Markers + reference

Sorbus

52 species · Rosaceae · Rosales

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Species 52
Genome length 159–161 kb
Candidate markers 271
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

10 hotspot labels from the diversity plot in genomic order, plus the top 10 remaining regions by MarkerSeek score (out of 271 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnH-GUG-psbA LSC 265 0.0227 1.00 63.0 yes View details
trnR-UCU-atpA LSC 675 0.0314 0.99 84.3 yes View details
petN-psbM LSC 1245 0.0095 1.00 49.2 yes View details
psbM-trnD-GUC LSC 1232 0.0044 1.00 50.7 yes View details
trnT-GGU-psbD LSC 1405 0.0059 1.00 62.9 yes View details
trnT-UGU-trnL-UAA LSC 1263 0.0086 0.99 59.4 yes View details
ndhC-trnV-UAC LSC 679 0.0260 0.92 72.5 yes View details
psaJ-rpl33 LSC 456 0.0042 1.00 43.1 yes View details
ndhF-rpl32 SSC 1050 0.0069 1.00 65.4 yes View details
rpl32-trnL-UAG SSC 1469 0.0079 0.99 58.0 yes View details
rpl22-rps19 LSC 66 0.0178 1.00 61.3 yes View details
atpH-atpI LSC 1168 0.0035 1.00 61.0 yes View details
rpl33-rps18 LSC 218 0.0160 1.00 59.1 yes View details
rps16-trnQ-UUG LSC 809 0.0051 1.00 58.7 yes View details
rps16 LSC 1140 0.0032 1.00 57.8 yes View details
rps19-trnH-GUG LSC 41 0.0271 1.00 57.0 no View details
trnF-GAA-ndhJ LSC 702 0.0033 1.00 56.2 yes View details
petA-psbJ LSC 984 0.0032 1.00 54.9 yes View details
rpoB-trnC-GCA LSC 1217 0.0044 1.00 54.6 yes View details
psbZ-trnG-UCC LSC 407 0.0056 1.00 54.3 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 GCGCTAACCTTGGTATGGAA 342–386 1.000 89.0
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 356–400 1.000 88.8
trnH-GUG-psbA_p3 trnH-GUG-psbA ATATTATGGGCGAACGACGG CCTCTAGACCTAGCTGCTGT 353–397 0.923 85.7
trnH-GUG-psbA_p4 trnH-GUG-psbA ATATTATGGGCGAACGACGG TTCCCTCTAGACCTAGCTGC 356–400 0.923 85.6
trnH-GUG-psbA_p5 trnH-GUG-psbA ATATTATGGGCGAACGACGG GCGCTAACCTTGGTATGGAA 403–447 0.923 85.5
rps16_p1 rps16 AGAAACAAAAAGGTTATACAAGGCT TATGTACCGACCGAACCGAT 1270–1284 1.000 43.3
rps16_p2 rps16 AGAAACAAAAAGGTTATACAAGGCT CCGACCGAACCGATGATTAT 1264–1278 1.000 43.3
rps16_p3 rps16 ACAAAAAGGTTATACAAGGCT TATGTACCGACCGAACCGAT 1266–1280 1.000 43.3
rps16_p4 rps16 AGAAACAAAAAGGTTATACAAGGCT ATTATGTACCGACCGAACCG 1272–1286 1.000 43.3
rps16_p5 rps16 GGAAATAGCAAAGAAACAAAAAGGT TATGTACCGACCGAACCGAT 1281–1295 0.962 41.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 873–912 1.000 83.9
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCTTTCTGCCACATCGTTTT GAGGTTCGAATCCTTCCGTC 850–889 1.000 82.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG CCACAGCTGATCATGTCCTT GAGGTTCGAATCCTTCCGTC 883–922 1.000 82.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TCCACAGCTGATCATGTCCT GAGGTTCGAATCCTTCCGTC 884–923 1.000 82.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GTGTCGACTAGAAATGGGGC 935–974 1.000 81.4
trnR-UCU-atpA_p1 trnR-UCU-atpA TGGAATGAAAAGCGTCCATTG AGACATTTACCGACGAAGCG 776–1335 0.962 74.9
trnR-UCU-atpA_p2 trnR-UCU-atpA GGAATGAAAAGCGTCCATTGT AGACATTTACCGACGAAGCG 775–1334 0.962 74.9
trnR-UCU-atpA_p3 trnR-UCU-atpA GGTTCAAATCCTATTGGACGC AGACATTTACCGACGAAGCG 715–1274 0.962 73.9
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGAATGAAAAGCGTCCATT AGACATTTACCGACGAAGCG 776–1335 0.962 70.8
trnR-UCU-atpA_p5 trnR-UCU-atpA TTGGAATGAAAAGCGTCCAT AGACATTTACCGACGAAGCG 777–1336 0.962 70.8
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT GCGAATCCATGGAAGGTCAT 1208–1262 1.000 85.0
atpH-atpI_p2 atpH-atpI AATAGAAGCAAGCCCGACAG GCGAATCCATGGAAGGTCAT 1242–1296 1.000 84.9
atpH-atpI_p3 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTTGCAACCTTAGCTGCG 1238–1292 1.000 84.0
atpH-atpI_p4 atpH-atpI AATAGAAGCAAGCCCGACAG TTTTTGCAACCTTAGCTGCG 1272–1326 1.000 83.9
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA GCGAATCCATGGAAGGTCAT 1209–1263 1.000 83.8
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TAAGCCCTGCTCAATGAACC CCGGATTTGAACTGGGGAAA 1363–1400 1.000 81.4
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TAAGCCCTGCTCAATGAACC AAAAGGATTTGCAGTCCCCC 1345–1382 1.000 79.3
rpoB-trnC-GCA_p3 rpoB-trnC-GCA TATTGCCTCATTTCCACCCC CCGGATTTGAACTGGGGAAA 1297–1334 1.000 79.0
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CTCTGTTAAGCCCTGCTCAA CCGGATTTGAACTGGGGAAA 1369–1406 1.000 78.6
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GTTCCTCTGTTAAGCCCTGC CCGGATTTGAACTGGGGAAA 1373–1410 1.000 78.0

