Markers + reference

Tillandsia

168 species · Bromeliaceae · Poales

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Species 168
Genome length 155–167 kb
Candidate markers 280
Primer pairs 105

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 280 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
rpl32-trnL-UAG SSC 754 0.0186 1.00 74.0 yes View details
ccsA SSC 954 0.0056 1.00 51.8 yes View details
ccsA-ndhD SSC 265 0.0386 1.00 63.6 yes View details
ycf1 SSC 5526 0.0075 1.00 62.7 yes View details
trnS-GCU-trnG-UCC LSC 1195 0.0154 0.98 65.0 yes View details
trnC-GCA-petN LSC 1028 0.0175 1.00 68.5 yes View details
trnT-GGU-psbD LSC 1042 0.0092 1.00 58.5 yes View details
trnT-UGU-trnL-UAA LSC 785 0.0129 1.00 71.8 yes View details
accD-psaI LSC 885 0.0133 0.99 67.2 yes View details
petA-psbJ LSC 1134 0.0122 1.00 74.4 yes View details
ycf1 IRa 2306 0.0031 0.46 32.1 no View details
ndhF-rpl32 SSC 797 0.0220 0.00 52.6 no View details
ndhC-trnV-UAC LSC 1041 0.0094 1.00 70.9 yes View details
atpB-rbcL LSC 780 0.0085 0.99 68.3 yes View details
psaJ-rpl33 LSC 524 0.0109 1.00 68.0 yes View details
psaA-ycf3 LSC 647 0.0122 1.00 67.7 yes View details
petN-psbM LSC 1237 0.0086 1.00 67.0 yes View details
trnF-GAA-ndhJ LSC 767 0.0072 1.00 66.1 yes View details
rps8-rpl14 LSC 172 0.0270 0.99 65.9 yes View details
psbE-petL LSC 1524 0.0096 1.00 64.0 yes View details
trnK-UUU-rps16 LSC 693 0.0121 1.00 63.5 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
rpl32-trnL-UAG_p1 rpl32-trnL-UAG CACCGGGCATTCAAAAAGTT AGCGTGTCTACCGATTTCAC 778–904 1.000 87.7
rpl32-trnL-UAG_p2 rpl32-trnL-UAG CACCGGGCATTCAAAAAGTT CAGCGTGTCTACCGATTTCA 779–905 1.000 87.7
rpl32-trnL-UAG_p3 rpl32-trnL-UAG CACCGGGCATTCAAAAAGTT TTTAGAAGATGCCGCCACTC 838–964 0.994 87.4
rpl32-trnL-UAG_p4 rpl32-trnL-UAG TTCCACCGGGCATTCAAAAA AGCGTGTCTACCGATTTCAC 781–876 0.982 86.5
rpl32-trnL-UAG_p5 rpl32-trnL-UAG TTTCCACCGGGCATTCAAAA AGCGTGTCTACCGATTTCAC 782–877 0.982 86.5
ccsA_p1 ccsA GCTAAAGCATCTCGGTTCGA CTTCATGTAGTTTATTCAATTAGATGT 1081–1096 0.964 48.0
ccsA_p2 ccsA AGTGGCGGCATCTTCTAAAA CTTCATGTAGTTTATTCAATTAGATGT 1056–1066 0.958 47.9
ccsA_p3 ccsA GCTAAAGCATCTCGGTTCGA TCTTCATGTAGTTTATTCAATTAGATG 1082–1097 0.958 47.8
ccsA_p4 ccsA GAGTGGCGGCATCTTCTAAA CTTCATGTAGTTTATTCAATTAGATGT 1057–1067 0.952 47.6
ccsA_p5 ccsA GAGTGGCGGCATCTTCTAAA TCTTCATGTAGTTTATTCAATTAGATG 1058–1068 0.946 47.4
ccsA-ndhD_p1 ccsA-ndhD AGGTCTACATAGTTATGGTTCA CAGTTGACAAGGTACACGCT 337–365 0.994 51.8
ccsA-ndhD_p2 ccsA-ndhD AGGTCTACATAGTTATGGTTCA TCAGTTGACAAGGTACACGC 338–366 0.994 51.8
ccsA-ndhD_p3 ccsA-ndhD AGGTCTACATAGTTATGGTTCATTCA CAGTTGACAAGGTACACGCT 337–365 0.976 51.0
ccsA-ndhD_p4 ccsA-ndhD AGGTCTACATAGTTATGGTTCATTCA TCAGTTGACAAGGTACACGC 338–366 0.976 51.0
