Markers + reference

Potentilla

95 species · Rosaceae · Rosales

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Species 95
Genome length 153–157 kb
Candidate markers 268
Primer pairs 95

Genome-wide nucleotide diversity

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

Candidate markers

12 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 357 0.0585 0.97 79.7 yes View details
trnK-UUU-rps16 LSC 844 0.0283 1.00 68.0 yes View details
rps16-trnQ-UUG LSC 1038 0.0331 1.00 77.3 yes View details
trnR-UCU-atpA LSC 640 0.0467 0.96 82.3 yes View details
trnT-UGU-trnL-UAA LSC 1128 0.0355 0.99 83.3 yes View details
ndhC-trnV-UAC LSC 580 0.0399 0.98 73.1 yes View details
petA-psbJ LSC 1030 0.0336 0.98 71.3 yes View details
trnP-UGG-psaJ LSC 435 0.0365 1.00 70.9 yes View details
ycf1 IRb 1104 0.0091 1.00 51.8 no View details
ndhF-rpl32 SSC 1126 0.0314 0.96 72.5 yes View details
rpl32-trnL-UAG SSC 549 0.0419 1.00 78.7 yes View details
ycf1 SSC 5682 0.0229 1.00 64.0 yes View details
psbM-trnD-GUC LSC 979 0.0239 1.00 74.8 yes View details
trnT-GGU-psbD LSC 1351 0.0221 1.00 73.9 yes View details
psbE-petL LSC 1218 0.0247 0.98 73.9 yes View details
ycf3-trnS-GGA LSC 707 0.0244 1.00 73.3 yes View details
rpl2-trnH-GUG IRa 61 0.0235 1.00 73.2 no View details
rpoB-trnC-GCA LSC 1163 0.0243 0.99 72.8 yes View details
atpF-atpH LSC 519 0.0277 1.00 72.7 yes View details
trnG-UCC-trnR-UCU LSC 186 0.0571 1.00 72.6 yes View details
rps16 LSC 1124 0.0177 1.00 72.1 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 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 317–511 1.000 90.4
trnH-GUG-psbA_p2 trnH-GUG-psbA GATCCACTTGGCTACATCCG GCGCTAACCTTGGTATGGAA 367–561 0.989 90.3
trnH-GUG-psbA_p3 trnH-GUG-psbA CAATCCACTGCCTTGATCCA GCGCTAACCTTGGTATGGAA 381–575 0.989 90.3
trnH-GUG-psbA_p4 trnH-GUG-psbA AATCCACTGCCTTGATCCAC GCGCTAACCTTGGTATGGAA 380–574 0.989 90.2
trnH-GUG-psbA_p5 trnH-GUG-psbA ACAATCCACTGCCTTGATCC GCGCTAACCTTGGTATGGAA 382–576 0.958 89.0
trnK-UUU-rps16_p1 trnK-UUU-rps16 TCAGGATCAGTCGTGGTCTT CGACGAGAGGGAAGAGATCT 1059–1186 1.000 91.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 TTCAGGATCAGTCGTGGTCT CGACGAGAGGGAAGAGATCT 1060–1187 1.000 91.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT CGACGAGAGGGAAGAGATCT 968–1095 1.000 90.3
trnK-UUU-rps16_p4 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT CGACGAGAGGGAAGAGATCT 967–1094 1.000 90.3
trnK-UUU-rps16_p5 trnK-UUU-rps16 GGACTCTCTAGAACCTCCCC CGACGAGAGGGAAGAGATCT 1599–1697 0.926 88.1
rps16_p1 rps16 ACTTGTGTTGGATTGGCACT TGTACCAACCGAACCAATGA 1355–1553 0.968 82.7
rps16_p2 rps16 GAAGACGGGGGAGAAGTAGA TGTACCAACCGAACCAATGA 1410–1478 0.905 79.5
rps16_p3 rps16 ACGAAAATCATCCCATCGGG TGTACCAACCGAACCAATGA 1314–1369 0.821 76.7
rps16_p4 rps16 TAAGGAAGACGGGGGAGAAG TGTACCAACCGAACCAATGA 1414–1482 0.842 76.6
rps16_p5 rps16 CCTCCTGGCTCTCTTCTCTT TGTACCAACCGAACCAATGA 1825–1884 0.537 62.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG CAGCGGATCATGTCCTTCAA GAGGTTCGAATCCTTCCGTC 796–1224 1.000 91.2
rps16-trnQ-UUG_p2 rps16-trnQ-UUG GCGGATCATGTCCTTCAAGT GAGGTTCGAATCCTTCCGTC 794–1222 1.000 91.2
rps16-trnQ-UUG_p3 rps16-trnQ-UUG AAGTCGCACGTTGCTTTCTA GAGGTTCGAATCCTTCCGTC 778–1206 0.989 89.9
rps16-trnQ-UUG_p4 rps16-trnQ-UUG GATGTAAGACTCCACAGCGG GAGGTTCGAATCCTTCCGTC 820–1238 0.947 88.7
rps16-trnQ-UUG_p5 rps16-trnQ-UUG GGATGTAAGACTCCACAGCG GAGGTTCGAATCCTTCCGTC 821–1239 0.947 88.7
trnG-UCC-trnR-UCU_p1 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGAAGACCTCTGTCCTATCCA 212–353 1.000 75.3
trnG-UCC-trnR-UCU_p2 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGAAGACCTCTGTCCTATCCA 215–356 1.000 75.1
trnG-UCC-trnR-UCU_p3 trnG-UCC-trnR-UCU AGCCTTCCAAGCTAACGATG AGGTTTAGAAGACCTCTGTCCT 218–359 1.000 74.7
trnG-UCC-trnR-UCU_p4 trnG-UCC-trnR-UCU CCTAGCCTTCCAAGCTAACG AGGTTTAGAAGACCTCTGTCCT 221–362 1.000 74.5
trnG-UCC-trnR-UCU_p5 trnG-UCC-trnR-UCU CCCTAGCCTTCCAAGCTAAC AGAAGACCTCTGTCCTATCCA 216–357 1.000 72.9
trnR-UCU-atpA_p1 trnR-UCU-atpA ATTGGAGTGAAAAGCGTCCA AGGAGCAAGTGGAACGTTTT 673–954 0.947 87.3
trnR-UCU-atpA_p2 trnR-UCU-atpA TGGAGTGAAAAGCGTCCATT AGGAGCAAGTGGAACGTTTT 671–952 0.947 87.3
trnR-UCU-atpA_p3 trnR-UCU-atpA TTGGAGTGAAAAGCGTCCAT AGGAGCAAGTGGAACGTTTT 672–953 0.947 87.3
trnR-UCU-atpA_p4 trnR-UCU-atpA TGGAGTGAAAAGCGTCCATT ATTCAGGAGCAAGTGGAACG 675–956 0.947 86.2
trnR-UCU-atpA_p5 trnR-UCU-atpA TTGGAGTGAAAAGCGTCCAT ATTCAGGAGCAAGTGGAACG 676–957 0.947 86.2

