RSAT - matrix-scan

Scan DNA sequences with position-specific scoring matrices (PSSM)

Citation: Jean Valéry Turatsinze, Morgane Thomas-Chollier, Matthieu Defrance and Jacques van Helden (2008). Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat Protoc, 3, 1578-1588. Pubmed 18802439
Sequence       Format Paste your sequence in the box below

Or select a file to upload (.gz compressed files supported)


Mask 
Matrix (or matrices)        Format 

Or select a file to upload


Or Dynamic selection of motifs from the available collections
(select the collection and a dropdown menu will appear to select motifs)

Input1 - Select a database in list:
2 - Select a collection in list:
3 - Select one or more matrix identifiers:

View matrix descriptions & download full collections

Fungi

Yeastract s_cerevisiae - [732 motifs] (20130918) - [local copy]
cisBP s_cerevisiae - [776 motifs] (2015-06_v1.02) - [local copy]
cisBP Saccharomyces_cerevisiae - [1288 motifs] (2019-06_v2.00) - [local copy]
JASPAR core redundant fungi - [184 motifs] (2020) - [local copy]
JASPAR core nonredundant fungi - [183 motifs] (2020) - [local copy]

Multi-organisms

footprintDB all - [11491 motifs] (2020-01) - [local copy]
RSAT non-redundant insects+plants+vertebrates - [2889 motifs] (2017) - [local copy]
JASPAR core nonredundant all - [1646 motifs] (2020) - [local copy]
JASPAR core redundant all - [1964 motifs] (2020) - [local copy]
JASPAR unvalidated - [337 motifs] (2020) - [local copy]

