******************************************************************************** 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 ------------- ------ ------ ------------- ------ ------ RSGA_BACSU 1.0000 298 RSGA_GEOSW 1.0000 293 RSGA2_OCEIH 1.0000 293 RSGA2_LISIN 1.0000 291 RSGA_STRP1 1.0000 290 RSGA_LACSS 1.0000 299 ******************************************************************************** ******************************************************************************** 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= 1764 N= 6 sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.055 C 0.015 D 0.060 E 0.091 F 0.045 G 0.062 H 0.022 I 0.077 K 0.066 L 0.091 M 0.015 N 0.036 P 0.044 Q 0.037 R 0.058 S 0.062 T 0.052 V 0.067 W 0.002 Y 0.043 Background letter frequencies (from dataset with add-one prior applied): A 0.055 C 0.016 D 0.060 E 0.090 F 0.045 G 0.062 H 0.022 I 0.077 K 0.066 L 0.090 M 0.016 N 0.036 P 0.044 Q 0.037 R 0.058 S 0.062 T 0.052 V 0.067 W 0.002 Y 0.043 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 50 sites = 6 llr = 701 E-value = 5.2e-101 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::::3:2:::2:2:5::::::::::::::2:::::::::::8:::::: pos.-specific C :::::::::::::::::::::::::::::::::::::::::::::::::: probability D ::::::::3:3::::::2::2::::::::::::::::::3::::a::::: matrix E ::::::::::3:::3::8::2::::::::::::8::2::::::::::::: F ::::::::::::::::::::::::::::::::::2::::::2::::::a: G ::::::::::::2:::2::::::8:a::::::::::::55a::2:::a:: H ::::::2::::::::::::::3:::::a:::8::::2:2::::::::::: I ::::2::5:::::::2::a:::::::::::::2::3:5::::2::::::: K a:::::::::2:::3:::::2:::::8:::::::::2::::2:::::::: L :::a8::5:::a2a::::::::a:::::::::::82:2:::7:::::::: M :::::::::::::::::::::::::::::::::::3:::::::::::::: N :::::a::2:::2:::3:::2::2::::::::::::2:22:::::::::: P :::::::::8::::::::::::::::::::::::::3:::::::::a::: Q ::::::::::::2:::::::2::::::::::::::::::::::::::::: R ::::::2:2:::::2:::::::::a:2:::a::::::::::::::::::: S :a5:::2:222::::::::a:7:::::::::::2::::2::::::::::a T ::5:::::::::2::8::::2:::::::aa:::::::3:::::::a:::: V ::::::2:::::::::::::::::::::::::8:::::::::8::::::: W :::::::::::::::::::::::::::::::::::::::::::::::::: Y :::::::::::::::::::::::::::::::::::2:::::::::::::: bits 8.8 7.9 7.0 6.2 Relative 5.3 * Entropy 4.4 * * * ** ***** * ****** (168.6 bits) 3.5 **** * * * * * ** ************ * ******** 2.6 ****** * * * * ***** *************** ************* 1.8 ************************************************** 0.9 ************************************************** 0.0 -------------------------------------------------- Multilevel KSSLLNAIDPDLxLETAEISxSLGRGKHTTRHVELIPIGGGLVADTPGFS consensus T L E K N H M T D sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------------- RSGA2_LISIN 170 1.31e-54 AVIAGQSGVG KSTLLNSLNSDLTLKTAEISNSLGRGKHTTRHVELMPIGDGFVADTPGFS SIEWDDLQPE RSGA_BACSU 177 1.42e-53 TVFAGQSGVG KSSLLNAISPELGLRTNEISEHLGRGKHTTRHVELIHTSGGLVADTPGFS SLEFTDIEEE RSGA_GEOSW 172 1.89e-53 SVFAGQSGVG KSSLLNALRPDLQLKTNDISTHLGRGKHTTRHVELLEIGGGLVADTPGFS ALELDDIELE RSGA2_OCEIH 172 4.24e-53 SVFAGQSGVG KSSLINVLDPSLLLETAEISKSLGRGKHTTRHVELMKIGNGLVADTPGFS VLEFREIEAE RSGA_LACSS 174 6.23e-52 TVFTGQTGAG KSTLLNHIDPKLNLATAEISQSLNRGKHTTRHIELIPLNDGLVGDTPGFS SLGILNVTSE RSGA_STRP1 162 2.44e-49 TVFMGQTGVG KSTLLNRIAPELALEIGEISDSLGRGRHTTRAVSFYNTHGGKIADTPGFS SLDYDIANAE -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RSGA2_LISIN 1.3e-54 169_[1]_72 RSGA_BACSU 1.4e-53 176_[1]_72 RSGA_GEOSW 1.9e-53 171_[1]_72 RSGA2_OCEIH 4.2e-53 171_[1]_72 RSGA_LACSS 6.2e-52 173_[1]_76 RSGA_STRP1 2.4e-49 161_[1]_79 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=50 seqs=6 RSGA2_LISIN ( 170) KSTLLNSLNSDLTLKTAEISNSLGRGKHTTRHVELMPIGDGFVADTPGFS 1 RSGA_BACSU ( 177) KSSLLNAISPELGLRTNEISEHLGRGKHTTRHVELIHTSGGLVADTPGFS 1 RSGA_GEOSW ( 172) KSSLLNALRPDLQLKTNDISTHLGRGKHTTRHVELLEIGGGLVADTPGFS 