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (95)

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

Species Accession Length (bp) Link
Potentilla acaulis NC_087010.1 156203 View on NCBI ↗
Potentilla alba PP541868.1 154828 View on NCBI ↗
Potentilla ancistrifolia NC_086992.1 156432 View on NCBI ↗
Potentilla angustiloba NC_087007.1 156221 View on NCBI ↗
Potentilla argentea NC_087011.1 156207 View on NCBI ↗
Potentilla argyrophylla MW344871.1 156387 View on NCBI ↗
Potentilla articulata NC_088441.1 155428 View on NCBI ↗
Potentilla asperrima NC_087000.1 156418 View on NCBI ↗
Potentilla aurea subsp. aurea PP541869.1 156267 View on NCBI ↗
Potentilla biflora var. biflora MW348947.1 155465 View on NCBI ↗
Potentilla biflora var. lahulensis MW331277.1 155401 View on NCBI ↗
Potentilla californica NC_087038.1 155789 View on NCBI ↗
Potentilla canadensis NC_087035.1 156237 View on NCBI ↗
Potentilla centigrana NC_041209.1 156392 View on NCBI ↗
Potentilla chinensis MN871983.1 157117 View on NCBI ↗
Potentilla chinensis var. chinensis MW338695.1 156232 View on NCBI ↗
Potentilla chinensis var. lineariloba OR601525.1 156326 View on NCBI ↗
Potentilla chrysantha NC_087006.1 156366 View on NCBI ↗
Potentilla clandestina NC_086988.1 155758 View on NCBI ↗
Potentilla clevelandii NC_087039.1 155841 View on NCBI ↗
Potentilla conferta NC_087013.1 156244 View on NCBI ↗
Potentilla coriandrifolia NC_086986.1 155705 View on NCBI ↗
Potentilla coriandrifolia var. dumosa MW309838.1 157046 View on NCBI ↗
Potentilla crebridens NC_086999.1 156451 View on NCBI ↗
Potentilla cryptotaeniae NC_087022.1 156059 View on NCBI ↗
Potentilla delavayi NC_087021.1 156334 View on NCBI ↗
Potentilla desertorum NC_087002.1 156362 View on NCBI ↗
Potentilla dickinsii var. glabrata NC_051504.1 155524 View on NCBI ↗
Potentilla erecta NC_087033.1 156013 View on NCBI ↗
Potentilla eriocarpa NC_080342.1 155769 View on NCBI ↗
Potentilla eriocarpa var. eriocarpa MW331280.1 155512 View on NCBI ↗
Potentilla eriocarpa var. tsarongensis MW316692.1 155711 View on NCBI ↗
Potentilla flagellaris NC_086989.1 156241 View on NCBI ↗
Potentilla fragarioides NC_086991.1 156350 View on NCBI ↗
Potentilla freyniana NC_041210.1 156381 View on NCBI ↗
Potentilla freyniana var. 'chejuensis' MK472813.1 156379 View on NCBI ↗
Potentilla gageodoensis OK267273.1 156397 View on NCBI ↗
Potentilla gelida NC_087009.1 156365 View on NCBI ↗
Potentilla gobica PX409049.1 156336 View on NCBI ↗
Potentilla gordonii NC_087041.1 155949 View on NCBI ↗
Potentilla hebiichigo NC_041199.1 156329 View on NCBI ↗
Potentilla hololeuca NC_087001.1 156395 View on NCBI ↗
Potentilla inclinata NC_086996.1 156079 View on NCBI ↗
Potentilla indica NC_041178.1 156050 View on NCBI ↗
Potentilla kleiniana NC_068636.1 156343 View on NCBI ↗
Potentilla laevipes PX409048.1 156273 View on NCBI ↗