Non-vertebrate Metazoa

DrosophilaTFs - [61 motifs] (2015-11) - [local copy]
Aniseed (Ciona robusta motifs detected by SELEX) - [275 motifs] (2020-08) - [local copy]
cisBP Octopus_bimaculoides - [3795 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_yakuba - [4326 motifs] (2019-06_v2.00) - [local copy]
cisBP Melitaea_cinxia - [3363 motifs] (2019-06_v2.00) - [local copy]
cisBP Tribolium_castaneum - [4101 motifs] (2019-06_v2.00) - [local copy]
cisBP Rhodnius_prolixus - [3380 motifs] (2019-06_v2.00) - [local copy]
cisBP Nasonia_vitripennis - [4064 motifs] (2019-06_v2.00) - [local copy]
cisBP Caenorhabditis_remanei - [3289 motifs] (2019-06_v2.00) - [local copy]
cisBP Daphnia_pulex - [678 motifs] (2019-06_v2.00) - [local copy]
cisBP Megaselia_scalaris - [2683 motifs] (2019-06_v2.00) - [local copy]
cisBP Pristionchus_pacificus - [2683 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_virilis - [4276 motifs] (2019-06_v2.00) - [local copy]
cisBP Dendroctonus_ponderosae - [3846 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_mojavensis - [4293 motifs] (2019-06_v2.00) - [local copy]
cisBP Culex_quinquefasciatus - [3982 motifs] (2019-06_v2.00) - [local copy]
cisBP Zootermopsis_nevadensis - [3945 motifs] (2019-06_v2.00) - [local copy]
cisBP Schistosoma_mansoni - [3181 motifs] (2019-06_v2.00) - [local copy]
cisBP Helobdella_robusta - [3660 motifs] (2019-06_v2.00) - [local copy]
cisBP Aedes_aegypti - [3985 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_sechellia - [4352 motifs] (2019-06_v2.00) - [local copy]
cisBP Atta_cephalotes - [3404 motifs] (2019-06_v2.00) - [local copy]
cisBP Ixodes_scapularis - [3701 motifs] (2019-06_v2.00) - [local copy]
cisBP Caenorhabditis_elegans - [3438 motifs] (2019-06_v2.00) - [local copy]
cisBP Solenopsis_invicta - [3658 motifs] (2019-06_v2.00) - [local copy]
cisBP Caenorhabditis_brenneri - [3169 motifs] (2019-06_v2.00) - [local copy]
cisBP Strigamia_maritima - [3791 motifs] (2019-06_v2.00) - [local copy]
cisBP Bombyx_mori - [3662 motifs] (2019-06_v2.00) - [local copy]
cisBP Trichoplax_adhaerens - [2901 motifs] (2019-06_v2.00) - [local copy]
cisBP Heliconius_melpomene - [3647 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_persimilis - [4161 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_melanogaster - [4514 motifs] (2019-06_v2.00) - [local copy]
cisBP drosophila - [1427 motifs] (2014-10_v0.9) - [local copy]
cisBP Loa_loa - [3085 motifs] (2019-06_v2.00) - [local copy]
cisBP Strongylocentrotus_purpuratus - [3989 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_erecta - [4347 motifs] (2019-06_v2.00) - [local copy]
cisBP Pediculus_humanus - [4057 motifs] (2019-06_v2.00) - [local copy]
cisBP Caenorhabditis_japonica - [3107 motifs] (2019-06_v2.00) - [local copy]
cisBP Amphimedon_queenslandica - [2325 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_simulans - [4023 motifs] (2019-06_v2.00) - [local copy]
cisBP Lottia_gigantea - [3989 motifs] (2019-06_v2.00) - [local copy]
cisBP Anopheles_darlingi - [3542 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_ananassae - [4154 motifs] (2019-06_v2.00) - [local copy]
cisBP Onchocerca_volvulus - [2988 motifs] (2019-06_v2.00) - [local copy]
cisBP Nematostella_vectensis - [3571 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_grimshawi - [4226 motifs] (2019-06_v2.00) - [local copy]
cisBP c_elegans - [1499 motifs] (2015-05_v1.02) - [local copy]
cisBP Brugia_malayi - [3105 motifs] (2019-06_v2.00) - [local copy]
cisBP Acyrthosiphon_pisum - [4022 motifs] (2019-06_v2.00) - [local copy]
cisBP Trichinella_spiralis - [3131 motifs] (2019-06_v2.00) - [local copy]
cisBP Tetranychus_urticae - [3909 motifs] (2019-06_v2.00) - [local copy]
cisBP Apis_mellifera - [4133 motifs] (2019-06_v2.00) - [local copy]
cisBP Caenorhabditis_briggsae - [3261 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_willistoni - [4319 motifs] (2019-06_v2.00) - [local copy]
cisBP Anopheles_gambiae - [4089 motifs] (2019-06_v2.00) - [local copy]
cisBP Danaus_plexippus - [3886 motifs] (2019-06_v2.00) - [local copy]
cisBP Drosophila_pseudoobscura - [4286 motifs] (2019-06_v2.00) - [local copy]
cisBP Ciona_intestinalis - [3788 motifs] (2019-06_v2.00) - [local copy]
cisBP Lucilia_cuprina - [3942 motifs] (2019-06_v2.00) - [local copy]
cisBP Crassostrea_gigas - [4030 motifs] (2019-06_v2.00) - [local copy]
footprintDB-metazoa [only metazoa DNA motifs] - [7763 motifs] (2020-01) - [local copy]
RSAT non-redundant insects - [350 motifs] (2017) - [local copy]
Drosophila DMMPMM - [41 motifs] (2010_11) - [local copy]
Drosophila IDMMPMM - [39 motifs] (2010_11) - [local copy]
Database of Drosophila DNA-binding specificities (FlyFactorSurvey) - [652 motifs] (2016_06) - [local copy]
JASPAR core nonredundant nematodes - [43 motifs] (2020) - [local copy]
JASPAR core redundant nematodes - [43 motifs] (2020) - [local copy]
JASPAR core nonredundant urochordates - [1 motifs] (2020) - [local copy]
JASPAR core nonredundant insects - [143 motifs] (2020) - [local copy]
JASPAR core redundant insects - [153 motifs] (2020) - [local copy]
JASPAR core redundant urochordates - [1 motifs] (2020) - [local copy]

