Markers + reference

Rosularia

2 species · Crassulaceae · Saxifragales

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Species 2
Genome length 151–151 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

11 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 270 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rps16-trnQ-UUG LSC 1279 0.1311 0.97 84.0 yes View details
rpoB-trnC-GCA LSC 1106 0.0925 0.98 80.0 yes View details
trnC-GCA-petN LSC 830 0.0984 0.99 82.2 yes View details
petN-psbM LSC 1031 0.1077 0.77 77.5 yes View details
psbM-trnD-GUC LSC 1008 0.0913 0.97 84.0 yes View details
trnF-GAA-ndhJ LSC 589 0.1107 0.98 80.8 yes View details
trnP-UGG-psaJ LSC 258 0.2255 0.91 76.6 yes View details
ycf1 IRb 1089 0.0101 1.00 51.5 no View details
ndhF-rpl32 SSC 590 0.1175 0.97 84.5 yes View details
rpl32-trnL-UAG SSC 428 0.1699 0.96 79.2 yes View details
ycf1 SSC 5010 0.0822 0.99 71.1 yes View details
trnS-GCU-trnG-GCC LSC 616 0.1158 1.00 86.0 yes View details
lhbA-trnG-UCC LSC 629 0.1039 0.90 85.0 yes View details
petA-psbJ LSC 941 0.0899 0.93 82.7 yes View details
atpH-atpI LSC 687 0.0798 0.95 82.1 yes View details
ndhC-trnV-UAC LSC 880 0.0826 0.98 82.1 yes View details
psbI-trnS-GCU LSC 168 0.0932 0.96 81.9 yes View details
trnE-UUC-trnT-GGU LSC 813 0.0702 0.98 81.5 yes View details
rps18-rpl20 LSC 239 0.0929 0.95 81.3 yes View details
trnT-GGU-psbD LSC 691 0.0821 0.95 81.1 yes View details
psbE-petL LSC 1124 0.0799 0.85 80.4 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
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1352–1631 1.000 88.6
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 1363–1642 1.000 88.0
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 1373–1652 1.000 86.3
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 1374–1653 1.000 86.3
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCCACAGCTGATCATGTCC GAGGTTCGAATCCTTCCGTC 1375–1654 1.000 84.6
psbI-trnS-GCU_p1 psbI-trnS-GCU GGACGTAATCCTGGACGAGA TGGACTAAAGCGTCGGATTG 268–274 1.000 81.6
psbI-trnS-GCU_p2 psbI-trnS-GCU GGACGTAATCCTGGACGAGA GTGGACTAAAGCGTCGGATT 269–275 1.000 81.5
psbI-trnS-GCU_p3 psbI-trnS-GCU GGACGTAATCCTGGACGAGA TGCTAATCCGTTGTACGAGC 250–256 1.000 81.4
psbI-trnS-GCU_p4 psbI-trnS-GCU GGACGTAATCCTGGACGAGA ATCCGTTGTACGAGCGATTC 245–251 1.000 80.9
psbI-trnS-GCU_p5 psbI-trnS-GCU GGACGTAATCCTGGACGAGA AATCCGTTGTACGAGCGATT 246–252 1.000 79.8
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA TGTTCGGAATACAAAGAAAACCG 740–774 1.000 63.0
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC TGTTCGGAATACAAAGAAAACCG 739–773 1.000 63.0
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA CGAAGGACCCCTTAACTATTAGG 719–753 1.000 62.3
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC CGAAGGACCCCTTAACTATTAGG 718–752 1.000 62.3
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC GCTCGTACAACGGATTAGCA TGTTCGGAATACAAAGAAAACCG 758–792 1.000 62.2
atpH-atpI_p1 atpH-atpI AACGGAAGCAGCAGAAATCA GAATACGGTCCTTGGGTTCC 1190–1194 1.000 85.5
atpH-atpI_p2 atpH-atpI AACGGAAGCAGCAGAAATCA TGGGGAAGAATACGGTCCTT 1197–1201 1.000 85.5
atpH-atpI_p3 atpH-atpI CTCCCGGAAATTGGGCATTA GAATACGGTCCTTGGGTTCC 1526 0.500 59.2
atpH-atpI_p4 atpH-atpI CTCCCGGAAATTGGGCATTA TGGGGAAGAATACGGTCCTT 1533 0.500 59.2
atpH-atpI_p5 atpH-atpI CTCCCGGAAATTGGGCATTA TTGGGGAAGAATACGGTCCT 1534 0.500 59.2
rpoB-trnC-GCA_p1 rpoB-trnC-GCA CCAAATTAATCCCGCGGGTA TTCCTGCTCTTTTCACACCC 1736–1766 1.000 87.1
rpoB-trnC-GCA_p2 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT TTCCTGCTCTTTTCACACCC 1984–2014 1.000 86.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA CGAGCCCATATCCTTGCTTT CTGCTCTTTTCACACCCACT 1981–2011 1.000 86.5
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG TTCCTGCTCTTTTCACACCC 2176–2206 1.000 86.1
rpoB-trnC-GCA_p5 rpoB-trnC-GCA CCGCCTACACAAGCAAATTG CTGCTCTTTTCACACCCACT 2173–2203 1.000 86.0
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG TTAAAGCAGCCCAAGCAAGA 901–908 1.000 87.1
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCAAGACTTACT 895–902 1.000 85.6
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT TTAAAGCAGCCCAAGCAAGA 919–926 1.000 84.7
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CAGCCCAAGCAAGACTTACT 913–920 1.000 83.3
trnC-GCA-petN_p5 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CATTAAAGCAGCCCAAGCAA 903–910 1.000 81.1

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
Rosularia adenotricha PZ168341.1 151264 View on NCBI ↗
Rosularia alpestris MN794333.1 151288 View on NCBI ↗