Potentilla laevissima PX409047.1 156275 View on NCBI ↗
Potentilla lancinata NC_087012.1 156659 View on NCBI ↗
Potentilla leucophylla NC_086994.1 156187 View on NCBI ↗
Potentilla lineata NC_058280.1 156985 View on NCBI ↗
Potentilla longifolia NC_086998.1 156138 View on NCBI ↗
Potentilla mandshurica OR601528.1 152934 View on NCBI ↗
Potentilla micrantha PP541871.1 154964 View on NCBI ↗
Potentilla micropetala NC_086980.1 156584 View on NCBI ↗
Potentilla microphylla NC_086983.1 156671 View on NCBI ↗
Potentilla muirii NC_087043.1 155887 View on NCBI ↗
Potentilla multicaulis NC_087017.1 155977 View on NCBI ↗
Potentilla multifida NC_086995.1 156130 View on NCBI ↗
Potentilla multifida var. ornithopoda NC_087015.1 156196 View on NCBI ↗
Potentilla multifoliolata NC_087045.1 156056 View on NCBI ↗
Potentilla nervosa NC_087008.1 156407 View on NCBI ↗
Potentilla nivea NC_087005.1 156135 View on NCBI ↗
Potentilla pamiroalaica NC_087003.1 155984 View on NCBI ↗
Potentilla parvifolia NC_053696.1 152898 View on NCBI ↗
Potentilla patellifera NC_087034.1 155855 View on NCBI ↗
Potentilla plumosa NC_087020.1 156362 View on NCBI ↗
Potentilla potaninii NC_087018.1 156198 View on NCBI ↗
Potentilla potaninii var. compsophylla MW344870.1 156163 View on NCBI ↗
Potentilla purpurascens NC_087044.1 155864 View on NCBI ↗
Potentilla purpurea NC_087032.1 154740 View on NCBI ↗
Potentilla reptans NC_087037.1 156718 View on NCBI ↗
Potentilla reptans var. sericophylla MW331281.1 156223 View on NCBI ↗
Potentilla sabulosa NC_087046.1 155830 View on NCBI ↗
Potentilla saundersiana NC_072931.1 156346 View on NCBI ↗
Potentilla saundersiana var. jacquemontii MW338701.1 156316 View on NCBI ↗
Potentilla saundersiana var. saundersiana MW338699.1 156354 View on NCBI ↗
Potentilla saundersiana var. subpinnata MW344872.1 156316 View on NCBI ↗
Potentilla schmakovii PX409050.1 156395 View on NCBI ↗
Potentilla sericata NC_087042.1 155987 View on NCBI ↗
Potentilla sericea NC_087004.1 156134 View on NCBI ↗
Potentilla sericoleuca NC_087040.1 156006 View on NCBI ↗
Potentilla sikkimensis NC_087031.1 155914 View on NCBI ↗
Potentilla simplex NC_087036.1 156223 View on NCBI ↗
Potentilla simulatrix NC_086990.1 156040 View on NCBI ↗
Potentilla sinonivea NC_087019.1 156307 View on NCBI ↗
Potentilla sischanensis var. peterae MW344874.1 156210 View on NCBI ↗
Potentilla stolonifera NC_044418.1 156440 View on NCBI ↗
Potentilla stolonifera var. quelpaertensis MK229189.1 156393 View on NCBI ↗
Potentilla suavis NC_050934.1 155044 View on NCBI ↗
Potentilla supina MW338682.1 156297 View on NCBI ↗
Potentilla tanacetifolia NC_087014.1 156236 View on NCBI ↗
Potentilla tetrandra NC_086987.1 156178 View on NCBI ↗
Potentilla verticillaris NC_087016.1 156302 View on NCBI ↗
Potentilla virgata NC_086997.1 156034 View on NCBI ↗
Potentilla x subdigitata MW338684.1 156208 View on NCBI ↗