Markers + reference

Echeveria

7 species · Crassulaceae · Saxifragales

Back to catalogue

Species 7
Genome length 149–150 kb
Candidate markers 264
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

11 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 264 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnS-GCU-trnG-GCC LSC 644 0.0154 0.99 66.1 yes View details
trnG-GCC-trnR-UCU LSC 256 0.1108 0.84 71.9 yes View details
rpoB-trnC-GCA LSC 1155 0.0098 0.99 59.7 yes View details
trnF-GAA-ndhJ LSC 647 0.0177 1.00 65.5 yes View details
ycf4-cemA LSC 616 0.0126 1.00 62.1 yes View details
psbE-petL LSC 1074 0.0098 1.00 58.1 yes View details
ycf1 SSC 4455 0.0090 1.00 48.4 yes View details
ndhD-ccsA SSC 250 0.0305 1.00 66.1 yes View details
ccsA SSC 960 0.0044 1.00 42.6 yes View details
trnL-UAG-rpl32 SSC 487 0.0196 1.00 56.4 yes View details
rpl32-ndhF SSC 633 0.0129 1.00 59.6 yes View details
rpl2-trnH-GUG IRa 164 0.0070 1.00 63.9 no View details
psaA-ycf3 LSC 646 0.0057 1.00 63.5 yes View details
rbcL-accD LSC 729 0.0093 0.97 63.0 yes View details
psbK-psbI LSC 386 0.0137 1.00 60.9 yes View details
rpl20-rps12 LSC 784 0.0056 0.99 60.9 yes View details
petN-psbM LSC 796 0.0063 1.00 60.8 yes View details
rps12-trnV-GAC IRb 1262 0.0015 1.00 60.7 yes View details
trnV-GAC-rps12 IRa 1262 0.0015 1.00 60.7 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 100 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnK-UUU_p1 trnK-UUU CTCCATCAGCATTTTTGAGCA AGACTTTCCTTTTTGGTTTG 2587–2620 1.000 41.8
trnK-UUU_p2 trnK-UUU TCCATCAGCATTTTTGAGCA AGACTTTCCTTTTTGGTTTG 2586–2619 1.000 41.8
trnK-UUU_p3 trnK-UUU CTCCATCAGCATTTTTGAGCAA AGACTTTCCTTTTTGGTTTG 2587–2620 1.000 41.8
trnK-UUU_p4 trnK-UUU TCCATCAGCATTTTTGAGCAA AGACTTTCCTTTTTGGTTTG 2586–2619 1.000 41.8
trnK-UUU_p5 trnK-UUU CTCCATCAGCATTTTTGAGC AGACTTTCCTTTTTGGTTTG 2587–2620 1.000 41.8
psbK-psbI_p1 psbK-psbI GTTTGGCAAGCTGCTGTAAG CTTCTCGTCCAGGATTACGTC 521–522 1.000 73.6
psbK-psbI_p2 psbK-psbI CCAAATTACCCGAGGCCTAC CTTCTCGTCCAGGATTACGTC 607–608 1.000 73.4
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG TTCTCGTCCAGGATTACGTC 520–521 1.000 72.4
psbK-psbI_p4 psbK-psbI CCAAATTACCCGAGGCCTAC TTCTCGTCCAGGATTACGTC 606–607 1.000 72.2
psbK-psbI_p5 psbK-psbI CCAAATTACCCGAGGCCTAC CTTCTCGTCCAGGATTACGT 607–608 1.000 72.1
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TGTTCGGAATACAAAGAAAACCG 755–768 1.000 60.2
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TGTTCGGAATACAAAGAAAACCG 754–767 1.000 60.2
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC GCTCGTACAACGGATTAGCA TGTTCGGAATACAAAGAAAACCG 773–786 1.000 59.5
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CGAAGGACCCCTTAACTATTAGG 734–747 1.000 59.5
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CGAAGGACCCCTTAACTATTAGG 733–746 1.000 59.5
trnG-GCC_p1 trnG-GCC CAATCCGACGCTTTAGTCCA CAATGGACGCGTTTCATTCC 1652–1728 1.000 87.3
trnG-GCC_p2 trnG-GCC AATCCGACGCTTTAGTCCAC CAATGGACGCGTTTCATTCC 1651–1727 1.000 87.3
trnG-GCC_p3 trnG-GCC CAATCCGACGCTTTAGTCCA AGGAACAGTTGGAACGCTTT 1812–1888 1.000 87.1
trnG-GCC_p4 trnG-GCC AATCCGACGCTTTAGTCCAC AGGAACAGTTGGAACGCTTT 1811–1887 1.000 87.1
trnG-GCC_p5 trnG-GCC GTCACCTGACAAAAGGCAGA AGGAACAGTTGGAACGCTTT 1250–1328 1.000 87.1
trnG-GCC-trnR-UCU_p1 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTACCGAT AGGTTTAGAAGACCTATGTCCT 289–368 1.000 55.3
trnG-GCC-trnR-UCU_p2 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTACCGAT AGAAGACCTATGTCCTATCCA 283–362 1.000 55.1
trnG-GCC-trnR-UCU_p3 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTACCGAT ACCAAAGGTTTAGAAGACCTATGT 294–373 1.000 54.7
trnG-GCC-trnR-UCU_p4 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTACCGAT AAGGTTTAGAAGACCTATGTCCT 290–369 1.000 53.3
trnG-GCC-trnR-UCU_p5 trnG-GCC-trnR-UCU TAGCCTTCCAAGCTACCGAT AGAAGACCTATGTCCTATCCAT 283–362 1.000 52.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TTTCCCTCATTTCCATCCCG CCGGATTTGAACTGGGGAAA 1215–1243 1.000 79.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TTTCCCTCATTTCCATCCCG GTCTTGTGTTGATCAGGCGA 1238–1266 1.000 78.8
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TTTCCCTCATTTCCATCCCG TCTTGTGTTGATCAGGCGAC 1237–1265 1.000 78.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TTTCCCTCATTTCCATCCCG AAAAGGATTTGCAGTCCCCC 1197–1225 1.000 77.8
rpoB-trnC-GCA_p5 rpoB-trnC-GCA TTTCCCTCATTTCCATCCCG CTTGTGTTGATCAGGCGACA 1236–1264 1.000 76.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (7)

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

Species Accession Length (bp) Link
Echeveria cante PX427673.1 149050 View on NCBI ↗
Echeveria lilacina NC_060813.1 150080 View on NCBI ↗
Echeveria peacockii PX436094.1 149052 View on NCBI ↗
Echeveria prolifica PX436092.1 149956 View on NCBI ↗
Echeveria pulidonis PX326348.1 150101 View on NCBI ↗
Echeveria secunda PX427674.1 149054 View on NCBI ↗
Echeveria strictiflora PX436093.1 148994 View on NCBI ↗