Markers + reference

Saxifraga

116 species · Saxifragaceae · Saxifragales

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Species 116
Genome length 146–156 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
rps16-trnQ-UUG LSC 657 0.0702 0.93 76.3 yes View details
psbK-psbI LSC 393 0.0596 0.89 74.0 yes View details
trnS-GCU-trnG-GCC LSC 789 0.0749 0.76 75.1 yes View details
trnT-GGU-psbD LSC 1372 0.0554 0.68 71.0 yes View details
psbZ-trnG-UCC LSC 662 0.0765 0.36 64.4 yes View details
trnT-UGU-trnL-UAA LSC 977 0.0561 0.90 81.8 yes View details
ndhC-trnV-UAC LSC 824 0.0695 0.65 68.8 yes View details
rpl16 LSC 1431 0.0452 0.82 72.4 yes View details
ycf1 IRb 1311 0.0139 0.99 60.1 no View details
ndhF-rpl32 SSC 601 0.0672 0.97 79.1 yes View details
rpl32-trnL-UAG SSC 492 0.0876 0.62 63.9 yes View details
ycf1 SSC 3771 0.0592 0.98 78.6 yes View details
ycf1-trnN-GUU IRa 1964 0.0219 0.99 65.4 yes View details
atpH-atpI LSC 895 0.0470 0.96 88.6 yes View details
rpoB-trnC-GCA LSC 1087 0.0497 0.92 81.5 yes View details
petA-psbJ LSC 568 0.0674 0.96 80.5 yes View details
psbE-petL LSC 1249 0.0445 0.97 79.7 yes View details
trnK-UUU-rps16 LSC 832 0.0597 0.93 77.6 yes View details
trnE-UUC-trnT-GGU LSC 561 0.0507 0.91 76.8 yes View details
trnC-GCA-petN LSC 726 0.0470 0.94 75.9 yes View details
psaA-ycf3 LSC 612 0.0438 0.94 74.9 yes View details
rbcL-accD LSC 1162 0.0334 0.97 74.9 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
trnK-UUU-rps16_p1 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG AAAAAGGCGCTCAACCTACA 810–1081 0.991 91.3
trnK-UUU-rps16_p2 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG AAAAAGGCGCTCAACCTACA 809–1080 0.991 91.3
trnK-UUU-rps16_p3 trnK-UUU-rps16 CCCTTTCAGGATCAGTCGTG GAAGGGAGGGGAGAGATCTC 903–1153 0.828 84.9
trnK-UUU-rps16_p4 trnK-UUU-rps16 CCTTTCAGGATCAGTCGTGG GAAGGGAGGGGAGAGATCTC 902–1152 0.828 84.9
trnK-UUU-rps16_p5 trnK-UUU-rps16 CGAATCCCTTGCTTCATCCA GAAGGGAGGGGAGAGATCTC 855–1105 0.828 84.7
rps16-trnQ-UUG_p1 rps16-trnQ-UUG TGGTGTTTCCTTGTTCCAGG GCAAAGGTATGACCGGCATA 1558–2141 0.948 89.1
rps16-trnQ-UUG_p2 rps16-trnQ-UUG TGGTGTTTCCTTGTTCCAGG GTAGGCCTCGGGTAATTTGG 1512–2095 0.931 88.4
rps16-trnQ-UUG_p3 rps16-trnQ-UUG TGGTGTTTCCTTGTTCCAGG CAACCCACTCACCCAATCAA 1317–1896 0.845 85.2
rps16-trnQ-UUG_p4 rps16-trnQ-UUG TGGGTTCTAGTCGAGCAGAA CAACCCACTCACCCAATCAA 915–1486 0.819 84.1
rps16-trnQ-UUG_p5 rps16-trnQ-UUG CGCGTGTTCCACTTTTTGTT CAACCCACTCACCCAATCAA 1361–1390 0.060 47.2
psbK-psbI_p1 psbK-psbI CCAAATTACCCGAGGCCTAC ACGAAGAGTTTGAGAGTAAGCA 422–542 1.000 71.0
psbK-psbI_p2 psbK-psbI TATGCCGGTCATACCTTTGC ACGAAGAGTTTGAGAGTAAGCA 376–496 1.000 71.0
psbK-psbI_p3 psbK-psbI GTTTGGCAAGCTGCTGTAAG ACGAAGAGTTTGAGAGTAAGCA 336–456 1.000 70.9
psbK-psbI_p4 psbK-psbI CCGGTCATACCTTTGCTGTT ACGAAGAGTTTGAGAGTAAGCA 372–492 0.983 69.2
