******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.0.0 (Release date: 2008-07-12 05:23:09 +1000 (Sat, 12 Jul 2008)) 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= /home/t.bailey/MEME/SVNROOT/trunk/scripts/../tests/common/farntrans5.s ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ RAM1_YEAST 1.0000 431 PFTB_RAT 1.0000 437 BET2_YEAST 1.0000 325 RATRABGERB 1.0000 331 CAL1_YEAST 1.0000 376 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme /home/t.bailey/MEME/SVNROOT/trunk/scripts/../tests/common/farntrans5.s -text -mod tcm -protein -nostatus -nmotifs 2 -minw 8 model: mod= tcm nmotifs= 2 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= 25 wnsites= 0.8 theta: prob= 1 spmap= pam spfuzz= 120 global: substring= yes branching= no wbranch= no em: prior= megap b= 9500 maxiter= 50 distance= 1e-05 data: n= 1900 N= 5 sample: seed= 0 seqfrac= 1 Dirichlet mixture priors file: prior30.plib Letter frequencies in dataset: A 0.061 C 0.037 D 0.062 E 0.061 F 0.044 G 0.075 H 0.030 I 0.053 K 0.051 L 0.114 M 0.021 N 0.034 P 0.041 Q 0.038 R 0.041 S 0.078 T 0.046 V 0.057 W 0.018 Y 0.041 Background letter frequencies (from dataset with add-one prior applied): A 0.061 C 0.037 D 0.061 E 0.060 F 0.044 G 0.075 H 0.030 I 0.053 K 0.051 L 0.113 M 0.021 N 0.034 P 0.041 Q 0.039 R 0.041 S 0.078 T 0.046 V 0.057 W 0.018 Y 0.041 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 30 sites = 24 llr = 854 E-value = 2.2e-094 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::2::::1:2:11:1:1413314:1:1:: pos.-specific C ::::1::::::::2::132::::1:::::: probability D ::::21::11:6::::::::::::::2:13 matrix E ::::::1114::::::::::::::::1111 F :16:::::::::111:31::::::::::1: G 861241:42:::221:::2:22::::3::1 H ::::::::11:4::2::::::::::::::1 I ::1:::1::::::::1:::1:1::42:11: K :::::1::3::::::::::::::::::2:: L ::21:::::2::31::1::5::9:55::4: M :::::::::::::::::::::::::::::: N :1:1:::21:::::::::::1:::::1::: P ::::::5:::2::::::::::::::::::: Q :::1::::1:::::1:::::1::::::::: R :::::3:::::::2:::::::::::::1:: S :1:2::::::2:::13:1::32:3::12:: T ::::::::::::2::5:1:1:1:1:1:::1 V :::::::1::3:2:::::12::::1::::: W ::::::::::::::::13:::::::::::: Y :::::::::::::14:31:::::::1:::: bits 5.8 5.2 4.6 4.0 Relative 3.5 * Entropy 2.9 * * * (51.4 bits) 2.3 *** * * ** * * 1.7 *** ** *** ***** * **** 1.2 ****************************** 0.6 ****************************** 0.0 ------------------------------ Multilevel GGFGGRPGKEVDLCYTFCALAALALLGSLD consensus LAH HSYWCVSS SI sequence P G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------------------ BET2_YEAST 223 6.98e-22 WWLCERQLPE GGLNGRPSKLPDVCYSWWVLSSLAIIGRLD WINYEKLTEF RATRABGERB 227 4.67e-21 WWLCERQLPS GGLNGRPEKLPDVCYSWWVLASLKIIGRLH WIDREKLRSF CAL1_YEAST 275 1.25e-19 LNASYDQSDD