Markers + reference

Rubus

85 species · Rosaceae · Rosales

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Species 85
Genome length 155–157 kb
Candidate markers 263
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 263 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
trnK-UUU-rps16 LSC 1029 0.0361 0.98 74.6 yes View details
rps16-trnQ-UUG LSC 856 0.0406 1.00 81.7 yes View details
petN-psbM LSC 1282 0.0273 1.00 77.2 yes View details
trnT-GGU-psbD LSC 1359 0.0241 0.99 73.0 yes View details
trnT-UGU-trnL-CAA LSC 1209 0.0315 0.99 77.4 yes View details
ndhC-trnV-UAC LSC 626 0.0364 0.95 81.4 yes View details
petA-psbJ LSC 983 0.0357 1.00 74.8 yes View details
psbE-petL LSC 1214 0.0214 0.99 75.4 yes View details
rpl16 LSC 1356 0.0185 1.00 65.6 yes View details
ndhF-rpl32 SSC 1102 0.0281 1.00 69.8 yes View details
rpl32-trnL-UAG SSC 778 0.0439 0.93 78.1 yes View details
rpl2-trnH-GUG IRa 40 0.0560 1.00 83.7 no View details
rpoB-trnC-GCA LSC 948 0.0246 0.99 82.3 yes View details
trnH-GUG-psbA LSC 282 0.0579 1.00 77.0 yes View details
psbM-trnD-GUC LSC 986 0.0197 1.00 72.8 yes View details
trnS-GCU-trnG-GCC LSC 598 0.0286 1.00 71.3 yes View details
trnC-GCA-petN LSC 770 0.0177 1.00 68.0 yes View details
rpl22-rps19 LSC 100 0.0500 1.00 67.6 yes View details
trnF-GAA-ndhJ LSC 736 0.0227 1.00 67.2 yes View details
rpl20-clpP1 LSC 1072 0.0166 1.00 67.2 yes View details
ndhA SSC 2342 0.0144 0.99 67.2 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 GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 349–430 0.988 90.2
trnH-GUG-psbA_p2 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 363–444 0.988 90.2
trnH-GUG-psbA_p3 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 362–443 0.988 90.2
trnH-GUG-psbA_p4 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 364–445 0.988 90.2
trnH-GUG-psbA_p5 trnH-GUG-psbA GATCCACTTGGCTACATCCG CCTCTAGACCTAGCTGCTGT 299–380 0.988 90.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG CGACGAGAGGGAAGAGATCT 1059–1381 1.000 91.6
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAAGGCGCTCAACCTACA 965–1287 0.988 91.2
trnK-UUU-rps16_p3 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT AAAAAGGCGCTCAACCTACA 961–1283 0.988 90.7
trnK-UUU-rps16_p4 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT AAAAAGGCGCTCAACCTACA 962–1284 0.988 90.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG TGTTGCTGCCGTTTTGAAAG 1555–1896 0.965 89.8
rps16-trnQ-UUG_p1 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 892–1074 0.988 89.8
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TCATGTCCTTCAAGTCGCAC GAGGTTCGAATCCTTCCGTC 903–1053 0.976 88.8
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TTCGGAGGTTCGAATCCTTC 896–1078 0.988 85.1
rps16-trnQ-UUG_p4 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA TAAGGCAACGGGTTTTGGTC 922–1104 0.988 85.0
rps16-trnQ-UUG_p5 rps16-trnQ-UUG ATCATGTCCTTCAAGTCGCA GAGGTTCGAATCCTTCCGTC 911–1054 0.941 82.9
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GGGGGTTATAGAACGAATCACA 637–707 0.965 71.3
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GGGGGTTATAGAACGAATCACA 636–706 0.965 71.3
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC ACGGAAAGAGAGGGATTCGA GGGGGTTATAGAACGAATCACA 691–761 0.965 70.1
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGGGGGTTATAGAACGAATCAC 638–708 0.965 69.1
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC AGGGGGTTATAGAACGAATCAC 637–707 0.965 69.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA TATTGCCTCATTTCCACCCC CCGGATTTGAACTGGGGAAA 869–1046 0.988 87.3
rpoB-trnC-GCA_p2 rpoB-trnC-GCA TATTGCCTCATTTCCACCCC AAAAGGATTTGCAGTCCCCC 851–1028 0.988 85.1
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATATTGCCTCATTTCCACCCC CCGGATTTGAACTGGGGAAA 870–1047 0.988 82.6
rpoB-trnC-GCA_p4 rpoB-trnC-GCA CATTTCCACCCCCAAGCAT CCGGATTTGAACTGGGGAAA 861–1038 0.965 81.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA GTTCCTCTGTTAAGCCCTGA CCGGATTTGAACTGGGGAAA 945–1122 0.988 81.7
trnC-GCA-petN_p1 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG CAGCCCAAGCGAGATTTACT 813–847 0.988 90.6
trnC-GCA-petN_p2 trnC-GCA-petN TTTCCCCAGTTCAAATCCGG AGAGTCCACTTCTTCCCCAT 873–907 1.000 88.5
trnC-GCA-petN_p3 trnC-GCA-petN GGGGGACTGCAAATCCTTTT CAGCCCAAGCGAGATTTACT 831–865 0.988 88.4
trnC-GCA-petN_p4 trnC-GCA-petN GGGGGACTGCAAATCCTTTT AGAGTCCACTTCTTCCCCAT 891–925 1.000 86.3
trnC-GCA-petN_p5 trnC-GCA-petN CCAGTTCAAATCCGGGTGTC CAGCCCAAGCGAGATTTACT 808–842 0.988 84.6