psbK-psbI_p5 psbK-psbI TACCCGAGGCCTACTCTTTT ACGAAGAGTTTGAGAGTAAGCA 416–536 0.974 68.3
trnS-GCU-trnG-GCC_p1 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA ACGAATCACACTTTTACCACT 491–932 1.000 63.7
trnS-GCU-trnG-GCC_p2 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC ACGAATCACACTTTTACCACT 490–931 1.000 63.7
trnS-GCU-trnG-GCC_p3 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA AGAACGAATCACACTTTTACCAC 494–935 1.000 62.6
trnS-GCU-trnG-GCC_p4 trnS-GCU-trnG-GCC CAATCCGACGCTTTAGTCCA GAACGAATCACACTTTTACCACT 493–934 1.000 62.6
trnS-GCU-trnG-GCC_p5 trnS-GCU-trnG-GCC AATCCGACGCTTTAGTCCAC GAACGAATCACACTTTTACCACT 492–933 1.000 62.6
atpH-atpI_p1 atpH-atpI ATAACGGAAGCGGCAGAAAT TTTTGCAACTTTAGCTGCGG 598–1028 0.940 88.2
atpH-atpI_p2 atpH-atpI AGCGGCAGAAATCAATGGAT TTTTGCAACTTTAGCTGCGG 590–1020 0.940 88.0
atpH-atpI_p3 atpH-atpI TACCTTGACCAACTCCAGGT TTTTGCAACTTTAGCTGCGG 654–1084 0.940 87.6
atpH-atpI_p4 atpH-atpI AAGCGGCAGAAATCAATGGA TTTTGCAACTTTAGCTGCGG 591–1021 0.940 87.2
atpH-atpI_p5 atpH-atpI AATAACGGAAGCGGCAGAAA TTTTGCAACTTTAGCTGCGG 599–1029 0.940 87.1
rpoB-trnC-GCA_p1 rpoB-trnC-GCA ATTTCCCCATTTCCATCCCG CCGGATTTGAACTGGGGAAA 780–1190 0.905 86.9
rpoB-trnC-GCA_p2 rpoB-trnC-GCA ATTTCCCCATTTCCATCCCG AAAAGGATTTGCAGTCCCCC 762–1172 0.905 84.7
rpoB-trnC-GCA_p3 rpoB-trnC-GCA ATTTCCCCATTTCCATCCCG GACACCCGGATTTGAACTGG 785–1195 0.905 80.8
rpoB-trnC-GCA_p4 rpoB-trnC-GCA ATTTCCCCATTTCCATCCCG CGACACCCGGATTTGAACTG 786–1196 0.905 77.9
rpoB-trnC-GCA_p5 rpoB-trnC-GCA ATTTCCCCATTTCCATCCCG CGACACCCGGATTTGAACT 786–1196 0.905 77.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (116)

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

Species Accession Length (bp) Link
Saxifraga aizoides PV423509.1 151971 View on NCBI ↗
Saxifraga androsacea PV426729.1 149600 View on NCBI ↗
Saxifraga angustata NC_070439.1 147942 View on NCBI ↗
Saxifraga aphylla PV426730.1 149217 View on NCBI ↗
Saxifraga aristulata NC_070440.1 156390 View on NCBI ↗
Saxifraga aristulata var. longipila ON720852.1 147677 View on NCBI ↗
Saxifraga atuntsiensis NC_070441.1 147441 View on NCBI ↗
Saxifraga aurantiaca NC_070442.1 147339 View on NCBI ↗
Saxifraga auriculata NC_070443.1 147560 View on NCBI ↗
Saxifraga auriculata var. conaensis ON720856.1 147958 View on NCBI ↗
Saxifraga balfourii NC_070444.1 148977 View on NCBI ↗
Saxifraga bergenioides NC_070445.1 148082 View on NCBI ↗
Saxifraga biflora PV426731.1 151552 View on NCBI ↗
Saxifraga brachypoda NC_070446.1 149036 View on NCBI ↗
Saxifraga brevicaulis NC_070447.1 149448 View on NCBI ↗
Saxifraga brunonis NC_070449.1 149805 View on NCBI ↗
Saxifraga bryoides PV426732.1 152082 View on NCBI ↗
Saxifraga caesia PV426733.1 151360 View on NCBI ↗
Saxifraga cernua NC_070450.1 151359 View on NCBI ↗
