psbA TAAGCGGACGTGGTGAAATT TACAGAAACGTTCCCACAGG 286–288 1.000 77.9
trnL(tag)-psbA_p4 trnL(tag)-psbA CGGACGTGGTGAAATTGGTA TACAGAAACGTTCCCACAGG 282–284 1.000 77.8
trnL(tag)-psbA_p5 trnL(tag)-psbA TAAGCGGACGTGGTGAAATT AGTACAGAAACGTTCCCACAG 288–290 1.000 73.4
rrl-trnA(tgc)_p1 rrl-trnA(tgc) TCATCGCTTCTGAATGCCAA GGTTCGAGTCCGCTTATCTC 120–122 1.000 82.1
rrl-trnA(tgc)_p2 rrl-trnA(tgc) TCATCGCTTCTGAATGCCAA GTTCGAGTCCGCTTATCTCC 119–121 1.000 82.1
rrl-trnA(tgc)_p3 rrl-trnA(tgc) TTCATCGCTTCTGAATGCCA GTTCGAGTCCGCTTATCTCC 120–122 1.000 82.1
rrl-trnA(tgc)_p4 rrl-trnA(tgc) TTCATCGCTTCTGAATGCCA GGTTCGAGTCCGCTTATCTC 121–123 1.000 82.0
rrl-trnA(tgc)_p5 rrl-trnA(tgc) TCATCGCTTCTGAATGCCAA CAGTTGGTAGAGTGCTGCTT 159–161 1.000 80.7
upp_p1 upp AACCATGGCAAGAAAGACGT CGTCCCTACGTTTTCTGCTA 1795 1.000 79.1
upp_p2 upp AAGAAAGACGTGCTGCTGAA CGTCCCTACGTTTTCTGCTA 1786 1.000 78.9
upp_p3 upp CACCTCGCTCATGGTTAACA CGTCCCTACGTTTTCTGCTA 1687 1.000 78.6
upp_p4 upp ATCAGCACAAGGACCAACTG CGTCCCTACGTTTTCTGCTA 1962 0.333 47.4
upp_p5 upp CATCAGCACAAGGACCAACT CGTCCCTACGTTTTCTGCTA 1963 0.333 47.4
ORF172_p1 ORF172 CGTAACGATGCTTGGGTACA TGCTATGGGGTACGATGCTA 983 1.000 85.0
ORF172_p2 ORF172 CGTAACGATGCTTGGGTACA TTTGCTATGGGGTACGATGC 985 1.000 84.7
ORF172_p3 ORF172 CGTAGGGACGGAAAAGCTTT TGCTATGGGGTACGATGCTA 1281 1.000 82.7
ORF172_p4 ORF172 CGTAACGATGCTTGGGTACA CCGGTTTTGCGGATAGAAGA 1572 0.667 69.6
ORF172_p5 ORF172 CGTAACGATGCTTGGGTACA GGCCGGCGCTTTAATTATTC 1094 0.333 53.0
groEL-trnR1(acg)_p1 groEL-trnR1(acg) TCCATACCTTTTTCTAAAGCTTTCC TTTTTATCGGGCAAGGAGGG 628–779 1.000 51.4
groEL-trnR1(acg)_p2 groEL-trnR1(acg) CCATACCTTTTTCTAAAGCTTTCCT TTTTTATCGGGCAAGGAGGG 627–778 1.000 51.4
groEL-trnR1(acg)_p3 groEL-trnR1(acg) ACATCCATACCTTTTTCTAAAGCT TTTTTATCGGGCAAGGAGGG 631–782 1.000 51.4
groEL-trnR1(acg)_p4 groEL-trnR1(acg) CCATACCTTTTTCTAAAGCTTTCC TTTTTATCGGGCAAGGAGGG 627–778 1.000 51.4
groEL-trnR1(acg)_p5 groEL-trnR1(acg) ACCTTTTTCTAAAGCTTTCCT TTTTTATCGGGCAAGGAGGG 623–774 1.000 51.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Corallina chilensis NC_042901.1 178350 View on NCBI ↗
Corallina ferreyrae NC_041636.1 176889 View on NCBI ↗
Corallina officinalis MT211884.1 178175 View on NCBI ↗