Markers + reference

Laurencia

4 species · Rhodomelaceae · Ceramiales

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Species 4
Genome length 172–174 kb
Candidate markers 479
Primer pairs 100

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 479 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf46-rpl34 Genome 528 0.2784 0.96 82.3 yes View details
ccsA-cpeA Genome 651 0.2495 0.88 81.7 yes View details
ycf80 Genome 1428 0.1215 1.00 78.8 yes View details
mat Genome 1044 0.1687 1.00 79.0 yes View details
psbI-ycf39 Genome 758 0.2472 0.87 80.1 yes View details
orf190 Genome 816 0.1574 0.99 79.6 yes View details
infB Genome 2280 0.1134 1.00 77.1 yes View details
dnaB Genome 1827 0.1266 1.00 78.6 yes View details
syfB Genome 1956 0.1308 1.00 78.0 yes View details
orf103 Genome 501 0.1590 0.97 76.4 yes View details
ompR-rns Genome 515 0.1842 0.98 83.3 no View details
mat-cemA Genome 830 0.0955 0.97 81.6 yes View details
trnL(tag)-trnN(gtt) Genome 139 0.1654 0.89 81.1 yes View details
ycf60 Genome 597 0.0678 1.00 80.8 yes View details
moeB Genome 1054 0.1170 0.98 80.2 yes View details
trnA(tgc)-rnl Genome 82 0.0802 0.99 80.1 yes View details
ntcA Genome 675 0.1094 1.00 80.1 yes View details
carA Genome 1170 0.0901 1.00 79.7 yes View details
acsF Genome 1050 0.0753 1.00 79.5 yes View details
rnz Genome 678 0.0944 1.00 79.4 yes View details
ycf38 Genome 873 0.0895 0.99 79.4 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnA(tgc)-rnl_p1 trnA(tgc)-rnl GGTTCGAGTCCGCTTATCTC ATGTTTCGTCGGTAGTCACG 173–175 1.000 84.8
trnA(tgc)-rnl_p2 trnA(tgc)-rnl GTTCGAGTCCGCTTATCTCC ATGTTTCGTCGGTAGTCACG 172–174 1.000 84.8
trnA(tgc)-rnl_p3 trnA(tgc)-rnl TTCGAGTCCGCTTATCTCCA ATGTTTCGTCGGTAGTCACG 171–173 1.000 83.9
trnA(tgc)-rnl_p4 trnA(tgc)-rnl GTTCGAGTCCGCTTATCTCC CGCCCTTCATCGCTTCTAAA 154–156 1.000 82.9
trnA(tgc)-rnl_p5 trnA(tgc)-rnl GCTTTTGCAAGGCAGATGTC ATGTTTCGTCGGTAGTCACG 196–198 1.000 82.7
ycf46-rpl34_p1 ycf46-rpl34 TTAAATTGCCTAAGCCGCCT CGCTGAACAGGAAAAAGGGA 1714 0.250 45.7
ycf46-rpl34_p2 ycf46-rpl34 TTAAATTGCCTAAGCCGCCT TCGCTGAACAGGAAAAAGGG 1715 0.250 45.7
ycf46-rpl34_p3 ycf46-rpl34 TTAAATTGCCTAAGCCGCCT AGGATGTCGCAGGTTCAAAT 1980 0.250 44.9
ycf46-rpl34_p4 ycf46-rpl34 TTAAATTGCCTAAGCCGCCT ATGTCGCAGGTTCAAATCCT 1977 0.250 44.9
ycf46-rpl34_p5 ycf46-rpl34 CCTAAGCCGCCTACATTGAT CGCTGAACAGGAAAAAGGGA 1706 0.250 42.4
carA_p1 carA TCTCCAGATAAGTGGGGTGG GCACCAGAAGGACACTTACC 1893–1905 0.750 76.1
carA_p2 carA AAGCGGGAGAACAGGTTTTT TGGACAACAAAAGCACCAGA 1659 0.250 48.4
carA_p3 carA TCTCCAGATAAGTGGGGTGG TGGACAACAAAAGCACCAGA 1917 0.250 47.9
carA_p4 carA AAGCGGGAGAACAGGTTTTT GCACCAGAAGGACACTTACC 1647 0.250 47.9
carA_p5 carA TGGCGCTAAGTTGGATGAAA TGGACAACAAAAGCACCAGA 1487 0.250 47.4
rnz_p1 rnz TAATTGCTGCTGGTTCCTGG TGCTACCTCTCTGACGTACA 1656–1675 0.500 64.0
rnz_p2 rnz TAATTGCTGCTGGTTCCTGG TCACGATACCGGAAACAAGC 1747 0.250 46.4
rnz_p3 rnz TAATTGCTGCTGGTTCCTGG CGATACCGGAAACAAGCGAA 1744 0.250 43.5
rnz_p4 rnz AGTAATTGCTGCTGGTTCCT TCACGATACCGGAAACAAGC 1749 0.250 40.6
rnz_p5 rnz TAATTGCTGCTGGTTCCTGG CGATACCGGAAACAAGCGA 1744 0.250 40.4
trnL(tag)-trnN(gtt)_p1 trnL(tag)-trnN(gtt) TCTAGCGTGTCTGCCAATTC ACTCCCCAGGAAGGATTTGA 230–245 1.000 91.4
trnL(tag)-trnN(gtt)_p2 trnL(tag)-trnN(gtt) TCTAGCGTGTCTGCCAATTC CCCCAGGAAGGATTTGAACC 227–242 1.000 90.7
trnL(tag)-trnN(gtt)_p3 trnL(tag)-trnN(gtt) TCTGCCAATTCCACCACATC ACTCCCCAGGAAGGATTTGA 221–236 1.000 90.2
trnL(tag)-trnN(gtt)_p4 trnL(tag)-trnN(gtt) TCTGCCAATTCCACCACATC CCCCAGGAAGGATTTGAACC 218–233 1.000 89.5
trnL(tag)-trnN(gtt)_p5 trnL(tag)-trnN(gtt) TCTAGCGTGTCTGCCAATTC ACCACTGAGCTACTGAGGAA 176–191 1.000 89.4
ycf60_p1 ycf60 TTGCGTATTGTACACGACGT GAGTTGACCATTCGCCTGAT 1206 0.750 77.2
ycf60_p2 ycf60 CGATGTGCCGCTATCGATAA GAGTTGACCATTCGCCTGAT 1169 0.250 49.6
ycf60_p3 ycf60 TAGTCCTTGACCTGAGCCAA GAGTTGACCATTCGCCTGAT 1568 0.250 49.6
ycf60_p4 ycf60 CCTGAGCCAATAGGTGAACC GAGTTGACCATTCGCCTGAT 1558 0.250 49.4
ycf60_p5 ycf60 TGACCTGAGCCAATAGGTGA GAGTTGACCATTCGCCTGAT 1561 0.250 49.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Laurencia australis OQ908868.1 173810 View on NCBI ↗
Laurencia catarinensis NC_082854.1 171833 View on NCBI ↗
Laurencia obtusa NC_082856.1 172020 View on NCBI ↗
Laurencia verruciformis OQ908870.1 172933 View on NCBI ↗