GGFQGRENKFADTCYAFWCLNSLHLLTKDW KMLCQTELVT PFTB_RAT 237 1.56e-19 EWIARCQNWE GGIGGVPGMEAHGGYTFCGLAALVILKKER SLNLKSLLQW PFTB_RAT 138 2.44e-19 QFLELCQSPD GGFGGGPGQYPHLAPTYAAVNALCIIGTEE AYNVINREKL RATRABGERB 179 6.47e-19 EFVLSCMNFD GGFGCRPGSESHAGQIYCCTGFLAITSQLH QVNSDLLGWW RATRABGERB 131 8.90e-19 AYVQSLQKED GSFAGDIWGEIDTRFSFCAVATLALLGKLD AINVEKAIEF BET2_YEAST 172 2.53e-18 DFVLKCYNFD GGFGLCPNAESHAAQAFTCLGALAIANKLD MLSDDQLEEI RATRABGERB 276 1.27e-17 FILACQDEET GGFADRPGDMVDPFHTLFGIAGLSLLGEEQ IKPVSPVFCM BET2_YEAST 124 2.77e-17 SFIRGNQLED GSFQGDRFGEVDTRFVYTALSALSILGELT SEVVDPAVDF RAM1_YEAST 247 4.93e-17 YLKNCQNYEG GFGSCPHVDEAHGGYTFCATASLAILRSMD QINVEKLLEW BET2_YEAST 272 7.19e-17 FILKCQDEKK GGISDRPENEVDVFHTVFGVAGLSLMGYDN LVPIDPIYCM RAM1_YEAST 145 8.68e-17 VKLFTISPSG GPFGGGPGQLSHLASTYAAINALSLCDNID GCWDRIDRKG PFTB_RAT 286 2.62e-16 WVTSRQMRFE GGFQGRCNKLVDGCYSFWQAGLLPLLHRAL HAQGDPALSM RAM1_YEAST 296 2.87e-16 WSSARQLQEE RGFCGRSNKLVDGCYSFWVGGSAAILEAFG YGQCFNKHAL PFTB_RAT 348 7.66e-15 YILMCCQCPA GGLLDKPGKSRDFYHTCYCLSGLSIAQHFG SGAMLHDVVM RATRABGERB 83 2.21e-14 VFIKSCQHEC GGVSASIGHDPHLLYTLSAVQILTLYDSIH VINVDKVVAY PFTB_RAT 189 3.29e-14 QYLYSLKQPD GSFLMHVGGEVDVRSAYCAASVASLTNIIT PDLFEGTAEW BET2_YEAST 73 7.21e-14 FVLSCWDDKY GAFAPFPRHDAHLLTTLSAVQILATYDALD VLGKDRKVRL CAL1_YEAST 205 1.14e-13 LLGYIMSQQC YNGAFGAHNEPHSGYTSCALSTLALLSSLE KLSDKFKEDT RAM1_YEAST 198 1.67e-13 WLISLKEPNG GFKTCLEVGEVDTRGIYCALSIATLLNILT EELTEGVLNY CAL1_YEAST 327 4.42e-13 LLDRTQKTLT GGFSKNDEEDADLYHSCLGSAALALIEGKF NGELCIPQEI RAM1_YEAST 349 5.11e-13 ILYCCQEKEQ PGLRDKPGAHSDFYHTNYCLLGLAVAESSY SCTPNDSPHN BET2_YEAST 24 2.82e-10 RYIESLDTNK HNFEYWLTEHLRLNGIYWGLTALCVLDSPE TFVKEEVISF -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- BET2_YEAST 2.8e-10 23_[1]_19_[1]_21_[1]_18_[1]_21_ [1]_19_[1]_24 RATRABGERB 2.2e-14 82_[1]_18_[1]_18_[1]_18_[1]_19_[1]_26 CAL1_YEAST 1.1e-13 204_[1]_40_[1]_22_[1]_20 PFTB_RAT 3.3e-14 137_[1]_21_[1]_18_[1]_19_[1]_32_ [1]_60 RAM1_YEAST 1.7e-13 144_[1]_23_[1]_19_[1]_19_[1]_23_ [1]_53 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=30 seqs=24 BET2_YEAST ( 223) GGLNGRPSKLPDVCYSWWVLSSLAIIGRLD 1 RATRABGERB ( 227) GGLNGRPEKLPDVCYSWWVLASLKIIGRLH 1 CAL1_YEAST ( 275) GGFQGRENKFADTCYAFWCLNSLHLLTKDW 1 PFTB_RAT ( 237) GGIGGVPGMEAHGGYTFCGLAALVILKKER 1 PFTB_RAT ( 138) GGFGGGPGQYPHLAPTYAAVNALCIIGTEE 1 RATRABGERB ( 179) GGFGCRPGSESHAGQIYCCTGFLAITSQLH 1 RATRABGERB ( 131) GSFAGDIWGEIDTRFSFCAVATLALLGKLD 1 BET2_YEAST ( 172) GGFGLCPNAESHAAQAFTCLGALAIANKLD 1 RATRABGERB ( 276) GGFADRPGDMVDPFHTLFGIAGLSLLGEEQ 1 BET2_YEAST ( 124) GSFQGDRFGEVDTRFVYTALSALSILGELT 1 RAM1_YEAST ( 247) GFGSCPHVDEAHGGYTFCATASLAILRSMD 1 BET2_YEAST ( 272) GGISDRPENEVDVFHTVFGVAGLSLMGYDN 1 RAM1_YEAST ( 145) GPFGGGPGQLSHLASTYAAINALSLCDNID 1 PFTB_RAT ( 286) GGFQGRCNKLVDGCYSFWQAGLLPLLHRAL 