******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 3.0 (Release date: 2004/08/18 09:07:01) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.sdsc.edu. 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.sdsc.edu. ******************************************************************************** ******************************************************************************** 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= 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 farntrans5.s -mod tcm -protein -nmotifs 2 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 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 Information 3.5 * content 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 7.28e-22 WWLCERQLPE GGLNGRPSKLPDVCYSWWVLSSLAIIGRLD WINYEKLTEF RATRABGERB 227 6.18e-21 WWLCERQLPS GGLNGRPEKLPDVCYSWWVLASLKIIGRLH WIDREKLRSF CAL1_YEAST 275 9.17e-20 LNASYDQSDD GGFQGRENKFADTCYAFWCLNSLHLLTKDW KMLCQTELVT PFTB_RAT 237 1.15e-19 EWIARCQNWE GGIGGVPGMEAHGGYTFCGLAALVILKKER SLNLKSLLQW PFTB_RAT 138 4.30e-19 QFLELCQSPD GGFGGGPGQYPHLAPTYAAVNALCIIGTEE AYNVINREKL RATRABGERB 179 7.36e-19 EFVLSCMNFD GGFGCRPGSESHAGQIYCCTGFLAITSQLH QVNSDLLGWW RATRABGERB 131 8.19e-19 AYVQSLQKED GSFAGDIWGEIDTRFSFCAVATLALLGKLD AINVEKAIEF BET2_YEAST 172 2.10e-18 DFVLKCYNFD GGFGLCPNAESHAAQAFTCLGALAIANKLD MLSDDQLEEI RATRABGERB 276 1.43e-17 FILACQDEET GGFADRPGDMVDPFHTLFGIAGLSLLGEEQ IKPVSPVFCM BET2_YEAST 124 3.41e-17 SFIRGNQLED GSFQGDRFGEVDTRFVYTALSALSILGELT SEVVDPAVDF RAM1_YEAST 247 5.00e-17 YLKNCQNYEG GFGSCPHVDEAHGGYTFCATASLAILRSMD QINVEKLLEW BET2_YEAST 272 6.64e-17 FILKCQDEKK GGISDRPENEVDVFHTVFGVAGLSLMGYDN LVPIDPIYCM RAM1_YEAST 145 1.27e-16 VKLFTISPSG GPFGGGPGQLSHLASTYAAINALSLCDNID GCWDRIDRKG PFTB_RAT 286 3.17e-16 WVTSRQMRFE GGFQGRCNKLVDGCYSFWQAGLLPLLHRAL HAQGDPALSM RAM1_YEAST 296 3.47e-16 WSSARQLQEE RGFCGRSNKLVDGCYSFWVGGSAAILEAFG YGQCFNKHAL PFTB_RAT 348 4.30e-15 YILMCCQCPA GGLLDKPGKSRDFYHTCYCLSGLSIAQHFG SGAMLHDVVM RATRABGERB 83 2.40e-14 VFIKSCQHEC GGVSASIGHDPHLLYTLSAVQILTLYDSIH VINVDKVVAY PFTB_RAT 189 2.81e-14 QYLYSLKQPD GSFLMHVGGEVDVRSAYCAASVASLTNIIT PDLFEGTAEW BET2_YEAST 73 7.78e-14 FVLSCWDDKY GAFAPFPRHDAHLLTTLSAVQILATYDALD VLGKDRKVRL CAL1_YEAST 205 1.14e-13 LLGYIMSQQC YNGAFGAHNEPHSGYTSCALSTLALLSSLE KLSDKFKEDT RAM1_YEAST 198 1.33e-13 WLISLKEPNG GFKTCLEVGEVDTRGIYCALSIATLLNILT EELTEGVLNY RAM1_YEAST 349 3.52e-13 ILYCCQEKEQ PGLRDKPGAHSDFYHTNYCLLGLAVAESSY SCTPNDSPHN CAL1_YEAST 327 5.47e-13 LLDRTQKTLT GGFSKNDEEDADLYHSCLGSAALALIEGKF NGELCIPQEI BET2_YEAST 24 3.11e-10 RYIESLDTNK HNFEYWLTEHLRLNGIYWGLTALCVLDSPE TFVKEEVISF -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- BET2_YEAST 