******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.1.1 (Release date: Tue Apr 21 15:00:06 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 ------------- ------ ------ ------------- ------ ------ PERR_BACSU 1.0000 145 PERR_STAAU 1.0000 148 FUR_SHIFL 1.0000 148 FUR_KLEPN 1.0000 155 FUR_VIBPA 1.0000 149 ZUR_BACSU 1.0000 145 ******************************************************************************** ******************************************************************************** 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= 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= 890 N= 6 sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.058 C 0.031 D 0.071 E 0.088 F 0.036 G 0.060 H 0.063 I 0.061 K 0.057 L 0.100 M 0.016 N 0.047 P 0.025 Q 0.037 R 0.047 S 0.052 T 0.057 V 0.054 W 0.001 Y 0.039 Background letter frequencies (from dataset with add-one prior applied): A 0.058 C 0.032 D 0.070 E 0.087 F 0.036 G 0.059 H 0.063 I 0.060 K 0.057 L 0.099 M 0.016 N 0.047 P 0.025 Q 0.037 R 0.047 S 0.052 T 0.057 V 0.054 W 0.002 Y 0.040 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 41 sites = 5 llr = 483 E-value = 2.1e-055 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::4::::::::::a:::::::::::6::::::::::2:::: pos.-specific C ::::::::::::::::::::::::::::::::::::::::: probability D :::::62::::::::::::::::68::::::::::4::::: matrix E ::::2:::66::::::::::::::2:::::4:::6:::::: F :::::::4::::::::::::::a::::::::::6::::::a G :::::2:6:::6::::::::::::::a:::::::466:::: H :::::::::::::::::::::::::::::::62:::::::: I ::::6:::::8::::2:::::::::2:8::::::::::::: K :82:::2::::::::::::::::2:::::4:::::::6::: L :::a::2:::::6::::::a:::::::2:::4::::::::: M ::::::4:::2:::::::::::::::::::::::::::::: N :::::::::4:::::::44:6:::::::::::4:::::::: P :::::2::4:::::::::::::::::::::::::::::::: Q :2:::::::::::::::::::6::::::::::::::::::: R ::4::::::::::::::6::4::2::::::6::::::::4: S ::::2::::::4:::::::::::::2::::::::::24a:: T ::::::::::::::a::::::::::::::6::4:::::::: V ::::::::::::4::8::6::4::::::a::::::::::6: W ::::::::::::::::::::::::::::::::::::::::: Y a:::::::::::::::a::::::::::::::::4::::::: bits 8.8 7.9 7.1 6.2 Relative 5.3 Entropy 4.4 * ** * * * * * * (139.2 bits) 3.5 ** * ** ** ********** **** * **** 2.6 ***************************************** 1.8 ***************************************** 0.9 ***************************************** 0.0 ----------------------------------------- Multilevel YKALIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF consensus QR EGDFPNMSV I NN RV KEI L KELTYGDAS R sequence K SPK R S H S L -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------------------- FUR_KLEPN 40 1.29e-49 DNHHVSAEDL YKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF ELTQQHHHDH FUR_SHIFL 40 1.29e-49 DNHHVSAEDL YKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF ELTQQHHHDH FUR_VIBPA 40 6.44e-45 DCQHISAEDL YKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEGGKSVF ELSTQHHHDH PERR_STAAU 50 3.12e-41 SHTHPTADEI YQALSPDFPNISVATIYNNLRVFKDIGIVKELTYGDSSSRF DFNTHNHYHI PERR_BACSU 44 1.83e-40 SMAHPTADDI YKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGDASSRF DFVTSDHYHA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- FUR_KLEPN 1.3e-49 39_[1]_75 FUR_SHIFL 1.3e-49 39_[1]_68 FUR_VIBPA 6.4e-45 39_[1]_69 PERR_STAAU 3.1e-41 49_[1]_58 PERR_BACSU 1.8e-40 43_[1]_61 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=41 seqs=5 FUR_KLEPN ( 40) YKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF 1 FUR_SHIFL ( 40) YKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF 1 FUR_VIBPA ( 40) YKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEGGKSVF 1 PERR_STAAU ( 50) YQALSPDFPNISVATIYNNLRVFKDIGIVKELTYGDSSSRF 1 PERR_BACSU ( 44) YKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGDASSRF 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 41 n= 650 bayes= 7.96 E= 2.1e-055 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 466 -897 -897 -897 -897 -897 -897 -897 -897 