Markers + reference

Sibbaldianthe

4 species · Rosaceae · Rosales

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Species 4
Genome length 155–155 kb
Candidate markers 269
Primer pairs 95

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 9 remaining regions by MarkerSeek score (out of 269 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 354 0.0254 0.85 71.2 yes View details
trnK-UUU-rps16 LSC 678 0.0150 1.00 67.9 yes View details
rps16 LSC 1144 0.0119 1.00 48.4 yes View details
rps16-trnQ-UUG LSC 999 0.0170 0.98 65.9 yes View details
trnR-UCU-atpA LSC 658 0.0195 0.97 61.3 yes View details
accD-psaI LSC 544 0.0208 1.00 72.9 yes View details
trnP-UGG-psaJ LSC 528 0.0165 0.94 65.2 yes View details
psaJ-rpl33 LSC 446 0.0183 0.98 59.3 yes View details
rpl36-rps8 LSC 508 0.0089 0.96 53.0 yes View details
ndhF-rpl32 SSC 615 0.0155 0.98 62.1 yes View details
rpl32-trnL-UAG SSC 687 0.0206 0.97 58.5 yes View details
ndhA SSC 2322 0.0070 0.98 63.8 yes View details
rpl20-rps12 LSC 772 0.0058 0.99 63.3 yes View details
trnC-GCA-petN LSC 835 0.0101 0.94 63.1 yes View details
atpH-atpI LSC 469 0.0036 0.95 63.0 yes View details
rpl2-trnH-GUG IRa 45 0.0000 1.00 62.2 no View details
trnT-UGU-trnL-UAA LSC 895 0.0095 0.99 59.2 yes View details
petN-psbM LSC 1309 0.0043 1.00 58.9 yes View details
psbE-petL LSC 1264 0.0083 0.96 57.8 yes View details
trnT-GGU-psbD LSC 1401 0.0048 0.97 57.7 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 95 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 372–420 1.000 85.1
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG TTCCCTCTAGACCTAGCTGC 375–423 1.000 85.0
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA CCTCTAGACCTAGCTGCTGT 386–434 1.000 84.9
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC CCTCTAGACCTAGCTGCTGT 385–433 1.000 84.9
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC CCTCTAGACCTAGCTGCTGT 387–435 1.000 84.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT ATTTCAAAAAGGGCGGGAGT 775–790 1.000 80.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT ATTTCAAAAAGGGCGGGAGT 774–789 1.000 80.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TCAAAAAGGGCGGGAGTTTT 771–786 1.000 78.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTCAAAAAGGGCGGGAGTTT 772–787 1.000 78.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT TTTCAAAAAGGGCGGGAGTT 773–788 1.000 78.7
rps16_p1 rps16 AAACCGGGTTAGTCCTTTGT TGGGTTCCAAACTGAAGGAA 1213–1241 1.000 64.1
rps16_p2 rps16 AACCGGGTTAGTCCTTTGTT TGGGTTCCAAACTGAAGGAA 1212–1240 1.000 64.1
rps16_p3 rps16 ACCGGGTTAGTCCTTTGTTT TGGGTTCCAAACTGAAGGAA 1211–1239 1.000 64.1
rps16_p4 rps16 AACCGGGTTAGTCCTTTGTT AGTACCAACCGAACCAATGA 1274–1302 1.000 63.2
rps16_p5 rps16 ACCGGGTTAGTCCTTTGTTT AGTACCAACCGAACCAATGA 1273–1301 1.000 63.2
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 1053–1091 1.000 84.5
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 1051–1089 1.000 84.5
rps16-trnQ-UUG_p3 rps16-trnQ-UUG GATGTAAGACTCCACAGCGG GAGGTTCGAATCCTTCCGTC 1067–1105 1.000 84.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GGATGTAAGACTCCACAGCG GAGGTTCGAATCCTTCCGTC 1068–1106 1.000 84.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 1035–1073 1.000 83.7
trnR-UCU-atpA_p1 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG CGGCAGCTCAAATTAAAGCC 1411–1451 1.000 83.0
trnR-UCU-atpA_p2 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG GCGTATCCGGGAGATGTTTT 1661–1701 1.000 82.8
trnR-UCU-atpA_p3 trnR-UCU-atpA CCTAGCCTTCCAAGCTAACG GCGTATCCGGGAGATGTTTT 1664–1704 1.000 82.6
trnR-UCU-atpA_p4 trnR-UCU-atpA AGCCTTCCAAGCTAACGATG TGGAAAGAGCCGCGAAATTA 1621–1661 1.000 82.5
trnR-UCU-atpA_p5 trnR-UCU-atpA AGGGATCGTCTAGAAAGCGA GCGTATCCGGGAGATGTTTT 1868–1908 1.000 82.3
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT AGGCGAATCAATGGAAGGTC 524–529 1.000 83.1
atpH-atpI_p2 atpH-atpI AATAGAAGCAAGCCCGACAG AGGCGAATCAATGGAAGGTC 558–563 1.000 83.0
atpH-atpI_p3 atpH-atpI AGCCAATCCAGCAGCAATAA AGGCGAATCAATGGAAGGTC 540–545 1.000 82.1
atpH-atpI_p4 atpH-atpI AATAACGGAAGCGGCAGAAA AGGCGAATCAATGGAAGGTC 525–530 1.000 82.0
atpH-atpI_p5 atpH-atpI GCCAATCCAGCAGCAATAAC AGGCGAATCAATGGAAGGTC 539–544 1.000 81.6

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
Sibbaldianthe adpressa NC_050935.1 155021 View on NCBI ↗
Sibbaldianthe moorcroftii NC_086972.1 155216 View on NCBI ↗
Sibbaldianthe semiglabra NC_086973.1 155092 View on NCBI ↗
Sibbaldianthe sericea NC_086974.1 154841 View on NCBI ↗