Markers + reference

Bostrychia

2 species · Rhodomelaceae · Ceramiales

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Species 2
Genome length 168–171 kb
Candidate markers 463
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 463 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
dsbD Genome 753 0.2755 0.13 60.6 yes View details
orf65-orf40 Genome 573 0.3732 0.98 80.4 yes View details
ycf58 Genome 435 0.2719 1.00 75.6 yes View details
ConsOrf4 Genome 780 0.2978 0.97 81.4 yes View details
infB Genome 2217 0.2273 0.99 78.6 yes View details
secG Genome 201 0.2438 1.00 72.5 yes View details
accB Genome 540 0.2430 1.00 77.7 yes View details
dnaB Genome 1869 0.2268 0.98 80.1 yes View details
rpl9 Genome 465 0.2559 1.00 75.9 yes View details
ConsOrf3 Genome 507 0.2459 0.97 79.7 yes View details
ConsOrf5 Genome 1065 0.2906 0.97 82.0 yes View details
ycf80 Genome 1455 0.2435 0.97 81.7 yes View details
moeB Genome 1077 0.2222 0.98 81.0 yes View details
ntcA Genome 600 0.2437 0.98 80.4 yes View details
tilS Genome 984 0.2041 0.99 80.2 yes View details
rps1 Genome 792 0.2008 0.99 80.0 yes View details
syfB Genome 1980 0.2367 0.98 80.0 yes View details
carA Genome 1176 0.1914 0.99 79.7 yes View details
rps3 Genome 645 0.1566 1.00 79.7 yes View details
secY Genome 1236 0.1557 0.99 79.6 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
carA_p1 carA GAAATGGGGAGGAGGCAAAA AGCACCTGAAGGGCATTTAC 1892 0.500 58.2
carA_p2 carA CTGCTTGTCATTCTGGTGGT AGCACCTGAAGGGCATTTAC 1606 0.500 57.9
carA_p3 carA GAAATGGGGAGGAGGCAAAA CACCTGAAGGGCATTTACCA 1890 0.500 57.8
carA_p4 carA CTGCTTGTCATTCTGGTGGT CACCTGAAGGGCATTTACCA 1604 0.500 57.5
carA_p5 carA TGTTGCTGAGAAATGGGGAG AGCACCTGAAGGGCATTTAC 1901 0.500 57.1
dsbD_p1 dsbD TTTCACCACGTCCGCTATTT CAAATTTCCATCGACGAGCA 1430 0.500 49.2
dsbD_p2 dsbD TTTCACCACGTCCGCTATTT ACAAATTTCCATCGACGAGC 1431 0.500 49.1
dsbD_p3 dsbD TAGCGTGTCTGCCAATTTCA CAAATTTCCATCGACGAGCA 1445 0.500 49.1
dsbD_p4 dsbD TAGCGTGTCTGCCAATTTCA ACAAATTTCCATCGACGAGC 1446 0.500 49.1
dsbD_p5 dsbD CTCAGTGGTAGAGCGATTGG CAAATTTCCATCGACGAGCA 1265 0.500 48.8
tilS_p1 tilS TGGTGCTCCTTTATGTCCTTG CCATTGAGTTAGCAGCCCTT 1570–1581 1.000 79.4
tilS_p2 tilS TGGTGCTCCTTTATGTCCTTG CTCGAACCCGGAACTAATCG 1610–1621 1.000 79.2
tilS_p3 tilS GGTGCTCCTTTATGTCCTTGT CCATTGAGTTAGCAGCCCTT 1569 0.500 50.3
tilS_p4 tilS TGGTGCTCCTTTATGTCCTTG ACAACCTGGTGCTTTTGACA 2185 0.500 50.2
tilS_p5 tilS GGTGCTCCTTTATGTCCTTGT ACAACCTGGTGCTTTTGACA 2184 0.500 50.2
orf65-orf40_p1 orf65-orf40 AGCCGGACAAATAGCTTCAG AGCCTCACCTTGACCTAGTT 1684–2359 1.000 88.0
orf65-orf40_p2 orf65-orf40 TGGTTGTAAAGCCGGACAAA AGCCTCACCTTGACCTAGTT 1693–2368 1.000 87.8
orf65-orf40_p3 orf65-orf40 AGCCGGACAAATAGCTTCAG ACGACCTACCCCACCAATTA 1465 0.500 59.4
orf65-orf40_p4 orf65-orf40 AGCCGGACAAATAGCTTCAG CGATAACCACCAGGAGAAGC 1566 0.500 59.3
orf65-orf40_p5 orf65-orf40 AGCCGGACAAATAGCTTCAG GCGATAACCACCAGGAGAAG 1567 0.500 59.3
ycf80_p1 ycf80 AAGAGCATGTAACTCAGCGG TACCAGCTGGAGAACATGGA 2673 0.500 59.5
ycf80_p2 ycf80 TCCCGCCAGTTCCATTTATG TACCAGCTGGAGAACATGGA 2104 0.500 59.2
ycf80_p3 ycf80 AATTCCCGCCAGTTCCATTT TACCAGCTGGAGAACATGGA 2107 0.500 59.1
ycf80_p4 ycf80 AAGAGCATGTAACTCAGCGG CAGCTGGAGAACATGGACAA 2670 0.500 58.4
ycf80_p5 ycf80 ATGGACGTGGGTTCAATTCC TACCAGCTGGAGAACATGGA 2121 0.500 58.3
trnM_p1 trnM GATTCCCACTACCCGCTTTT ATCTCCTTCAGCTGTCGCTA 2001 0.500 57.2
trnM_p2 trnM GATTCCCACTACCCGCTTTT CTTGCAGCGTTTCGAAGAAA 2469 0.500 55.9
trnM_p3 trnM ATGATGTGGGTTCGATTCCC ATCTCCTTCAGCTGTCGCTA 2014 0.500 55.4
trnM_p4 trnM ATGATGTGGGTTCGATTCCC CTTGCAGCGTTTCGAAGAAA 2482 0.500 54.1
trnM_p5 trnM GATTCCCACTACCCGCTTTT ACTTGCAGCGTTTCGAAGAA 2470 0.500 53.4

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
Bostrychia simpliciuscula NC_035268.1 167514 View on NCBI ↗
Bostrychia tenella NC_035264.1 170809 View on NCBI ↗