380 -897 -897 -897 -897 242 -897 -897 -897 -897 -897 -897 278 -897 -897 -897 -897 -897 -897 -897 181 -897 -897 -897 -897 -897 308 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 334 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 120 -897 -897 -897 331 -897 -897 -897 -897 -897 -897 -897 195 -897 -897 -897 -897 -897 -897 309 -897 -897 175 -897 -897 -897 -897 -897 -897 298 -897 -897 -897 -897 -897 -897 -897 -897 -897 151 -897 -897 -897 -897 -897 181 101 460 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 346 334 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 279 -897 -897 -897 -897 -897 -897 -897 -897 398 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 279 -897 -897 -897 -897 -897 -897 -897 308 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 372 -897 -897 360 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 334 -897 -897 -897 -897 -897 -897 -897 -897 -897 295 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 260 -897 -897 -897 -897 -897 -897 -897 289 -897 -897 410 -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 -897 -897 -897 -897 -897 -897 -897 -897 -897 413 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 172 -897 -897 -897 -897 -897 -897 -897 -897 -897 389 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 466 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 308 -897 -897 366 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 308 -897 -897 -897 -897 -897 348 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 334 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 366 -897 -897 308 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 400 -897 -897 -897 289 -897 -897 -897 -897 -897 -897 478 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 309 -897 -897 -897 -897 -897 181 -897 -897 -897 -897 -897 208 -897 -897 -897 -897 -897 -897 -897 351 120 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 336 -897 -897 -897 -897 -897 -897 172 -897 -897 -897 -897 -897 -897 -897 195 -897 -897 -897 -897 -897 -897 -897 -897 -897 407 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 372 -897 101 -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 -897 421 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 280 -897 -897 -897 -897 -897 -897 -897 339 -897 -897 -897 -897 -897 -897 220 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 366 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 326 -897 -897 201 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 167 -897 -897 -897 -897 308 -897 -897 -897 -897 280 -897 -897 -897 -897 -897 -897 -897 405 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 334 -897 -897 -897 279 -897 275 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 251 -897 -897 334 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 178 -897 -897 -897 -897 334 -897 -897 -897 -897 -897 -897 -897 -897 -897 195 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 339 -897 -897 -897 -897 -897 -897 295 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 427 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 308 -897 -897 348 -897 -897 -897 -897 -897 -897 478 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 41 nsites= 5 E= 2.1e-055 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 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 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- Y[KQ][ARK]L[IES][DGP][MDKL][GF][EP][EN][IM][GS][LV]AT[VI]Y[RN][VN]L[NR][QV]F[DKR][DE][AIS]G[IL]V[TK][RE][HL][NTH][FY][EG][GD][GAS][KS]S[VR]F -------------------------------------------------------------------------------- Time 0.72 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 41 sites = 5 llr = 457 E-value = 3.9e-043 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::::::::::::::2::::484::::::::::::::::: pos.