******************************************************************************** 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= temp.fasta ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ YDAF_BACSU 1.0000 183 RIML_ECOLI 1.0000 179 RIMJ_SHIFL 1.0000 194 RIMJ_PSEAE 1.0000 189 Y802_MYCTU 1.0000 218 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme temp.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= 5 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= 963 N= 5 sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.084 C 0.015 D 0.060 E 0.069 F 0.043 G 0.069 H 0.031 I 0.048 K 0.035 L 0.113 M 0.022 N 0.039 P 0.040 Q 0.046 R 0.089 S 0.047 T 0.035 V 0.056 W 0.022 Y 0.037 Background letter frequencies (from dataset with add-one prior applied): A 0.083 C 0.015 D 0.060 E 0.068 F 0.043 G 0.068 H 0.032 I 0.048 K 0.036 L 0.112 M 0.022 N 0.040 P 0.041 Q 0.046 R 0.089 S 0.047 T 0.036 V 0.056 W 0.022 Y 0.038 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 38 sites = 5 llr = 352 E-value = 1.6e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :422:::2::224:22:::22::4:22:::::::::6: pos.-specific C :2:::::::::::22::::::::::::::::::::2:: probability D :::::::::::::::::4:::::2::::::::2:::2: matrix E :::44:6::::::::::::2::2:::4::::428:::: F 2:6:::::::2::::2::::::::::::::8::::::: G :::::22::::::::::2::::2::::::a::::a::: H 2:::::2:4:::::2::2:::::::::::::::::::: I :::::::2::4:4:::::::::2:::::2::2:::::: K :::::::::::::2:::::22:::::::::::4::2:4 L :::::6:6:::::::2::::::::442:4::22::22: M :2:::::::::4:::2:::::::::::::::::::::: N ::::::::2::::2::::a:::2:::::4::::2:::: P ::::::::::::::::4::4:::::2:::::::::::: Q ::2222::2:::::::::::2::2:::::::::::::: R :::2::::28:::2:2:2::4:22::28:::2:::::6 S ::::2:::::::222::::::a:::2:2:::::::::: T ::::2::::::2:::::::::::::::::::::::::: V :::::::::222::::6:::::::6::::::::::::: W :::::::::::::::::::::::::::::::::::::: Y 62::::::::::::2:::::::::::::::2::::4:: bits 6.0 5.4 4.8 * 4.2 * * Relative 3.6 * * * * ** * Entropy 3.0 *** * * * * * * * * ** *** * (101.6 bits) 2.4 *** *********** **** * * **** ****** 1.8 ************************************** 1.2 ************************************** 0.6 ************************************** 0.0 -------------------------------------- Multilevel YAFEELELHRIMACAAVDNPRSEAVLERLGFEKEGYAR consensus FCAAQGGANVAAIKCFPG AA GDLAASN YIDN CDK sequence HMQQSQHIQ FTSNHL H EK IQ PL I LE KL Y RT R VV RSM R KQ NR SR RL L SYR R -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------- RIMJ_SHIFL 131 7.93e-35 MFEALTAAIR YMQRTQHIHRIMANYMPHNKRSGDLLARLGFEKEGYAK DYLLIDGQWR RIMJ_PSEAE 130 2.03e-33 MARALRVANR YCFEQLGLHRIMASHLPRNARSERLLESLGFEKEGYAR AYLKIAGVWE YDAF_BACSU 120 1.90e-32 ITAACRKLIT YAFEELELNRVAICAAVGNEKSRAVPERIGFLEEGKAR DGLYVNGMHH RIML_ECOLI 120 1.13e-31 ISQALQALIH HYAQSGELRRFVIKCRVDNPQSNQVALRNGFILEGCLK QAEFLNDAYD Y802_MYCTU 133 5.13e-30 GTEMRAAVLY FAFAELEAQVATSRSFVDNPASIAVSRRNGYRDNGLDR VAREGAMAEA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RIMJ_SHIFL 7.9e-35 130_[1]_26 RIMJ_PSEAE 2e-33 129_[1]_22 YDAF_BACSU 1.9e-32 119_[1]_26 RIML_ECOLI 1.1e-31 119_[1]_22 Y802_MYCTU 5.1e-30 132_[1]_48 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=38 seqs=5 RIMJ_SHIFL ( 131) YMQRTQHIHRIMANYMPHNKRSGDLLARLGFEKEGYAK 1 RIMJ_PSEAE ( 130) YCFEQLGLHRIMASHLPRNARSERLLESLGFEKEGYAR 1 YDAF_BACSU ( 120) YAFEELELNRVAICAAVGNEKSRAVPERIGFLEEGKAR 1 RIML_ECOLI ( 120) HYAQSGELRRFVIKCRVDNPQSNQVALRNGFILEGCLK 1 Y802_MYCTU ( 133) FAFAELEAQVATSRSFVDNPASIAVSRRNGYRDNGLDR 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 38 n= 778 bayes= 8.22029 E= 1.6e-010 -897 -897 -897 -897 222 -897 266 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 399 226 371 -897 -897 -897 -897 -897 -897 -897 -897 316 -897 -897 -897 -897 -897 -897 -897 -897 241 126 -897 -897 -897 381 -897 -897 -897 -897 -897 -897 -897 -897 213 -897 -897 -897 -897 -897 -897 126 -897 -897 255 -897 -897 -897 -897 -897 -897 -897 -897 -897 213 117 -897 -897 -897 -897 -897 -897 -897 -897 255 -897 -897 -897 -897 -897 -897 -897 -897 -897 213 -897 209 249 -897 -897 -897 -897 -897 -897 -897 -897 155 -897 -897 -897 242 -897 -897 -897 213 -897 -897 -897 -897 -897 -897 -897 -897 -897 314 -897 155 266 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 126 -897 -897 -897 -897 -897 -897 206 -897 242 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 366 -897 -897 -897 -897 233 -897 213 117 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 