Markers + reference

Sibbaldia

4 species · Rosaceae · Rosales

Back to catalogue

Species 4
Genome length 153–154 kb
Candidate markers 268
Primer pairs 105

Genome-wide nucleotide diversity

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

Candidate markers

13 hotspot labels from the diversity plot in genomic order, plus the top 9 remaining regions by MarkerSeek score (out of 268 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 312 0.0386 0.95 82.1 yes View details
trnK-UUU-rps16 LSC 725 0.0166 0.96 60.0 yes View details
trnR-UCU-atpA LSC 685 0.0156 0.99 65.7 yes View details
rpoB-trnC-GCA LSC 1225 0.0138 0.98 65.2 yes View details
trnT-GGU-psbD LSC 1309 0.0191 0.98 65.8 yes View details
ycf3-trnS-GGA LSC 855 0.0080 0.99 59.3 yes View details
ndhC-trnV-UAC LSC 593 0.0187 0.92 65.4 yes View details
psbE-petL LSC 1256 0.0135 0.97 60.4 yes View details
ycf1 IRb 1161 0.0017 1.00 49.1 no View details
rpl32-trnL-UAG SSC 608 0.0147 0.97 69.3 yes View details
ccsA-ndhD SSC 266 0.0327 1.00 61.1 yes View details
rps15-ycf1 SSC 397 0.0176 1.00 53.1 yes View details
ycf1 SSC 5730 0.0094 1.00 48.8 yes View details
trnG-GCC-trnfM-CAU LSC 157 0.0385 0.99 74.6 yes View details
rpl22-rps19 LSC 97 0.0464 1.00 73.2 yes View details
petN-psbM LSC 1119 0.0082 0.99 66.7 yes View details
psaA-ycf3 LSC 767 0.0082 0.98 66.5 yes View details
petA-psbJ LSC 685 0.0105 0.99 66.0 yes View details
psbM-trnD-GUC LSC 598 0.0087 0.93 65.3 yes View details
ndhF-rpl32 SSC 634 0.0073 0.97 63.8 yes View details
rpl2-trnH-GUG IRa 45 0.0000 1.00 62.5 no View details
atpB-rbcL LSC 742 0.0047 1.00 62.1 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 105 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnH-GUG-psbA_p1 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 356–378 1.000 87.0
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 359–381 1.000 86.9
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 370–392 1.000 86.8
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 369–391 1.000 86.8
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 371–393 1.000 86.8
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAAGGCGCTCAACCTACA 899–952 1.000 86.0
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGACGAGAGGGAAGAGATCT 993–1046 1.000 85.7
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT AAAAAGGCGCTCAACCTACA 895–948 1.000 85.5
trnK-UUU-rps16_p4 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT AAAAAGGCGCTCAACCTACA 896–949 1.000 85.5
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT CGACGAGAGGGAAGAGATCT 989–1042 1.000 85.1
trnR-UCU-atpA_p1 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGAGGAAGCG 772–854 1.000 70.0
trnR-UCU-atpA_p2 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC GAGGAAGCGGAAACCCTTTT 761–843 1.000 69.3
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TCAGGACCAAATGGAACGTT 729–811 1.000 67.3
trnR-UCU-atpA_p4 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC TTCAGGACCAAATGGAACGT 730–812 1.000 67.3
trnR-UCU-atpA_p5 trnR-UCU-atpA TGGATAGGACAGAGGTCTTCT AGACATTTACCGAGGAAGCG 807–889 1.000 67.0
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TAAGCCCCGATCAATGAACC CCGGATTTGAACTGGGGAAA 1360–1380 1.000 80.0
rpoB-trnC-GCA_p2 rpoB-trnC-GCA GCCCCGATCAATGAACCTAC CCGGATTTGAACTGGGGAAA 1357–1377 1.000 79.5
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TTCCTCTGTTAAGCCCCGAT CCGGATTTGAACTGGGGAAA 1369–1389 1.000 79.3
rpoB-trnC-GCA_p4 rpoB-trnC-GCA TATTGCCTCATTTCCACCCC CCGGATTTGAACTGGGGAAA 1294–1314 1.000 79.3
rpoB-trnC-GCA_p5 rpoB-trnC-GCA AGCCCCGATCAATGAACCTA CCGGATTTGAACTGGGGAAA 1358–1378 1.000 78.8
petN-psbM_p1 petN-psbM AGTAAATCTCGCTTGGGCTG CAGTCAGCCAAGGTGATTGA 1221–1311 1.000 80.8
petN-psbM_p2 petN-psbM AGTAAATCTCGCTTGGGCTG AAAACAGTCAGCCAAGGTGA 1225–1315 1.000 78.8
petN-psbM_p3 petN-psbM ATGGGGAAGAAGTGGACTCT CAGTCAGCCAAGGTGATTGA 1161–1251 1.000 78.4
petN-psbM_p4 petN-psbM AGTAAATCTCGCTTGGGCTG AAACAGTCAGCCAAGGTGAT 1224–1314 1.000 77.0
petN-psbM_p5 petN-psbM AGTAAATCTCGCTTGGGCTG AACAGTCAGCCAAGGTGATT 1223–1313 1.000 77.0
psbM-trnD-GUC_p1 psbM-trnD-GUC CAATCACCTTGGCTGACTGT TTCAATTGGTCAGAGCACCG 719–766 1.000 80.4
psbM-trnD-GUC_p2 psbM-trnD-GUC TCAATCACCTTGGCTGACTG TTCAATTGGTCAGAGCACCG 720–767 1.000 79.6
psbM-trnD-GUC_p3 psbM-trnD-GUC TCACCTTGGCTGACTGTTTT TTCAATTGGTCAGAGCACCG 716–763 1.000 77.7
psbM-trnD-GUC_p4 psbM-trnD-GUC CAATCACCTTGGCTGACTGT GTTCAATTGGTCAGAGCACC 720–767 1.000 76.2
psbM-trnD-GUC_p5 psbM-trnD-GUC ATCACCTTGGCTGACTGTTT TTCAATTGGTCAGAGCACCG 717–764 1.000 75.8

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (4)

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

Species Accession Length (bp) Link
Sibbaldia aphanopetala NC_050967.1 153491 View on NCBI ↗
Sibbaldia cuneata NC_086969.1 153179 View on NCBI ↗
Sibbaldia cuneifolia NC_086968.1 153944 View on NCBI ↗
Sibbaldia procumbens NC_087023.1 153520 View on NCBI ↗