1 RSGA2_OCEIH ( 172) KSSLINVLDPSLLLETAEISKSLGRGKHTTRHVELMKIGNGLVADTPGFS 1 RSGA_LACSS ( 174) KSTLLNHIDPKLNLATAEISQSLNRGKHTTRHIELIPLNDGLVGDTPGFS 1 RSGA_STRP1 ( 162) KSTLLNRIAPELALEIGEISDSLGRGRHTTRAVSFYNTHGGKIADTPGFS 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 50 n= 1470 bayes= 8.37977 E= 5.2e-101 -923 -923 -923 -923 -923 -923 -923 -923 393 -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 -923 402 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 302 328 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 347 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 112 -923 320 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 478 -923 -923 -923 -923 -923 -923 -923 -923 260 -923 -923 -923 -923 -923 289 -923 -923 -923 -923 -923 -923 -923 151 143 -923 131 -923 -923 -923 -923 -923 -923 -923 -923 -923 270 -923 247 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 160 -923 247 -923 -923 -923 -923 -923 -923 -923 -923 219 -923 -923 151 143 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 425 -923 -923 143 -923 -923 -923 -923 -923 -923 247 188 -923 -923 -923 -923 134 -923 -923 -923 -923 -923 -923 143 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 347 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 160 -923 -923 -923 -923 142 -923 -923 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-923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 374 -923 -923 -923 -923 -923 219 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 410 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 400 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 367 -923 -923 -923 -923 -923 151 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 548 -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 -923 428 -923 -923 -923 -923 -923 -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 -923 410 -923 -923 -923 -923 -923 160 -923 -923 -923 -923 -923 521 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 112 -923 -923 -923 -923 -923 -923 -923 -923 -923 363 -923 -923 -923 -923 -923 320 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 143 -923 -923 -923 -923 -923 -923 -923 -923 187 -923 -923 -923 -923 320 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 212 -923 88 441 -923 -923 -923 -923 -923 -923 -923 -923 197 -923 -923 -923 88 -923 -923 289 -923 134 -923 -923 219 293 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 270 -923 88 -923 -923 -923 -923 -923 -923 269 -923 -923 -923 -923 -923 -923 -923 -923 300 289 -923 -923 -923 -923 219 -923 -923 -923 143 -923 -923 -923 -923 -923 -923 247 -923 -923 300 -923 -923 -923 -923 -923 219 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 400 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 187 -923 -923 -923 134 288 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 112 -923 -923 -923 -923 -923 -923 -923 -923 -923 363 -923 -923 392 -923 -923 -923 -923 142 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 406 -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 -923 -923 428 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 451 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 400 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 446 -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 -923 402 -923 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: 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0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- KS[ST]LLNA[IL]DP[DE]LxL[EK]T[AN]EISx[SH]LGRGKHTTRHVEL[IM]P[IT]G[GD]GLVADTPGFS -------------------------------------------------------------------------------- Time 0.62 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 50 sites = 6 llr = 690 E-value = 1.3e-095 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::::::::::2::::a::3a::3:::3:::::::::::2::::::::: pos.