317 -897 -897 184 -897 -897 126 -897 -897 -897 222 -897 -897 306 -897 -897 -897 -897 -897 -897 -897 -897 -897 184 -897 -897 126 -897 -897 -897 -897 -897 -897 -897 -897 -897 416 -897 -897 -897 -897 -897 249 184 -897 -897 226 -897 -897 -897 -897 -897 -897 306 -897 -897 -897 -897 -897 -897 -897 209 -897 -897 -897 -897 -897 371 -897 -897 -897 -897 -897 -897 249 -897 -897 233 -897 -897 117 209 -897 -897 -897 -897 126 371 -897 -897 -897 -897 266 -897 -897 -897 -897 -897 -897 -897 -897 209 -897 -897 -897 241 126 -897 -897 -897 222 -897 -897 -897 -897 84 316 -897 -897 -897 117 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 329 -897 -897 -897 -897 342 -897 -897 -897 -897 273 -897 -897 155 266 -897 -897 -897 -897 -897 -897 -897 117 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 465 -897 -897 -897 -897 -897 -897 -897 -897 126 -897 -897 155 -897 -897 -897 -897 249 -897 -897 -897 329 -897 -897 -897 -897 -897 -897 -897 126 -897 -897 -897 -897 -897 -897 -897 249 -897 -897 -897 -897 213 217 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 441 -897 -897 -897 -897 -897 -897 -897 155 -897 155 -897 206 -897 -897 -897 233 -897 -897 117 -897 -897 -897 -897 -897 226 -897 173 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 213 117 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 184 -897 -897 -897 -897 -897 -897 -897 342 -897 -897 126 -897 -897 -897 -897 -897 -897 -897 -897 184 -897 -897 229 -897 -897 209 -897 -897 -897 -897 126 -897 -897 255 -897 -897 -897 -897 -897 84 -897 -897 -897 -897 117 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 317 209 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 206 -897 184 -897 333 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 387 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 422 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 241 -897 -897 -897 255 -897 -897 -897 206 -897 84 -897 -897 -897 -897 117 -897 -897 -897 -897 -897 -897 -897 173 155 -897 -897 -897 -897 349 84 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 355 -897 -897 -897 -897 -897 -897 -897 233 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 387 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 371 -897 -897 -897 -897 -897 -897 249 84 -897 -897 -897 -897 -897 -897 -897 -897 -897 341 284 -897 173 -897 -897 -897 -897 -897 -897 84 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 349 -897 -897 -897 -897 -897 276 -897 -897 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 38 nsites= 5 E= 1.6e-010 0.000000 0.000000 0.000000 0.000000 0.200000 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 0.600000 0.400000 0.200000 0.000000 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 0.200000 0.200000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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0.000000 0.200000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.200000 0.000000 0.000000 0.000000 0.000000 0.400000 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 0.800000 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 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 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.200000 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 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 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [YFH][ACMY][FAQ][EAQR][EQST][LGQ][EGH][LAI][HNQR][RV][IAFV][MATV][AIS][CKNRS][ACHSY][AFLMR][VP][DGHR]N[PAEK][RAKQ]S[EGINR][ADQR][VL][LAPS][EALR][RS][LNI]G[FY][EILR][KDEL][EN]G[YCKL][ADL][RK] -------------------------------------------------------------------------------- Time 0.40 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 21 sites = 5 llr = 207 E-value = 2.0e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::44::::::4222::::::2 pos.