ccsA-ndhD_p5 ccsA-ndhD GGTCTACATAGTTATGGTTCATTCAC CAGTTGACAAGGTACACGCT 336–364 0.976 51.0
ycf1_p1 ycf1 CCCTTGTCTCTTCCTCCTCA ATCCGCCTGATAGGGAATCA 678–792 0.964 89.9
ycf1_p2 ycf1 CCCTTGTCTCTTCCTCCTCA TCCGCCTGATAGGGAATCAT 677–791 0.964 89.9
ycf1_p3 ycf1 CCCTTGTCTCTTCCTCCTCA AGAATCCGCCTGATAGGGAA 681–795 0.887 86.2
ycf1_p4 ycf1 TCTCTCCCCACCAAATTCCT ATCCGCCTGATAGGGAATCA 658–667 0.762 81.1
ycf1_p5 ycf1 TCTCTCCCCACCAAATTCCT TCCGCCTGATAGGGAATCAT 657–666 0.762 81.1
trnK-UUU_p1 trnK-UUU GACTCCCAAGCACACGTATT TTTGATAGGGTCGTGCAGTG 2863–2992 0.988 90.0
trnK-UUU_p2 trnK-UUU TTTCAAGGACTCCCAAGCAC TTTGATAGGGTCGTGCAGTG 2870–2999 0.970 89.9
trnK-UUU_p3 trnK-UUU GACTCCCAAGCACACGTATT GTCGTGCAGTGCAATTCAAT 2854–2983 0.976 87.6
trnK-UUU_p4 trnK-UUU TTTCAAGGACTCCCAAGCAC GTCGTGCAGTGCAATTCAAT 2861–2990 0.958 87.5
trnK-UUU_p5 trnK-UUU TTTCAAGGACTCCCAAGCAC TGTTTTGATAGGGTCGTGCA 2873–3000 0.911 83.9
trnK-UUU-rps16_p1 trnK-UUU-rps16 AAAGCCGAGTACTCTACCGT GGTGCTCAACCTACAGGAAC 641–840 1.000 89.1
trnK-UUU-rps16_p2 trnK-UUU-rps16 AAGCCGAGTACTCTACCGTT GGTGCTCAACCTACAGGAAC 640–839 1.000 89.1
trnK-UUU-rps16_p3 trnK-UUU-rps16 TACCGTTGAGTTAGCAACCC GGTGCTCAACCTACAGGAAC 627–826 1.000 86.8
trnK-UUU-rps16_p4 trnK-UUU-rps16 AGTCGCACTTAAAAGCCGAG GGTGCTCAACCTACAGGAAC 652–851 0.994 85.7
trnK-UUU-rps16_p5 trnK-UUU-rps16 TCGCACTTAAAAGCCGAGTA GGTGCTCAACCTACAGGAAC 650–849 0.994 84.4

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (168)

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

Species Accession Length (bp) Link
Tillandsia achyrostachys NC_065171.1 159171 View on NCBI ↗
Tillandsia aeranthos NC_081610.1 156895 View on NCBI ↗
Tillandsia albertiana NC_081611.1 156188 View on NCBI ↗
Tillandsia albida NC_081612.1 157378 View on NCBI ↗
Tillandsia alfredo-lauii NC_081613.1 158883 View on NCBI ↗
Tillandsia alvareziae NC_081614.1 157680 View on NCBI ↗
Tillandsia andicola PZ270549.1 156304 View on NCBI ↗
Tillandsia andrieuxii NC_081615.1 158966 View on NCBI ↗
Tillandsia arequitae NC_081616.1 155795 View on NCBI ↗
Tillandsia arroyoensis NC_081617.1 159375 View on NCBI ↗
Tillandsia australis NC_065172.1 157679 View on NCBI ↗
Tillandsia balbisiana NC_081618.1 157554 View on NCBI ↗
Tillandsia bartramii NC_081619.1 157665 View on NCBI ↗
Tillandsia bermejoensis NC_065173.1 155985 View on NCBI ↗
Tillandsia bochilensis NC_081620.1 157872 View on NCBI ↗
Tillandsia botterii NC_081621.1 157744 View on NCBI ↗
Tillandsia bourgaei NC_081622.1 158591 View on NCBI ↗
Tillandsia brachycaulos NC_065174.1 157145 View on NCBI ↗
Tillandsia cacticola NC_065175.1 157057 View on NCBI ↗
Tillandsia caliginosa NC_081623.1 156507 View on NCBI ↗
Tillandsia calothyrsus NC_081624.1 159293 View on NCBI ↗
Tillandsia capitata NC_081625.1 157699 View on NCBI ↗
