Markers + reference

Dudleya

3 species · Crassulaceae · Saxifragales

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Species 3
Genome length 150–151 kb
Candidate markers 270
Primer pairs 100

Genome-wide nucleotide diversity

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

Candidate markers

9 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 272 0.0172 1.00 52.0 yes View details
atpF-atpH LSC 389 0.0034 1.00 44.0 yes View details
rpoB-trnC-GCA LSC 1123 0.0030 1.00 48.6 yes View details
trnT-GGU-psbD LSC 734 0.0054 0.93 65.7 yes View details
accD LSC 1437 0.0009 1.00 45.5 yes View details
pafII-cemA LSC 614 0.0063 0.86 64.0 yes View details
cemA LSC 690 0.0010 1.00 39.8 yes View details
petA-psbJ LSC 728 0.0055 1.00 45.9 yes View details
psbB-psbT LSC 179 0.0037 1.00 40.9 yes View details
matK LSC 1503 0.0031 1.00 60.7 yes View details
trnF-GAA-ndhJ LSC 577 0.0035 1.00 60.5 yes View details
psbZ-trnG-UCC LSC 670 0.0020 1.00 60.0 yes View details
rps16 LSC 1051 0.0013 1.00 59.8 yes View details
psbC-trnS-UGA LSC 178 0.0094 1.00 58.8 yes View details
ndhA SSC 2083 0.0016 1.00 58.6 yes View details
atpF LSC 1286 0.0016 1.00 58.3 yes View details
psaB LSC 2205 0.0009 1.00 57.9 yes View details
clpP1 LSC 2015 0.0013 1.00 57.9 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
trnH-GUG-psbA_p1 trnH-GUG-psbA AATCCACTTGGCTACATCCG TGAAGTCCCATCTTTAAATGG 316–319 1.000 42.8
trnH-GUG-psbA_p2 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TGAAGTCCCATCTTTAAATGG 323–326 1.000 42.7
trnH-GUG-psbA_p3 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TGAAGTCCCATCTTTAAATGG 324–327 1.000 42.7
trnH-GUG-psbA_p4 trnH-GUG-psbA CTGCCTTAATCCACTTGGCT TTGAAGTCCCATCTTTAAATGG 324–327 1.000 42.7
trnH-GUG-psbA_p5 trnH-GUG-psbA ACTGCCTTAATCCACTTGGC TTGAAGTCCCATCTTTAAATGG 325–328 1.000 42.7
trnK-UUU_p1 trnK-UUU TCCATCAGCATTTTTGAGCA AGACTTTCCGTTTTGGCTTG 2571–2572 1.000 54.3
trnK-UUU_p2 trnK-UUU TCCATCAGCATTTTTGAGCAA AGACTTTCCGTTTTGGCTTG 2571–2572 1.000 52.5
trnK-UUU_p3 trnK-UUU GATCCATCAGCATTTTTGAGCA AGACTTTCCGTTTTGGCTTG 2573–2574 1.000 52.0
trnK-UUU_p4 trnK-UUU ATCCATCAGCATTTTTGAGCA AGACTTTCCGTTTTGGCTTG 2572–2573 1.000 50.8
trnK-UUU_p5 trnK-UUU AGATCCATCAGCATTTTTGAGC AGACTTTCCGTTTTGGCTTG 2574–2575 1.000 49.8
matK_p1 matK CCTTAGGGGATTCTAAGAACA CCTTGTTTTGACTGTATCGCA 1709 1.000 40.3
matK_p2 matK CCTTAGGGGATTCTAAGAACA ACCTTGTTTTGACTGTATCGC 1710 1.000 40.3
matK_p3 matK CCTTAGGGGATTCTAAGAACA CCTTGTTTTGACTGTATCGCAC 1709 1.000 40.3
matK_p4 matK CCTTAGGGGATTCTAAGAACA ACCTTGTTTTGACTGTATCGCA 1710 1.000 40.3
matK_p5 matK CCTTAGGGGATTCTAAGAACAT CCTTGTTTTGACTGTATCGCA 1709 1.000 40.3
rps16_p1 rps16 CCGAATCATGCCCACACTTT GCGGACCAAACCAATGACTA 1124–1125 1.000 72.2
rps16_p2 rps16 TAGATCCGAATCATGCCCAC GCGGACCAAACCAATGACTA 1129–1130 1.000 72.1
rps16_p3 rps16 CCGAATCATGCCCACACTTT TATATACGGAGTGCGGACCA 1136–1137 1.000 71.5
rps16_p4 rps16 TAGATCCGAATCATGCCCAC TATATACGGAGTGCGGACCA 1141–1142 1.000 71.4
rps16_p5 rps16 CGAATCATGCCCACACTTTT GCGGACCAAACCAATGACTA 1123–1124 1.000 70.7
trnG-GCC_p1 trnG-GCC AGGGGGTTCCGTTGTTTAAC TGGACGCGTTTCATTACGAT 1251–1253 1.000 80.3
trnG-GCC_p2 trnG-GCC CAATCCGACGCTTTAGTCCA ATGGACGCGTTTCATTACGA 1650–1652 1.000 80.2
trnG-GCC_p3 trnG-GCC CAATCCGACGCTTTAGTCCA TGGACGCGTTTCATTACGAT 1649–1651 1.000 80.2
trnG-GCC_p4 trnG-GCC AATCCGACGCTTTAGTCCAC ATGGACGCGTTTCATTACGA 1649–1651 1.000 80.2
trnG-GCC_p5 trnG-GCC AATCCGACGCTTTAGTCCAC TGGACGCGTTTCATTACGAT 1648–1650 1.000 80.2
atpF_p1 atpF CGCTCAATACGGTCACGAAT GGGCGAAGTGATCCAAAAAG 1455–1456 1.000 71.5
atpF_p2 atpF CGCTCAATACGGTCACGAAT GGGGCGAAGTGATCCAAAAA 1456–1457 1.000 70.6
atpF_p3 atpF CGCTCAATACGGTCACGAAT GGGGCGAAGTGATCCAAAA 1456–1457 1.000 68.3
atpF_p4 atpF CGCTCAATACGGTCACGAA GGGCGAAGTGATCCAAAAAG 1455–1456 1.000 66.9
atpF_p5 atpF CGCTCAATACGGTCACGAA GGGGCGAAGTGATCCAAAAA 1456–1457 1.000 66.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (3)

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

Species Accession Length (bp) Link
Dudleya candelabrum PX244393.1 150419 View on NCBI ↗
Dudleya farinosa NC_085682.1 150780 View on NCBI ↗
Dudleya lanceolata PX244391.1 150313 View on NCBI ↗