Saxifraga chumbiensis NC_070451.1 147841 View on NCBI ↗
Saxifraga cinerascens NC_070452.1 149745 View on NCBI ↗
Saxifraga congestiflora NC_070453.1 147569 View on NCBI ↗
Saxifraga consanguinea NC_070454.1 149963 View on NCBI ↗
Saxifraga depressa PV426735.1 149685 View on NCBI ↗
Saxifraga diversifolia var. angustibracteata NC_070456.1 147352 View on NCBI ↗
Saxifraga drabiformis NC_070457.1 147316 View on NCBI ↗
Saxifraga egregia NC_070459.1 147385 View on NCBI ↗
Saxifraga egregia var. eciliata ON720873.1 147553 View on NCBI ↗
Saxifraga erectisepala NC_070460.1 147356 View on NCBI ↗
Saxifraga exarata PV426736.1 150001 View on NCBI ↗
Saxifraga filicaulis NC_070461.1 149036 View on NCBI ↗
Saxifraga flaccida NC_070462.1 148718 View on NCBI ↗
Saxifraga fortunei NC_070463.1 151393 View on NCBI ↗
Saxifraga fortunei var. pilosissima ON920922.1 151186 View on NCBI ↗
Saxifraga gemmigera NC_070464.1 147143 View on NCBI ↗
Saxifraga gemmigera var. gemmuligera ON720879.1 147144 View on NCBI ↗
Saxifraga gemmipara NC_070465.1 149580 View on NCBI ↗
Saxifraga giraldiana NC_085615.1 147267 View on NCBI ↗
Saxifraga glabricaulis NC_070495.1 147371 View on NCBI ↗
Saxifraga glacialis NC_070466.1 147051 View on NCBI ↗
Saxifraga gouldii NC_070467.1 149394 View on NCBI ↗
Saxifraga gouldii var. eglandulosa ON720883.1 149300 View on NCBI ↗
Saxifraga granulifera NC_070468.1 151323 View on NCBI ↗
Saxifraga gyalana NC_070469.1 147165 View on NCBI ↗
Saxifraga heleonastes NC_070470.1 147564 View on NCBI ↗
Saxifraga hemisphaerica NC_070471.1 149210 View on NCBI ↗
Saxifraga hirculoides NC_070472.1 147625 View on NCBI ↗
Saxifraga hispidula NC_070473.1 148550 View on NCBI ↗
Saxifraga hookeri NC_070474.1 147286 View on NCBI ↗
Saxifraga hostii PV426737.1 151913 View on NCBI ↗
Saxifraga hypericoides NC_070475.1 147720 View on NCBI ↗
Saxifraga isophylla NC_070478.1 147658 View on NCBI ↗
Saxifraga josephii PP849681.1 150489 View on NCBI ↗
Saxifraga kingdonii NC_070479.1 147570 View on NCBI ↗
Saxifraga limprichtii ON720942.1 147178 View on NCBI ↗
Saxifraga litangensis NC_070481.1 147653 View on NCBI ↗
Saxifraga lychnitis NC_070482.1 147358 View on NCBI ↗
Saxifraga mengtzeana NC_073564.1 150670 View on NCBI ↗
Saxifraga montana NC_061958.1 147646 View on NCBI ↗
Saxifraga moschata PP622684.1 149922 View on NCBI ↗
Saxifraga mutata PV426739.1 152017 View on NCBI ↗
Saxifraga nanella NC_070490.1 147426 View on NCBI ↗
Saxifraga nangqenica NC_070491.1 147759 View on NCBI ↗
Saxifraga nangxianensis NC_070492.1 147675 View on NCBI ↗
Saxifraga nigroglandulifera NC_070493.1 148055 View on NCBI ↗
Saxifraga oresbia NC_070494.1 147313 View on NCBI ↗
Saxifraga paniculata PP622685.1 152089 View on NCBI ↗
Saxifraga pardanthina NC_070496.1 147310 View on NCBI ↗
