Markers + reference

Emilia

2 species · Asteraceae · Asterales

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Species 2
Genome length 151–151 kb
Candidate markers 267
Primer pairs 70

Genome-wide nucleotide diversity

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

Candidate markers

6 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 267 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ndhF SSC 2223 0.4491 0.90 80.7 yes View details
ccsA SSC 972 0.4524 0.90 82.1 yes View details
ndhD SSC 1521 0.4903 0.85 81.0 yes View details
ndhA SSC 2198 0.4845 0.87 80.0 yes View details
ndhH SSC 1179 0.4543 0.81 79.6 yes View details
ycf1 SSC 5034 0.3740 0.78 72.7 yes View details
ndhF-rpl32 SSC 1161 0.4290 0.89 81.9 yes View details
ndhG-ndhI SSC 450 0.4723 0.92 79.8 yes View details
rpl2-trnH-GUG IRa 107 0.0280 0.98 78.3 no View details
psaC SSC 246 0.4698 0.94 77.1 yes View details
rps15 SSC 270 0.5020 0.93 77.0 yes View details
ndhE-ndhG SSC 232 0.4769 0.93 76.9 yes View details
ndhG SSC 531 0.4409 0.76 76.9 yes View details
ndhH-rps15 SSC 91 0.4118 0.93 76.9 yes View details
ndhI SSC 501 0.4482 0.77 76.5 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
ndhF_p1 ndhF CTAGCACTGGGTAGACCTCA AGGTAAAATCCGGTGAGTCG 2642 0.500 53.5
ndhF_p2 ndhF TCGTTGTGGTCGGACTCTAT AGGTAAAATCCGGTGAGTCG 2821 0.500 53.3
ndhF_p3 ndhF ATCAATTCGGTCGTTGTGGT AGGTAAAATCCGGTGAGTCG 2831 0.500 53.2
ndhF_p4 ndhF TCTCTTCCTTCTCCGAGCTC AGGTAAAATCCGGTGAGTCG 2763 0.500 52.7
ndhF_p5 ndhF TGTTTCGATGCAACAGCAAG AGGTAAAATCCGGTGAGTCG 2416 0.500 51.4
ndhF-rpl32_p1 ndhF-rpl32 CGCCCACACGATTAGTTACA AGCGTGTCTACCGATTTCAC 2258 0.500 59.9
ndhF-rpl32_p2 ndhF-rpl32 CGCCCACACGATTAGTTACA CAGCGTGTCTACCGATTTCA 2259 0.500 59.9
ndhF-rpl32_p3 ndhF-rpl32 GTTGCCGTCGGAAAAAGAAG AGCGTGTCTACCGATTTCAC 1800 0.500 59.7
ndhF-rpl32_p4 ndhF-rpl32 GTTGCCGTCGGAAAAAGAAG CAGCGTGTCTACCGATTTCA 1801 0.500 59.7
ndhF-rpl32_p5 ndhF-rpl32 TGCCGTCGGAAAAAGAAGAA AGCGTGTCTACCGATTTCAC 1798 0.500 59.6
ccsA_p1 ccsA GTGAAATCGGTAGACACGCT GTTTTTGATTCTGGACCGCG 1578 0.500 59.6
ccsA_p2 ccsA TGAAATCGGTAGACACGCTG GTTTTTGATTCTGGACCGCG 1577 0.500 59.6
ccsA_p3 ccsA GTGTGGTGGGGAGTCTTTTT GTTTTTGATTCTGGACCGCG 1704 0.500 59.2
ccsA_p4 ccsA GTGAAATCGGTAGACACGCT GCATTACCGGGTATGAGTGG 1779 0.500 59.0
ccsA_p5 ccsA TGAAATCGGTAGACACGCTG GCATTACCGGGTATGAGTGG 1778 0.500 59.0
ndhD_p1 ndhD GGGCTCATATTGGAGTTGGG GGGACGGATGTAAAGCCAAA 2282 0.500 58.5
ndhD_p2 ndhD GGGGCTCATATTGGAGTTGG GGGACGGATGTAAAGCCAAA 2283 0.500 58.5
ndhD_p3 ndhD GGGCTCATATTGGAGTTGGG TGGCACTGTCAATCCAGAAG 2513 0.500 58.4
ndhD_p4 ndhD GGGGCTCATATTGGAGTTGG TGGCACTGTCAATCCAGAAG 2514 0.500 58.4
ndhD_p5 ndhD GGGCTCATATTGGAGTTGGG GGCACTGTCAATCCAGAAGT 2512 0.500 58.4
psaC_p1 psaC TTTCTTTCCTCCCCACATGC TGGCACTGTCAATCCAGAAG 976 0.500 57.9
psaC_p2 psaC TTTCTTTCCTCCCCACATGC GGCACTGTCAATCCAGAAGT 975 0.500 57.9
psaC_p3 psaC GAGACGTTTCTTTCCTCCCC TGGCACTGTCAATCCAGAAG 982 0.500 57.7
psaC_p4 psaC GAGACGTTTCTTTCCTCCCC GGCACTGTCAATCCAGAAGT 981 0.500 57.7
psaC_p5 psaC TCCTCCCCACATGCATAGAA TGGCACTGTCAATCCAGAAG 970 0.500 57.6
ndhE-ndhG_p1 ndhE-ndhG TTTGGCTTTACATCCGTCCC TGGAGTAACTTCCGTGGTCT 1138 0.500 58.6
ndhE-ndhG_p2 ndhE-ndhG CTTCTGGATTGACAGTGCCA TGGAGTAACTTCCGTGGTCT 907 0.500 58.4
ndhE-ndhG_p3 ndhE-ndhG ACTTCTGGATTGACAGTGCC TGGAGTAACTTCCGTGGTCT 908 0.500 58.4
ndhE-ndhG_p4 ndhE-ndhG ACATCCGTCCCATGGTATCA TGGAGTAACTTCCGTGGTCT 1129 0.500 58.4
ndhE-ndhG_p5 ndhE-ndhG GGACACATTGAGTACACCCG TGGAGTAACTTCCGTGGTCT 1082 0.500 57.7

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
Emilia prenanthoidea NC_088757.1 151406 View on NCBI ↗
Emilia sonchifolia NC_058645.1 151474 View on NCBI ↗