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (52)

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

Species Accession Length (bp) Link
Sorbus aestivalis NC_068530.1 159903 View on NCBI ↗
Sorbus albopilosa NC_068534.1 159904 View on NCBI ↗
Sorbus americana NC_062338.1 160054 View on NCBI ↗
Sorbus aucuparia subsp. pohuashanensis OR915917.1 160067 View on NCBI ↗
Sorbus buschiana NC_085656.1 159538 View on NCBI ↗
Sorbus californica NC_085651.1 159973 View on NCBI ↗
Sorbus cashmiriana NC_085671.1 160054 View on NCBI ↗
Sorbus cibagouensis NC_068532.1 159800 View on NCBI ↗
Sorbus commixta MK920288.1 159952 View on NCBI ↗
Sorbus cuspidata NC_085639.1 159968 View on NCBI ↗
Sorbus decora NC_085652.1 160340 View on NCBI ↗
Sorbus discolor NC_068723.1 160139 View on NCBI ↗
Sorbus dumosa NC_085653.1 160167 View on NCBI ↗
Sorbus epidendron NC_085670.1 159711 View on NCBI ↗
Sorbus filipes NC_068533.1 160074 View on NCBI ↗
Sorbus foliolosa NC_068526.1 160006 View on NCBI ↗
Sorbus helenae NC_068536.1 159910 View on NCBI ↗
Sorbus hupehensis NC_068721.1 159955 View on NCBI ↗
Sorbus hupehensis var. paucijuga MT916771.1 160050 View on NCBI ↗
Sorbus hypoglauca NC_068535.1 160178 View on NCBI ↗
Sorbus insignis NC_051947.1 159993 View on NCBI ↗
Sorbus keissleri OQ100079.1 159753 View on NCBI ↗
Sorbus kiukiangensis NC_085636.1 160083 View on NCBI ↗
Sorbus macrantha NC_085631.1 159899 View on NCBI ↗
Sorbus matsumurana NC_062341.1 160289 View on NCBI ↗
Sorbus microphylla NC_085633.1 159938 View on NCBI ↗
Sorbus monbeigii PQ308348.1 160174 View on NCBI ↗
Sorbus multijuga NC_068724.1 159850 View on NCBI ↗
Sorbus oligodonta NC_085634.1 159937 View on NCBI ↗
Sorbus poteriifolia NC_085663.1 160060 View on NCBI ↗
Sorbus prattii NC_085635.1 160089 View on NCBI ↗
Sorbus pseudovilmorinii NC_085664.1 159974 View on NCBI ↗
Sorbus pteridophylla NC_062342.1 159805 View on NCBI ↗
Sorbus randaiensis NC_085665.1 159460 View on NCBI ↗
Sorbus reducta NC_068722.1 160280 View on NCBI ↗
Sorbus rehderiana NC_068525.1 160034 View on NCBI ↗
Sorbus rehderiana var. grosseserrata OR897860.1 160107 View on NCBI ↗
Sorbus rufopilosa NC_085638.1 159802 View on NCBI ↗
Sorbus rutilans NC_068528.1 159998 View on NCBI ↗
Sorbus salwinensis NC_085666.1 159795 View on NCBI ↗
Sorbus sambucifolia NC_085654.1 159900 View on NCBI ↗
Sorbus sargentiana NC_068529.1 159657 View on NCBI ↗
Sorbus scalaris NC_085637.1 160065 View on NCBI ↗
Sorbus scopulina NC_085658.1 160301 View on NCBI ↗
Sorbus sitchensis var. grayi OR897861.1 160197 View on NCBI ↗
Sorbus slavnicensis (nom. inval.) NC_085649.1 160341 View on NCBI ↗
Sorbus tapashana NC_085591.1 160055 View on NCBI ↗
Sorbus tianschanica NC_068599.1 160024 View on NCBI ↗
Sorbus ulleungensis NC_037022.1 159632 View on NCBI ↗
Sorbus vilmorinii MK920285.1 159936 View on NCBI ↗
Sorbus wilsoniana NC_068531.1 159646 View on NCBI ↗
Sorbus xanthoneura NC_085586.1 160609 View on NCBI ↗