Plants

Cistrome (A thaliana motifs detected by DAP-seq) - [862 motifs] (2016-06) - [local copy]
Athamap (A thaliana) - [84 motifs] (2015-11) - [local copy]
cisBP Oryza_meridionalis - [1289 motifs] (2019-06_v2.00) - [local copy]
cisBP Brassica_napus - [25 motifs] (2019-06_v2.00) - [local copy]
cisBP Solanum_lycopersicum - [1399 motifs] (2019-06_v2.00) - [local copy]
cisBP Zea_mays - [1334 motifs] (2019-06_v2.00) - [local copy]
cisBP Populus_trichocarpa - [1428 motifs] (2019-06_v2.00) - [local copy]
cisBP Gossypium_raimondii - [1448 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_nivara - [1297 motifs] (2019-06_v2.00) - [local copy]
cisBP a_thaliana - [309 motifs] (2015-06_v1.02) - [local copy]
cisBP Vitis_vinifera - [1418 motifs] (2019-06_v2.00) - [local copy]
cisBP Helianthus_annuus - [4 motifs] (2019-06_v2.00) - [local copy]
cisBP Medicago_truncatula - [1422 motifs] (2019-06_v2.00) - [local copy]
cisBP Fragaria_vesca - [1363 motifs] (2019-06_v2.00) - [local copy]
cisBP Brachypodium_distachyon - [1295 motifs] (2019-06_v2.00) - [local copy]
cisBP Manihot_esculenta - [1425 motifs] (2019-06_v2.00) - [local copy]
cisBP Chlamydomonas_reinhardtii - [340 motifs] (2019-06_v2.00) - [local copy]
cisBP Solanum_tuberosum - [1361 motifs] (2019-06_v2.00) - [local copy]
cisBP Arabidopsis_lyrata - [1556 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_glaberrima - [1281 motifs] (2019-06_v2.00) - [local copy]
cisBP Triticum_aestivum - [1293 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_rufipogon - [1302 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_punctata - [1341 motifs] (2019-06_v2.00) - [local copy]
cisBP Prunus_persica - [1406 motifs] (2019-06_v2.00) - [local copy]
cisBP Glycine_max - [1491 motifs] (2019-06_v2.00) - [local copy]
cisBP Leersia_perrieri - [1300 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_barthii - [1296 motifs] (2019-06_v2.00) - [local copy]
cisBP Physcomitrella_patens - [1033 motifs] (2019-06_v2.00) - [local copy]
cisBP Amborella_trichopoda - [1291 motifs] (2019-06_v2.00) - [local copy]
cisBP Musa_acuminata - [1391 motifs] (2019-06_v2.00) - [local copy]
cisBP Aegilops_tauschii - [1177 motifs] (2019-06_v2.00) - [local copy]
cisBP Ostreococcus_lucimarinus - [418 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_sativa - [1321 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_glumaepatula - [1311 motifs] (2019-06_v2.00) - [local copy]
cisBP Setaria_italica - [1305 motifs] (2019-06_v2.00) - [local copy]
cisBP Triticum_urartu - [1124 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_indica - [1310 motifs] (2019-06_v2.00) - [local copy]
cisBP Arabidopsis_thaliana - [1653 motifs] (2019-09_v2.00) - [local copy]
cisBP Brassica_oleracea - [1539 motifs] (2019-06_v2.00) - [local copy]
cisBP Sorghum_bicolor - [1306 motifs] (2019-06_v2.00) - [local copy]
cisBP Prunus_mume - [1386 motifs] (2019-06_v2.00) - [local copy]
cisBP Brassica_rapa - [1532 motifs] (2019-06_v2.00) - [local copy]
cisBP Hordeum_vulgare - [1279 motifs] (2019-06_v2.00) - [local copy]
cisBP Phaseolus_vulgaris - [12 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_longistaminata - [1151 motifs] (2019-06_v2.00) - [local copy]
cisBP Selaginella_moellendorffii - [1077 motifs] (2019-06_v2.00) - [local copy]
cisBP Cucumis_sativus - [1398 motifs] (2019-06_v2.00) - [local copy]
cisBP Oryza_brachyantha - [1264 motifs] (2019-06_v2.00) - [local copy]
footprintDB-plants [only plant DNA motifs] - [1997 motifs] (2020-01) - [local copy]
RSAT non-redundant plants - [306 motifs] (2017) - [local copy]
ArabidopsisPBM (A thaliana) - [108 motifs] (2015-11) - [local copy]
JASPAR core nonredundant plants - [530 motifs] (2020) - [local copy]
JASPAR core redundant plants - [572 motifs] (2020) - [local copy]

