Markers + reference

Lophurella

5 species · Rhodomelaceae · Ceramiales

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Species 5
Genome length 167–168 kb
Candidate markers 455
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 455 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf37 Genome 492 0.1118 1.00 76.5 yes View details
dsbD Genome 738 0.0898 1.00 78.8 yes View details
ycf23 Genome 849 0.0869 1.00 81.4 yes View details
ilvH Genome 537 0.0507 1.00 77.5 yes View details
ycf58 Genome 414 0.1302 1.00 77.9 yes View details
QQP83_pgp116 Genome 798 0.1223 1.00 79.6 yes View details
dnaB Genome 1818 0.0829 1.00 78.6 yes View details
syfB Genome 2019 0.0913 1.00 78.1 yes View details
ompR-rns Genome 365 0.1286 1.00 80.6 no View details
trnM-cemA Genome 187 0.1975 0.99 81.3 yes View details
tilS Genome 984 0.0734 1.00 81.2 yes View details
carA Genome 1170 0.0643 1.00 81.0 yes View details
argB Genome 861 0.0633 1.00 81.0 yes View details
trnY-trnV.2 Genome 88 0.1545 1.00 81.0 yes View details
ycf29 Genome 621 0.0651 1.00 80.2 yes View details
ycf46 Genome 1464 0.0719 1.00 80.0 yes View details
ycf80 Genome 1515 0.0810 1.00 79.9 yes View details
petN-acsF Genome 248 0.0747 1.00 79.5 yes View details
accD Genome 870 0.0524 1.00 79.3 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
ycf46_p1 ycf46 AAACCATTCCGAACTTGGCT AATTAGACGGGGCCAAAGAC 2230 0.200 47.0
ycf46_p2 ycf46 ATCTCCCCCAAGAGTTCACA AATTAGACGGGGCCAAAGAC 2728 0.200 46.6
ycf46_p3 ycf46 TCTCCCCCAAGAGTTCACAT AATTAGACGGGGCCAAAGAC 2727 0.200 46.6
ycf46_p4 ycf46 CAAGTCGAGCAGAGACGAAA AATTAGACGGGGCCAAAGAC 2828 0.200 46.6
ycf46_p5 ycf46 CAAACCATTCCGAACTTGGC AATTAGACGGGGCCAAAGAC 2231 0.200 46.5
ycf37_p1 ycf37 ACCACTTTTTGTTTTCATCCGA TGGTTGGGTAAGGAGACCAT 1233–1245 0.400 37.7
ycf37_p2 ycf37 GACCACTTTTTGTTTTCATCCGA TGGTTGGGTAAGGAGACCAT 1234–1246 0.400 37.1
ycf37_p3 ycf37 ACCACTTTTTGTTTTCATCCGA TTGGTTGGGTAAGGAGACCA 1234–1246 0.400 36.7
ycf37_p4 ycf37 ACCACTTTTTGTTTTCATCCGA GACTTTGTGACTCGGTTGGT 1249 0.200 23.7
ycf37_p5 ycf37 GACCACTTTTTGTTTTCATCCGA GACTTTGTGACTCGGTTGGT 1250 0.200 23.0
accD_p1 accD TGGAGCTGGTTTAACATGGG TCTCTAGCAGGAGTCGCTAA 1725–1736 1.000 81.1
accD_p2 accD ACTGCTCCTCATCCTAAGCT TCTCTAGCAGGAGTCGCTAA 2073 0.200 40.9
accD_p3 accD ACTGCTCCTCATCCTAAGCT CACCGTTATGACATTGAGCG 2003 0.200 40.9
accD_p4 accD TGGAGCTGGTTTAACATGGG CACCGTTATGACATTGAGCG 1656 0.200 40.5
accD_p5 accD ACTGCTCCTCATCCTAAGCT CGTTATGACATTGAGCGCAA 2000 0.200 40.2
carA_p1 carA AATGGTTATGGTCCGATGCC GTGGACGATAGATGCACCAG 1468–1489 0.600 70.9
carA_p2 carA AATGGTTATGGTCCGATGCC GCACCAGAAGGACACTTACC 1455–1476 0.600 70.4
carA_p3 carA AATGGTTATGGTCCGATGCC GATGCACCAGAAGGACACTT 1458–1479 0.600 70.4
carA_p4 carA AATGGTTATGGTCCGATGCC TGGACGATAGATGCACCAGA 1467–1488 0.600 70.2
carA_p5 carA AATGGTTATGGTCCGATGCC ATGTGGACGATAGATGCACC 1470–1491 0.600 67.7
dsbD_p1 dsbD ATCCTTCCTGGGGAGTTTCA AGGAGCAATACGACCATACA 1336 0.200 31.9
dsbD_p2 dsbD TCAAATCCTTCCTGGGGAGT AGGAGCAATACGACCATACA 1340 0.200 31.9
dsbD_p3 dsbD GGTTCAAATCCTTCCTGGGG AGGAGCAATACGACCATACA 1343 0.200 31.2
dsbD_p4 dsbD TCCTTCCTGGGGAGTTTCAA AGGAGCAATACGACCATACA 1335 0.200 31.0
dsbD_p5 dsbD TACCAATTTCACCACGTCCG AGGAGCAATACGACCATACA 1541 0.200 30.7
tilS_p1 tilS AGGTCTTGCTCGACACAAAG TATCAAGCATGAACAGCGCT 1823 0.200 46.7
tilS_p2 tilS GAAGGTCTTGCTCGACACAA TATCAAGCATGAACAGCGCT 1825 0.200 46.7
tilS_p3 tilS GGTCTTGCTCGACACAAAGA TATCAAGCATGAACAGCGCT 1822 0.200 46.7
tilS_p4 tilS TTGAAGGTCTTGCTCGACAC TATCAAGCATGAACAGCGCT 1827 0.200 46.7
tilS_p5 tilS AGGTCTTGCTCGACACAAAG AAGCATGAACAGCGCTTCTA 1819 0.200 46.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Lophurella caespitosa NC_079641.1 167946 View on NCBI ↗
Lophurella hookeriana NC_079642.1 168141 View on NCBI ↗
Lophurella mutabilis NC_079643.1 168279 View on NCBI ↗
Lophurella pseudocorticata OQ731399.1 167005 View on NCBI ↗
Lophurella stichidiosa NC_079644.1 168119 View on NCBI ↗