-specific C :::a::::a:::::::a::::::::::::::::::::::::::::::::: probability D ::2::::::::3:::::::::::22::::2:::2::::::::::3::::: matrix E :23::::::::::a::::::3::8:28::::::3:::2::3a:22::2:: F :::::a::::::::::::::::::::::::3:::::::8::::::::::: G 2:2::::7:::::::::::::::::7:::::::::::::::::::::::: H :3::::::::a:2:::::::::::::::::::::7::::::::::::::: I :::::::::::2:::::::::::::::7::::::::3:2:::7::2:::: K ::::a:::::::3::8:::8::::::2:2::::2:::::::::7::7::: L ::2::::::3:2::::::::::2::::3::::::::5::5::3::::::: M 2::::::::3::2:::::::::::::::2::::::::::2:::::::::: N ::::::::::::2::2::::::::22:::::::23:::::::::3::::: P ::::::::::::::a:::::::::::::22:::::::::::::::::8:: Q :2:::::::2::::::::::2::::::::3:::::::5::2::2:::::: R 2:::::a::::::::::::2:::::::::::a:::::2:2:::::83:7: S 532::::2::::::::::::::::2::::22::::::2::2::::::::: T :::::::2:2:2::::::::2:::2::::::::2::::::2:::2:::2: V :::::::::::2::::::a:::8::::::22:::::2::2::::::::2: W ::::::::::::::::::::::::::::2::::::::::::::::::::: Y ::::::::::::::::::::::::::::::3:a::a:::::::::::::a bits 8.8 7.9 7.0 6.2 * * * Relative 5.3 * * * * Entropy 4.4 * ** * * * ** * ** ** * (165.9 bits) 3.5 **** * * ******* ** ** ** * * * * * 2.6 ** ******** ******** *** **** *** ** *** ********* 1.8 ************************************************** 0.9 ************************************************** 0.0 -------------------------------------------------- Multilevel SHECKFRGCLHDKEPKCAVKAAVEAGEIAQFRYEHYLQFLEEIKDRKPRY consensus S M E L Y N I L N R sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------------- RSGA2_OCEIH 244 5.49e-54 ADSFPEFNAR MHLCKFRGCMHDKEPKCAVKEAVENEEIAVFRYNHYLRFLEEIQTRKPRY RSGA2_LISIN 242 1.01e-52 QFCFPEMEDR RSGCKFRGCMHDNEPNCAVKTAVEANEIADFRYKHYIQILQELKNRKPRY RSGA_BACSU 249 2.22e-52 GYTFPDIREK SSSCKFRGCLHLKEPKCAVKQAVEDGELKQYRYDHYVEFMTEIKDRKPRY RSGA_STRP1 234 2.89e-51 NEAFPELRRL SHECKFRSCTHTHEPKCAVKAALETGELWPVRYEHYLQFLSEIENRRETY KKVIKRK RSGA_LACSS 246 1.84e-50 VSRYPEFREI GQDCKFRTCQHVMEPKCAVKAAVDAGEIMQSRYTNYLQFRAELKDIRPVY KKSK RSGA_GEOSW 244 9.51e-50 PLYFPEFCER SEECKFRGCLHIAEPKCAVREAVESGKIPSYRYENYISFVEEIKERKPRY -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RSGA2_OCEIH 5.5e-54 243_[2] RSGA2_LISIN 1e-52 241_[2] RSGA_BACSU 2.2e-52 248_[2] RSGA_STRP1 2.9e-51 233_[2]_7 RSGA_LACSS 1.8e-50 245_[2]_4 RSGA_GEOSW 9.5e-50 243_[2] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=50 seqs=6 RSGA2_OCEIH ( 244) MHLCKFRGCMHDKEPKCAVKEAVENEEIAVFRYNHYLRFLEEIQTRKPRY 1 RSGA2_LISIN ( 242) RSGCKFRGCMHDNEPNCAVKTAVEANEIADFRYKHYIQILQELKNRKPRY 1 RSGA_BACSU ( 249) SSSCKFRGCLHLKEPKCAVKQAVEDGELKQYRYDHYVEFMTEIKDRKPRY 1 RSGA_STRP1 ( 234) SHECKFRSCTHTHEPKCAVKAALETGELWPVRYEHYLQFLSEIENRRETY 1 RSGA_LACSS ( 246) GQDCKFRTCQHVMEPKCAVKAAVDAGEIMQSRYTNYLQFRAELKDIRPVY 1 RSGA_GEOSW ( 244) SEECKFRGCLHIAEPKCAVREAVESGKIPSYRYENYISFVEEIKERKPRY 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 50 n= 1470 bayes= 8.37977 E= 1.3e-095 -923 -923 -923 -923 -923 142 -923 -923 -923 -923 341 -923 -923 -923 151 302 -923 -923 -923 -923 -923 -923 -923 88 -923 -923 389 -923 -923 -923 -923 -923 -923 217 -923 243 -923 -923 -923 -923 -923 -923 147 188 -923 142 -923 -923 -923 88 -923 -923 -923 -923 -923 143 -923 -923 -923 -923 -923 599 -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 -923 393 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 446 -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 -923 410 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 342 -923 -923 -923 -923 -923 -923 -923 -923 -923 143 169 -923 -923 -923 -923 599 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 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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 0.000000 0.666667 0.000000 0.166667 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 -------------------------------------------------------------------------------- S[HS]ECKFRGC[LM]HDKEPKCAVK[AE]AVEAGE[IL]AQ[FY]RYE[HN]Y[LI]QFLEE[IL]K[DN]R[KR]PRY -------------------------------------------------------------------------------- Time 1.05 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 50 sites = 6 llr = 691 E-value = 2.1e-093 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::7::::a:::::a:::::::2:2:::::2::2:2:::::::::::: pos.