Markers + reference

Boeica

2 species · Gesneriaceae · Lamiales

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Species 2
Genome length 154–154 kb
Candidate markers 264
Primer pairs 75

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 6 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhD SSC 1530 0.4833 0.70 76.6 yes View details
psaC-ndhE SSC 260 0.5181 0.96 76.6 yes View details
ndhE SSC 306 0.4913 0.94 77.1 yes View details
ndhI SSC 492 0.5074 0.82 77.7 yes View details
ndhA SSC 2139 0.4768 0.83 79.2 yes View details
ndhH SSC 1182 0.5028 0.92 82.8 yes View details
rps15-ycf1 SSC 356 0.4726 0.97 76.1 yes View details
ycf1 SSC 3510 0.4573 0.90 78.4 yes View details
ycf1-trnN-GUU IRa 2176 0.2221 0.92 81.4 yes View details
ndhF SSC 2247 0.4521 0.89 80.7 yes View details
ccsA SSC 963 0.4747 0.82 80.0 yes View details
ndhG SSC 531 0.4671 0.86 79.7 yes View details
ndhG-ndhI SSC 362 0.4326 0.88 76.7 yes View details
ndhF-trnL-UAG SSC 1577 0.4203 0.71 76.6 yes View details
rps15 SSC 273 0.4661 0.92 76.5 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
ndhF_p1 ndhF GCAGAATACCGTCACCCATT TCGGGAAAATACGCCCAATT 2540 0.500 58.6
ndhF_p2 ndhF GCAGAATACCGTCACCCATT CTCGGGAAAATACGCCCAAT 2541 0.500 57.1
ndhF_p3 ndhF GCAGAATACCGTCACCCATT CAAACTCGGGAAAATACGCC 2545 0.500 55.4
ndhF_p4 ndhF GCAGAATACCGTCACCCATT AAACTCGGGAAAATACGCCC 2544 0.500 55.3
ndhF_p5 ndhF GCAGAATACCGTCACCCATT TGAGAACCCAACTTTCCGTT 2603 0.500 53.9
ndhF-trnL-UAG_p1 ndhF-trnL-UAG CAAGAGGTCGTGTGAACCAA GAAGTAGCAAAGCCTTGGGT 2598 0.500 58.9
ndhF-trnL-UAG_p2 ndhF-trnL-UAG CAAGAGGTCGTGTGAACCAA TGAAGTAGCAAAGCCTTGGG 2599 0.500 58.9
ndhF-trnL-UAG_p3 ndhF-trnL-UAG CAAGAGGTCGTGTGAACCAA TCCTAAGAGCAGCGTGTCTA 2127 0.500 58.6
ndhF-trnL-UAG_p4 ndhF-trnL-UAG CAAGAGGTCGTGTGAACCAA AGCAGCGTGTCTACCAATTT 2120 0.500 58.1
ndhF-trnL-UAG_p5 ndhF-trnL-UAG CAAGAGGTCGTGTGAACCAA CTAAGAGCAGCGTGTCTACC 2125 0.500 58.0
ccsA_p1 ccsA TTCGTTTTCAAGGTGGGGAG TCAGTAGCTTTTCGATGGCC 2138 0.500 59.6
ccsA_p2 ccsA TTCGTTTTCAAGGTGGGGAG CAGTAGCTTTTCGATGGCCT 2137 0.500 59.6
ccsA_p3 ccsA TTCGTTTTCAAGGTGGGGAG TTCTCGCCTGTTCACACAAA 1613 0.500 59.6
ccsA_p4 ccsA TTCGTTTTCAAGGTGGGGAG TGGTGCTGCACTCTTTTTCT 2248 0.500 59.3
ccsA_p5 ccsA TTCGTTTTCAAGGTGGGGAG TTTTTGATTCTGGACCGCGA 1910 0.500 58.9
ndhD_p1 ndhD TTTGTGTGAACAGGCGAGAA TGGTCCTGGCTCCTAAATCA 2176 0.500 59.5
ndhD_p2 ndhD TTTGTGTGAACAGGCGAGAA GACCGAAGACTGTGTTGGTT 1906 0.500 59.3
ndhD_p3 ndhD TTTGTGTGAACAGGCGAGAA CCGACCGATTTCTTGAGTGT 1863 0.500 59.1
ndhD_p4 ndhD TTGGAGTTGGGACCCAAAAG TGGTCCTGGCTCCTAAATCA 2458 0.500 59.1
ndhD_p5 ndhD TTGGAGTTGGGACCCAAAAG GACCGAAGACTGTGTTGGTT 2188 0.500 59.0
psaC-ndhE_p1 psaC-ndhE TTTGCCCACTGTACATTGCT TACGTCGTGGTATGGGATCA 1681 0.500 59.5
psaC-ndhE_p2 psaC-ndhE AACCAACACAGTCTTCGGTC TACGTCGTGGTATGGGATCA 1096 0.500 59.2
psaC-ndhE_p3 psaC-ndhE ACACTCAAGAAATCGGTCGG TACGTCGTGGTATGGGATCA 1139 0.500 58.9
psaC-ndhE_p4 psaC-ndhE ACATCCGTCCCAAGGTATCA TACGTCGTGGTATGGGATCA 1047 0.500 58.5
psaC-ndhE_p5 psaC-ndhE ACGCTCGAACACATTGTGTA TACGTCGTGGTATGGGATCA 1006 0.500 58.4
ndhE_p1 ndhE TGATTTAGGAGCCAGGACCA TTTCTCTTTGGACCGTTGGG 908 0.500 59.5
ndhE_p2 ndhE AACCAACACAGTCTTCGGTC TTTCTCTTTGGACCGTTGGG 1178 0.500 59.4
ndhE_p3 ndhE TGATTTAGGAGCCAGGACCA TACGTCGTGGTATGGGATCA 826 0.500 59.3
ndhE_p4 ndhE ACACTCAAGAAATCGGTCGG TTTCTCTTTGGACCGTTGGG 1221 0.500 59.2
ndhE_p5 ndhE AACCAACACAGTCTTCGGTC TACGTCGTGGTATGGGATCA 1096 0.500 59.2

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
Boeica ferruginea NC_070431.1 154309 View on NCBI ↗
Boeica multinervia NC_070432.1 154058 View on NCBI ↗