******************************************************************************** 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 ------------- ------ ------ ------------- ------ ------ NRDI_STACT 1.0000 130 NRDI_DEIRA 1.0000 141 NRDI_SHIBS 1.0000 136 NRDI_KLEP7 1.0000 136 NRDI_WIGBR 1.0000 141 NRDI_BACSU 1.0000 130 ******************************************************************************** ******************************************************************************** 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= 814 N= 6 sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.066 C 0.007 D 0.042 E 0.052 F 0.055 G 0.080 H 0.023 I 0.055 K 0.057 L 0.075 M 0.018 N 0.063 P 0.047 Q 0.038 R 0.068 S 0.058 T 0.055 V 0.095 W 0.012 Y 0.034 Background letter frequencies (from dataset with add-one prior applied): A 0.066 C 0.008 D 0.042 E 0.052 F 0.055 G 0.079 H 0.024 I 0.055 K 0.056 L 0.074 M 0.019 N 0.062 P 0.047 Q 0.038 R 0.067 S 0.058 T 0.055 V 0.094 W 0.013 Y 0.035 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 50 sites = 6 llr = 633 E-value = 1.9e-069 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::22:::::272:::::::2:5:83:::52::2::::2:::::::22::2 pos.-specific C :::::::::::::::::::::2:::::::::3:::::::::::::::::: probability D ::::::::::::::::::3::::::8::::2:::::::::::::::2a:: matrix E ::::::::::::::::::2:::::::::::2:::::::::8::::::::5 F :::22:::::::::::5:::7::::::::::::::::::8:::::::::: G ::3::::a::3:a::::a:2:3::5:::::::2:::::::::2a:::::: H 72:3:::::::::::2::2::::::::::::::::::2:::::::::::: I :::::3:::5::::::::::::2:::2a:::::::2::::::::::::32 K 2:2:::2:::::::3:::::::3::::::35:2:::::7::2:::25::: L ::::772::::::::::::::::::::::::::::38::2:72::::::: M ::::2:::::::::::::::::::::::::::2::::2::::3::::::: N :7:::::::::::8:7:::7:::::2::::::::::::::2::::2:::2 P ::::::::::::::::::::::::::::::::::a::::::::::2:::: Q :::2::::::::::::::2::::::::::22:2:::::::::2::2:::: R ::3:::7:::::::5:::::::5::::::3::2:::::3:::::::::2: S :::::::::::8:2:::::::::22:::5:::::::::::::2::22::: T 2::2::::::::::::::::::::::3:::::::::::::::::a::::: V ::::::::a3:::::2::2:::::::5::::::a:22::::2::::::5: W ::::::::::::::::5:::2::::::::::::::2:::::::::::::: Y :2::::::::::::2:::::2::::::::::7:::2:5:::::::::::: bits 6.9 6.2 5.5 4.8 * * Relative 4.1 * * * * * * * Entropy 3.4 ** ** *** ** * * * * * ** **** ** * (152.2 bits) 2.8 ** ************** ***** * ** ** ** ****** ** * 2.1 ********************************************* **** 1.4 ************************************************** 0.7 ************************************************** 0.0 -------------------------------------------------- Multilevel HNGHLLRGVIASGNRNFGDNFARAGDVIAKKYxVPLLYKFELMGTxKDVE consensus R I VG K W GK A T SR C R I sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------------- NRDI_SHIBS 70 1.76e-50 RQVIRFLNDE HNRALLRGVIASGNRNFGEAYGRAGDVIARKCGVPWLYRFELMGTQSDIE NVRKGVTEFW NRDI_STACT 63 1.05e-49 VPDVVQTFLR HNGTMIRGVVGSGNRNWGQNFAKASDTISKDYMVPLLMKFEVQGTKKDVE EFKDKVGHFY NRDI_KLEP7 70 3.19e-49 RQAIRFLNDV HNRQLIRGVIAAGNRNFGDGWGRAGDVIAQKCAVPYLYRFELMGTPDDIN TVRKGVSEFW NRDI_BACSU 60 4.24e-47 VPASTQSFLE KYAHLLLGVAASGNKVWGDNFAKSADTISRQYQVPILHKFELSGTSKDVE LFTQEVERVV NRDI_WIGBR 70 1.01e-46 HQVTNFLNTL HNKFFLKGVIGSGNKNFGVNFCIAGNIISKKYKVPLLYKFELLGTNKDVI NVKNGINKFW NRDI_DEIRA 62 6.41e-44 VPASTRRLLT THGHLLRGVVASGSYHWGHNFARAADVIAAEYRVPVVAKLNKGGTAADRA AVRRWLLHYA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- NRDI_SHIBS 