Markers + reference

Coelastrum

5 species · Scenedesmaceae · Sphaeropleales

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Species 5
Genome length 170–299 kb
Candidate markers 228
Primer pairs 95

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 228 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
psbD-trnS-UGA Genome 1099 0.4005 0.40 73.8 yes View details
infA-psbB Genome 1417 0.4490 0.60 74.0 yes View details
rpl20-psbA Genome 1183 0.4576 0.68 74.8 yes View details
psbA Genome 6616 0.3531 0.86 70.9 yes View details
psbC Genome 1386 0.4742 0.37 70.8 yes View details
rpl12-cemA Genome 4655 0.3703 0.12 62.5 yes View details
clpP-rpoC1 Genome 1608 0.4370 0.55 72.9 yes View details
trnG-GCC-rpoA Genome 629 0.4483 0.54 73.1 yes View details
ycf1-trnS-GCU Genome 3753 0.3900 0.40 67.3 yes View details
psbC Genome 1386 NA 0.00 30.3 no View details
rbcL Genome 1428 0.0981 1.00 83.9 yes View details
ccsA Genome 1113 0.1876 0.96 83.6 yes View details
rpoA Genome 1473 0.2393 0.97 83.5 yes View details
rrn23 Genome 2073 0.0652 0.99 83.0 yes View details
rrn23 Genome 2073 0.0560 0.98 82.7 yes View details
chlN Genome 1539 0.1579 0.99 82.5 yes View details
cemA Genome 1137 0.1690 0.96 82.5 yes View details
rrn23-rrn23 Genome 1438 0.1615 0.90 82.1 yes View details
clpP Genome 1647 0.1137 0.99 81.6 yes View details
rpoBb Genome 1641 0.1646 0.99 81.0 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 95 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
chlN_p1 chlN GAACAAAAGACAAGCAGGACA TGCAAATTTCGACTCGAGTT 2300 0.200 15.6
chlN_p2 chlN TGAACAAAAGACAAGCAGGAC TGCAAATTTCGACTCGAGTT 2301 0.200 15.6
chlN_p3 chlN GAACAAAAGACAAGCAGGACA ATGCAAATTTCGACTCGAGT 2301 0.200 13.8
chlN_p4 chlN TGAACAAAAGACAAGCAGGAC ATGCAAATTTCGACTCGAGT 2302 0.200 13.8
chlN_p5 chlN ACAAAAGACAAGCAGGACAA TGCAAATTTCGACTCGAGTT 2298 0.200 13.7
rpoBb_p1 rpoBb TGGAGAAAAGGATTCGGCTT TAATGCGTACTGAAAGGCCC 2359 0.200 40.7
rpoBb_p2 rpoBb TTGGAGAAAAGGATTCGGCT TAATGCGTACTGAAAGGCCC 2360 0.200 40.7
rpoBb_p3 rpoBb TGGAGAAAAGGATTCGGCTT TGCAAAGACAAGCAGTTCCT 2380 0.200 40.5
rpoBb_p4 rpoBb TTGGAGAAAAGGATTCGGCT TGCAAAGACAAGCAGTTCCT 2381 0.200 40.5
rpoBb_p5 rpoBb TGGAGAAAAGGATTCGGCTT GGTACTGGATTGGAAGCTCG 2333 0.200 40.5
psbD-trnS-UGA_p1 psbD-trnS-UGA GCATCATCAAACCATGTACGT GGTTCGAATCCCTCCCTTTC 361–1177 1.000 75.4
psbD-trnS-UGA_p2 psbD-trnS-UGA GCATCATCAAACCATGTACGT GTTCGAATCCCTCCCTTTCC 360–1176 1.000 75.4
psbD-trnS-UGA_p3 psbD-trnS-UGA GCATCATCAAACCATGTACGTT GGTTCGAATCCCTCCCTTTC 361–1177 1.000 72.8
psbD-trnS-UGA_p4 psbD-trnS-UGA GCATCATCAAACCATGTACGTT GTTCGAATCCCTCCCTTTCC 360–1176 1.000 72.8
psbD-trnS-UGA_p5 psbD-trnS-UGA GCATCATCAAACCATGTACG GTTCGAATCCCTCCCTTTCC 360–1176 1.000 68.9
infA-psbB_p1 infA-psbB GGGGTTGAAGTTATTGGGCA AAAGTGTCATCGATCCAGCC 1670 0.200 47.2
infA-psbB_p2 infA-psbB GGGGTTGAAGTTATTGGGCA CACCGCTAATTGTCCATCCA 1799 0.200 47.2
infA-psbB_p3 infA-psbB GGGGTTGAAGTTATTGGGCA TTTGTAGCTGTTTCACCGCT 1812 0.200 47.1
infA-psbB_p4 infA-psbB GGGGTTGAAGTTATTGGGCA ACCGCTAATTGTCCATCCAC 1798 0.200 47.1
infA-psbB_p5 infA-psbB GGGGTTGAAGTTATTGGGCA TGTTACGTGGAAAGCACCAA 2029 0.200 47.1
rbcL_p1 rbcL GATTTACAATCCGCCCCCAT GATCGGCGGTTAAAAGAGGT 2008 0.200 47.8
rbcL_p2 rbcL GATTTACAATCCGCCCCCAT TCCACCTGCAGAAAGAGGTA 1977 0.200 47.8
rbcL_p3 rbcL TCGCTGCTTCTTTCTTCGAA GATCGGCGGTTAAAAGAGGT 2101 0.200 46.6
rbcL_p4 rbcL TTCGCTGCTTCTTTCTTCGA GATCGGCGGTTAAAAGAGGT 2102 0.200 46.6
rbcL_p5 rbcL TCGCTGCTTCTTTCTTCGAA TCCACCTGCAGAAAGAGGTA 2070 0.200 46.6
rpl20-psbA_p1 rpl20-psbA ACGAGCAATCCATACACGTC GAAACGTTGGTTCTCATGCG 2122 0.200 47.0
rpl20-psbA_p2 rpl20-psbA ACGAGCAATCCATACACGTC GCTGCTTTTTCAACGTGGTT 1982 0.200 46.8
rpl20-psbA_p3 rpl20-psbA ACGAGCAATCCATACACGTC GGTTGCTGCTTTTTCAACGT 1986 0.200 46.8
rpl20-psbA_p4 rpl20-psbA ACGAGCAATCCATACACGTC TGGTTGCTGCTTTTTCAACG 1987 0.200 46.7
rpl20-psbA_p5 rpl20-psbA ACGAGCAATCCATACACGTC TTGCTGCTTTTTCAACGTGG 1984 0.200 46.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (5)

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

Species Accession Length (bp) Link
Coelastrum astroideum PX512535.1 186201 View on NCBI ↗
Coelastrum cambricum PX512541.1 171270 View on NCBI ↗
Coelastrum microporum NC_068582.1 169961 View on NCBI ↗
Coelastrum morum PX512671.1 298895 View on NCBI ↗
Coelastrum pseudomicroporum PX512550.1 179623 View on NCBI ↗