-specific C :::4::::::::::::::::: probability D ::::2:::::2:::::::::: matrix E ::::4::::::22:2:::::: F 4::::::2:::::2::::::2 G ::::::a:::4::::a:a:2: H :2::2::::::::2::2:::: I :::::4:::4::::::::44: K :22::::::::22:::4:::: L :::::4:::6:2::::::4:: M :::::::::::::::::::4: N 4:::::::::::::::::::: P ::::::::::::::::::::: Q :22::::::::2::8:2:::: R :4::::::::::2:::2:::: S :::::2:24:::2:::::::2 T 2:2:::::::::::::::::4 V :::2::::::::::::::::: W ::::::::6::::2::::::: Y ::::2::6:::::2::::2:: bits 6.0 5.4 4.8 4.2 * Relative 3.6 * * ** * Entropy 3.0 * * *** ** * * (59.7 bits) 2.4 *********** ******** 1.8 ********************* 1.2 ********************* 0.6 ********************* 0.0 --------------------- Multilevel FRAAEIGYWLAAAAQGKGIIT consensus NHKCDL FSIGEEFE H LMA sequence TKQVHS S DKKH Q YGF QT Y LRW R S QSY -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- RIMJ_SHIFL 102 5.74e-22 ANFSNVVRGS FHACYLGYSIGQKWQGKGLMF EALTAAIRYM YDAF_BACSU 91 1.12e-20 MISLHNLDQV NRKAEIGYWIAKEFEGKGIIT AACRKLITYA RIML_ECOLI 91 3.56e-20 VISFNRIEPL NKTAEIGYWLDESHQGQGIIS QALQALIHHY RIMJ_PSEAE 101 3.09e-18 CSYTNIVRGV FQACHLGFSLAAAAQGRGLMA RALRVANRYC Y802_MYCTU 104 3.58e-18 QALSSKDFPI TRQVDSGSWLGLRYQGHGYGT EMRAAVLYFA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RIMJ_SHIFL 5.7e-22 101_[2]_72 YDAF_BACSU 1.1e-20 90_[2]_72 RIML_ECOLI 3.6e-20 90_[2]_68 RIMJ_PSEAE 3.1e-18 100_[2]_68 Y802_MYCTU 3.6e-18 103_[2]_94 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 RIMJ_SHIFL ( 102) FHACYLGYSIGQKWQGKGLMF 1 YDAF_BACSU ( 91) NRKAEIGYWIAKEFEGKGIIT 1 RIML_ECOLI ( 91) NKTAEIGYWLDESHQGQGIIS 1 RIMJ_PSEAE ( 101) FQACHLGFSLAAAAQGRGLMA 1 Y802_MYCTU ( 104) TRQVDSGSWLGLRYQGHGYGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 21 n= 863 bayes= 7.42291 E= 2.0e-006 -897 -897 -897 -897 322 -897 -897 -897 -897 -897 -897 333 -897 -897 -897 -897 249 -897 -897 -897 -897 -897 -897 -897 -897 -897 266 -897 249 -897 -897 -897 -897 213 217 -897 -897 -897 -897 -897 226 -897 -897 -897 -897 -897 -897 -897 249 -897 -897 -897 -897 213 -897 -897 249 -897 -897 -897 226 471 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 184 -897 -897 -897 -897 173 255 -897 -897 266 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 241 -897 -897 -897 -897 -897 -897 -897 306 -897 184 -897 -897 -897 -897 -897 209 -897 -897 -897 -897 -897 -897 -897 -897 -897 387 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 222 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 209 -897 -897 -897 399 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 309 -897 -897 474 -897 -897 -897 -897 -897 -897 -897 -897 306 -897 242 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 226 -897 173 -897 -897 255 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 126 -897 -897 155 -897 -897 -897 -897 249 84 -897 -897 -897 213 -897 -897 -897 -897 -897 -897 126 -897 -897 155 -897 -897 -897 -897 249 -897 -897 -897 -897 -897 117 209 -897 -897 -897 -897 126 -897 -897 -897 222 -897 266 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 316 241 -897 -897 -897 155 -897 -897 -897 -897 -897 -897 -897 -897 -897 412 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 387 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 266 -897 349 -897 -897 -897 -897 213 117 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 387 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 306 -897 184 -897 -897 -897 -897 -897 -897 -897 -897 -897 241 -897 -897 -897 -897 -897 155 -897 306 -897 -897 416 -897 -897 -897 -897 -897 -897 -897 -897 -897 126 -897 -897 -897 222 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 209 349 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 21 nsites= 5 E= 2.0e-006 0.000000 0.000000 0.000000 0.000000 0.400000 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 0.200000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.200000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 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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 0.000000 0.400000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.200000 0.000000 0.000000 0.400000 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 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.200000 0.200000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.200000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.200000 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 0.200000 0.200000 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 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 0.000000 0.000000 0.200000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.200000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 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 0.000000 0.000000 0.000000 0.400000 0.000000 0.400000 0.000000 0.000000 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 0.200000 0.000000 0.400000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 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 0.200000 0.400000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [FNT][RHKQ][AKQT][ACV][EDHY][ILS]G[YFS][WS][LI][AGD][AEKLQ][AEKRS][AFHWY][QE]G[KHQR]G[ILY][IMG][TAFS] -------------------------------------------------------------------------------- Time 0.64 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 21 sites = 2 llr = 109 E-value = 3.