******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.3.0 (Release date: Sat Sep 26 01:51:56 PDT 2009) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= tmp.fasta ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ YVDD_BACSU 1.0000 191 Y4923_PSEAE 1.0000 195 LOG_ORYSJ 1.0000 242 LOG1_ARATH 1.0000 213 FAS6_RHOFA 1.0000 198 YJF5_YEAST 1.0000 245 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme tmp.fasta -mod zoops -nmotifs 3 -prior dirichlet -nostatus -protein -text model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 50 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 6 wnsites= 0.8 theta: prob= 1 spmap= pam spfuzz= 120 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 1284 N= 6 sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.096 C 0.012 D 0.035 E 0.086 F 0.033 G 0.115 H 0.030 I 0.061 K 0.049 L 0.089 M 0.037 N 0.025 P 0.044 Q 0.023 R 0.046 S 0.061 T 0.043 V 0.076 W 0.011 Y 0.030 Background letter frequencies (from dataset with add-one prior applied): A 0.095 C 0.013 D 0.035 E 0.086 F 0.033 G 0.114 H 0.031 I 0.061 K 0.049 L 0.088 M 0.037 N 0.025 P 0.044 Q 0.023 R 0.046 S 0.061 T 0.043 V 0.075 W 0.012 Y 0.030 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 50 sites = 6 llr = 715 E-value = 1.8e-111 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::2::8::8::5:8::8:::::::2:::::::::5:::::2::::::::: pos.-specific C ::::::::::::::::::::::::::::::2:2::::::::::2:::::: probability D ::::::::::::a:::::::::::::::::::::::::::2:::::::23 matrix E ::3:::3::5:::::::::::::::aa::a:::::::::::::::::2:2 F ::::::::::2:::a::::::2::2::25:::::::::::::::::2::: G :::::::::::2:2:::::aa:a:::::::::::2::a::::::7::::: H :a::::::::2::::::::::::::::::::::::2:::a:::::::::: I :::::::::::::::8:::::::::::2:::5::::2:7::::32:::2: K ::::a:2::2::::::::::::::::::::::::::::::2a:::::::: L ::::::2:::7::::::7:::2::5::73::3::::8:2::::2:a7::: M a:::::2a:::::::::3::::::::::2::::::::::::::::::::: N :::::::::2::::::::::::::::::::::::::::::3::::::8:5 P ::::::::::::::::::a:::::::::::::::::::::::a::::::: Q ::3::::::::::::::::::::::::::::::::8::::2::::::::: R :::a:22::2:::::::::::::::::::::::::::::::::::::::: S ::::::::2::3::::2:::::::::::::::::3::::::::::::::: T ::2::::::::::::::::::::a::::::::8::::::::::::::::: V :::::::::::::::2:::::2::::::::8::::::::::::32:::7: W :::::::::::::::::::::::::::::::2:a:::::::::::::::: Y :::::::::::::::::::::5::2:::::::::::::2:::::::2::: bits 6.4 * 5.8 * 5.2 * * * * 4.5 ** ** * * * * * * * * ** * Relative 3.9 ** ** * * * * * ** * * ** * Entropy 3.2 ** *** * * ** **** ** ** *** ** *** * ** * * * (171.9 bits) 2.6 ****** **** ************ ********* ********* ***** 1.9 ************************************************** 1.3 ************************************************** 0.6 ************************************************** 0.0 -------------------------------------------------- Multilevel MHERKAEMAELADAFIALPGGYGTLEELFEVITWAQLGIHNKPIGLLNVN consensus Q S M L L S V D sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------------- LOG1_ARATH 93 6.07e-55 TVGEVKAVAD MHQRKAEMAKHSDAFIALPGGYGTLEELLEVITWAQLGIHDKPVGLLNVE GYYNSLLSFI LOG_ORYSJ 121 6.07e-55 PVGEVRAVSG MHERKAEMARFADAFIALPGGYGTLEELLEVITWAQLGIHKKPVGLLNVD GFYDPFLSFI YJF5_YEAST 130 1.94e-53 EYGETTIVPD MHTRKRMMANLSDAFVAMPGGYGTFEEIMECITWSQLGIHNKPIILFNID GFYDKLLEFL YVDD_BACSU 87 8.66e-53 NLTELIEVNG MHERKAKMSELADGFISMPGGFGTYEELFEVLCWAQIGIHQKPIGLYNVN GYFEPMMKMV FAS6_RHOFA 106 1.54e-52 GLTELHVVHD MHQRKALMAELGDAFIALPGGVGTAEEFFEVLTWSHLGLHNKPCVLLNDN EYYRPLLSYI Y4923_PSEAE 89 2.87e-52 GLTRLEVVDG MHARKARMAELADAFIALPGGLGTLEELFEVWTWGQLGYHAKPLGLLEVN GFYDPLLTFL -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- LOG1_ARATH 6.1e-55 92_[1]_71 