Tillandsia caput-medusae NC_081626.1 157147 View on NCBI ↗
Tillandsia cardenasii NC_081627.1 156248 View on NCBI ↗
Tillandsia carlos-hankii NC_081628.1 158700 View on NCBI ↗
Tillandsia castellanii PZ270550.1 156784 View on NCBI ↗
Tillandsia caulescens NC_081629.1 156493 View on NCBI ↗
Tillandsia cauligera NC_081630.1 156698 View on NCBI ↗
Tillandsia cees-goudae NC_081631.1 157383 View on NCBI ↗
Tillandsia cereicola NC_065176.1 157533 View on NCBI ↗
Tillandsia chaetophylla NC_081632.1 157668 View on NCBI ↗
Tillandsia chapalillaensis NC_081633.1 157699 View on NCBI ↗
Tillandsia circinnatioides NC_081634.1 157290 View on NCBI ↗
Tillandsia complanata NC_081635.1 157480 View on NCBI ↗
Tillandsia concolor NC_081636.1 157175 View on NCBI ↗
Tillandsia copalaensis NC_081637.1 157404 View on NCBI ↗
Tillandsia copanensis NC_081638.1 157447 View on NCBI ↗
Tillandsia cossoni NC_081639.1 158729 View on NCBI ↗
Tillandsia cotagaitensis PZ270554.1 156575 View on NCBI ↗
Tillandsia crocata PZ270555.1 156285 View on NCBI ↗
Tillandsia cyanea NC_064985.1 157602 View on NCBI ↗
Tillandsia dasyliriifolia NC_081640.1 157347 View on NCBI ↗
Tillandsia denudata NC_081641.1 157011 View on NCBI ↗
Tillandsia disticha NC_065178.1 156538 View on NCBI ↗
Tillandsia divaricata NC_081679.1 156809 View on NCBI ↗
Tillandsia dugesii NC_081642.1 158821 View on NCBI ↗
Tillandsia duratii NC_065179.1 155373 View on NCBI ↗
Tillandsia edithae NC_065180.1 156777 View on NCBI ↗
Tillandsia ehlersiana NC_081643.1 157626 View on NCBI ↗
Tillandsia eistetteri NC_081644.1 157197 View on NCBI ↗
Tillandsia elongata var. subimbricata OQ935633.1 158086 View on NCBI ↗
Tillandsia erubescens NC_081645.1 159328 View on NCBI ↗
Tillandsia espinosae NC_065181.1 158115 View on NCBI ↗
Tillandsia esseriana NC_081646.1 156839 View on NCBI ↗
Tillandsia extensa NC_081647.1 156838 View on NCBI ↗
Tillandsia fasciculata NC_081648.1 157726 View on NCBI ↗
Tillandsia filifolia NC_081649.1 156843 View on NCBI ↗
Tillandsia flexuosa var. vivipara OQ935639.1 157944 View on NCBI ↗
Tillandsia floribunda NC_081650.1 157139 View on NCBI ↗
Tillandsia fuchsii NC_081651.1 157372 View on NCBI ↗
Tillandsia funckiana NC_081652.1 157981 View on NCBI ↗
Tillandsia gilliesii PZ270556.1 156817 View on NCBI ↗
Tillandsia grossispicata NC_081655.1 157729 View on NCBI ↗
Tillandsia gymnobotrya NC_065182.1 159182 View on NCBI ↗
Tillandsia hammeri NC_081656.1 157647 View on NCBI ↗
Tillandsia harrisii NC_081657.1 157692 View on NCBI ↗
Tillandsia hildae NC_081660.1 158017 View on NCBI ↗
Tillandsia hintoniana NC_081661.1 158732 View on NCBI ↗
Tillandsia hirta PZ270557.1 156737 View on NCBI ↗
Tillandsia hondurensis NC_081662.1 157649 View on NCBI ↗
Tillandsia huarazensis NC_081663.1 157147 View on NCBI ↗