3.1e-10 23_[1]_19_[1]_21_[1]_18_[1]_21_ [1]_19_[1]_24 RATRABGERB 2.4e-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 4.3e-15 137_[1]_21_[1]_18_[1]_19_[1]_32_ [1]_60 RAM1_YEAST 1.3e-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 RAM1_YEAST ( 349) PGLRDKPGAHSDFYHTNYCLLGLAVAESSY 1 CAL1_YEAST ( 327) GGFSKNDEEDADLYHSCLGSAALALIEGKF 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 -470 -327 -377 -1 330 -398 -485 -347 -566 -404 54 -81 -396 -330 -9 -350 -421 -467 -482 -244 -349 -513 -434 367 -26 -384 59 -61 38 -123 -357 -404 -371 -364 -348 -238 -14 -322 -240 127 -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 -186 -16 -179 -195 -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 -374 0 15 -233 -169 -288 -259 375 -235 -26 -97 -231 -75 -473 -424 -148 -438 -204 99 -31 196 38 -302 -85 -335 -202 205 -266 -99 26 -54 6 33 83 -304 47 -444 33 57 -349 84 122 -315 209 -342 79 121 -263 109 -118 -53 -144 -265 -389 -305 -160 -416 82 250 -25 -316 123 -254 -111 61 85 -136 -283 -122 -146 -60 -156 -221 -375 -14 161 -320 -465 -373 -228 -392 -333 13 -325 -90 -101 -301 208 -309 -7 90 -181 221 -331 -288 -438 -650 318 -350 -594 -396 355 -672 -341 -686 -596 -158 -495 -373 4 -357 -386 -623 -637 -514 47 -316 -480 -387 82 91 -337 -111 -338 103 -98 -307 -15 -318 -312 -83 170 152 -328 -285 94 221 -398 -311 80 90 -301 -129 -266 -30 -111 21 -354 -263 179 -282 -178 -115 -329 139 -167 -305 -309 -259 149 -77 196 -221 -241 -249 -153 -216 -75 19 -217 -54 -68 -205 -133 341 71 -383 -460 -463 -428 -445 -427 86 -370 -442 -260 -234 -417 -351 -356 143 348 -55 -479 -484 -170 21 -317 -268 232 -354 -39 -217 -250 -54 -152 -36 -288 -261 -224 -116 -223 -78 132 328 46 272 -489 -397 84 -402 -334 -118 -347 -90 -105 -314 -378 -325 -320 -1 82 -106 351 88 277 240 -625 -594 -564 141 -583 -514 -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 -247 -196 -412 97 -258 -374 -166 -146 -278 178 -325 106 -202 153 0 -314 -457 -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 -320 -554 -562 -243 -564 290 -164 -543 -528 -491 -503 -489 -418 -296 -502 -500 317 38 -358 -284 -334 -229 -37 -276 -81 -332 -204 -260 -82 -270 -263 99 23 -47 -389 -383 -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 -192 -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 -------------------------------------------------------------------------------- Time 32.68 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 14 sites = 21 llr = 376 E-value = 3.1e-019 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::111::::1:: pos.