1.8e-50 69_[1]_17 NRDI_STACT 1.1e-49 62_[1]_18 NRDI_KLEP7 3.2e-49 69_[1]_17 NRDI_BACSU 4.2e-47 59_[1]_21 NRDI_WIGBR 1e-46 69_[1]_22 NRDI_DEIRA 6.4e-44 61_[1]_30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=50 seqs=6 NRDI_SHIBS ( 70) HNRALLRGVIASGNRNFGEAYGRAGDVIARKCGVPWLYRFELMGTQSDIE 1 NRDI_STACT ( 63) HNGTMIRGVVGSGNRNWGQNFAKASDTISKDYMVPLLMKFEVQGTKKDVE 1 NRDI_KLEP7 ( 70) HNRQLIRGVIAAGNRNFGDGWGRAGDVIAQKCAVPYLYRFELMGTPDDIN 1 NRDI_BACSU ( 60) KYAHLLLGVAASGNKVWGDNFAKSADTISRQYQVPILHKFELSGTSKDVE 1 NRDI_WIGBR ( 70) HNKFFLKGVIGSGNKNFGVNFCIAGNIISKKYKVPLLYKFELLGTNKDVI 1 NRDI_DEIRA ( 62) THGHLLRGVVASGSYHWGHNFARAADVIAAEYRVPVVAKLNKGGTAADRA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 50 n= 520 bayes= 6.8726 E= 1.9e-069 -923 -923 -923 -923 -923 -923 479 -923 156 -923 -923 -923 -923 -923 -923 -923 159 -923 -923 -923 -923 -923 -923 -923 -923 -923 279 -923 -923 -923 -923 342 -923 -923 -923 -923 -923 -923 -923 226 134 -923 -923 -923 -923 207 -923 -923 156 -923 -923 -923 -923 -923 231 -923 -923 -923 -923 -923 134 -923 -923 -923 159 -923 379 -923 -923 -923 -923 -923 -923 212 -923 -923 159 -923 -923 -923 -923 -923 -923 -923 159 -923 -923 -923 -923 316 312 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 259 -923 316 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 156 116 -923 -923 -923 -923 331 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 366 -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 -923 342 -923 -923 134 -923 -923 -923 -923 -923 -923 318 -923 -923 -923 -923 -923 -923 -923 -923 -923 183 -923 -923 334 -923 -923 -923 -923 207 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 134 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 385 -923 -923 -923 -923 -923 -923 -923 -923 -923 366 -923 -923 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289 -923 -923 -923 -923 -923 366 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 153 -923 -923 -923 -923 234 -923 -923 -923 -923 266 -923 -923 -923 -923 -923 -923 -923 -923 -923 153 -923 -923 -923 -923 -923 -923 431 -923 -923 -923 -923 -923 -923 -923 -923 142 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 159 -923 -923 -923 -923 -923 -923 -923 -923 259 242 -923 -923 -923 -923 -923 -923 -923 -923 -923 418 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 292 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 312 -923 -923 -923 -923 134 -923 -923 -923 -923 -923 -923 -923 256 -923 -923 -923 -923 212 231 -923 -923 -923 -923 -923 -923 -923 199 169 -923 -923 -923 -923 315 -923 -923 -923 -923 212 -923 -923 -923 -923 -923 -923 -923 531 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 426 134 -923 -923 -923 -923 107 -923 -923 156 -923 312 -923 -923 212 131 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 342 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 442 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 159 -923 216 -923 -923 -923 -923 -923 -923 -923 83 366 226 -923 -923 -923 -923 -923 -923 -923 -923 -923 348 -923 -923 -923 -923 -923 -923 -923 83 -923 -923 134 -923 -923 -923 -923 -923 279 -923 -923 -923 312 -923 -923 -923 -923 -923 -923 -923 -923 384 -923 -923 -923 -923 -923 -923 -923 -923 356 -923 -923 -923 -923 -923 231 -923 -923 -923 -923 -923 -923 -923 -923 -923 392 -923 -923 -923 -923 116 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 401 -923 -923 -923 -923 -923 -923 -923 142 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 