LOG_ORYSJ 6.1e-55 120_[1]_72 YJF5_YEAST 1.9e-53 129_[1]_66 YVDD_BACSU 8.7e-53 86_[1]_55 FAS6_RHOFA 1.5e-52 105_[1]_43 Y4923_PSEAE 2.9e-52 88_[1]_57 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=50 seqs=6 LOG1_ARATH ( 93) MHQRKAEMAKHSDAFIALPGGYGTLEELLEVITWAQLGIHDKPVGLLNVE 1 LOG_ORYSJ ( 121) MHERKAEMARFADAFIALPGGYGTLEELLEVITWAQLGIHKKPVGLLNVD 1 YJF5_YEAST ( 130) MHTRKRMMANLSDAFVAMPGGYGTFEEIMECITWSQLGIHNKPIILFNID 1 YVDD_BACSU ( 87) MHERKAKMSELADGFISMPGGFGTYEELFEVLCWAQIGIHQKPIGLYNVN 1 FAS6_RHOFA ( 106) MHQRKALMAELGDAFIALPGGVGTAEEFFEVLTWSHLGLHNKPCVLLNDN 1 Y4923_PSEAE ( 89) MHARKARMAELADAFIALPGGLGTLEELFEVWTWGQLGYHAKPLGLLEVN 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 50 n= 990 bayes= 7.35755 E= 1.8e-111 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 476 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 502 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 81 -923 -923 195 -923 -923 -923 -923 -923 -923 -923 -923 -923 385 -923 -923 195 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 444 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 435 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 313 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 186 -923 -923 -923 -923 -923 -923 -923 -923 195 -923 -923 -923 -923 176 92 218 -923 -923 -923 186 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 476 -923 -923 -923 -923 -923 -923 -923 -923 -923 313 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 146 -923 -923 -923 -923 -923 -923 -923 254 -923 -923 -923 -923 176 -923 -923 272 -923 -923 186 -923 -923 -923 -923 -923 -923 -923 -923 -923 234 -923 244 -923 -923 292 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 239 -923 -923 -923 -923 54 -923 -923 -923 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-923 -923 -923 -923 -923 115 -923 406 -923 -923 -923 -923 -923 313 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 454 -923 -923 -923 81 -923 -923 -923 234 -923 -923 -923 -923 250 -923 -923 -923 -923 -923 -923 -923 -923 -923 248 -923 -923 -923 354 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 354 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 234 -923 -923 146 -923 292 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 392 -923 -923 -923 -923 192 218 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 354 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 367 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 347 -923 -923 -923 -923 -923 -923 -923 -923 -923 304 -923 192 -923 -923 -923 -923 -923 -923 -923 -923 385 -923 -923 367 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 428 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 644 -923 239 -923 -923 -923 -923 54 -923 -923 -923 -923 -923 -923 -923 -923 -923 246 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 244 -923 -923 -923 -923 -923 -923 518 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 146 -923 324 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 313 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 346 -923 92 -923 -923 -923 -923 -923 -923 -923 -923 -923 248 -923 -923 -923 -923 -923 -923 502 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 81 -923 224 -923 -923 -923 -923 -923 176 -923 -923 372 -923 285 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 435 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 451 -923 -923 -923 -923 -923 -923 -923 -923 367 -923 -923 -923 -923 -923 246 -923 92 -923 -923 -923 -923 -923 -923 -923 215 -923 -923 -923 -923 -923 -923 -923 254 -923 146 -923 -923 -923 -923 -923 -923 -923 -923 -923 115 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 350 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 234 -923 -923 -923 -923 292 -923 -923 -923 -923 -923 -923 -923 -923 -923 248 -923 -923 -923 96 -923 -923 -923 -923 -923 -923 -923 504 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 224 -923 -923 -923 -923 146 -923 -923 -923 -923 -923 -923 -923 -923 -923 315 -923 -923 -923 -923 324 96 -923 -923 -923 -923 -923 -923 -923 430 -923 -923 -923 -923 -923 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix 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0.333333 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- MH[EQ]RKAEMAEL[AS]DAFIA[LM]PGGYGTLEEL[FL]EV[IL]TW[AS]QLGIHNKP[IV]GLLNV[ND] -------------------------------------------------------------------------------- Time 0.53 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 50 sites = 6 llr = 606 E-value = 1.1e-056 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::::2:322:3:32:::5a22::22:5::::::::::22:::::::7: pos.-specific C :::8::8::::::::::::::::::::::::::::::::::::::::::: probability D ::::::::::::::::::3::::::::::::::3:::::::::::::::3 matrix E ::::::::::::::2:::3::37:::3::5:::::::::::::::::::: F :::::7::::2::::::::::::::::2:::::::::::::::::::::: G :::::::a:::a22:::2::::2:a::::::7:2:::aa7::a::a:::: H ::::::::::::::::::::::::::2:2::::::::::::::::::::2 I ::5::::::::::::::::::2:::::2::::5::::::::3:::::5:: K 7:::::::::2::5:2:3:2:::::2:::2:2:2::::::::::::2::: L :::::::::::::::2:::2:::8::25::2:3:a::::::::a::32:: M :::::::::2:::::::::::::2:::2::::::::::::::::a::::: N :::::::::2::22:::::::::::::::::2:::::::::::::::::2 P ::::::::::5:::2::::::::::::::::::::::::::::::::::: Q :::::::::::::::::32:::::::::::2::::::::::::::::::2 R 33::::::::::3:::::2::::::3:::25::2::::::3::::::::2 S :5::::::75:::2:3:2:2:::::::::22::::::::23:::::::3: T :2:2::::::::::2::::::::::2:::::::2::::::22::::5::: V ::5:a:::::::::22:::::3:::2::3::::::a:::::5:::::3:: W ::::::::::::::::::::::::::::::::2::::::::::::::::: Y :::::3::::::::::a:::::::::2:::::::::a::::::::::::: bits 6.4 5.8 5.2 * * * * 4.5 * * * * * Relative 3.9 **** * ** * Entropy 3.2 * ****** * * * ** ***** **** (145.6 bits) 2.6 ************ * *** * ** * *** ***** ********* 1.9 ************** ********************************** 1.3 ************************************************** 0.6 ************************************************** 0.0 -------------------------------------------------- Multilevel KSICVFCGSSPGAKASYKDAAEELGRELAERGIDLVYGGGRVGLMGTIAD consensus RRV Y A R QE V V L SI LVS sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------------- LOG1_ARATH 8 6.51e-49 MEIESKF KRICVFCGSSAGNKVSYKDAAIELGTELVSRNIDLVYGGGSIGLMGLISQ AVFNGGRHVI LOG_ORYSJ 36 2.30e-48 GGAGERRSRF RRICVYCGSAKGRKASYQDAAVELGKELVERGIDLVYGGGSIGLMGLVSH AVHDGGRHVI Y4923_PSEAE 4 1.07e-46 MTL RSVCVFCGASPGASPVYQEAAVALGRHLAERGLTLVYGGGAVGLMGTVAD AALAAGGEVI YJF5_YEAST 19 1.18e-44 NSSRGGQVGG KSVCVYCGSSFGAKALYSESAEELGALFHKLGWKLVYGGGTTGLMGKIAR STMGPDLSGQ YVDD_BACSU 2 1.69e-44 M KTICVFAGSNPGGNEAYKRKAAELGVYMAEQGIGLVYGGSRVGLMGTIAD AIMENGGTAI FAS6_RHOFA 20 1.97e-42 TVSAQARPTP KSVTVFCGAMPGRGTKYGQLAEGMGRAIARSKLRLVYGGARVGLMGTLAN AALDSGGTVV -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- LOG1_ARATH 6.5e-49 7_[2]_156 LOG_ORYSJ 2.3e-48 35_[2]_157 Y4923_PSEAE 1.1e-46 3_[2]_142 YJF5_YEAST 1.2e-44 18_[2]_177 YVDD_BACSU 1.7e-44 1_[2]_140 FAS6_RHOFA 2e-42 19_[2]_129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=50 seqs=6 LOG1_ARATH ( 8) KRICVFCGSSAGNKVSYKDAAIELGTELVSRNIDLVYGGGSIGLMGLISQ 1 LOG_ORYSJ ( 36) RRICVYCGSAKGRKASYQDAAVELGKELVERGIDLVYGGGSIGLMGLVSH 1 Y4923_PSEAE ( 4) RSVCVFCGASPGASPVYQEAAVALGRHLAERGLTLVYGGGAVGLMGTVAD 1 YJF5_YEAST ( 19) KSVCVYCGSSFGAKALYSESAEELGALFHKLGWKLVYGGGTTGLMGKIAR 1 YVDD_BACSU ( 2) KTICVFAGSNPGGNEAYKRKAAELGVYMAEQGIGLVYGGSRVGLMGTIAD 1 FAS6_RHOFA ( 20) KSVTVFCGAMPGRGTKYGQLAEGMGRAIARSKLRLVYGGARVGLMGTLAN 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 50 n= 990 bayes= 7.80735 E= 1.1e-056 -923 -923 -923 -923 -923 -923 -923 -923 376 -923 -923 -923 -923 -923 285 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 285 304 195 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 304 -923 -923 -923 -923 -923 -923 -923 -923 -923 273 -923 -923 -923 600 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 195 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 373 -923 -923 -923 -923 -923 -923 434 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 348 81 600 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 313 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 181 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 346 -923 -923 -923 -923 81 -923 -923 -923 -923 -923 -923 -923 -923 -923 218 272 -923 -923 -923 304 -923 -923 -923 -923 81 -923 -923 -923 234 -923 -923 -923 176 -923 -923 -923 351 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 313 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 181 -923 -923 -923 -923 54 -923 -923 -923 -923 -923 272 -923 -923 285 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 54 -923 -923 335 -923 -923 272 -923 -923 -923 146 -923 -923 -923 -923 181 -923 -923 96 -923 -923 -923 -923 -923 -923 -923 -923 193 -923 -923 -923 195 115 -923 -923 81 -923 -923 -923 -923 -923 -923 -923 176 92 -923 -923 -923 -923 -923 246 -923 115 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 506 -923 -923 -923 -923 -923 54 -923 -923 276 -923 -923 -923 -923 385 -923 146 -923 -923 -923 -923 -923 -923 324 195 -923 -923 -923 -923 -923 -923 -923 -923 -923 285 186 -923 -923 -923 -923 -923 239 -923 -923 -923 -923 -923 -923 -923 176 92 -923 -923 -923 -923 -923 146 -923 -923 -923 -923 339 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 81 -923 -923 195 -923 -923 -923 146 -923 -923 -923 -923 -923 -923 -923 -923 -923 215 -923 -923 81 -923 -923 295 -923 54 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 324 218 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 313 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 81 -923 -923 -923 -923 -923 -923 -923 176 -923 -923 -923 -923 -923 285 -923 195 115 -923 -923 81 -923 -923 195 -923 -923 244 -923 -923 92 -923 -923 -923 -923 -923 -923 -923 -923 -923 248 -923 -923 -923 -923 234 -923 -923 146 -923 250 218 -923 -923 -923 -923 -923 -923 -923 -923 -923 239 -923 -923 -923 -923 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246 -923 -923 -923 -923 -923 -923 324 -923 -923 -923 244 -923 -923 -923 -923 272 -923 285 186 -923 -923 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 50 nsites= 6 E= 1.1e-056 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.500000 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 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0.000000 0.500000 0.000000 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.166667 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [KR][SR][IV]CV[FY]CG[SA]SPG[AR]KASY[KQ][DE]AA[EV]ELGREL[AV]ERG[IL]DLVYGGG[RS][VI]GLMG[TL][IV][AS]D -------------------------------------------------------------------------------- Time 0.84 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 45 sites = 5 llr = 445 E-value = 4.7e-022 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::::::::::::4::::::22:4::::::62:4:2:::2:22::: pos.