-specific C ::::::::::::61 probability D 12:11::1:::::: matrix E 1::61::2:::::: F 1:::::::5::::: G ::::1::::::::: H :::::::::::::: I 5::::12::4:::: K ::313:::::11:1 L 11:::53::24:1: M :::::::::::::: N :4:::::::::::: P :::::::::::::: Q ::1::::2:::::6 R ::1:::1::::11: S ::::1::1:114:: T ::1::1:::::::: V :12::21::3:::: W ::::::::2::::: Y ::::::::3::::: bits 5.8 5.2 4.6 4.0 Information 3.5 * content 2.9 * ** (25.8 bits) 2.3 * ** ** 1.7 **** * ** ** 1.2 ************** 0.6 ************** 0.0 -------------- Multilevel INKEKLLEFILSCQ consensus YV sequence WL -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- BET2_YEAST 254 2.24e-13 SLAIIGRLDW INYEKLTEFILKCQ DEKKGGISDR RATRABGERB 258 1.30e-12 SLKIIGRLHW IDREKLRSFILACQ DEETGGFADR RATRABGERB 162 4.20e-12 TLALLGKLDA INVEKAIEFVLSCM NFDGGFGCRP RATRABGERB 66 9.60e-12 VMDLMGQLHR MNKEEILVFIKSCQ HECGGVSASI RAM1_YEAST 278 5.08e-11 SLAILRSMDQ INVEKLLEWSSARQ LQEERGFCGR CAL1_YEAST 190 5.01e-10 CRSKEDFDEY IDTEKLLGYIMSQQ CYNGAFGAHN BET2_YEAST 55 6.90e-10 ALCVLDSPET FVKEEVISFVLSCW DDKYGAFAPF RATRABGERB 114 1.57e-09 ILTLYDSIHV INVDKVVAYVQSLQ KEDGSFAGDI PFTB_RAT 172 2.34e-09 IIGTEEAYNV INREKLLQYLYSLK QPDGSFLMHV RAM1_YEAST 330 4.59e-09 ILEAFGYGQC FNKHALRDYILYCC QEKEQPGLRD CAL1_YEAST 126 1.65e-08 LRDYEYFETI LDKRSLARFVSKCQ RPDRGSFVSC PFTB_RAT 268 1.65e-08 ALVILKKERS LNLKSLLQWVTSRQ MRFEGGFQGR PFTB_RAT 220 1.65e-08 VASLTNIITP DLFEGTAEWIARCQ NWEGGIGGVP RAM1_YEAST 229 2.54e-08 IATLLNILTE ELTEGVLNYLKNCQ NYEGGFGSCP PFTB_RAT 330 4.58e-08 DPALSMSHWM FHQQALQEYILMCC QCPAGGLLDK CAL1_YEAST 239 5.86e-08 LLSSLEKLSD KFKEDTITWLLHRQ VSSHGCMKFE PFTB_RAT 121 1.52e-07 LELLDEPIPQ IVATDVCQFLELCQ SPDGGFGGGP CAL1_YEAST 362 1.91e-07 IEGKFNGELC IPQEIFNDFSKRCC F BET2_YEAST 107 4.34e-07 TYDALDVLGK DRKVRLISFIRGNQ LEDGSFQGDR BET2_YEAST 155 5.01e-07 ALSILGELTS EVVDPAVDFVLKCY NFDGGFGLCP RAM1_YEAST 180 5.78e-07 CDNIDGCWDR IDRKGIYQWLISLK EPNGGFKTCL -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- BET2_YEAST 4.3e-07 54_[2]_38_[2]_34_[2]_85_[2]_58 RATRABGERB 1.6e-09 65_[2]_34_[2]_34_[2]_82_[2]_60 RAM1_YEAST 5.8e-07 179_[2]_35_[2]_35_[2]_38_[2]_88 CAL1_YEAST 5.9e-08 125_[2]_50_[2]_35_[2]_109_[2]_1 PFTB_RAT 2.3e-09 120_[2]_37_[2]_34_[2]_34_[2]_48_ [2]_94 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=14 seqs=21 BET2_YEAST ( 254) INYEKLTEFILKCQ 1 RATRABGERB ( 258) IDREKLRSFILACQ 1 RATRABGERB ( 162) INVEKAIEFVLSCM 1 RATRABGERB ( 66) MNKEEILVFIKSCQ 1 RAM1_YEAST ( 278) INVEKLLEWSSARQ 1 CAL1_YEAST ( 190) IDTEKLLGYIMSQQ 1 BET2_YEAST ( 55) FVKEEVISFVLSCW 1 RATRABGERB ( 114) INVDKVVAYVQSLQ 1 PFTB_RAT ( 172) INREKLLQYLYSLK 1 RAM1_YEAST ( 330) FNKHALRDYILYCC 1 CAL1_YEAST ( 126) LDKRSLARFVSKCQ 1 PFTB_RAT ( 