Prokaryotes

RegulonDB prokaryotes - [93 motifs] (2015_08) - [local copy]
DBTBS (Bacillus Subtilis) - [88 motifs] (2015-11) - [local copy]

RNA binding

ATtRACT - [1322 motifs] (2017) - [local copy]
CISBP-RNA - [11897 motifs] (2017) - [local copy]
RBPDB - [71 motifs] (2017) - [local copy]

Vertebrates

Epigram (Human Histone marks related motifs) - [589 motifs] (2016-06) - [local copy]
Methylated motifs GM12878 (Human TFs) - [60 motifs] (2018-11) - [local copy]
Methylated motifs HEK293T (Human TFs) - [9 motifs] (2018-11) - [local copy]
Methylated motifs MCF-7 (Human TFs) - [52 motifs] (2018-11) - [local copy]
Methylated motifs A549 (Human TFs) - [21 motifs] (2018-11) - [local copy]
Methylated motifs SK-N-SH (Human TFs) - [21 motifs] (2018-11) - [local copy]
Methylated motifs HCT116 (Human TFs) - [16 motifs] (2018-11) - [local copy]
Methylated motifs HepG2 (Human TFs) - [66 motifs] (2018-11) - [local copy]
Methylated motifs HEK293 (Human TFs) - [88 motifs] (2018-11) - [local copy]
Methylated motifs HeLa-S3 (Human TFs) - [31 motifs] (2018-11) - [local copy]
Methylated motifs IMR-90 (Human TFs) - [11 motifs] (2018-11) - [local copy]
Methylated motifs H1-hESC (Human TFs) - [35 motifs] (2018-11) - [local copy]
Methylated motifs K562 (Human TFs) - [108 motifs] (2018-11) - [local copy]
Methylated motifs SNU398 (Human TFs) - [1 motifs] (2018-11) - [local copy]
hPDI (Human TFs identified by protein microarray assays) - [437 motifs] (2016-06) - [local copy]
cisBP Oreochromis_niloticus - [5296 motifs] (2019-06_v2.00) - [local copy]
cisBP Xenopus_tropicalis - [5393 motifs] (2019-06_v2.00) - [local copy]
cisBP Dipodomys_ordii - [4810 motifs] (2019-06_v2.00) - [local copy]
cisBP Dasypus_novemcinctus - [5871 motifs] (2019-06_v2.00) - [local copy]
cisBP human - [1832 motifs] (2014-10_v0.9) - [local copy]
cisBP Rattus_norvegicus - [5946 motifs] (2019-06_v2.00) - [local copy]
cisBP Anas_platyrhynchos - [5038 motifs] (2019-06_v2.00) - [local copy]
cisBP Chlorocebus_sabaeus - [6176 motifs] (2019-06_v2.00) - [local copy]
cisBP Homo_sapiens - [6607 motifs] (2019-06_v2.00) - [local copy]
cisBP Choloepus_hoffmanni - [4069 motifs] (2019-06_v2.00) - [local copy]
cisBP Equus_caballus - [5765 motifs] (2019-06_v2.00) - [local copy]
cisBP Ailuropoda_melanoleuca - [5863 motifs] (2019-06_v2.00) - [local copy]
cisBP Gallus_gallus - [5272 motifs] (2019-06_v2.00) - [local copy]
cisBP Callithrix_jacchus - [6089 motifs] (2019-06_v2.00) - [local copy]
cisBP Erinaceus_europaeus - [4783 motifs] (2019-06_v2.00) - [local copy]
cisBP Echinops_telfairi - [4813 motifs] (2019-06_v2.00) - [local copy]