-specific C ::::::::::::::::::::::::::::::::::::::::::::: probability D :::6::::::6:::2::::::2:::::::::::2:::4:::2::: matrix E :::2:::2::::::2a::::42::2::::::::28::2::62::: F :62::2::8::::::::a::::::::::::::::::::::::::: G a:::::::::::::::6::::::22::::2::::::::::::::: H :::::::::::4::::::::::4:2::2::::::::::::::::: I :::::::::4:::4::::6::::::682::::::::2::2::::: K ::::2::2::42:::::::::2::2::::::::2:::26::2::: L :::::68::4::2::::::::::2:22::::::::822:6::::: M :::::22:2::2:::::::::::::2:::::::::::::2::::: N :::2:::::::::::::::2::2::::::::::::::::::2::: P ::::6:::::::::::::::2:::::::::4:6:::::::::::6 Q ::::::::::::::4::::::::::::4:::::2::::2:2:::: R ::::::::::::::::4::2:::62:::2::2:2::::::::::: S ::::2::4::::4:2:::24:2::::::6244:::::::::::2: T :::::::2:::::::::::::2:::::::::4:::::::::::2: V :::::::::2:::6::::2:2::::::22::::::26::::::62 W ::::::::::::::::::::::::::::::::::::::::::2:: Y :48::::::::2::::::::::::::::::::::::::::::8:2 bits 6.4 5.8 5.2 * 4.5 * * * Relative 3.9 ** * * * * Entropy 3.2 ***** * * ** * * * * * * * * (128.3 bits) 2.6 ******* * ** ******* ** **** *** ******* *** 1.9 ********************************************* 1.3 ********************************************* 0.6 ********************************************* 0.0 --------------------------------------------- Multilevel GFYDPLLSFIDHAVQEGFISEDAREIIQSAPSPDELVDKLEAYVP consensus YFEKFMEMLKKSID R SAAEHGGLLHRGSTAEAVIEAIADWSV sequence NSM K V ML E VNPKNLHM IVSAR K LKQMQE TY T Y S RVS K V Q L K T R R N -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------------------------------- LOG_ORYSJ 171 9.83e-43 KKPVGLLNVD GFYDPFLSFIDMAVSEGFIAEDARRIIISAPTARELVLKLEEYVP EYEVGLVWDD LOG1_ARATH 143 3.81e-42 DKPVGLLNVE GYYNSLLSFIDKAVEEGFISPTARHIIVSAPSAKELVKKLEDYVP RHEKVASKKS YJF5_YEAST 180 5.62e-42 NKPIILFNID GFYDKLLEFLKHSIQERFISVKNGEIIQVASTPQEVVDKIEKYVV PEGRFNLNWS YVDD_BACSU 137 2.30e-38 QKPIGLYNVN GYFEPMMKMVKYSIQEGFSNESHLKLIHSSSRPDELIEQMQNYSY PILEKKWTEI Y4923_PSEAE 139 5.21e-38 AKPLGLLEVN GFYDPLLTFLDHLVDERFVRAEHRGMLQRGASPEALLDALAAWTP SVAPKWVDRT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- LOG_ORYSJ 9.8e-43 170_[3]_27 LOG1_ARATH 3.8e-42 142_[3]_26 YJF5_YEAST 5.6e-42 179_[3]_21 YVDD_BACSU 2.3e-38 136_[3]_10 Y4923_PSEAE 5.2e-38 138_[3]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=45 seqs=5 LOG_ORYSJ ( 171) GFYDPFLSFIDMAVSEGFIAEDARRIIISAPTARELVLKLEEYVP 1 LOG1_ARATH ( 143) GYYNSLLSFIDKAVEEGFISPTARHIIVSAPSAKELVKKLEDYVP 1 YJF5_YEAST ( 180) GFYDKLLEFLKHSIQERFISVKNGEIIQVASTPQEVVDKIEKYVV 1 YVDD_BACSU ( 137) GYFEPMMKMVKYSIQEGFSNESHLKLIHSSSRPDELIEQMQNYSY 1 Y4923_PSEAE ( 139) GFYDPLLTFLDHLVDERFVRAEHRGMLQRGASPEALLDALAAWTP 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 45 n= 1020 bayes= 8.61216 E= 4.7e-022 -897 -897 -897 -897 -897 313 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 418 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 374 -897 -897 -897 -897 260 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 474 -897 -897 409 122 -897 -897 -897 -897 -897 -897 -897 298 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 202 -897 -897 -897 378 -897 -897 172 -897 -897 -897 -897 -897 -897 -897 -897 260 -897 -897 -897 -897 276 244 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 318 244 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 122 -897 -897 -897 -897 202 -897 -897 -897 -897 -897 -897 272 222 -897 -897 -897 -897 -897 -897 -897 460 -897 -897 -897 -897 -897 244 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 272 -897 218 -897 -897 -897 -897 -897 -897 -897 141 -897 -897 -897 -897 409 -897 -897 -897 -897 -897 302 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 370 -897 202 -897 244 -897 -897 -897 -897 -897 -897 -897 -897 274 207 -897 -897 -897 -897 -897 -897 -897 -897 118 -897 -897 -897 -897 -897 272 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 272 -897 -897 -897 -897 -897 -897 -897 -897 -897 299 -897 -897 -897 -897 250 122 -897 -897 -897 -897 -897 -897 -897 -897 -897 412 -897 