Markers + reference

Lepechiniella

2 species · Boraginaceae · Boraginales

Back to catalogue

Species 2
Genome length 147–148 kb
Candidate markers 266
Primer pairs 90

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 266 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpoB-trnC-GCA LSC 1200 0.0143 0.99 68.2 yes View details
trnE-UUC-trnT-GGU LSC 725 0.0085 0.97 66.4 yes View details
ndhC-trnV-UAC LSC 566 0.0068 0.78 55.7 yes View details
ycf4-cemA LSC 830 0.0122 0.98 67.3 yes View details
psaJ-rpl33 LSC 351 0.0233 0.98 69.1 yes View details
rpl16 LSC 1483 0.0088 0.99 59.5 yes View details
ycf1 IRb 1107 0.0037 0.99 57.6 yes View details
ndhD SSC 1518 0.0020 1.00 47.4 yes View details
ycf1 SSC 5328 0.0026 1.00 54.3 no View details
ndhD-psaC SSC 102 0.0490 1.00 70.3 yes View details
trnV-UAC-trnM-CAU LSC 182 0.0220 1.00 65.1 yes View details
psaA-ycf3 LSC 723 0.0043 0.97 64.6 yes View details
trnG-UCC LSC 48 0.0208 1.00 64.5 yes View details
psbZ-trnG-GCC LSC 283 0.0111 0.95 63.3 yes View details
trnT-UGU-trnL-UAA LSC 636 0.0063 0.99 63.2 yes View details
trnH-GUG-psbA LSC 273 0.0121 0.91 63.0 yes View details
ccsA-ndhD SSC 144 0.0208 1.00 62.5 yes View details
trnK-UUU-rps16 LSC 763 0.0027 0.98 62.3 yes View details
ndhF-rpl32 SSC 612 0.0049 0.99 62.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CAACCGTGCTAACCTTGGTA 370–395 1.000 82.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CAACCGTGCTAACCTTGGTA 384–409 1.000 82.2
trnH-GUG-psbA_p3 trnH-GUG-psbA GATCCACTTGGCTACATCCG ATCAACCGTGCTAACCTTGG 372–397 1.000 82.2
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CAACCGTGCTAACCTTGGTA 383–408 1.000 82.1
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CAACCGTGCTAACCTTGGTA 385–410 1.000 82.1
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCGATGGTATGGACGAATCC GGTGCTCAACCTACAGGAAC 937–948 1.000 79.4
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 876–887 1.000 78.8
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 875–886 1.000 78.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAGGAAC 885–896 1.000 77.8
trnK-UUU-rps16_p5 trnK-UUU-rps16 TGGACGAATCCTTCCCTTCA GGTGCTCAACCTACAGGAAC 928–939 1.000 77.2
trnG-UCC_p1 trnG-UCC AAAGGAGCCGAATGAAACCA TGTGAAAAATTTTCGGGAATTGT 202 1.000 40.4
trnG-UCC_p2 trnG-UCC AAGGAGCCGAATGAAACCAA TGTGAAAAATTTTCGGGAATTGT 201 1.000 40.4
trnG-UCC_p3 trnG-UCC AGGAGCCGAATGAAACCAAA TGTGAAAAATTTTCGGGAATTGT 200 1.000 40.4
trnG-UCC_p4 trnG-UCC GGAGCCGAATGAAACCAAAG TGTGAAAAATTTTCGGGAATTGT 199 1.000 40.4
trnG-UCC_p5 trnG-UCC AGGAGCCGAATGAAACCAAA GGATTGTATGTGAAAAATTTTCGGG 208 1.000 40.4
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCTCATTTCCATTACCGAGCA CCGGATTTGAACTGGGGAAA 1284–1293 1.000 72.7
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CCTCATTTCCATTACCGAGCA AAAAGGATTTGCAGTCCCCC 1266–1275 1.000 70.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CCTCATTTCCATTACCGAGC CCGGATTTGAACTGGGGAAA 1284–1293 1.000 67.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCTCATTTCCATTACCGAGCA TTTGTTGATCAGGCGACACC 1303–1312 1.000 67.2
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCCTCATTTCCATTACCGAGC CCGGATTTGAACTGGGGAAA 1285–1294 1.000 67.1
trnE-UUC-trnT-GGU_p1 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA GAACCGATGACTTACGCCTT 791–812 1.000 81.5
trnE-UUC-trnT-GGU_p2 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA GAACCGATGACTTACGCCTT 789–810 1.000 81.5
trnE-UUC-trnT-GGU_p3 trnE-UUC-trnT-GGU TTTCGTAGTACCCTACCCCC GAACCGATGACTTACGCCTT 845–866 1.000 81.2
trnE-UUC-trnT-GGU_p4 trnE-UUC-trnT-GGU AGAGATGTCCTGAACCGCTA CCATGGCGTTACTCTACCAC 770–791 1.000 81.1
trnE-UUC-trnT-GGU_p5 trnE-UUC-trnT-GGU AGATGTCCTGAACCGCTAGA CCATGGCGTTACTCTACCAC 768–789 1.000 81.1
psbZ-trnG-GCC_p1 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG AATCGAACCCGCATCTTCTC 443–451 1.000 80.8
psbZ-trnG-GCC_p2 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG GAATCGAACCCGCATCTTCT 444–452 1.000 80.7
psbZ-trnG-GCC_p3 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC AATCGAACCCGCATCTTCTC 441–449 1.000 80.4
psbZ-trnG-GCC_p4 psbZ-trnG-GCC GCTTCTCCTGATGGTTGGTC GAATCGAACCCGCATCTTCT 442–450 1.000 80.4
psbZ-trnG-GCC_p5 psbZ-trnG-GCC TTGCTTCTCCTGATGGTTGG ACGGGCAACTATACCAAACC 500–508 1.000 80.0

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
Lepechiniella alatavica PV548682.1 147555 View on NCBI ↗
Lepechiniella sarawschanica PV548708.1 146974 View on NCBI ↗