1 RAM1_YEAST ( 296) RGFCGRSNKLVDGCYSFWVGGSAAILEAFG 1 PFTB_RAT ( 348) GGLLDKPGKSRDFYHTCYCLSGLSIAQHFG 1 RATRABGERB ( 83) GGVSASIGHDPHLLYTLSAVQILTLYDSIH 1 PFTB_RAT ( 189) GSFLMHVGGEVDVRSAYCAASVASLTNIIT 1 BET2_YEAST ( 73) GAFAPFPRHDAHLLTTLSAVQILATYDALD 1 CAL1_YEAST ( 205) YNGAFGAHNEPHSGYTSCALSTLALLSSLE 1 RAM1_YEAST ( 198) GFKTCLEVGEVDTRGIYCALSIATLLNILT 1 CAL1_YEAST ( 327) GGFSKNDEEDADLYHSCLGSAALALIEGKF 1 RAM1_YEAST ( 349) PGLRDKPGAHSDFYHTNYCLLGLAVAESSY 1 BET2_YEAST ( 24) HNFEYWLTEHLRLNGIYWGLTALCVLDSPE 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 30 n= 1755 bayes= 6.12445 E= 2.2e-094 -218 -476 -324 -369 -492 351 -61 -474 -334 -558 -392 -225 -103 -392 -86 -303 -361 -418 -449 -109 -81 -469 -328 -377 -1 329 -398 -485 -348 -567 -404 54 -81 -396 -330 -9 -350 -421 -467 -482 -258 -349 -504 -436 380 -47 -393 39 -82 20 -134 -364 -401 -385 -376 -350 -259 -35 -300 -200 127 -17 -201 -5 -348 114 -187 -312 -81 -63 -205 120 -263 155 27 92 7 -262 -388 -304 -26 143 115 -207 -17 219 -252 -171 -9 -112 95 -185 -16 -179 -194 -235 -164 -152 -351 -13 -146 -17 33 -115 -32 45 38 -310 85 -143 -204 47 -13 -95 271 -53 -143 -50 83 -303 -47 -38 -90 6 -396 -375 0 15 -233 -169 -289 -260 375 -236 -26 -97 -232 -75 -474 -425 -148 -438 -204 99 -31 196 38 -302 -85 -336 -202 205 -266 -99 26 -54 6 33 83 -304 47 -444 34 57 -349 84 122 -315 209 -342 79 121 -263 109 -118 -53 -144 -265 -389 -305 -160 -417 82 250 -25 -316 123 -255 -111 61 85 -136 -283 -122 -146 -60 -157 -222 -376 -14 161 -320 -465 -373 -228 -392 -333 13 -325 -90 -101 -301 208 -309 -7 90 -181 221 -331 -288 -441 -652 318 -353 -595 -399 355 -674 -343 -688 -599 -160 -497 -375 4 -359 -388 -625 -638 -515 47 -316 -480 -387 82 91 -336 -111 -338 103 -98 -307 -15 -317 -312 -83 170 152 -328 -285 94 221 -399 -311 80 90 -301 -130 -267 -30 -111 21 -354 -263 179 -282 -179 -116 -328 140 -167 -305 -308 -259 149 -77 196 -221 -241 -249 -153 -216 -75 19 -217 -54 -68 -205 -133 341 70 -383 -459 -463 -428 -445 -427 85 -369 -442 -260 -233 -417 -350 -355 143 348 -55 -479 -484 -171 21 -317 -268 232 -354 -39 -217 -251 -54 -152 -36 -288 -261 -224 -116 -223 -78 132 327 46 272 -490 -397 84 -403 -334 -119 -348 -90 -105 -315 -379 -326 -320 0 82 -107 351 88 277 240 -625 -594 -564 141 -583 -515 -585 -580 -446 -452 -451 4 -521 -277 -297 107 -614 -619 45 -317 -489 -395 -222 -96 -340 81 -346 184 -95 -313 -373 -323 -316 -85 81 179 -327 -285 211 -440 -248 -197 -413 97 -259 -375 -167 -146 -278 178 -326 106 -203 153 0 -315 -458 -377 213 -308 -476 -384 -5 88 -337 123 -337 -91 -99 -307 -372 -318 -311 118 79 12 -328 -287 87 -518 -675 -601 -319 -555 -562 -243 -565 290 -164 -543 -528 -491 -504 -490 -418 -296 -502 -500 317 38 -357 -284 -333 -228 -37 -275 -81 -332 -203 -259 -82 -270 -263 98 23 -47 -389 -382 -408 -489 -735 -670 -387 -688 -678 294 -638 194 -240 -597 -632 -619 -631 -623 -16 84 -602 -556 91 0 -492 -398 -220 -404 -343 158 -348 187 109 -317 -375 -324 -318 -313 78 -100 -329 80 -159 -454 121 100 -362 163 39 -329 20 -356 -221 172 -274 38 24 13 5 -279 -402 -316 47 -443 -200 57 -348 -88 38 37 160 -341 -205 47 -262 41 145 120 7 -264 -388 -19 -28 -364 22 86 69 -344 -250 108 -9 153 95 -185 -17 -174 -191 -72 -165 -153 -352 -294 -146 -443 171 100 -32 -6 175 -314 -80 -144 -205 47 -262 41 27 -178 126 -263 82 -19 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 30 nsites= 24 E= 2.2e-094 0.000000 0.000000 0.000000 0.000000 0.000000 0.833333 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.041667 0.041667 0.000000 0.000000 0.000000 0.083333 0.625000 0.000000 0.000000 0.000000 0.000000 0.000000 0.083333 0.041667 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.583333 0.083333 0.000000 0.083333 0.041667 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000 0.166667 0.041667 0.000000 0.041667 0.000000 0.208333 0.000000 0.000000 0.000000 0.083333 0.000000 0.083333 0.000000 0.125000 0.041667 0.166667 0.041667 0.000000 0.000000 0.000000 0.041667 0.125000 0.166667 0.000000 0.041667 0.416667 0.000000 0.000000 0.041667 0.041667 0.041667 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.041667 0.083333 0.000000 0.041667 0.125000 0.041667 0.000000 0.083333 0.041667 0.000000 0.041667 0.041667 0.000000 0.333333 0.041667 0.000000 0.041667 0.041667 0.000000 0.041667 0.041667 0.041667 0.083333 0.000000 0.000000 0.041667 0.083333 0.000000 0.041667 0.000000 0.000000 0.500000 0.000000 0.041667 0.041667 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.041667 0.375000 0.041667 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.041667 0.041667 0.041667 0.083333 0.041667 0.000000 0.083333 0.000000 0.083333 0.083333 0.000000 0.166667 0.083333 0.000000 0.250000 0.000000 0.041667 0.083333 0.000000 0.083333 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.416667 0.041667 0.000000 0.083333 0.000000 0.000000 0.208333 0.041667 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000 0.000000 0.041667 0.208333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.041667 0.000000 0.000000 0.208333 0.000000 0.041667 0.166667 0.000000 0.291667 0.000000 0.000000 0.000000 0.000000 0.583333 0.000000 0.000000 0.000000 0.375000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.083333 0.000000 0.000000 0.000000 0.083333 0.166667 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.041667 0.000000 0.000000 0.041667 0.166667 0.166667 0.000000 0.000000 0.125000 0.208333 0.000000 0.000000 0.083333 0.166667 0.000000 0.000000 0.000000 0.083333 0.000000 0.041667 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 