268) LNLKSLLQWVTSRQ 1 PFTB_RAT ( 220) DLFEGTAEWIARCQ 1 RAM1_YEAST ( 229) ELTEGVLNYLKNCQ 1 PFTB_RAT ( 330) FHQQALQEYILMCC 1 CAL1_YEAST ( 239) KFKEDTITWLLHRQ 1 PFTB_RAT ( 121) IVATDVCQFLELCQ 1 CAL1_YEAST ( 362) IPQEIFNDFSKRCC 1 BET2_YEAST ( 107) DRKVRLISFIRGNQ 1 BET2_YEAST ( 155) EVVDPAVDFVLKCY 1 RAM1_YEAST ( 180) IDRKGIYQWLISLK 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 14 n= 1835 bayes= 7.42721 E= 3.1e-019 -180 -316 28 36 140 -376 -308 299 -24 -14 117 -265 -348 -268 -271 -280 -167 -65 -321 -275 -149 -393 133 -139 -11 -301 50 -227 -104 -40 -165 317 0 -117 32 -189 -143 106 -363 -290 -9 -383 -234 -146 -8 -309 -205 -210 224 -111 -154 -135 -277 119 160 -196 94 147 -356 0 -174 -491 57 300 -396 -328 51 -351 95 -378 -243 -145 -289 50 33 -217 12 -38 -433 -348 61 -430 48 71 -335 60 -173 -37 243 -328 -192 -95 2 -80 41 27 -130 -250 -375 -291 55 -332 -507 -413 10 -422 -361 96 -365 194 -94 -334 -390 -340 -334 -331 92 167 -344 -304 61 19 -456 -363 -205 -378 -316 176 -315 118 -79 32 -352 14 98 -285 19 91 -309 10 -6 -431 96 174 -336 -74 -174 -302 -67 -329 -193 61 -249 205 41 72 21 -37 -376 -291 -585 -591 -675 -658 339 -654 -303 -494 -585 -478 -424 -461 -604 -498 -508 -576 -538 -496 362 282 -333 -431 -610 -551 -351 -574 -548 290 -506 94 -192 -471 -535 -506 -502 6 -316 227 -516 -458 -7 -410 -200 4 -314 -290 -182 -28 139 137 97 -106 -256 51 38 25 20 -221 -366 -4 61 -428 -188 -102 -334 -74 52 -298 141 -130 93 61 -249 -81 112 195 -129 -248 -374 -5 -318 386 -431 -324 -470 -438 -297 -372 -61 20 -304 47 -439 41 186 -360 -300 -347 -474 -424 -264 97 -402 -180 -325 -446 -118 -335 29 -335 49 -229 -343 411 -155 -328 -274 -317 47 -50 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 14 nsites= 21 E= 3.1e-019 0.000000 0.000000 0.095238 0.095238 0.142857 0.000000 0.000000 0.476190 0.047619 0.095238 0.047619 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.190476 0.000000 0.047619 0.000000 0.047619 0.000000 0.000000 0.095238 0.000000 0.380952 0.047619 0.000000 0.047619 0.000000 0.000000 0.142857 0.000000 0.000000 0.047619 0.000000 0.000000 0.000000 0.047619 0.000000 0.000000 0.000000 0.285714 0.047619 0.000000 0.000000 0.000000 0.095238 0.142857 0.000000 0.095238 0.190476 0.000000 0.047619 0.000000 0.000000 0.095238 0.571429 0.000000 0.000000 0.047619 0.000000 0.095238 0.000000 0.000000 0.000000 0.000000 0.047619 0.047619 0.000000 0.047619 0.047619 0.000000 0.000000 0.095238 0.000000 0.095238 0.095238 0.000000 0.142857 0.000000 0.047619 0.333333 0.000000 0.000000 0.000000 0.047619 0.000000 0.047619 0.095238 0.000000 0.000000 0.000000 0.000000 0.095238 0.000000 0.000000 