-specific C a::a::::::::::::::::::::::::::::::::::::a probability D ::6:::::4::66::2::::::::::2:2:::::::::::: matrix E :4:::2::6::::::66:4:6::::::::::::::4::::: F :::::::::a:::::::::::::::::4::::::::::::: G ::::a::::::::2:::::2::::::6:::::::::::a:: H ::::::::::2::::::::::::4:4:::::4a::::::4: I ::::::46:::::26::2:::6:::::4::::::::4:::: K :::::8::::::::::::::::::4:::2::::::::::2: L :6::::::::::::4:2:::4::::::::6::::8:6:::: M ::::::::::::::::::::::::2:::::::::2:::::: N ::2::::::::::::2::::::::::2::::6::::::::: P ::::::::::::4:::::::::::::::::::::::::::: Q ::2:::::::2::2::::62::2:::::::::::::::::: R :::::::::::::::::6:6::::2:::4::::4::::::: S ::::::::::6::4:::::::::2::::::2::6::::::: T :::::::::::::::::::::::::4::2:8:::::::::: V ::::::64:::::::::2::::::2::2:4:::::::::4: W ::::::::::::::::::::::::::::::::::::::::: Y :::::::::::4:::::::::::::2:::::::::6:a::: bits 8.8 7.9 7.1 6.2 Relative 5.3 * * * Entropy 4.4 * ** * * ** * (131.8 bits) 3.5 * ***** * ** * ** ****** ** * 2.6 ***************************************** 1.8 ***************************************** 0.9 ***************************************** 0.0 ----------------------------------------- Multilevel CLDCGKVIEFSDDSIEERQREIAAKHGFRLTNHSLYLYGHC consensus EN EIVD HYPGLDAIEGLAQHMTDIDVSH RMEI V sequence Q Q I NLV Q SRYNVK K Q V T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------------------- FUR_SHIFL 93 1.05e-44 TQQHHHDHLI CLDCGKVIEFSDDSIEARQGEIAAKHGIRLTNHSLYLYGHC AEGDCREDEH FUR_KLEPN 93 1.64e-44 TQQHHHDHLI CLDCGKVIEFSDDSIELRQREIASRHGIRLTNHSLYLYGHC AEGDCRETNT FUR_VIBPA 93 1.18e-41 STQHHHDHLV CLDCGEVIEFSDDIIEERQREIAAKYNVTLTNHSLYLYGKC SDGGCKENPD PERR_STAAU 102 7.43e-40 FNTHNHYHII CEQCGKIVDFQYPQLNEIERLAQHMTDFDVTHHRMEIYGVC KECQDK PERR_BACSU 96 3.67e-39 FVTSDHYHAI CENCGKIVDFHYPGLDEVEQLAAHVTGFKVSHHRLEIYGVC QECSKKENH -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- FUR_SHIFL 1e-44 92_[2]_15 FUR_KLEPN 1.6e-44 92_[2]_22 FUR_VIBPA 1.2e-41 92_[2]_16 PERR_STAAU 7.4e-40 101_[2]_6 PERR_BACSU 3.7e-39 95_[2]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=41 seqs=5 FUR_SHIFL ( 93) CLDCGKVIEFSDDSIEARQGEIAAKHGIRLTNHSLYLYGHC 1 FUR_KLEPN ( 93) CLDCGKVIEFSDDSIELRQREIASRHGIRLTNHSLYLYGHC 1 FUR_VIBPA ( 93) CLDCGEVIEFSDDIIEERQREIAAKYNVTLTNHSLYLYGKC 1 PERR_STAAU ( 102) CEQCGKIVDFQYPQLNEIERLAQHMTDFDVTHHRMEIYGVC 1 PERR_BACSU ( 96) CENCGKIVDFHYPGLDEVEQLAAHVTGFKVSHHRLEIYGVC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 41 n= 650 bayes= 7.96 E= 3.9e-043 -897 497 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 -897 220 -897 -897 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-------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 41 nsites= 5 E= 3.9e-043 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 0.000000 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 0.600000 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 0.000000 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 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C[LE][DNQ]CG[KE][VI][IV][ED]F[SHQ][DY][DP][SGIQ][IL][EDN][EAL][RIV][QE][RGQ][EL][IA][AQ][AHS][KMRV][HTY][GDN][FIV][RDKT][LV][TS][NH]H[SR][LM][YE][LI]YG[HVK]C -------------------------------------------------------------------------------- Time 1.08 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 29 sites = 6 llr = 360 E-value = 6.8e-031 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::7:::::::::3:::::2:::2:::55 pos.-specific C :::::::::::::::::::::::2::::: probability D ::2::::::::::2::::::2:7:::::3 matrix E ::3:::::::::2:::7:::3:::::::: F ::::::::::::::::::2:::::::::: G ::::a:::::::::::::::::::::::: H ::::::::::::2:::::::::2:75::: I :::::::3::::::8::::2::::::2:: K :83:::5:::2::5::::::::::::::2 L a::::5:::5::5::a:28::::::2::: M ::::::::::::::2:::::::2:::::: N :::2:::::2::::::::::2::3::::: P :::::::::35::::::::::5:::3::: Q ::2:::::::3:2:::2::52:::2:::: R :2::::5::::a::::2::::::2::::: S ::::::::::::::::::::25:::::5: T :::2::::a::::::::::::::2::5:: V :::::3:5:::::::::5:2::::::3:: W ::::::::::::::::::::::::::::: Y :::::2:2:::::::::3::::::2:::: bits 8.8 7.9 7.1 6.2 Relative 5.3 Entropy 4.4 * * * (86.5 bits) 3.5 ** * * * ** ** * * 2.6 ** ********* ******* ** ***** 