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (85)

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

Species Accession Length (bp) Link
Rubus alceifolius NC_082581.1 156266 View on NCBI ↗
Rubus amabilis NC_047211.1 155279 View on NCBI ↗
Rubus arcticus NC_062417.1 156668 View on NCBI ↗
Rubus argutus OR972714.1 156630 View on NCBI ↗
Rubus bambusarum NC_056916.1 156309 View on NCBI ↗
Rubus biflorus NC_080344.1 155810 View on NCBI ↗
Rubus boninensis NC_046015.1 155807 View on NCBI ↗
Rubus buergeri NC_072261.1 156276 View on NCBI ↗
Rubus calophyllus PP566881.1 156406 View on NCBI ↗
Rubus calycacanthus PP566882.1 156321 View on NCBI ↗
Rubus calycinus PP566883.1 156280 View on NCBI ↗
Rubus chingii NC_062414.1 155563 View on NCBI ↗
Rubus chingii var. suavissimus NC_083088.1 155502 View on NCBI ↗
Rubus chrysobotrys PP566884.1 156238 View on NCBI ↗
Rubus cochinchinensis NC_056289.1 156235 View on NCBI ↗
Rubus columellaris NC_056932.1 155470 View on NCBI ↗
Rubus conduplicatus NC_064143.1 155731 View on NCBI ↗
Rubus corchorifolius NC_056942.1 155526 View on NCBI ↗
Rubus crassifolius NC_056941.1 156241 View on NCBI ↗
Rubus crataegifolius NC_039704.1 155714 View on NCBI ↗
Rubus ellipticus NC_056929.1 155553 View on NCBI ↗
Rubus ellipticus var. obcordatus MZ352083.1 155656 View on NCBI ↗
Rubus eucalyptus NC_057620.1 155672 View on NCBI ↗
Rubus flosculosus PP566885.1 155977 View on NCBI ↗
Rubus fockeanus PP566886.1 156429 View on NCBI ↗
Rubus foliaceistipulatus PP566887.1 156500 View on NCBI ↗
Rubus glandulosopunctatus NC_057624.1 155742 View on NCBI ↗
Rubus henryi NC_056945.1 156159 View on NCBI ↗
Rubus hirsutus NC_059905.1 156005 View on NCBI ↗
Rubus hirtus PP541890.1 156770 View on NCBI ↗
Rubus hunanensis NC_060618.1 156217 View on NCBI ↗
Rubus hybrid cultivar NC_042716.1 156621 View on NCBI ↗
Rubus ichangensis NC_056935.1 156315 View on NCBI ↗
Rubus idaeus PZ264131.1 155723 View on NCBI ↗
Rubus idaeus subsp. idaeus PP541891.1 155722 View on NCBI ↗
Rubus incanus NC_057625.1 155843 View on NCBI ↗
Rubus innominatus NC_056939.1 155496 View on NCBI ↗
Rubus irenaeus PP566888.1 156232 View on NCBI ↗
Rubus irritans NC_057600.1 155286 View on NCBI ↗
Rubus kawakamii NC_057626.1 155935 View on NCBI ↗
Rubus laciniatostipulatus NC_057627.1 156236 View on NCBI ↗