0.000000 0.083333 0.083333 0.208333 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.083333 0.000000 0.083333 0.041667 0.000000 0.000000 0.375000 0.125000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.458333 0.041667 0.000000 0.000000 0.000000 0.083333 0.000000 0.000000 0.291667 0.000000 0.000000 0.000000 0.000000 0.125000 0.000000 0.041667 0.000000 0.000000 0.000000 0.041667 0.000000 0.041667 0.083333 0.291667 0.083333 0.291667 0.000000 0.000000 0.083333 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.083333 0.083333 0.000000 0.250000 0.083333 0.416667 0.208333 0.000000 0.000000 0.000000 0.208333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000 0.000000 0.125000 0.000000 0.000000 0.083333 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.083333 0.000000 0.458333 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.083333 0.208333 0.000000 0.000000 0.291667 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 0.041667 0.000000 0.125000 0.000000 0.083333 0.000000 0.250000 0.041667 0.000000 0.000000 0.000000 0.291667 0.000000 0.000000 0.000000 0.041667 0.166667 0.000000 0.125000 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.208333 0.083333 0.041667 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.875000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.416667 0.083333 0.000000 0.000000 0.000000 0.000000 0.041667 0.000000 0.041667 0.000000 0.000000 0.000000 0.041667 0.000000 0.000000 0.250000 0.083333 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.416667 0.000000 0.458333 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.041667 0.083333 0.000000 0.000000 0.125000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.458333 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.083333 0.000000 0.000000 0.083333 0.000000 0.000000 0.166667 0.125000 0.000000 0.291667 0.041667 0.000000 0.041667 0.000000 0.000000 0.125000 0.000000 0.041667 0.041667 0.083333 0.041667 0.000000 0.000000 0.000000 0.083333 0.000000 0.000000 0.083333 0.000000 0.041667 0.041667 0.083333 0.166667 0.000000 0.000000 0.041667 0.000000 0.041667 0.125000 0.208333 0.041667 0.000000 0.000000 0.041667 0.041667 0.000000 0.083333 0.125000 0.083333 0.000000 0.000000 0.125000 0.041667 0.375000 0.041667 0.000000 0.041667 0.000000 0.000000 0.041667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.125000 0.041667 0.083333 0.125000 0.000000 0.000000 0.041667 0.000000 0.041667 0.000000 0.041667 0.041667 0.000000 0.125000 0.000000 0.041667 0.041667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GGFGGRPGK[EL][VAP][DH]LC[YH][TS][FY][CW][ACG][LV][AS][AS]L[AS][LI]LGSLD -------------------------------------------------------------------------------- Time 9.37 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 14 sites = 21 llr = 383 E-value = 6.1e-021 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::1:1:::11:: pos.