-specific C :::::2:::::::::::::::::::::::::::::::::::::3:::::: probability D ::::::::8:::::::::2:7::::::a:::::::::3::::::::::a: matrix E ::::::::2:::::::::7:2:::::::::::::a:2::::::::::::: F ::::::::::::::5::::::a:::::::a:::::::::::::::::::: G ::::::::::::::::::::::::::::::::::::::::2::::::::: H :::::::::::::::::::::::::::::::::::2:3:2:::::::::: I 3:::7::7:2:523:::::::::::::::::3:3::::a::57:7::::: K :::::::::::::::::2:::::::::::::::::25:::::::::a::: L ::::::::::::5::::::::::22a8:::a:73::2::::2:22::::8 M ::::::::::::::2::::::::::::::::::::::::::::::::7:2 N ::::::a:::::::::::::::2:5:::::::::::22:::::::2:::: P ::aa:::::::::::::::a::::::::::::::::::::8::::::::: Q :::::::::8::::::::2::::::::::::::::::::7:::::::::: R :a::::::::::::::::::::::2:::a::::::::::2:::::::::: S ::::::::::::::2a::::2:72:::::::::::5:::::::::3:::: T ::::::::::::::::::::::27:::::::::::::::::::::5:2:: V 7:::32:3:::5372::8:::::::::::::7:3:::::::3322::2:: W :::::::::::::::::::::::::::::::::::::::::::::::::: Y ::::::::::::::::::::::::::::::::2::::::::::3:::::: bits 8.8 7.9 7.0 6.2 Relative 5.3 Entropy 4.4 *** * * ** * * *** ** (166.2 bits) 3.5 *** ** *** *** * * * **** * *** **** 2.6 ************ ******************** ** ************* 1.8 ************************************************** 0.9 ************************************************** 0.0 -------------------------------------------------- Multilevel VRPPIANIDQAILVFSAVEPDFSTNLLDRFLVLIESKDIQPIICITKMDL consensus I V V VVI I L H VVY S sequence V -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------------- RSGA_BACSU 71 3.43e-54 MEIKERTNEL IRPPICNVDQAVLVFSAVQPSFSTALLDRFLVLVEANDIQPIICITKMDL IEDQDTEDTI RSGA2_LISIN 67 5.71e-53 LDVLSRENAL VRPPVANIDIAILVFSAVEPDFSTNLADRFLVAIEKEDIQPVICISKMDL ATDAEKEQIA RSGA_GEOSW 67 1.56e-52 MNIRERKNWL VRPPIANVEQAILVFSAVEPDFSTRLLDRFLVLVESKHIRPIIVVNKMDL VDDQTKPTME RSGA2_OCEIH 67 1.08e-51 MEIKERSNEL VRPPIANIDQAIIVSSAVDPDFTTLLLDRFLVLIESKHIQPIILITKVDL LNEDQLENIK RSGA_STRP1 66 1.01e-50 LAIHPRKNSL VRPPIVNIDQAVVIMSAKEPEFNSNLLDRFLILLEHKAIHPVVYISKMDL LDSPEEIKAI RSGA_LACSS 68 2.60e-49 LEILDRKNEM IRPPVANIDQAVVIVSAVEPDFSLNLLDRFLIYLESLNIQGLVYLTKTDM ISDEKYQEIK -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RSGA_BACSU 3.4e-54 70_[3]_178 RSGA2_LISIN 5.7e-53 66_[3]_175 RSGA_GEOSW 1.6e-52 66_[3]_177 RSGA2_OCEIH 1.1e-51 66_[3]_177 RSGA_STRP1 1e-50 65_[3]_175 RSGA_LACSS 2.6e-49 67_[3]_182 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=50 seqs=6 RSGA_BACSU ( 71) IRPPICNVDQAVLVFSAVQPSFSTALLDRFLVLVEANDIQPIICITKMDL 1 RSGA2_LISIN ( 67) VRPPVANIDIAILVFSAVEPDFSTNLADRFLVAIEKEDIQPVICISKMDL 1 RSGA_GEOSW ( 67) VRPPIANVEQAILVFSAVEPDFSTRLLDRFLVLVESKHIRPIIVVNKMDL 1 RSGA2_OCEIH ( 67) VRPPIANIDQAIIVSSAVDPDFTTLLLDRFLVLIESKHIQPIILITKVDL 1 RSGA_STRP1 ( 66) VRPPIVNIDQAVVIMSAKEPEFNSNLLDRFLILLEHKAIHPVVYISKMDL 1 RSGA_LACSS ( 68) IRPPVANIDQAVVIVSAVEPDFSLNLLDRFLIYLESLNIQGLVYLTKTDM 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 50 n= 1470 bayes= 8.37977 E= 2.1e-093 -923 -923 -923 -923 -923 -923 -923 212 -923 -923 -923 -923 -923 -923 -923 -923 -923 331 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 410 -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 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 451 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 312 -923 -923 -923 -923 -923 -923 -923 -923 -923 231 -923 -923 360 341 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 131 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 478 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 312 -923 -923 -923 -923 -923 -923 -923 -923 -923 231 -923 -923 -923 -923 379 88 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 112 -923 -923 -923 -923 -923 449 -923 -923 -923 -923 -923 -923 418 -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 -923 270 -923 -923 -923 -923 -923 -923 -923 -923 -923 289 -923 -923 -923 -923 -923 -923 -923 -923 -923 112 -923 247 -923 -923 -923 -923 -923 -923 -923 231 -923 -923 -923 -923 -923 -923 -923 -923 -923 212 -923 -923 -923 -923 -923 -923 -923 -923 -923 331 -923 -923 -923 -923 -923 -923 346 -923 -923 -923 -923 -923 341 -923 -923 -923 -923 143 -923 131 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 402 -923 -923 -923 -923 418 -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 -923 134 -923 -923 -923 -923 -923 -923 -923 -923 363 -923 -923 -923 -923 147 288 -923 -923 -923 -923 -923 -923 -923 -923 -923 217 -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 -923 347 88 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 143 -923 -923 -923 -923 -923 -923 -923 -923 446 -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 -923 219 -923 -923 -923 343 169 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 88 -923 -923 -923 -923 -923 143 369 -923 -923 -923 160 -923 -923 -923 -923 -923 -923 -923 -923 88 -923 378 -923 -923 151 -923 -923 -923 -923 -923 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-923 219 -923 -923 -923 243 328 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 393 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 -923 541 -923 -923 -923 -923 -923 169 131 -923 -923 -923 -923 406 -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 -923 320 341 -923 -923 -923 -923 -923 -923 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 50 nsites= 6 E= 2.1e-093 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 0.666667 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 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.166667 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 0.000000 0.000000 0.000000 0.000000 0.500000 0.166667 0.000000 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.333333 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 0.000000 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 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.166667 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 0.833333 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 0.166667 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 0.666667 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 0.333333 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 0.166667 0.000000 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.166667 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 0.166667 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 0.000000 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 0.666667 0.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.166667 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 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [VI]RPP[IV]AN[IV]DQA[IV][LV][VI]FSAVEPDFSTNLLDRFL[VI]L[ILV]ESK[DH]IQP[IV][IV][CY]I[TS]KMDL -------------------------------------------------------------------------------- Time 1.41 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RSGA_BACSU 1.01e-146 70_[3(3.43e-54)]_56_[1(1.42e-53)]_22_[2(2.22e-52)] RSGA_GEOSW 2.32e-142 66_[3(1.56e-52)]_55_[1(1.89e-53)]_22_[2(9.51e-50)] RSGA2_OCEIH 2.17e-145 66_[3(1.08e-51)]_55_[1(4.24e-53)]_22_[2(5.49e-54)] RSGA2_LISIN 6.50e-147 66_[3(5.71e-53)]_53_[1(1.31e-54)]_22_[2(1.01e-52)] RSGA_STRP1 5.36e-138 65_[3(1.01e-50)]_46_[1(2.44e-49)]_22_[2(2.89e-51)]_7 RSGA_LACSS 2.52e-138 67_[3(2.60e-49)]_56_[1(6.23e-52)]_22_[2(1.84e-50)]_4 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: kodomo ********************************************************************************