156 316 -923 -923 -923 -923 -923 -923 -923 83 -923 -923 -923 -923 -923 -923 -923 107 -923 -923 -923 116 412 -923 -923 212 -923 153 -923 -923 -923 -923 -923 -923 -923 -923 -923 366 -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 -923 418 -923 -923 -923 134 -923 -923 -923 -923 -923 -923 -923 156 -923 -923 142 183 212 -923 153 -923 -923 -923 -923 134 -923 199 -923 -923 -923 -923 -923 315 -923 -923 -923 -923 -923 -923 153 -923 -923 -923 -923 -923 -923 457 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 259 -923 -923 -923 -923 -923 -923 131 -923 -923 242 -923 -923 134 -923 -923 328 -923 -923 -923 159 -923 -923 -923 142 -923 -923 -923 -923 -923 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 50 nsites= 6 E= 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0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- HN[GR]HL[LI]RGV[IV][AG]SGN[RK]N[FW]GDNF[AG][RK]A[GA]D[VT]I[AS][KR]K[YC]xVPLLY[KR]FELMGTxKD[VI]E -------------------------------------------------------------------------------- Time 0.25 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 49 sites = 3 llr = 379 E-value = 1.7e-030 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::::::::::::::::::::::a:::::::::::::::::::::::: pos.-specific C :::::::::::::::::::::3::::::::::::::::::::::::::: probability D :::::::::::::::::::::::::::::::3::::::7:::::::::: matrix E :::::::::::a::::::3::::::::::::7:73::::7::::::::: F ::::::a:::::::::a::::::::::::::::::3::::::::::::: G :::::::::::::::::::::7::::::::::::::::::::::::::: H ::::::::::::::7:::::::::::::::::::3:::::::::::::: I :::3:::::::::::::3::::3::::a::3::::3:3::::a:73::: K ::::::::::::::::::33:::::3::::::33::::3:::::::::: L ::37::::::::::::::::a:3::::::a:::::3:::::::a::::: M a:::::::::::::::::::::3:::::::::::::::::::::::::: N ::::::::::::a:::::::::::::::::7:::::::::::::::::: P :::::::::::::::::::::::a::::a:::::::::::a:::::a:: Q ::3:::::::::::3:::3:::::::::::::::::7:::::::::::: R :::::::::3:::::a:::7::::::a:::::7:3:3:::::::::::: S :a:::::aa7a::::::::::::::::::::::::::::3:::::::a: T :::::::::::::a::::::::::::::::::::::::::::::::::: V ::3:a::::::::::::7:::::::7:::::::::::7::::::37::: W ::::::::::::::::::::::::::::::::::::::::::::::::: Y :::::a:::::::::::::::::::::::::::::::::::a::::::a bits 6.9 6.2 5.5 * 4.8 * * * * Relative 4.1 ** **** ******* * ** *** *** *** Entropy 3.4 ** ************* ** ** ****** * * ****** *** (182.1 bits) 2.8 ** ********************************************** 2.1 ************************************************* 1.4 ************************************************* 0.7 ************************************************* 0.0 ------------------------------------------------- Multilevel MSLLVYFSSSSENTHRFVERLGIPAVRIPLNEREEFQVDEPYILIVPSY consensus QI R Q IKK CL K IDKKHIRIKS VI sequence V Q M RL -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------------------------- NRDI_SHIBS 1 5.22e-58 . MSQLVYFSSSSENTQRFIERLGMPAVRIPLNERERIQVDEPYILIVPSY GGGGTAGAVP NRDI_KLEP7 1 1.61e-56 . MSLIVYFSSRSENTHRFVQRLGLPAVRIPLNEREHLRVDEPYILIVPSY GGGGTAGAVP NRDI_WIGBR 1 3.60e-55 . MSVLVYFSSSSENTHRFVKKLCIPAKRIPLIDKKEFQIKSPYILVIPSY NNGILDTAVP -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- NRDI_SHIBS 5.2e-58 [2]_87 NRDI_KLEP7 1.6e-56 [2]_87 NRDI_WIGBR 3.6e-55 [2]_92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=49 seqs=3 NRDI_SHIBS ( 1) MSQLVYFSSSSENTQRFIERLGMPAVRIPLNERERIQVDEPYILIVPSY 1 