Markers + reference

Chloropicon

6 species · Chloropicaceae · Chloropicales

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Species 6
Genome length 64–65 kb
Candidate markers 196
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 196 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
chlB-psbI Genome 792 0.3501 0.97 80.4 yes View details
tilS Genome 978 0.2677 0.99 81.2 yes View details
rpoB Genome 3465 0.1996 0.99 75.7 yes View details
rpoC2 Genome 2310 0.2303 0.99 78.1 yes View details
ftsH Genome 1275 0.2284 0.99 81.4 yes View details
psbB Genome 1539 0.1246 1.00 80.1 yes View details
minD Genome 918 0.1809 0.99 79.8 yes View details
petA Genome 915 0.1935 1.00 79.5 yes View details
petB Genome 648 0.0910 1.00 79.5 yes View details
atpI Genome 714 0.1267 1.00 79.3 yes View details
atpB Genome 1443 0.1126 1.00 79.2 yes View details
ycf12-rbcL Genome 104 0.1744 1.00 79.2 yes View details
trnS(gcu)-trnL(uag) Genome 56 0.3244 1.00 78.9 yes View details
psbD Genome 1059 0.0891 1.00 78.8 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
chlB-psbI_p1 chlB-psbI CAAGTGGACTCCAGATGCTC ATTCTGGAGATGGGTGGTGA 1563 0.167 46.3
chlB-psbI_p2 chlB-psbI CAAGTGGACTCCAGATGCTC TCTGGAGATGGGTGGTGAAT 1561 0.167 46.3
chlB-psbI_p3 chlB-psbI ATGTTGTTTGTGCGGGTACT ATTCTGGAGATGGGTGGTGA 1957 0.167 46.2
chlB-psbI_p4 chlB-psbI ATGTTGTTTGTGCGGGTACT TCTGGAGATGGGTGGTGAAT 1955 0.167 46.2
chlB-psbI_p5 chlB-psbI CAAGTGGACTCCAGATGCTC GGGTTACGGCTTGGATCATT 1044 0.167 46.1
atpB_p1 atpB AATGATCCAAGCCGTAACCC ACTTGGCAACGTGATTCTGT 2237 0.167 46.0
atpB_p2 atpB AATGATCCAAGCCGTAACCC AGTCACTTGGCAACGTGATT 2241 0.167 46.0
atpB_p3 atpB AATGATCCAAGCCGTAACCC GAATACGTAAACGCGTCCCT 2173 0.167 45.6
atpB_p4 atpB AATGATCCAAGCCGTAACCC AACGTAACGGCCCAATTTCT 1770 0.167 45.4
atpB_p5 atpB AATGATCCAAGCCGTAACCC CCAGACTCAGCCTGGTTTAC 1873 0.167 45.4
psbD_p1 psbD CCTTCACTTCCACAAGCCTT CTGACCAGATGAATGCACGA 2375 0.167 46.4
psbD_p2 psbD CCTTCACTTCCACAAGCCTT GTTACCAGACCACCAAGCAA 1690 0.167 46.4
psbD_p3 psbD CCTTCACTTCCACAAGCCTT TTCTGGAACGAAGTGTGCAA 1807 0.167 46.3
psbD_p4 psbD CCTTCACTTCCACAAGCCTT TTTCTGGAACGAAGTGTGCA 1808 0.167 46.3
psbD_p5 psbD AGGGTGAATATGCTGAAGCG CTGACCAGATGAATGCACGA 2539 0.167 46.2
petA_p1 petA AAGGATACGGGATAGACGGG ACGACCTGGACGTTTTGAAA 2023 0.167 45.8
petA_p2 petA CCTACGCTGGTTCAAATCCA ACGACCTGGACGTTTTGAAA 2220 0.167 45.6
petA_p3 petA TGGTTAAAGGAGGCGGATTG ACGACCTGGACGTTTTGAAA 2257 0.167 45.5
petA_p4 petA GGTTAAAGGAGGCGGATTGT ACGACCTGGACGTTTTGAAA 2256 0.167 45.5
petA_p5 petA GTGGTTAAAGGAGGCGGATT ACGACCTGGACGTTTTGAAA 2258 0.167 45.5
ftsH_p1 ftsH TTGCTTCACGTGGTTCTTCA AAAGCGCTCGATGGTTACAT 1937–1938 0.333 61.3
ftsH_p2 ftsH TCTTCGTAACGGGCAAGAAG AAAGCGCTCGATGGTTACAT 1784–1787 0.333 60.9
ftsH_p3 ftsH GTAACGGGCAAGAAGGGATT AAAGCGCTCGATGGTTACAT 1779–1782 0.333 60.6
ftsH_p4 ftsH TAAACTTGTCCACGACCACG AAAGCGCTCGATGGTTACAT 2358–2359 0.333 60.3
ftsH_p5 ftsH TTGCTTCACGTGGTTCTTCA AAAAGCGCTCGATGGTTACA 1938–1939 0.333 59.9
ycf12-rbcL_p1 ycf12-rbcL AATATAGGGACGGTGAGCGA CACCACGTAAGCACTCGTAA 920 0.167 46.2
ycf12-rbcL_p2 ycf12-rbcL AATATAGGGACGGTGAGCGA CCACGTAAGCACTCGTAACA 918 0.167 46.2
ycf12-rbcL_p3 ycf12-rbcL AATATAGGGACGGTGAGCGA AACAAGCACGACCGTAGTTT 902 0.167 46.1
ycf12-rbcL_p4 ycf12-rbcL AATATAGGGACGGTGAGCGA ACAAGCACGACCGTAGTTTT 901 0.167 46.1
ycf12-rbcL_p5 ycf12-rbcL AATATAGGGACGGTGAGCGA GTAACAAGCACGACCGTAGT 904 0.167 46.1

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (6)

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

Species Accession Length (bp) Link
Chloropicon laureae NC_042484.1 64740 View on NCBI ↗
Chloropicon mariensis NC_042485.1 64323 View on NCBI ↗
Chloropicon maureeniae NC_042488.1 64094 View on NCBI ↗
Chloropicon primus KJ746601.1 64335 View on NCBI ↗
Chloropicon roscoffensis NC_042486.1 64534 View on NCBI ↗
Chloropicon sieburthii NC_042483.1 64565 View on NCBI ↗