Markers + reference

Chloroparvula

2 species · Chloropicaceae · Chloropicales

Back to catalogue

Species 2
Genome length 70–71 kb
Candidate markers 192
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

4 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 192 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl19 Genome 366 0.5367 0.97 77.1 yes View details
rps8 Genome 429 0.5074 0.95 79.9 yes View details
rps9 Genome 597 0.4907 0.90 82.1 yes View details
rbcL Genome 1428 0.5307 0.82 80.0 yes View details
atpF Genome 555 0.3270 0.95 82.4 yes View details
rps3 Genome 669 0.2720 0.97 82.0 yes View details
rpoC1 Genome 2349 0.3480 0.95 81.8 yes View details
chlB Genome 1533 0.4739 0.86 81.1 yes View details
accD Genome 1164 0.2781 0.98 80.8 yes View details
psbA Genome 1062 0.4148 0.99 79.8 yes View details
psbD Genome 1059 0.4480 0.99 79.7 yes View details
psbC Genome 1386 0.4465 0.99 79.7 yes View details
psaA Genome 2259 0.4814 0.86 79.6 yes View details
chlL Genome 852 0.4837 0.79 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 70 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
psbD_p1 psbD GCCGAGGCATACTAATAGGC ACCACCAAAGCCAAGTACAG 1761 0.500 59.8
psbD_p2 psbD GCCGAGGCATACTAATAGGC GGTACAAAATGCGCAACCTC 1604 0.500 59.7
psbD_p3 psbD GGTACATGAGCTGGGTTCAG ACCACCAAAGCCAAGTACAG 2113 0.500 59.6
psbD_p4 psbD GGTACATGAGCTGGGTTCAG GGTACAAAATGCGCAACCTC 1956 0.500 59.6
psbD_p5 psbD CCCATGAAAGCGGTACATGA ACCACCAAAGCCAAGTACAG 2124 0.500 59.6
psbC_p1 psbC TCAGGTTGGTTCTTTGCTCC ATGGGGGCGGATTGTAAATC 2395 0.500 59.8
psbC_p2 psbC GGCGGTCTATGGACATTTGT ATGGGGGCGGATTGTAAATC 2566 0.500 59.7
psbC_p3 psbC TGGTGCAACGGTAGAAAACA ATGGGGGCGGATTGTAAATC 2246 0.500 59.6
psbC_p4 psbC TCAGGTTGGTTCTTTGCTCC TTGAACCCCTAACCTACGGT 2199 0.500 59.6
psbC_p5 psbC CACTTTCCGTGCATTCAACC ATGGGGGCGGATTGTAAATC 2198 0.500 59.6
psbA_p1 psbA GATTTACAATCCGCCCCCAT TCCTACAATTCGAGCAGCAC 1894 0.500 59.9
psbA_p2 psbA GATTTACAATCCGCCCCCAT TTGGCTCCTACAATTCGAGC 1899 0.500 59.8
psbA_p3 psbA GATTTACAATCCGCCCCCAT CGAGCAAAAGAAGCAACAGG 1977 0.500 59.6
psbA_p4 psbA GATTTACAATCCGCCCCCAT TATATAATCGGCGGCATGGC 1519 0.500 59.5
psbA_p5 psbA GATTTACAATCCGCCCCCAT TATTATTCACGCCGTGGTGG 1584 0.500 59.5
rps3_p1 rps3 CACATGTACGTGGAAGCGTA GGTGAATAGGACGCGTTTCT 1714 0.500 59.8
rps3_p2 rps3 TTGCACTTGGTCAACGTACA GGTGAATAGGACGCGTTTCT 1609 0.500 59.7
rps3_p3 rps3 GCACAATGGTCGTCAACATG GGTGAATAGGACGCGTTTCT 1354 0.500 59.7
rps3_p4 rps3 CCGAATTGCACTTGGTCAAC GGTGAATAGGACGCGTTTCT 1614 0.500 59.5
rps3_p5 rps3 CACATGTACGTGGAAGCGTA CGGTAAGGGGCAAGAAGATC 1802 0.500 59.5
accD_p1 accD CGTGATCGTCTAGTAGCACG AATGCGACTGAGTGACATCC 2574 0.500 59.8
accD_p2 accD CGTGATCGTCTAGTAGCACG ATGGAATGCGACTGAGTGAC 2578 0.500 59.8
accD_p3 accD CGTGATCGTCTAGTAGCACG GGAATGCGACTGAGTGACAT 2576 0.500 59.8
accD_p4 accD TGCTCAAGGGCGTATTCTTC AATGCGACTGAGTGACATCC 2395 0.500 59.7
accD_p5 accD TGCTCAAGGGCGTATTCTTC GGAATGCGACTGAGTGACAT 2397 0.500 59.7
rpoC1_p1 rpoC1 AAAGGAGGTCAAAGGCTTGG CTTGCTCAAAGCCTAGACGT 2856 0.500 59.3
rpoC1_p2 rpoC1 AAAGGAGGTCAAAGGCTTGG GTCACCAGCTCCAATGGAAA 2891 0.500 59.3
rpoC1_p3 rpoC1 AAAGGAGGTCAAAGGCTTGG TCACCAGCTCCAATGGAAAC 2890 0.500 59.3
rpoC1_p4 rpoC1 AAAGGAGGTCAAAGGCTTGG GTTTGCTCGTAGACCACCAT 2816 0.500 59.2
rpoC1_p5 rpoC1 AAAGGAGGTCAAAGGCTTGG TCACCAGCTGTCAATTGACC 2992 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
Chloroparvula japonica NC_042487.1 71262 View on NCBI ↗
Chloroparvula pacifica NC_042489.1 69644 View on NCBI ↗