-specific C ::::::::::::4: probability D 12:::::1:::::: matrix E 1::61::2:::::: F 1:::::::3::::: G ::::1:::::::1: H :::::1:1:::::: I 4::::23::41::: K ::315:::::21:1 L 221::43::22:21 M :::::::::::::: N :5::::::::::1: P :::::::::::::: Q :::::::1:::::5 R ::21::11:::11: S ::::1::1:116:: T ::1::::::::::: V ::2::1:::2:::: W ::::::::2::::: Y ::::::::5::::: bits 5.8 5.2 4.6 4.0 Relative 3.5 * Entropy 2.9 * (26.3 bits) 2.3 * ** * * 1.7 ****** ** *** 1.2 ************** 0.6 ************** 0.0 -------------- Multilevel INKEKLIxYILSCQ consensus L R L FV sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- RATRABGERB 66 2.71e-12 VMDLMGQLHR MNKEEILVFIKSCQ HECGGVSASI BET2_YEAST 254 5.70e-12 SLAIIGRLDW INYEKLTEFILKCQ DEKKGGISDR RATRABGERB 258 6.43e-12 SLKIIGRLHW IDREKLRSFILACQ DEETGGFADR RATRABGERB 162 2.61e-11 TLALLGKLDA INVEKAIEFVLSCM NFDGGFGCRP CAL1_YEAST 190 6.30e-11 CRSKEDFDEY IDTEKLLGYIMSQQ CYNGAFGAHN RAM1_YEAST 278 2.70e-10 SLAILRSMDQ INVEKLLEWSSARQ LQEERGFCGR PFTB_RAT 172 4.03e-10 IIGTEEAYNV INREKLLQYLYSLK QPDGSFLMHV RATRABGERB 114 1.27e-09 ILTLYDSIHV INVDKVVAYVQSLQ KEDGSFAGDI BET2_YEAST 7 3.17e-09 MSGSLT LLKEKHIRYIESLD TNKHNFEYWL PFTB_RAT 268 6.39e-09 ALVILKKERS LNLKSLLQWVTSRQ MRFEGGFQGR RAM1_YEAST 414 6.96e-09 DVNPVYGLPI ENVRKIIHYFKSNL SSPS CAL1_YEAST 126 1.06e-08 LRDYEYFETI LDKRSLARFVSKCQ RPDRGSFVSC PFTB_RAT 220 1.26e-08 VASLTNIITP DLFEGTAEWIARCQ NWEGGIGGVP BET2_YEAST 55 1.37e-08 ALCVLDSPET FVKEEVISFVLSCW DDKYGAFAPF RAM1_YEAST 229 2.07e-08 IATLLNILTE ELTEGVLNYLKNCQ NYEGGFGSCP RAM1_YEAST 330 4.96e-08 ILEAFGYGQC FNKHALRDYILYCC QEKEQPGLRD RATRABGERB 18 1.15e-07 VTIKSDAPDT LLLEKHADYIASYG SKKDDYEYCM RAM1_YEAST 180 1.44e-07 CDNIDGCWDR IDRKGIYQWLISLK EPNGGFKTCL PFTB_RAT 73 1.55e-07 KFNHLVPRLV LQREKHFHYLKRGL RQLTDAYECL BET2_YEAST 107 1.93e-07 TYDALDVLGK DRKVRLISFIRGNQ LEDGSFQGDR CAL1_YEAST 36 5.20e-07 LLPSSHQGHD VNRMAIIFYSISGL SIFDVNVSAK -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RATRABGERB 1.2e-07 17_[2]_34_[2]_34_[2]_34_[2]_82_[2]_60 BET2_YEAST 1.4e-08 6_[2]_34_[2]_38_[2]_133_[2]_58 CAL1_YEAST 1.1e-08 35_[2]_76_[2]_50_[2]_173 RAM1_YEAST 5e-08 179_[2]_35_[2]_35_[2]_38_[2]_70_[2]_4 PFTB_RAT 1.3e-08 72_[2]_85_[2]_34_[2]_34_[2]_156 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=14 seqs=21 RATRABGERB ( 66) MNKEEILVFIKSCQ 1 BET2_YEAST ( 254) INYEKLTEFILKCQ 1 RATRABGERB ( 258) IDREKLRSFILACQ 1 RATRABGERB ( 162) INVEKAIEFVLSCM 1 CAL1_YEAST ( 190) IDTEKLLGYIMSQQ 1 RAM1_YEAST ( 278) INVEKLLEWSSARQ 1 PFTB_RAT ( 172) INREKLLQYLYSLK 1 RATRABGERB ( 114) INVDKVVAYVQSLQ 1 BET2_YEAST ( 7) LLKEKHIRYIESLD 1 PFTB_RAT ( 268) LNLKSLLQWVTSRQ 1 RAM1_YEAST ( 