cisBP Astyanax_mexicanus - [5191 motifs] (2019-06_v2.00) - [local copy]
cisBP Bos_taurus - [5895 motifs] (2019-06_v2.00) - [local copy]
cisBP Cavia_porcellus - [5683 motifs] (2019-06_v2.00) - [local copy]
cisBP Danio_rerio - [5320 motifs] (2019-06_v2.00) - [local copy]
cisBP Mus_musculus - [6014 motifs] (2019-06_v2.00) - [local copy]
cisBP mouse - [1715 motifs] (2014-10_v0.9) - [local copy]
Human_TF_dimers (Human TFs dimers) - [664 motifs] (2016-05) - [local copy]
Jolma_2013 (Human TFs) - [818 motifs] (2015-11) - [local copy]
ENCODE (Human TFs) - [2065 motifs] (2018-03) - [local copy]
Hocomoco (Mouse TFs) - [531 motifs] (2017-10) - [local copy]
Hocomoco (Human TFs) - [771 motifs] (2017-10) - [local copy]
RSAT non-redundant vertebrates - [2233 motifs] (2017) - [local copy]
HT-Methyl-Selex (Human TFs) - [923 motifs] (2018-03) - [local copy]
HT-Selex (Human TFs) - [864 motifs] (2018-03) - [local copy]
ZF_ChIP-seq (C2H2 zinc fingers) - [109 motifs] (2020-07) - [local copy]
NCAP-SELEX (HUMAN TFs) - [195 motifs] (2018-09) - [local copy]
CAP-SELEX (HUMAN TFs) - [186 motifs] (2018-09) - [local copy]
Homer (Human TF motifs) - [332 motifs] (2016-07) - [local copy]
JASPAR core redundant vertebrates - [1011 motifs] (2020) - [local copy]
JASPAR core nonredundant vertebrates - [746 motifs] (2020) - [local copy]
ZF_ChIP-exo (C2H2 zinc fingers) - [126 motifs] (2020-07) - [local copy]

Pseudo-counts distributed in an equiprobable waydistributed proportionally to residues priors

Background model estimation method

    Markov order     High orders can be time-consuming, but order 0 is generally not representative. We recommend orders 1 or 2.
    Estimate residue probabilities from input sequences

    Organism-specific

      Organism 
      [List of organisms] not seeing your favorite organism in the list ? Contact us to have it installed
      Sequence type  

Pseudo-frequencies

Scanning options

Search strands      Origin     Offset   score decimals   handling of N characters

Return (Select one return type)


Individual matches
CRERs
(Cis-Regulatory element
Enriched Regions)
Enrichment of hits
in the whole input sequence set
Fields to
return






   sort by   
Other fields to return
Thresholds
Field Lower
Threshold 		Upper
Threshold
Weight
score
P-value
Sig
P(S|M)
proba_M
P(S|B)
proba_B
Normalized
weight
Rank
Field Lower
Threshold 		Upper
Threshold
CRER size*
site P-value*
CRER sites
CRER pval
CRER sig
* =mandatory field
Field Lower
Threshold 		Upper
Threshold
Occurrences
Weight
score
Occurrences
above the score
Enrichment
Expected
occurrences
Occ P-value
Occ E-value
Occ sig
Rank

Output  
      MANUAL MAIL