Markers + reference

Liagora

2 species · Liagoraceae · Nemaliales

Back to catalogue

Species 2
Genome length 183–183 kb
Candidate markers 482
Primer pairs 110

Genome-wide nucleotide diversity

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

Candidate markers

12 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 482 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf35 Genome 387 0.0672 1.00 70.3 yes View details
tilS Genome 1008 0.0605 1.00 78.5 yes View details
trpA Genome 795 0.0491 1.00 72.0 yes View details
ycf23 Genome 798 0.0576 1.00 73.5 yes View details
ORF_8 Genome 168 0.0595 1.00 67.5 yes View details
ORF_4 Genome 2247 0.0641 1.00 75.4 yes View details
petN-acsF Genome 345 0.0986 1.00 74.8 yes View details
chlB Genome 3392 0.0419 1.00 64.6 yes View details
psbZ-trnG Genome 427 0.1007 1.00 83.5 yes View details
dnaB Genome 1770 0.0508 1.00 72.2 yes View details
syfB Genome 2001 0.0575 1.00 72.8 yes View details
ompR Genome 732 0.0410 1.00 68.1 yes View details
ompR-rns Genome 293 0.1024 1.00 79.8 no View details
trnR-trnV Genome 26 0.1154 1.00 78.2 yes View details
trnC-cbbX Genome 63 0.0952 1.00 77.7 yes View details
rps9-rpl31 Genome 22 0.1000 0.91 77.3 yes View details
trnG-trnM Genome 48 0.2917 1.00 76.5 yes View details
accB Genome 498 0.0542 1.00 76.5 yes View details
trnY-trnV Genome 74 0.1486 1.00 76.2 yes View details
rps18-infB Genome 212 0.0955 0.94 76.0 yes View details
rpl20-rpl35 Genome 13 0.1538 1.00 76.0 yes View details
carA-petJ Genome 112 0.1071 1.00 75.9 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
ycf35_p1 ycf35 GTGATAAAGCTGAAGGCCGA ATACGATCGTAAGGGCCAGA 872 0.500 59.7
ycf35_p2 ycf35 GTGATAAAGCTGAAGGCCGA CGATCGTAAGGGCCAGAAAA 869 0.500 59.7
ycf35_p3 ycf35 GTGATAAAGCTGAAGGCCGA CATACGATCGTAAGGGCCAG 873 0.500 59.3
ycf35_p4 ycf35 GTGGAATTGGTAGACACGCT ATACGATCGTAAGGGCCAGA 543 0.500 59.2
ycf35_p5 ycf35 GTGGAATTGGTAGACACGCT CGATCGTAAGGGCCAGAAAA 540 0.500 59.1
carA-petJ_p1 carA-petJ TGTTTTATAGGTTTTTGTGTCAAACA AAGCGGAACAAGGTTGGTAA 159–165 1.000 45.9
carA-petJ_p2 carA-petJ TGTTTTATAGGTTTTTGTGTCAAACA CAAGCGGAACAAGGTTGGTA 160–166 1.000 45.9
carA-petJ_p3 carA-petJ TGTTTTATAGGTTTTTGTGTCAAACA AAGTCAAGCGGAACAAGGTT 164–170 1.000 45.7
carA-petJ_p4 carA-petJ TGTTTTATAGGTTTTTGTGTCAAACA TTGGAGGACGTTTAGAGGCT 216–222 1.000 44.4
carA-petJ_p5 carA-petJ TGTTTTATAGGTTTTTGTGTCAAACA TTTGGAGGACGTTTAGAGGC 217–223 1.000 44.4
trnR-trnV_p1 trnR-trnV GGTCCCTGTCCTAATCCCTT CTGGTTCAAGTCCAGTACCG 84 1.000 81.4
trnR-trnV_p2 trnR-trnV AAGGTCCCTGTCCTAATCCC CTGGTTCAAGTCCAGTACCG 86 1.000 81.3
trnR-trnV_p3 trnR-trnV AAGGTCCCTGTCCTAATCCC TTACAAGCAGGTGGTCACTG 103 1.000 79.5
trnR-trnV_p4 trnR-trnV GGTCCCTGTCCTAATCCCTT TTACAAGCAGGTGGTCACTG 101 1.000 79.5
trnR-trnV_p5 trnR-trnV GGTCCCTGTCCTAATCCCTT CTATAAAGTTGGGTGGGCGG 146 1.000 78.2
tilS_p1 tilS GCCTTATTGATCAATCGTATGCC ACTAAATTCATATCACTAGCACC 1064 1.000 44.6
tilS_p2 tilS GCCTTATTGATCAATCGTATGCC AACTAAATTCATATCACTAGCACC 1065 1.000 44.6
tilS_p3 tilS GCCTTATTGATCAATCGTATGCC ATCAAGACCTAACTCAAAACT 1082 1.000 44.5
tilS_p4 tilS TGCCTTATTGATCAATCGTATGC ATCAAGACCTAACTCAAAACT 1083 1.000 44.5
tilS_p5 tilS GCCTTATTGATCAATCGTATGCC TCAAGACCTAACTCAAAACTAA 1081 1.000 44.5
trpA_p1 trpA CGATTAGTTCCGGGTTCGAG ATACGGCATGGCAAGAACAT 1301 1.000 81.9
trpA_p2 trpA CGATTAGTTCCGGGTTCGAG CGAAGCTACGGACAACAAGA 1242 1.000 81.9
trpA_p3 trpA TTTGAGTCGTGTCTTGCCTC ATACGGCATGGCAAGAACAT 1627 0.500 58.5
trpA_p4 trpA TTTGAGTCGTGTCTTGCCTC CGAAGCTACGGACAACAAGA 1568 0.500 58.4
trpA_p5 trpA TTTGAGTCGTGTCTTGCCTC CAATTAAGGCCAGGGCTGAT 1685 0.500 58.3
ycf23_p1 ycf23 ATGCTTTAGCCTTTGGAGTT AGCTAATACATGACATCCAATCA 857 1.000 44.4
ycf23_p2 ycf23 ATGCTTTAGCCTTTGGAGTT GCTAATACATGACATCCAATCATCA 856 1.000 44.4
ycf23_p3 ycf23 ATGCTTTAGCCTTTGGAGTT ACATGACATCCAATCATCAT 850 1.000 44.4
ycf23_p4 ycf23 ATGCTTTAGCCTTTGGAGTT AAGCTAATACATGACATCCAATCA 858 1.000 44.4
ycf23_p5 ycf23 ATGCTTTAGCCTTTGGAGTT ACATGACATCCAATCATCATT 850 1.000 44.4

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
Liagora brachyclada NC_031667.1 182937 View on NCBI ↗
Liagora harveyana NC_031661.1 182933 View on NCBI ↗