1.8 ***************************** 0.9 ***************************** 0.0 ----------------------------- Multilevel LKEAGLKVTLPRLKILEVLQEPDNHHTAA consensus K VRI PQ A Y S PVSD sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------------------- FUR_SHIFL 8 3.51e-32 MTDNNTA LKKAGLRVTLPRLKILEVLQEPDNHHVSA EDLYKRLIDM FUR_KLEPN 8 6.35e-32 MTDNNTA LKKAGLKVTLPRLKILEVLQEPDNHHVSA EDLYKRLIDM FUR_VIBPA 8 3.06e-29 MSDNNQA LKDAGLKVTLPRLKILEVLQQPDCQHISA EDLYKKLIDL PERR_BACSU 13 2.12e-27 AHELKEALET LKETGVRITPQRHAILEYLVNSMAHPTAD DIYKALEGKF PERR_STAAU 19 1.00e-26 EHELEESIAS LRQAGVRITPQRQAILRYLISSHTHPTAD EIYQALSPDF ZUR_BACSU 10 3.82e-24 MNVQEALNL LKENGYKYTNKREDMLQLFADSDRYLTAK NVLSALNDDY -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- FUR_SHIFL 3.5e-32 7_[3]_112 FUR_KLEPN 6.4e-32 7_[3]_119 FUR_VIBPA 3.1e-29 7_[3]_113 PERR_BACSU 2.1e-27 12_[3]_104 PERR_STAAU 1e-26 18_[3]_101 ZUR_BACSU 3.8e-24 9_[3]_107 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=29 seqs=6 FUR_SHIFL ( 8) LKKAGLRVTLPRLKILEVLQEPDNHHVSA 1 FUR_KLEPN ( 8) LKKAGLKVTLPRLKILEVLQEPDNHHVSA 1 FUR_VIBPA ( 8) LKDAGLKVTLPRLKILEVLQQPDCQHISA 1 PERR_BACSU ( 13) LKETGVRITPQRHAILEYLVNSMAHPTAD 1 PERR_STAAU ( 19) LRQAGVRITPQRQAILRYLISSHTHPTAD 1 ZUR_BACSU ( 10) LKENGYKYTNKREDMLQLFADSDRYLTAK 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 29 n= 722 bayes= 6.89885 E= 6.8e-031 -923 -923 -923 -923 -923 -923 -923 -923 -923 334 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 386 -923 -923 -923 -923 -923 182 -923 -923 -923 -923 -923 -923 -923 124 194 -923 -923 -923 -923 254 -923 -923 -923 -923 216 -923 -923 -923 -923 -923 -923 351 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 182 -923 -923 -923 -923 154 -923 -923 -923 -923 -923 -923 -923 -923 407 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 234 -923 -923 -923 -923 -923 -923 -923 263 -923 207 -923 -923 -923 -923 -923 -923 -923 -923 313 -923 -923 -923 -923 -923 340 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 246 -923 -923 -923 -923 -923 -923 -923 -923 -923 321 -923 207 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 413 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 234 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-------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 29 nsites= 6 E= 6.8e-031 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 0.833333 0.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.333333 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 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0.166667 0.000000 0.166667 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 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.166667 0.000000 0.166667 0.000000 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 0.000000 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.166667 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 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.333333 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 0.500000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.166667 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 -------------------------------------------------------------------------------- LK[EK]AG[LV][KR][VI]T[LP][PQ]RL[KA]ILE[VY]LQE[PS]DNH[HP][TV][AS][AD] -------------------------------------------------------------------------------- Time 1.30 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- PERR_BACSU 4.79e-95 12_[3(2.12e-27)]_2_[1(1.83e-40)]_11_[2(3.67e-39)]_9 PERR_STAAU 8.61e-96 18_[3(1.00e-26)]_2_[1(3.12e-41)]_11_[2(7.43e-40)]_6 FUR_SHIFL 2.48e-114 7_[3(3.51e-32)]_3_[1(1.29e-49)]_12_[2(1.05e-44)]_15 FUR_KLEPN 8.37e-114 7_[3(6.35e-32)]_3_[1(1.29e-49)]_12_[2(1.64e-44)]_22 FUR_VIBPA 1.03e-103 7_[3(3.06e-29)]_3_[1(6.44e-45)]_12_[2(1.18e-41)]_16 ZUR_BACSU 4.59e-24 9_[3(3.82e-24)]_2_[1(1.46e-07)]_64 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo-count ********************************************************************************