0.000000 0.047619 0.000000 0.000000 0.095238 0.000000 0.476190 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.095238 0.190476 0.000000 0.000000 0.095238 0.047619 0.000000 0.000000 0.000000 0.000000 0.000000 0.190476 0.000000 0.285714 0.000000 0.047619 0.000000 0.047619 0.095238 0.000000 0.047619 0.095238 0.000000 0.047619 0.047619 0.000000 0.142857 0.238095 0.000000 0.047619 0.000000 0.000000 0.000000 0.000000 0.000000 0.047619 0.000000 0.190476 0.047619 0.142857 0.047619 0.047619 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.476190 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 0.238095 0.285714 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.380952 0.000000 0.238095 0.000000 0.000000 0.000000 0.000000 0.000000 0.095238 0.000000 0.285714 0.000000 0.000000 0.047619 0.000000 0.000000 0.047619 0.000000 0.000000 0.000000 0.047619 0.142857 0.380952 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 0.047619 0.000000 0.142857 0.047619 0.047619 0.047619 0.000000 0.000000 0.095238 0.380952 0.000000 0.000000 0.000000 0.047619 0.000000 0.619048 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.000000 0.047619 0.000000 0.047619 0.142857 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.095238 0.000000 0.047619 0.000000 0.000000 0.619048 0.000000 0.000000 0.000000 0.000000 0.047619 0.047619 -------------------------------------------------------------------------------- Time 51.86 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RAM1_YEAST 2.14e-20 144_[1(1.27e-16)]_5_[2(5.78e-07)]_4_[1(1.33e-13)]_1_[2(2.54e-08)]_4_[1(5.00e-17)]_1_[2(5.08e-11)]_4_[1(3.47e-16)]_4_[2(4.59e-09)]_5_[1(3.52e-13)]_35_[2(9.16e-05)]_4 PFTB_RAT 2.44e-21 120_[2(1.52e-07)]_3_[1(4.30e-19)]_4_[2(2.34e-09)]_3_[1(2.81e-14)]_1_[2(1.65e-08)]_3_[1(1.15e-19)]_1_[2(1.65e-08)]_4_[1(3.17e-16)]_14_[2(4.58e-08)]_4_[1(4.30e-15)]_60 BET2_YEAST 1.02e-27 6_[2(5.17e-05)]_3_[1(3.11e-10)]_1_[2(6.90e-10)]_4_[1(7.78e-14)]_4_[2(4.34e-07)]_3_[1(3.41e-17)]_1_[2(5.01e-07)]_3_[1(2.10e-18)]_21_[1(7.28e-22)]_1_[2(2.24e-13)]_4_[1(6.64e-17)]_24 RATRABGERB 4.90e-26 65_[2(9.60e-12)]_3_[1(2.40e-14)]_1_[2(1.57e-09)]_3_[1(8.19e-19)]_1_[2(4.20e-12)]_3_[1(7.36e-19)]_18_[1(6.18e-21)]_1_[2(1.30e-12)]_4_[1(1.43e-17)]_26 CAL1_YEAST 3.16e-22 125_[2(1.65e-08)]_50_[2(5.01e-10)]_1_[1(1.14e-13)]_4_[2(5.86e-08)]_22_[1(9.17e-20)]_22_[1(5.47e-13)]_5_[2(1.91e-07)]_1 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 2 reached. ******************************************************************************** CPU: pmgm2 ********************************************************************************