Markers + reference

Laportea

10 species · Urticaceae · Rosales

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Species 10
Genome length 149–162 kb
Candidate markers 267
Primer pairs 75

Genome-wide nucleotide diversity

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

Candidate markers

5 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 507 0.1614 0.94 79.1 yes View details
rps16-trnQ-UUG LSC 425 0.2283 0.88 75.9 yes View details
psbE-petL LSC 1080 0.1056 0.98 84.8 yes View details
ndhF-rpl32 SSC 915 0.1167 0.77 76.9 yes View details
ycf1 IRa 5583 0.1090 0.99 77.9 yes View details
trnC-GCA-petN LSC 901 0.1012 0.99 89.7 yes View details
rpl20-rps12 LSC 810 0.0652 0.97 87.7 yes View details
trnS-GCU-trnG-UCC LSC 616 0.1075 0.98 86.3 yes View details
atpF LSC 1306 0.0535 0.98 84.5 yes View details
atpB-rbcL LSC 755 0.0773 0.99 84.3 yes View details
rbcL-accD LSC 725 0.0843 0.96 84.0 yes View details
rpoB-trnC-GCA LSC 1130 0.1008 0.98 83.8 yes View details
rpl16 LSC 1294 0.0641 0.97 83.7 yes View details
clpP LSC 1965 0.0594 0.98 83.3 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 75 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU-rps16_p1 trnK-UUU-rps16 CGACATGCTGCTTTTTCCAG CGTTGCAATTGATGTTCGCT 875–1110 0.500 71.5
trnK-UUU-rps16_p2 trnK-UUU-rps16 CGACATGCTGCTTTTTCCAG ATTTCAACGAAGGCAGGTGT 724–959 0.400 67.6
trnK-UUU-rps16_p3 trnK-UUU-rps16 TGCTCGTGGTAAAAGCCTTT ATTTCAACGAAGGCAGGTGT 1009–1151 0.200 54.4
trnK-UUU-rps16_p4 trnK-UUU-rps16 TGCTCGTGGTAAAAGCCTTT CGTTGCAATTGATGTTCGCT 1160–1302 0.200 54.0
trnK-UUU-rps16_p5 trnK-UUU-rps16 TGCTCGTGGTAAAAGCCTTT TCGTTGCAATTGATGTTCGC 1161–1303 0.200 54.0
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG GAGGTTCGAATCCTTCCGTC 490–739 0.800 77.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCACGTTGCTTTCTACCACA GAGGTTCGAATCCTTCCGTC 493–742 0.800 74.9
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CGTTGCTTTCTACCACATCG TTCGGAGGTTCGAATCCTTC 494–743 0.800 72.4
rps16-trnQ-UUG_p4 rps16-trnQ-UUG CACGTTGCTTTCTACCACATC GAGGTTCGAATCCTTCCGTC 492–741 0.800 71.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CACGTTGCTTTCTACCACAT GAGGTTCGAATCCTTCCGTC 492–741 0.800 70.3
trnS-GCU-trnG-UCC_p1 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 655–727 1.000 63.7
trnS-GCU-trnG-UCC_p2 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 654–726 1.000 63.7
trnS-GCU-trnG-UCC_p3 trnS-GCU-trnG-UCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 657–729 1.000 62.6
trnS-GCU-trnG-UCC_p4 trnS-GCU-trnG-UCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 656–728 1.000 62.6
trnS-GCU-trnG-UCC_p5 trnS-GCU-trnG-UCC ACGGAAAGAGAGGGATTCGA ACGAATCACACTTTTACCACT 709–781 1.000 62.5
trnG-UCC_p1 trnG-UCC CAATCCGACGCTTTAGTCCA GGTCAGCGATTACGTGAGTT 2107–2224 0.900 87.9
trnG-UCC_p2 trnG-UCC AATCCGACGCTTTAGTCCAC GGTCAGCGATTACGTGAGTT 2106–2223 0.900 87.9
trnG-UCC_p3 trnG-UCC ACGGAAAGAGAGGGATTCGA GGTCAGCGATTACGTGAGTT 2161–2278 0.900 86.7
trnG-UCC_p4 trnG-UCC CTGGGCCTGGCTTCTTTTAT GGTCAGCGATTACGTGAGTT 1905–1959 0.400 64.0
trnG-UCC_p5 trnG-UCC CAATCCGACGCTTTAGTCCA GAGGTCAGCGATTACGTGAG 2109–2115 0.200 51.0
atpF_p1 atpF ATACGAGCAATACCATCGCC ATTTCTGCCGCTTCCGTTAT 2110–2177 0.800 83.1
atpF_p2 atpF CTGAAATTTCACCCCGACCA ATTTCTGCCGCTTCCGTTAT 2401–2422 0.700 78.9
atpF_p3 atpF AGCAATTCCTACCGTACCCT TAATTGGGGGAGGGGGAATT 1868–1877 0.200 51.5
atpF_p4 atpF CTGAAATTTCACCCCGACCA TAATTGGGGGAGGGGGAATT 2046–2055 0.200 51.4
atpF_p5 atpF ATACGAGCAATACCATCGCC TAATTGGGGGAGGGGGAATT 1810 0.100 43.2
rpoB-trnC-GCA_p1 rpoB-trnC-GCA AGAGGTTCCCAGGGAATTCA CCGGATTTGAACTGGGGAAA 1432–1580 0.900 86.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CCGGATTTGAACTGGGGAAA 1605–1753 0.800 83.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT TTTGCCCTATGACCCAATCG 2253–2271 0.300 59.7
rpoB-trnC-GCA_p4 rpoB-trnC-GCA AGAGGTTCCCAGGGAATTCA TTTGCCCTATGACCCAATCG 2080–2095 0.200 51.0
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GCTCTCCGCTTACACAAGAA TTTGCCCTATGACCCAATCG 2450–2465 0.200 50.3

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (10)

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

Species Accession Length (bp) Link
Laportea aestuans NC_064746.1 153521 View on NCBI ↗
Laportea bulbifera NC_063590.1 150042 View on NCBI ↗
Laportea canadensis NC_064747.1 150253 View on NCBI ↗
Laportea cuspidata NC_064748.1 149149 View on NCBI ↗
Laportea decumana NC_064977.1 151855 View on NCBI ↗
Laportea grossa NC_064976.1 161930 View on NCBI ↗
Laportea medogensis NC_064975.1 150196 View on NCBI ↗
Laportea mooreana NC_064749.1 150827 View on NCBI ↗
Laportea oligoloba NC_064971.1 152919 View on NCBI ↗
Laportea ovalifolia NC_064750.1 153659 View on NCBI ↗