NRDI_KLEP7 ( 1) MSLIVYFSSRSENTHRFVQRLGLPAVRIPLNEREHLRVDEPYILIVPSY 1 NRDI_WIGBR ( 1) MSVLVYFSSSSENTHRFVKKLCIPAKRIPLIDKKEFQIKSPYILVIPSY 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 49 n= 526 bayes= 7.89537 E= 1.7e-030 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 570 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 411 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 216 -823 -823 -823 311 -823 -823 -823 183 -823 -823 -823 -823 -823 -823 -823 -823 -823 259 -823 316 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 341 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 484 -823 -823 -823 -823 418 -823 -823 -823 -823 -823 -823 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-823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 259 -823 -823 -823 -823 -823 -823 -823 -823 -823 283 -823 -823 -823 -823 -823 269 -823 -823 -823 -823 256 -823 -823 -823 -823 311 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 256 -823 -823 -823 -823 -823 331 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 375 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 531 -823 -823 -823 307 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 259 -823 216 411 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 441 -823 -823 -823 -823 -823 -823 -823 392 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 256 -823 -823 -823 -823 -823 -823 -823 -823 283 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 -823 389 -823 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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 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 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- MS[LQV][LI]VYFSS[SR]SENT[HQ]RF[VI][EKQ][RK]L[GC][ILM]PA[VK]RIPL[NI][ED][RK][EK][EHR][FIL][QR][VI][DK][ES]PYIL[IV][VI]PSY -------------------------------------------------------------------------------- Time 0.35 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 15 sites = 6 llr = 175 E-value = 3.2e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::3:5::3:2:::: pos.-specific C ::::::::::::::: probability D :::2::::2:::::: matrix E :::::3::::::::: F :2:3:::::::::8: G 533:8:::::::::: H ::::::::2:::::: I :3:::::::::3::: K ::::::::::::::: L ::2::::::::::2a M ::::::::::::::: N ::2:::::::::2:: P :::::::a::::::: Q :::::2:::5:3::: R ::::::::3::25:: S :::2:::::3::2:: T 523:2:::::322:: V ::::::a::25:::: W ::::::::::::::: Y ::::::::::::::: bits 6.9 6.2 5.5 4.8 Relative 4.1 * Entropy 3.4 ** ** (42.2 bits) 2.8 * **** * ** 2.1 *************** 1.4 *************** 0.7 *************** 0.0 --------------- Multilevel GGGAGAVPAQVIRFL consensus TITF E RSTQ sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- NRDI_SHIBS 52 6.89e-16 YILIVPSYGG GGTAGAVPRQVIRFL NDEHNRALLR NRDI_KLEP7 52 4.03e-15 YILIVPSYGG GGTAGAVPRQAIRFL NDVHNRQLIR NRDI_BACSU 44 5.85e-14 VDTPFVLVTY TTNFGQVPASTQSFL EKYAHLLLGV NRDI_STACT 47 5.85e-14 IDEPYILVTS TIGFGEVPDVVQTFL RHNGTMIRGV NRDI_WIGBR 52 1.64e-13 YILVIPSYNN GILDTAVPHQVTNFL NTLHNKFFLK NRDI_DEIRA 46 3.00e-13 PTDAYLLLTY TFGSGEVPASTRRLL TTHGHLLRGV -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- NRDI_SHIBS 6.9e-16 51_[3]_70 NRDI_KLEP7 4e-15 51_[3]_70 NRDI_BACSU 5.9e-14 43_[3]_72 NRDI_STACT 5.9e-14 46_[3]_69 NRDI_WIGBR 1.6e-13 51_[3]_75 NRDI_DEIRA 3e-13 45_[3]_81 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=6 NRDI_SHIBS ( 52) GGTAGAVPRQVIRFL 1 NRDI_KLEP7 ( 52) GGTAGAVPRQAIRFL 