172 -897 -897 -897 -897 -897 -897 -897 354 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 239 -897 -897 -897 -897 -897 -897 -897 -897 312 -897 -897 -897 -897 -897 -897 -897 -897 -897 492 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 331 -897 -897 -897 -897 -897 -897 -897 172 -897 141 -897 -897 107 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 298 -897 -897 212 272 -897 -897 -897 -897 107 -897 -897 222 -897 -897 -897 -897 -897 -897 -897 -897 219 -897 -897 -897 -897 141 -897 -897 -897 -897 250 122 -897 -897 -897 -897 202 -897 -897 -897 -897 -897 -897 172 222 -897 -897 -897 207 -897 -897 -897 -897 -897 370 -897 -897 -897 -897 298 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 81 -897 -897 -897 118 -897 -897 -897 -897 370 -897 -897 -897 -897 -897 -897 -897 -897 122 -897 81 270 -897 202 -897 -897 -897 -897 -897 212 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 331 -897 118 244 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 372 -897 118 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 270 172 -897 -897 -897 -897 -897 412 -897 -897 -897 141 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 212 331 -897 141 -897 -897 266 -897 -897 -897 -897 81 -897 -897 -897 -897 -897 -897 -897 -897 -897 172 -897 -897 -897 -897 107 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 319 -897 -897 272 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 212 272 322 -897 -897 -897 207 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 378 -897 -897 -897 -897 -897 -897 -897 -897 -897 250 122 -897 -897 -897 -897 202 -897 -897 -897 -897 312 212 -897 -897 -897 -897 -897 107 -897 -897 322 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 318 -897 -897 -897 -897 -897 -897 -897 141 -897 -897 -897 -897 -897 -897 -897 -897 -897 172 -897 118 -897 -897 -897 -897 -897 -897 -897 299 -897 -897 -897 -897 350 122 -897 -897 -897 -897 202 118 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 107 -897 -897 -897 -897 -897 -897 -897 361 -897 -897 -897 -897 312 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 172 -897 276 244 -897 -897 -897 -897 -897 -897 -897 -897 -897 107 -897 -897 280 -897 -897 -897 -897 -897 -897 -897 -897 -897 312 -897 -897 -897 -897 -897 -897 107 -897 250 122 -897 -897 -897 -897 202 -897 -897 298 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 412 474 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 172 222 299 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 378 -897 -897 -897 -897 141 -897 274 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 45 nsites= 5 E= 4.7e-022 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.600000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.200000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[FY][YF][DEN][PKS][LFM][LM][SEKT][FM][ILV][DK][HKMY][ASL][VI][QDES]E[GR]F[ISV][SANR][EAPV][DEKST][AHN][RGL][EGHKR][ILM][IL][QHIV][SRV][AGS][PSA][STR][PA][DEKQR][EA][LV][VIL][DEKL][KAQ][LIM][EAQ][ADEKN][YW][VST][PVY] -------------------------------------------------------------------------------- Time 1.02 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- YVDD_BACSU 4.31e-123 1_[2(1.69e-44)]_35_[1(8.66e-53)]_[3(2.30e-38)]_10 Y4923_PSEAE 2.26e-124 3_[2(1.07e-46)]_35_[1(2.87e-52)]_[3(5.21e-38)]_12 LOG_ORYSJ 5.05e-133 35_[2(2.30e-48)]_35_[1(6.07e-55)]_[3(9.83e-43)]_27 LOG1_ARATH 3.43e-133 7_[2(6.51e-49)]_35_[1(6.07e-55)]_[3(3.81e-42)]_26 FAS6_RHOFA 1.41e-85 19_[2(1.97e-42)]_36_[1(1.54e-52)]_43 YJF5_YEAST 4.55e-127 18_[2(1.18e-44)]_61_[1(1.94e-53)]_[3(5.62e-42)]_21 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo.fbb.msu.ru ********************************************************************************