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::55:::::5::::::::::: pos.-specific C ::::::::::::::::::::5 probability D ::::::::::::::::a:::: matrix E :5:5::5:::::a::::5::: F :::::::5::::::::::::5 G ::::::::::::::::::5:: H ::::::55:::::::::::5: I ::::::::::::::::::::: K :::::::::5::::::::::: L ::::::::a:::::5:::::: M ::::::::::::::::::::: N ::5:a:::::::::::::::: P ::::::::::a::a:::5::: Q ::::::::::::::::::::: R :::::a:::::::::a::::: S ::::::::::::::::::5:: T ::::::::::::::::::::: V ::::::::::::::5:::::: W :::::::::::a::::::::: Y a5:::::::::::::::::5: bits 6.0 5.4 * 4.8 * * ** * 4.2 * * ** * * * Relative 3.6 * **** **** ** ** Entropy 3.0 ************** ****** (78.9 bits) 2.4 ********************* 1.8 ********************* 1.2 ********************* 0.6 ********************* 0.0 --------------------- Multilevel YEAANREFLAPWEPLRDEGHC consensus YNE HH K V PSYF sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- RIMJ_SHIFL 34 2.18e-26 HDRDAWRLAD YYAENRHFLKPWEPVRDESHC YPSGWQARLG RIMJ_PSEAE 33 2.01e-24 QPDDFVRTSR YENANREHLAPWEPLRDPGYF SVDNARARTL -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RIMJ_SHIFL 2.2e-26 33_[3]_140 RIMJ_PSEAE 2e-24 32_[3]_136 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=2 RIMJ_SHIFL ( 34) YYAENRHFLKPWEPVRDESHC 1 RIMJ_PSEAE ( 33) YENANREHLAPWEPLRDPGYF 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 21 n= 863 bayes= 8.74987 E= 3.9e+000 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 472 -765 -765 -765 287 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 372 258 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 365 -765 -765 -765 -765 -765 -765 -765 -765 258 -765 -765 287 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 465 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 349 -765 -765 -765 -765 -765 -765 -765 -765 287 -765 -765 398 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 354 -765 398 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 315 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 258 -765 -765 -765 -765 -765 -765 -765 381 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 461 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 547 -765 -765 -765 -765 387 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 461 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 215 -765 -765 -765 -765 -765 -765 -765 315 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 349 -765 -765 -765 -765 -765 -765 -765 405 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 287 -765 -765 -765 -765 -765 -765 -765 -765 361 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 287 -765 -765 -765 -765 -765 -765 -765 -765 -765 341 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 398 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 372 -765 503 -765 -765 354 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 21 nsites= 2 E= 3.9e+000 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 1.000000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 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 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 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 0.000000 0.000000 0.500000 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 0.000000 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 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 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- Y[EY][AN][AE]NR[EH][FH]L[AK]PWEP[LV]RD[EP][GS][HY][CF] -------------------------------------------------------------------------------- Time 0.82 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- YDAF_BACSU 1.36e-44 90_[2(1.12e-20)]_8_[1(1.90e-32)]_26 RIML_ECOLI 2.68e-43 90_[2(3.56e-20)]_8_[1(1.13e-31)]_22 RIMJ_SHIFL 7.00e-71 33_[3(2.18e-26)]_47_[2(5.74e-22)]_8_[1(7.93e-35)]_26 RIMJ_PSEAE 6.64e-64 32_[3(2.01e-24)]_47_[2(3.09e-18)]_8_[1(2.03e-33)]_22 Y802_MYCTU 2.83e-39 103_[2(3.58e-18)]_8_[1(5.13e-30)]_48 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo.fbb.msu.ru ********************************************************************************