Markers + reference

Kumanoa

2 species · Batrachospermaceae · Batrachospermales

Back to catalogue

Species 2
Genome length 184–184 kb
Candidate markers 462
Primer pairs 120

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 462 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
petP-ycf45 Genome 319 0.2069 1.00 73.5 yes View details
chlB Genome 3525 0.1337 1.00 75.1 yes View details
bas1-rpl35 Genome 736 0.3024 0.57 73.6 yes View details
ycf92 Genome 825 0.2140 0.99 80.2 yes View details
ycf80-BIZ62_gs002 Genome 281 0.2115 0.99 74.6 yes View details
ycf91 Genome 354 0.1864 1.00 73.6 yes View details
gltB-rpoZ Genome 526 0.2327 0.96 81.1 yes View details
psaM-chlL Genome 666 0.2433 0.95 83.9 yes View details
BIZ62_gt017-dsbD Genome 263 0.3077 0.99 74.2 yes View details
BIZ62_gr001-ycf27 Genome 562 0.3098 0.98 82.5 yes View details
orf172 Genome 510 0.2098 1.00 76.9 yes View details
clpC-rpl19 Genome 666 0.1925 1.00 79.3 yes View details
ycf33-argB Genome 340 0.2748 0.89 76.9 yes View details
BIZ62_gt013-BIZ62_gt014 Genome 51 0.1250 0.94 82.6 yes View details
BIZ62_gt019-BIZ62_gr001 Genome 53 0.1400 0.94 81.6 yes View details
rpl34-BIZ62_gt015 Genome 491 0.1933 0.97 81.2 yes View details
BIZ62_gr002-BIZ62_gt018 Genome 51 0.2143 0.82 80.8 yes View details
rps2 Genome 702 0.1029 1.00 80.2 yes View details
ycf80 Genome 1497 0.1690 0.99 79.8 yes View details
orf466 Genome 1398 0.1674 1.00 79.5 yes View details
ycf53 Genome 750 0.1379 1.00 79.4 yes View details
upp Genome 627 0.1923 1.00 79.3 yes View details
ORF198 Genome 1212 0.1922 1.00 79.2 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 120 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
petP-ycf45_p1 petP-ycf45 AGATTCGTTTGGTGCAGGAG TTGTTTTCCCTACACCAGGC 1321 0.500 58.4
petP-ycf45_p2 petP-ycf45 GATTCGTTTGGTGCAGGAGA TTGTTTTCCCTACACCAGGC 1320 0.500 58.4
petP-ycf45_p3 petP-ycf45 AAGATTCGTTTGGTGCAGGA TTGTTTTCCCTACACCAGGC 1322 0.500 57.8
petP-ycf45_p4 petP-ycf45 ATTCGTTTGGTGCAGGAGAA TTGTTTTCCCTACACCAGGC 1319 0.500 57.8
petP-ycf45_p5 petP-ycf45 AGATTCGTTTGGTGCAGGAG AGGACGCCTACCTAAATCCA 1035 0.500 57.1
chlB_p1 chlB AGAACCTCAATGGACAGCAA GGAGTATGAAACAACCAGTTGG 951 0.500 30.2
chlB_p2 chlB ACCTCAATGGACAGCAAAACT GGAGTATGAAACAACCAGTTGG 948 0.500 29.5
chlB_p3 chlB AGAACCTCAATGGACAGCAAA GGAGTATGAAACAACCAGTTGG 951 0.500 28.0
chlB_p4 chlB AGAACCTCAATGGACAGCAA ACAAGGAGTATGAAACAACCAGT 955 0.500 28.0
chlB_p5 chlB ACCTCAATGGACAGCAAAACT ACAAGGAGTATGAAACAACCAGT 952 0.500 27.2
orf466_p1 orf466 CAGGACCAGCCCATATAGGA CCAAGCTCGAGGCAGTAATT 2621 0.500 59.5
orf466_p2 orf466 CAGGACCAGCCCATATAGGA TTAAACCAAGCTCGAGGCAG 2626 0.500 58.2
orf466_p3 orf466 ATGCAGGACCAGCCCATATA CCAAGCTCGAGGCAGTAATT 2624 0.500 57.7
orf466_p4 orf466 TATGCAGGACCAGCCCATAT CCAAGCTCGAGGCAGTAATT 2625 0.500 57.7
orf466_p5 orf466 CAGGACCAGCCCATATAGGA CCAGAAGTACATCCGCTGTT 2337 0.500 56.7
bas1-rpl35_p1 bas1-rpl35 CAGACAGAACGGGAGAATGG CAACAGCTATTTGGGCAAGC 1634 0.500 59.9
bas1-rpl35_p2 bas1-rpl35 GCAGCCAGGAGATAAGACAC CAACAGCTATTTGGGCAAGC 1368 0.500 59.6
bas1-rpl35_p3 bas1-rpl35 AGACAGAACGGGAGAATGGA CAACAGCTATTTGGGCAAGC 1633 0.500 59.5
bas1-rpl35_p4 bas1-rpl35 CAGACAGAACGGGAGAATGG ACAGCTATTTGGGCAAGCAT 1632 0.500 58.7
bas1-rpl35_p5 bas1-rpl35 AGAACGGGAGAATGGAGGAT CAACAGCTATTTGGGCAAGC 1629 0.500 58.5
rps2_p1 rps2 TTGCAAGCAAACTGGATTGG CTGTTGTGCTACGATGAGCT 1296 0.500 55.7
rps2_p2 rps2 TTGCAAGCAAACTGGATTGG TCTGTTGTGCTACGATGAGC 1297 0.500 55.7
rps2_p3 rps2 TTGCAAGCAAACTGGATTGG ACAATCCATCATACCCGCAC 1190 0.500 55.5
rps2_p4 rps2 TTGCAAGCAAACTGGATTGG TGCAGCTATTTGCATGGCTA 1433 0.500 55.3
rps2_p5 rps2 TTGCAAGCAAACTGGATTGG CCCGCACCAGTTTTAACTCT 1177 0.500 54.9
ycf92_p1 ycf92 GCGAGTATTCGGTGGAATGT TTTGATCGAAAGCGCGAGTA 2112 0.500 59.4
ycf92_p2 ycf92 GCGAGTATTCGGTGGAATGT TGCGTATACCAATTTCGCCA 1745 0.500 59.3
ycf92_p3 ycf92 GCAGAAAGATCCGTCGCTAA TTTGATCGAAAGCGCGAGTA 2091 0.500 59.3
ycf92_p4 ycf92 GCAGAAAGATCCGTCGCTAA TGCGTATACCAATTTCGCCA 1724 0.500 59.2
ycf92_p5 ycf92 GCGAGTATTCGGTGGAATGT AAAGCGCGAGTAGTAGAAGC 2104 0.500 58.8

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
Kumanoa americana NC_031178.1 184025 View on NCBI ↗
Kumanoa mahlacensis MK641509.1 183893 View on NCBI ↗