Rubus lambertianus NC_056931.1 156316 View on NCBI ↗
Rubus lambertianus var. paykouangensis MZ352082.1 156263 View on NCBI ↗
Rubus lasiostylus PP566889.1 155898 View on NCBI ↗
Rubus leucanthus MK105853.1 156068 View on NCBI ↗
Rubus lineatus NC_056943.1 156286 View on NCBI ↗
Rubus longisepalus NC_059904.1 155957 View on NCBI ↗
Rubus menglaensis PP566890.1 156248 View on NCBI ↗
Rubus niveus NC_056930.1 155946 View on NCBI ↗
Rubus occidentalis NC_060646.1 156253 View on NCBI ↗
Rubus pacificus NC_064142.1 156255 View on NCBI ↗
Rubus paniculatus PP566891.1 156299 View on NCBI ↗
Rubus parviaraliifolius NC_057628.1 155832 View on NCBI ↗
Rubus parviflorus OR972719.1 156882 View on NCBI ↗
Rubus parvifolius NC_060617.1 155906 View on NCBI ↗
Rubus pectinaris NC_056944.1 156506 View on NCBI ↗
Rubus pedunculosus NC_080345.1 155144 View on NCBI ↗
Rubus peltatus NC_056937.1 155582 View on NCBI ↗
Rubus pentagonus NC_056936.1 156287 View on NCBI ↗
Rubus phoenicolasius NC_057144.1 155144 View on NCBI ↗
Rubus pileatus NC_056947.1 155464 View on NCBI ↗
Rubus pinfaensis MZ352081.1 155523 View on NCBI ↗
Rubus pyrifolius var. permollis MT576950.1 156316 View on NCBI ↗
Rubus quinquefoliolatus NC_063615.1 156489 View on NCBI ↗
Rubus reflexus var. lanceolobus PV955414.1 156222 View on NCBI ↗
Rubus rosifolius PP566893.1 156006 View on NCBI ↗
Rubus rubroangustifolius NC_057629.1 155566 View on NCBI ↗
Rubus rufus NC_056798.1 156232 View on NCBI ↗
Rubus sachalinensis NC_056965.1 155787 View on NCBI ↗
Rubus semiplenus PV590107.1 156017 View on NCBI ↗
Rubus setchuenensis NC_056946.1 156295 View on NCBI ↗
Rubus stans PP566894.1 155530 View on NCBI ↗
Rubus subinopertus PP566895.1 155866 View on NCBI ↗
Rubus sumatranus PP737792.1 155935 View on NCBI ↗
Rubus swinhoei NC_077571.1 156335 View on NCBI ↗
Rubus taitoensis NC_057630.1 155948 View on NCBI ↗
Rubus taiwanicola NC_057631.1 155616 View on NCBI ↗
Rubus takesimensis NC_037991.1 155760 View on NCBI ↗
Rubus tephrodes NC_060615.1 156217 View on NCBI ↗
Rubus trianthus NC_060616.1 155546 View on NCBI ↗
Rubus trifidus NC_046585.1 155823 View on NCBI ↗
Rubus tsangii NC_056940.1 155995 View on NCBI ↗
Rubus wallichianus NC_056933.1 155703 View on NCBI ↗
Rubus xanthocarpus NC_056938.1 156052 View on NCBI ↗
Rubus xanthoneurus NC_056934.1 156300 View on NCBI ↗