414) ENVRKIIHYFKSNL 1 CAL1_YEAST ( 126) LDKRSLARFVSKCQ 1 PFTB_RAT ( 220) DLFEGTAEWIARCQ 1 BET2_YEAST ( 55) FVKEEVISFVLSCW 1 RAM1_YEAST ( 229) ELTEGVLNYLKNCQ 1 RAM1_YEAST ( 330) FNKHALRDYILYCC 1 RATRABGERB ( 18) LLLEKHADYIASYG 1 RAM1_YEAST ( 180) IDRKGIYQWLISLK 1 PFTB_RAT ( 73) LQREKHFHYLKRGL 1 BET2_YEAST ( 107) DRKVRLISFIRGNQ 1 CAL1_YEAST ( 36) VNRMAIIFYSISGL 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 14 n= 1835 bayes= 7.42721 E= 6.1e-021 -194 -317 27 33 90 -398 -339 275 -338 92 120 -307 -371 -319 -313 -306 -180 36 -324 -282 -222 -483 147 -172 -406 -315 -236 -354 -129 52 -272 359 -329 41 35 -228 -207 -34 -450 -365 -188 -337 -387 -289 7 -375 -285 -136 226 -18 -114 -245 -348 -225 230 -277 96 162 -335 8 -196 -516 -17 314 -424 -350 51 -371 97 -398 97 -168 -309 -122 114 -242 -204 -38 -455 -372 57 -486 -252 66 -412 69 -223 -363 316 -386 -255 -149 -317 -125 56 23 -197 -315 -430 -355 -17 -311 -484 -390 -214 -395 194 176 -341 175 -85 -308 -368 -318 -311 -304 16 135 -322 -280 110 -299 -471 -377 14 -381 -321 227 -327 119 -77 -294 -355 -305 98 -289 19 30 -308 10 -5 -429 47 147 -18 -74 136 -300 -66 -327 -191 61 -248 170 112 72 -129 -37 -374 -290 -579 -589 -670 -653 290 -651 -301 -492 -581 -477 -422 -459 -601 -496 -506 -572 -535 -493 330 351 -272 -391 -471 -429 -53 -471 -431 331 -374 30 -82 -346 -434 -383 -376 -56 -242 175 -401 -346 61 -413 -197 5 -319 -288 -180 55 173 72 96 -103 -254 52 39 26 21 -226 -368 -4 40 -393 -233 -177 -373 -93 -230 -345 73 -379 -242 46 -291 -148 91 273 -32 -308 -411 -25 -199 322 -288 -222 -303 15 -252 -214 -123 57 -175 136 -334 36 117 -250 -188 -194 -377 6 -198 -75 -116 -128 -366 -156 -97 -296 13 -63 37 -167 -289 400 -154 -252 -207 -271 23 -359 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 14 nsites= 21 E= 6.1e-021 0.000000 0.000000 0.095238 0.095238 0.095238 0.000000 0.000000 0.380952 0.000000 0.238095 0.047619 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.047619 0.000000 0.000000 0.000000 0.000000 0.190476 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.190476 0.000000 0.476190 0.000000 0.047619 0.047619 0.000000 0.000000 0.047619 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.047619 0.000000 0.000000 0.000000 0.285714 0.095238 0.000000 0.000000 0.000000 0.000000 0.238095 0.000000 0.095238 0.190476 0.000000 0.047619 0.000000 0.000000 0.047619 0.619048 0.000000 0.000000 0.047619 0.000000 0.095238 0.000000 0.047619 0.000000 0.000000 0.000000 0.095238 0.000000 0.000000 0.047619 0.000000 0.000000 0.095238 0.000000 0.000000 0.095238 0.000000 0.142857 0.000000 0.000000 0.523810 0.000000 0.000000 0.000000 0.000000 0.000000 0.047619 0.095238 0.000000 0.000000 0.000000 0.000000 0.047619 0.