Markers + reference

Chroomonas

2 species · Chroomonadaceae · Pyrenomonadales

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Species 2
Genome length 137–146 kb
Candidate markers 356
Primer pairs 90

Genome-wide nucleotide diversity

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

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 356 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
groEL-ycf65 Genome 1038 0.4565 0.85 80.9 yes View details
minE-rpl32 Genome 907 0.3995 0.97 82.3 yes View details
rbcR-rpl27 Genome 1078 0.3971 0.83 80.6 yes View details
rps4-rbcL Genome 1753 0.4013 0.94 82.9 yes View details
rne Genome 1314 0.3832 0.97 81.9 yes View details
infB Genome 2343 0.3336 0.98 78.9 yes View details
psbN-psbN Genome 2264 0.3931 0.79 78.0 yes View details
psbN-psbH Genome 1007 0.4044 0.82 80.8 yes View details
ycf26 Genome 699 0.3853 0.95 83.3 yes View details
ccsA Genome 978 0.2700 0.97 81.3 yes View details
trnK-UUU-ycf12 Genome 554 0.3745 0.86 81.3 yes View details
ycf36 Genome 495 0.3758 0.95 81.3 yes View details
dnaB Genome 1806 0.3521 0.97 80.8 yes View details
trnA-UGC-rnl Genome 72 0.1429 0.97 80.7 yes View details
rnl-trnA-UGC Genome 72 0.1429 0.97 80.7 yes View details
ycf29 Genome 693 0.3765 0.98 80.6 yes View details
rps2 Genome 699 0.2014 0.99 80.3 yes View details
rps3 Genome 660 0.2277 0.98 80.2 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 90 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
groEL-ycf65_p1 groEL-ycf65 TGCGACTAAAGCAGCTGTAG TCCCCAAACGAATGAAAGCA 1868 0.500 59.9
groEL-ycf65_p2 groEL-ycf65 CGCGTTCTGGACTTCAAAAC TCCCCAAACGAATGAAAGCA 1566 0.500 59.8
groEL-ycf65_p3 groEL-ycf65 CGTTCTGGACTTCAAAACGC TCCCCAAACGAATGAAAGCA 1564 0.500 59.8
groEL-ycf65_p4 groEL-ycf65 GCGTTCTGGACTTCAAAACG TCCCCAAACGAATGAAAGCA 1565 0.500 59.8
groEL-ycf65_p5 groEL-ycf65 GGACTTCAAAACGCAGCTTC TCCCCAAACGAATGAAAGCA 1558 0.500 59.6
trnA-UGC-rnl_p1 trnA-UGC-rnl GGGGGTATAGCTCAGTTGGT TCATCGCTTCTGAATGCCAA 197–200 1.000 80.0
trnA-UGC-rnl_p2 trnA-UGC-rnl GGGGGTATAGCTCAGTTGGT TTCATCGCTTCTGAATGCCA 198–201 1.000 80.0
trnA-UGC-rnl_p3 trnA-UGC-rnl GGGGGTATAGCTCAGTTGGT CGCTTCTGAATGCCAAGGTA 193–196 1.000 78.9
trnA-UGC-rnl_p4 trnA-UGC-rnl GGGGGTATAGCTCAGTTGGT GCCCTTCATCGCTTCTGAAT 202–205 1.000 78.2
trnA-UGC-rnl_p5 trnA-UGC-rnl GGGGGTATAGCTCAGTTGGT AATGCTTACTTCCAGCTCCC 245–248 1.000 76.5
ccsA_p1 ccsA AAGCGGAAACTGCTACACAA AGGCTGGACAAATTGCTTCA 2163 0.500 59.7
ccsA_p2 ccsA AGCGGAAACTGCTACACAAA AGGCTGGACAAATTGCTTCA 2162 0.500 59.7
ccsA_p3 ccsA AAATCGTCGTATGGCTGCAT AGGCTGGACAAATTGCTTCA 2145 0.500 59.6
ccsA_p4 ccsA AAGCGGAAACTGCTACACAA TGAATGACATAGCGTCCTGC 1788 0.500 59.2
ccsA_p5 ccsA AGCGGAAACTGCTACACAAA TGAATGACATAGCGTCCTGC 1787 0.500 59.2
minE-rpl32_p1 minE-rpl32 TTGTATTAGCCCATGACCGC CGTCTAGCAAACTGGAGCAA 1248 0.500 58.1
minE-rpl32_p2 minE-rpl32 GCTTGTCGATTAGATGGGCA CGTCTAGCAAACTGGAGCAA 1464 0.500 58.0
minE-rpl32_p3 minE-rpl32 CCGCTCTACGTTAAATGCCT CGTCTAGCAAACTGGAGCAA 1232 0.500 57.9
minE-rpl32_p4 minE-rpl32 TAAAACGCTTGCGCAGTTTT CGTCTAGCAAACTGGAGCAA 1400 0.500 56.8
minE-rpl32_p5 minE-rpl32 TTAAAACGCTTGCGCAGTTT CGTCTAGCAAACTGGAGCAA 1401 0.500 56.8
rbcR-rpl27_p1 rbcR-rpl27 TACTCGACGCATTTCTTGGG GGGAATGTAAGTGTAGGGCG 2101 0.500 59.6
rbcR-rpl27_p2 rbcR-rpl27 TACTCGACGCATTTCTTGGG TGCGTCCGAAGAAAAAGACA 2004 0.500 59.5
rbcR-rpl27_p3 rbcR-rpl27 TACTCGACGCATTTCTTGGG CGGCGATGATACTGAAGGAG 2344 0.500 59.5
rbcR-rpl27_p4 rbcR-rpl27 TACTCGACGCATTTCTTGGG AGGAGGGATCCTTTGGGAAA 2329 0.500 59.4
rbcR-rpl27_p5 rbcR-rpl27 GGTCTTCTTCATTGGGCCAA GGGAATGTAAGTGTAGGGCG 1713 0.500 59.0
rnl-trnA-UGC_p1 rnl-trnA-UGC TCATCGCTTCTGAATGCCAA GGGGGTATAGCTCAGTTGGT 197–200 1.000 80.0
rnl-trnA-UGC_p2 rnl-trnA-UGC TTCATCGCTTCTGAATGCCA GGGGGTATAGCTCAGTTGGT 198–201 1.000 80.0
rnl-trnA-UGC_p3 rnl-trnA-UGC CGCTTCTGAATGCCAAGGTA GGGGGTATAGCTCAGTTGGT 193–196 1.000 78.9
rnl-trnA-UGC_p4 rnl-trnA-UGC GCCCTTCATCGCTTCTGAAT GGGGGTATAGCTCAGTTGGT 202–205 1.000 78.2
rnl-trnA-UGC_p5 rnl-trnA-UGC AATGCTTACTTCCAGCTCCC GGGGGTATAGCTCAGTTGGT 245–248 1.000 76.5

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
Chroomonas collegionis LC648955.1 137219 View on NCBI ↗
Chroomonas debatzensis LC648962.1 146033 View on NCBI ↗