Saxifraga parnassifolia NC_070497.1 147997 View on NCBI ↗
Saxifraga parva NC_070498.1 147586 View on NCBI ↗
Saxifraga perpusilla NC_070499.1 147423 View on NCBI ↗
Saxifraga pratensis NC_070500.1 147355 View on NCBI ↗
Saxifraga przewalskii NC_070501.1 147623 View on NCBI ↗
Saxifraga pseudohirculus NC_070502.1 147522 View on NCBI ↗
Saxifraga punctulata NC_070503.1 147071 View on NCBI ↗
Saxifraga rotundifolia PV426742.1 152282 View on NCBI ↗
Saxifraga rotundifolia subsp. rotundifolia PP622686.1 152322 View on NCBI ↗
Saxifraga rudolphiana PV426740.1 151875 View on NCBI ↗
Saxifraga rufescens NC_070504.1 151394 View on NCBI ↗
Saxifraga saginoides NC_066000.1 147716 View on NCBI ↗
Saxifraga sanguinea NC_070505.1 146800 View on NCBI ↗
Saxifraga saxicola PQ932579.1 151565 View on NCBI ↗
Saxifraga sediformis NC_070506.1 147126 View on NCBI ↗
Saxifraga sedoides PV426743.1 149363 View on NCBI ↗
Saxifraga sessiliflora NC_065999.1 149569 View on NCBI ↗
Saxifraga sibirica PV426744.1 151420 View on NCBI ↗
Saxifraga signata NC_070507.1 147072 View on NCBI ↗
Saxifraga signatella NC_070508.1 146562 View on NCBI ↗
Saxifraga sinomontana MN104589.1 147240 View on NCBI ↗
Saxifraga sinomontana var. amabilis ON720929.1 147682 View on NCBI ↗
Saxifraga stella-aurea NC_070510.1 147403 View on NCBI ↗
Saxifraga stellariifolia NC_070511.1 147620 View on NCBI ↗
Saxifraga stolonifera NC_037882.1 151066 View on NCBI ↗
Saxifraga subaequifoliata NC_070512.1 147396 View on NCBI ↗
Saxifraga substrigosa NC_070513.1 148747 View on NCBI ↗
Saxifraga sunhangiana PP796439.1 151501 View on NCBI ↗
Saxifraga tangutica NC_070514.1 147696 View on NCBI ↗
Saxifraga tangutica var. platyphylla ON720935.1 147564 View on NCBI ↗
Saxifraga taraktophylla NC_070515.1 147247 View on NCBI ↗
Saxifraga tibetica NC_070516.1 147905 View on NCBI ↗
Saxifraga tombeanensis PV426745.1 152092 View on NCBI ↗
Saxifraga tridactylites PP622688.1 150025 View on NCBI ↗
Saxifraga tsangchanensis NC_070517.1 148264 View on NCBI ↗
Saxifraga umbellulata NC_070518.1 146377 View on NCBI ↗
Saxifraga unguiculata NC_070519.1 147451 View on NCBI ↗
Saxifraga unguiculata var. subglabra ON720943.1 147356 View on NCBI ↗
Saxifraga uninervia NC_070520.1 147183 View on NCBI ↗
Saxifraga vandellii PV426746.1 151925 View on NCBI ↗
Saxifraga vilmoriniana NC_070521.1 146830 View on NCBI ↗
Saxifraga viridipetala NC_070522.1 149600 View on NCBI ↗
Saxifraga viscidula NC_070523.1 147595 View on NCBI ↗
Saxifraga wallichiana NC_070524.1 149418 View on NCBI ↗
Saxifraga wardii NC_070525.1 149264 View on NCBI ↗
Saxifraga xiaozhongdianensis NC_070526.1 147662 View on NCBI ↗
Saxifraga yarlungzangboensis NC_070527.1 147373 View on NCBI ↗
Saxifraga yushuensis NC_070528.1 146923 View on NCBI ↗