1 NRDI_BACSU ( 44) TTNFGQVPASTQSFL 1 NRDI_STACT ( 47) TIGFGEVPDVVQTFL 1 NRDI_WIGBR ( 52) GILDTAVPHQVTNFL 1 NRDI_DEIRA ( 46) TFGSGEVPASTRRLL 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 15 n= 730 bayes= 6.91488 E= 3.2e-006 -923 -923 -923 -923 -923 266 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 318 -923 -923 -923 -923 -923 -923 -923 159 207 -923 259 -923 -923 -923 -923 -923 -923 -923 -923 159 -923 -923 -923 -923 -923 -923 -923 -923 207 -923 -923 -923 116 -923 142 -923 -923 -923 -923 259 -923 -923 -923 234 -923 199 -923 259 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 153 -923 -923 -923 -923 -923 -923 -923 -923 -923 339 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 159 -923 -923 -923 292 -923 -923 269 -923 -923 -923 -923 -923 -923 -923 -923 -923 212 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 342 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 442 -923 -923 -923 -923 -923 -923 -923 234 -923 199 -923 -923 -923 279 -923 -923 -923 -923 -923 -923 -923 231 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 370 -923 253 -923 83 -923 -923 134 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 259 242 -923 -923 -923 -923 -923 -923 -923 -923 -923 259 -923 -923 -923 -923 -923 312 131 -923 159 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 142 -923 -923 289 153 159 -923 -923 -923 -923 -923 -923 -923 392 -923 -923 -923 -923 116 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 375 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 15 nsites= 6 E= 3.2e-006 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 0.166667 0.333333 0.000000 0.333333 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 0.333333 0.000000 0.000000 0.000000 0.166667 0.000000 0.166667 0.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.333333 0.000000 0.166667 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.166667 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.166667 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 0.000000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.333333 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 0.333333 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 0.500000 0.000000 0.333333 0.000000 0.166667 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 0.000000 0.000000 0.000000 0.000000 0.333333 0.500000 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 0.333333 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 0.166667 0.000000 0.000000 0.500000 0.166667 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.000000 0.000000 0.000000 0.166667 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 0.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GT][GI][GT][AF]G[AE]VP[AR][QS][VT][IQ]RFL -------------------------------------------------------------------------------- Time 0.42 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- NRDI_STACT 2.22e-55 46_[3(5.85e-14)]_1_[1(1.05e-49)]_18 NRDI_DEIRA 1.57e-48 45_[3(3.00e-13)]_1_[1(6.41e-44)]_30 NRDI_SHIBS 2.14e-112 [2(5.22e-58)]_2_[3(6.89e-16)]_3_[1(1.76e-50)]_17 NRDI_KLEP7 6.54e-109 [2(1.61e-56)]_2_[3(4.03e-15)]_3_[1(3.19e-49)]_17 NRDI_WIGBR 1.99e-103 [2(3.60e-55)]_2_[3(1.64e-13)]_3_[1(1.01e-46)]_22 NRDI_BACSU 1.87e-52 43_[3(5.85e-14)]_1_[1(4.24e-47)]_21 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo ********************************************************************************