Tillandsia hubertiana NC_081664.1 157732 View on NCBI ↗
Tillandsia incarnata NC_081665.1 156764 View on NCBI ↗
Tillandsia inopinata NC_081666.1 157728 View on NCBI ↗
Tillandsia intermedia NC_081667.1 157403 View on NCBI ↗
Tillandsia ionantha NC_081668.1 157373 View on NCBI ↗
Tillandsia ixioides NC_065185.1 156950 View on NCBI ↗
Tillandsia jaguactalensis NC_081669.1 157172 View on NCBI ↗
Tillandsia jaliscomonticola NC_081670.1 157717 View on NCBI ↗
Tillandsia joel-mandimboensis NC_081671.1 159237 View on NCBI ↗
Tillandsia juncea NC_081672.1 157673 View on NCBI ↗
Tillandsia kirchhoffiana NC_081673.1 158630 View on NCBI ↗
Tillandsia klausii NC_081674.1 157420 View on NCBI ↗
Tillandsia krahnii NC_081675.1 156729 View on NCBI ↗
Tillandsia lajensis NC_081676.1 157529 View on NCBI ↗
Tillandsia landbeckii NC_081677.1 156082 View on NCBI ↗
Tillandsia langlasseana NC_081678.1 158767 View on NCBI ↗
Tillandsia lautneri NC_081680.1 157955 View on NCBI ↗
Tillandsia leiboldiana NC_081681.1 157275 View on NCBI ↗
Tillandsia limbata NC_081682.1 157324 View on NCBI ↗
Tillandsia lotteae NC_081683.1 155914 View on NCBI ↗
Tillandsia lucida NC_081684.1 157333 View on NCBI ↗
Tillandsia lymanii NC_081685.1 157689 View on NCBI ↗
Tillandsia macdougallii NC_081686.1 159235 View on NCBI ↗
Tillandsia machupicchuensis NC_081687.1 156906 View on NCBI ↗
Tillandsia macrochlamys NC_081688.1 158883 View on NCBI ↗
Tillandsia magnusiana NC_081689.1 157725 View on NCBI ↗
Tillandsia makoyana NC_081690.1 157733 View on NCBI ↗
Tillandsia malzinei NC_065186.1 157759 View on NCBI ↗
Tillandsia mandonii PZ270558.1 156271 View on NCBI ↗
Tillandsia marnieri-lapostollei NC_081691.1 157826 View on NCBI ↗
Tillandsia may-patii NC_081693.1 157328 View on NCBI ↗
Tillandsia maya NC_081692.1 157200 View on NCBI ↗
Tillandsia micans NC_081694.1 157491 View on NCBI ↗
Tillandsia multicaulis NC_081695.1 156888 View on NCBI ↗
Tillandsia myosura PZ270559.1 156275 View on NCBI ↗
Tillandsia neglecta NC_081696.1 156459 View on NCBI ↗
Tillandsia nicolasensis NC_081697.1 156825 View on NCBI ↗
Tillandsia nidus NC_081698.1 157373 View on NCBI ↗
Tillandsia oaxacana NC_081699.1 159185 View on NCBI ↗
Tillandsia ovatispicata NC_081700.1 157049 View on NCBI ↗
Tillandsia paleacea NC_081701.1 155830 View on NCBI ↗
Tillandsia parryi NC_081702.1 158686 View on NCBI ↗
Tillandsia paucifolia NC_081703.1 157160 View on NCBI ↗
Tillandsia polystachia NC_081705.1 157644 View on NCBI ↗
Tillandsia prodigiosa NC_081706.1 159113 View on NCBI ↗
Tillandsia propagulifera NC_081707.1 157119 View on NCBI ↗
Tillandsia pruinosa NC_081708.1 157196 View on NCBI ↗
Tillandsia pseudo-floribunda NC_081710.1 157168 View on NCBI ↗