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.190476 0.000000 0.428571 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.047619 0.142857 0.000000 0.000000 0.142857 0.000000 0.000000 0.000000 0.047619 0.000000 0.000000 0.285714 0.000000 0.285714 0.000000 0.000000 0.000000 0.000000 0.095238 0.000000 0.047619 0.047619 0.000000 0.047619 0.047619 0.000000 0.095238 0.190476 0.047619 0.047619 0.095238 0.000000 0.000000 0.000000 0.000000 0.047619 0.000000 0.142857 0.095238 0.142857 0.000000 0.047619 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 0.190476 0.476190 0.000000 0.000000 0.000000 0.000000 0.047619 0.000000 0.000000 0.428571 0.000000 0.190476 0.000000 0.000000 0.000000 0.000000 0.000000 0.095238 0.000000 0.238095 0.000000 0.000000 0.095238 0.000000 0.000000 0.047619 0.000000 0.000000 0.000000 0.095238 0.190476 0.238095 0.047619 0.000000 0.000000 0.047619 0.047619 0.095238 0.047619 0.000000 0.000000 0.047619 0.095238 0.000000 0.000000 0.000000 0.000000 0.047619 0.000000 0.000000 0.095238 0.000000 0.000000 0.047619 0.000000 0.000000 0.095238 0.571429 0.000000 0.000000 0.000000 0.047619 0.000000 0.428571 0.000000 0.000000 0.000000 0.095238 0.000000 0.000000 0.000000 0.190476 0.000000 0.095238 0.000000 0.047619 0.095238 0.000000 0.000000 0.000000 0.000000 0.047619 0.000000 0.047619 0.047619 0.000000 0.000000 0.047619 0.000000 0.000000 0.095238 0.142857 0.047619 0.000000 0.000000 0.523810 0.000000 0.000000 0.000000 0.000000 0.047619 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [IL]N[KR]EKL[IL]x[YF][IV]LSCQ -------------------------------------------------------------------------------- Time 13.92 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RAM1_YEAST 1.09e-19 144_[1(8.68e-17)]_5_[2(1.44e-07)]_4_[1(1.67e-13)]_1_[2(2.07e-08)]_4_[1(4.93e-17)]_1_[2(2.70e-10)]_4_[1(2.87e-16)]_4_[2(4.96e-08)]_5_[1(5.11e-13)]_35_[2(6.96e-09)]_4 PFTB_RAT 5.87e-22 72_[2(1.55e-07)]_51_[1(2.44e-19)]_4_[2(4.03e-10)]_3_[1(3.29e-14)]_1_[2(1.26e-08)]_3_[1(1.56e-19)]_1_[2(6.39e-09)]_4_[1(2.62e-16)]_32_[1(7.66e-15)]_60 BET2_YEAST 2.36e-26 6_[2(3.17e-09)]_3_[1(2.82e-10)]_1_[2(1.37e-08)]_4_[1(7.21e-14)]_4_[2(1.93e-07)]_3_[1(2.77e-17)]_18_[1(2.53e-18)]_21_[1(6.98e-22)]_1_[2(5.70e-12)]_4_[1(7.19e-17)]_24 RATRABGERB 7.64e-26 17_[2(1.15e-07)]_34_[2(2.71e-12)]_3_[1(2.21e-14)]_1_[2(1.27e-09)]_3_[1(8.90e-19)]_1_[2(2.61e-11)]_3_[1(6.47e-19)]_18_[1(4.67e-21)]_1_[2(6.43e-12)]_4_[1(1.27e-17)]_26 CAL1_YEAST 5.59e-23 35_[2(5.20e-07)]_76_[2(1.06e-08)]_50_[2(6.30e-11)]_1_[1(1.14e-13)]_40_[1(1.25e-19)]_22_[1(4.42e-13)]_20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 2 reached. ******************************************************************************** CPU: tlb-sayonara.imb.uq.edu.au ********************************************************************************