Tillandsia pseudobaileyi NC_081709.1 157301 View on NCBI ↗
Tillandsia pseudomicans NC_081711.1 157388 View on NCBI ↗
Tillandsia pseudooaxacana NC_081712.1 159183 View on NCBI ↗
Tillandsia punctulata NC_065187.1 159113 View on NCBI ↗
Tillandsia purpurea NC_084189.1 167164 View on NCBI ↗
Tillandsia quaquaflorifera NC_081713.1 159219 View on NCBI ↗
Tillandsia rauhii NC_081714.1 157788 View on NCBI ↗
Tillandsia recurvata NC_081716.1 156652 View on NCBI ↗
Tillandsia recurvifolia NC_081717.1 156376 View on NCBI ↗
Tillandsia remota NC_081718.1 157756 View on NCBI ↗
Tillandsia retorta PZ270567.1 156322 View on NCBI ↗
Tillandsia reversa NC_081719.1 157129 View on NCBI ↗
Tillandsia riohondoensis NC_081720.1 157728 View on NCBI ↗
Tillandsia roezlii NC_081721.1 157116 View on NCBI ↗
Tillandsia roland-gosselinii NC_081722.1 157392 View on NCBI ↗
Tillandsia roseospicata NC_081723.1 158547 View on NCBI ↗
Tillandsia rothii NC_081724.1 157377 View on NCBI ↗
Tillandsia rubella NC_081725.1 157597 View on NCBI ↗
Tillandsia rubroviolacea NC_081726.1 156852 View on NCBI ↗
Tillandsia schiedeana NC_065188.1 157155 View on NCBI ↗
Tillandsia seleriana NC_081727.1 157106 View on NCBI ↗
Tillandsia setacea NC_081728.1 157670 View on NCBI ↗
Tillandsia sierrajuarezensis NC_081729.1 158892 View on NCBI ↗
Tillandsia somnians NC_081730.1 157000 View on NCBI ↗
Tillandsia sphaerocephala NC_065189.1 157384 View on NCBI ↗
Tillandsia spiraliflora NC_081731.1 157449 View on NCBI ↗
Tillandsia stoltenii NC_081732.1 157229 View on NCBI ↗
Tillandsia streptocarpa NC_081733.1 155781 View on NCBI ↗
Tillandsia streptophylla NC_081734.1 157207 View on NCBI ↗
Tillandsia stricta NC_081735.1 156615 View on NCBI ↗
Tillandsia subteres NC_081736.1 157683 View on NCBI ↗
Tillandsia suesilliae NC_081737.1 158676 View on NCBI ↗
Tillandsia supermexicana NC_081738.1 158683 View on NCBI ↗
Tillandsia tecolometl NC_081739.1 159217 View on NCBI ↗
Tillandsia tectorum NC_081740.1 156980 View on NCBI ↗
Tillandsia tehuacana NC_081741.1 157810 View on NCBI ↗
Tillandsia tenebra PZ270568.1 156214 View on NCBI ↗
Tillandsia tricolor NC_081743.1 157747 View on NCBI ↗
Tillandsia ulrici NC_081744.1 159182 View on NCBI ↗
Tillandsia usneoides NC_065190.1 155929 View on NCBI ↗
Tillandsia utriculata NC_065191.1 157294 View on NCBI ↗
Tillandsia utriculata subsp. pringlei OQ935696.1 157681 View on NCBI ↗
Tillandsia variabilis NC_081745.1 157655 View on NCBI ↗
Tillandsia violacea NC_081746.1 159155 View on NCBI ↗
Tillandsia welzii NC_081747.1 157334 View on NCBI ↗
Tillandsia werdermannii NC_081748.1 156306 View on NCBI ↗
Tillandsia wuelfinghoffii NC_081749.1 158902 View on NCBI ↗
Tillandsia xiphioides NC_081750.1 156261 View on NCBI ↗
Tillandsia zecheri NC_081751.1 156123 View on NCBI ↗