******************************************************************************** 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 zoops -protein -nostatus -nmotifs 2 -minw 8 model: mod= zoops 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= 5 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 = 32 sites = 5 llr = 352 E-value = 2.1e-031 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::::::::::::2::::2:::22:24:::2 pos.-specific C :::::::2::2::::::a::::2::::::::: probability D ::22:::::::::::a:::::::::::::::: matrix E ::26::::::22::::::::::::::::::2: F ::2:::6::::::2::::::6::::::::::: G ::::8a::a:::::::4::::::24:::::4: H :::::::::::::::::::::::::::2::2: I ::::::::::::::::::::::::::::64:: K ::::::::::::a::::::::::::::2:::2 L 24::::4::::::8:::::::::6:28:46:: M 2::::::::::::::::::::::::::::::: N :::::::4:::6::::::::::::2::::::: P ::4:::::::4:::4::::::::::::2:::: Q 62:::::4::::::::::::::2::::::::: R :2::2::::a:::::::::::::::::::::6 S :2:2::::::22:::::::8::::28:::::: T ::::::::::::::::2:::::::::::::2: V ::::::::::::::4:4:::::6::::::::: W ::::::::::::::::::::4a:::::::::: Y ::::::::::::::::::a::::::::::::: bits 5.8 * 5.2 * 4.6 * ** * 4.0 * * * ** ** Relative 3.5 * ** *** * * ** ** Entropy 2.9 * ******* ***** ****** ** ** * (101.7 bits) 2.3 * ****************************** 1.7 ******************************** 1.2 ******************************** 0.6 ******************************** 0.0 -------------------------------- Multilevel QLPEGGFNGRPNKLPDGCYSFWVLGSLAILGR consensus LQDDR LQ CE FV V AW CAALAHLIEA sequence MRES C ES A T QGN K HK SF S S P T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------- BET2_YEAST 219 6.27e-34 EEIGWWLCER QLPEGGLNGRPSKLPDVCYSWWVLSSLAIIGR LDWINYEKLT RATRABGERB 223 1.37e-32 DLLGWWLCER QLPSGGLNGRPEKLPDVCYSWWVLASLKIIGR LHWIDREKLR PFTB_RAT 282 3.49e-29 SLLQWVTSRQ MRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHR ALHAQGDPAL RAM1_YEAST 292 4.70e-27 KLLEWSSARQ LQEERGFCGRSNKLVDGCYSFWVGGSAAILEA FGYGQCFNKH CAL1_YEAST 271 5.14e-27 FESELNASYD QSDDGGFQGRENKFADTCYAFWCLNSLHLLTK DWKMLCQTEL -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- BET2_YEAST 6.3e-34 218_[1]_75 RATRABGERB 1.4e-32 222_[1]_77 PFTB_RAT 3.5e-29 281_[1]_124 RAM1_YEAST 4.7e-27 291_[1]_108 CAL1_YEAST 5.1e-27 270_[1]_74 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=32 seqs=5 BET2_YEAST ( 219) QLPEGGLNGRPSKLPDVCYSWWVLSSLAIIGR 1 RATRABGERB ( 223) QLPSGGLNGRPEKLPDVCYSWWVLASLKIIGR 1 PFTB_RAT ( 282) MRFEGGFQGRCNKLVDGCYSFWQAGLLPLLHR 1 RAM1_YEAST ( 292) LQEERGFCGRSNKLVDGCYSFWVGGSAAILEA 1 CAL1_YEAST ( 271) QSDDGGFQGRENKFADTCYAFWCLNSLHLLTK 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 32 n= 1745 bayes= 9.38835 E= 2.1e-031 -200 -366 -346 -114 -278 -398 -55 -204 -204 -76 113 -179 -279 420 -150 -275 -216 -219 -307 -343 -65 -312 -142 -47 -216 -217 -93 -145 45 112 -67 -35 -180 179 174 68 -56 -121 -271 -200 -75 -366 85 113 89 -230 -153 -247 -61 -279 -167 -57 327 -57 -100 -127 -100 -198 -345 -229 -174 -549 101 341 -468 -299 -249 -379 -137 -418 -292 -106 -278 -80 -220 24 -207 -314 -499 -405 -159 -414 -264 -305 -433 350 -327 -413 -255 -492 -331 -164 -347 -318 10 -242 -294 -356 -392 -408 -176 -427 -286 -332 -447 358 -350 -433 -298 -511 -353 -188 -360 -351 -277 -261 -315 -375 -406 -425 -295 -345 -493 -448 386 -479 -353 -101 -421 103 -36 -379 -389 -380 -389 -376 -313 -158 -218 -95 -108 135 -103 -92 -294 -198 -86 -250 -50 -292 -163 312 -221 296 -75 -115 -99 -213 -328 -256 -176 -427 -286 -332 -447 358 -350 -433 -298 -511 -353 -188 -360 -351 -277 -261 -315 -375 -406 -425 -313 -372 -445 -422 -458 -408 -222 -384 -97 -421 -338 -267 -326 -213 447 -368 -328 -436 -331 -424 -63 97 -195 61 -293 -240 -195 -245 -109 -282 -182 -111 361 -114 -134 40 -105 -195 -363 -300 -188 -396 -78 72 -356 -209 -114 -319 -131 -393 -266 416 -262 -129 -176 44 -137 -306 -374 -308 -318 -451 -472 -400 -523 -459 -377 -378 416 -489 -351 -290 -406 -335 -3 -426 -332 -427 -439 -479 -275 -363 -497 -397 107 -473 -349 -47 -357 273 40 -362 -358 -288 -300 -390 -255 -107 -288 -248 110 -266 -305 -241 -261 -248 -272 -112 -216 -236 -143 -212 334 -208 -214 -157 -116 217 -356 -320 -291 -459 383 -92 -417 -370 -283 -390 -349 -461 -350 -37 -416 -318 -335 -325 -328 -362 -427 -393 -22 -224 -301 -251 -224 200 -264 -74 -218 -202 -97 -170 -249 -214 -211 -129 165 242 -315 -275 -344 470 -543 -486 -480 -544 -495 -404 -511 -506 -366 -443 -508 -491 -440 -470 -354 -442 -579 -559 -337 -420 -443 -429 -10 -430 -166 -333 -382 -337 -272 -310 -395 -352 -334 -376 -351 -327 -146 441 113 -235 -329 -333 -350 -220 -330 -332 -274 -391 -248 -138 -259 -279 -251 313 70 -257 -398 -367 -354 -384 -477 -454 367 -462 -176 -258 -400 -236 -195 -305 -405 -341 -343 -378 -346 -274 394 67 -365 -421 -423 -406 -135 -423 -374 -380 -369 -284 -257 -332 -414 -342 -312 -415 -356 -331 562 -179 -53 46 -338 -273 -214 -323 -266 26 -237 -176 -88 -237 -267 39 -210 -243 -90 346 -328 -301 123 -242 -334 -259 -171 57 -268 -76 -224 220 -22 -201 -255 -208 -210 -159 -113 -73 -293 -258 111 -316 -158 -185 -366 274 -220 -340 -168 -393 -255 166 -262 -181 -189 58 -141 -258 -383 -337 -97 -258 -306 -301 -282 -277 -295 -238 -223 -58 -185 -114 -266 -251 -213 312 99 -226 -355 -301 34 -327 -446 -350 -140 -393 -336 -50 -310 271 27 -315 -325 -264 -267 -310 -211 -87 -308 -291 189 -313 -107 -23 -238 -190 169 -197 149 -231 -103 -13 190 0 -2 -79 -47 -146 -284 -193 -251 -354 -464 -420 -167 -466 -418 341 -366 117 0 -343 -410 -355 -362 -380 -224 68 -346 -311 -257 -346 -516 -432 -126 -481 -398 250 -388 228 27 -379 -393 -331 -346 -405 -239 -16 -318 -306 -71 -348 -72 118 -275 203 177 -240 -18 -277 -145 22 -186 -31 -55 -90 133 -192 -315 -225 -8 -374 -345 -245 -419 -350 -178 -333 102 -360 -255 -180 -295 -111 415 -279 -230 -333 -324 -357 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 32 nsites= 5 E= 2.1e-031 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.200000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.200000 0.200000 0.200000 0.000000 0.000000 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0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.200000 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 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.200000 0.000000 0.000000 0.000000 0.200000 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 0.600000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.400000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [QLM][LQRS][PDEF][EDS][GR]G[FL][NQC]GR[PCES][NES]K[LF][PVA]D[GVT]CY[SA][FW]W[VCQ][LAG][GANS][SL][LA][AHKP][IL][LI][GEHT][RAK] -------------------------------------------------------------------------------- Time 2.91 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 50 sites = 4 llr = 429 E-value = 3.0e-023 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::::::3::a33353::::::3:::::53:::3::::::::::::::3: pos.-specific C :::::::::8:::::::::::::::::::::::::a::::::::35:::: probability D :::a:::::::::::::::::3:3::3:::3::::::::5:::::::::3 matrix E :a:::::::::::::::::3::35::8:::5::::::::5:::::::::8 F ::::::5:3::::::::::::::::3:::::5::::::5:::8::::::: G a:::::3:::::::::::5::::::::5::::::::::::aa:a3::5:: H :::::::::::::::::::::::::::::::::::::::::::::::3:: I ::3::::3:::::3::3::53::3:::::3::3:::::::::3::::::: K :::::::::::::::::::3:::::::3:::::33::::::::::::::: L :::::::::::5::5:88::8:::5::::3::35::::::::::3::::: M ::::::::::::::::::::::::::::::::::::3:::::::::::3: N ::::::::::::::::::5:::::3:::::3:::3::a:::::::::3:: P ::::::::::::::::::::::3::::3::::::::::::::::::a::: Q ::::::::::::::::::::::::::::::::::::5::::::::::::: R :::::a::::::::::::::::::::::::::::3::::::::::3:::: S ::::::33::::8::5::::::3:::::::::::3:::::::::3:::3: T ::::8::::3:::3:3:3:::8:::3::3::::::::::::::::::::: V ::8:3::3:::3:3::::::::::35::33::5::::::::::::3::3: W :::::::::::::::::::::::::::::::3::::::3::::::::::: Y ::::::::8::::::::::::::::::::::3::::3:3::::::::::: bits 5.8 5.2 4.6 * * * * 4.0 * * * *** * * * Relative 3.5 ****** *** * * * * **** **** * * Entropy 2.9 ******* *** * ****** ** * ** ********* *** * (154.9 bits) 2.3 ***************************** ************** ***** 1.7 ************************************************** 1.2 ************************************************** 0.6 ************************************************** 0.0 -------------------------------------------------- Multilevel GEVDTRFAYCALSAASLLGILTAELVEGAAEFVLKCQNFDGGFGCCPGAE consensus I V GIFT AAILAITNEIDEDNFDKTIDWIAN M WE I GR HMD sequence SS V T T K PIVT PVLNYLKR Y Y LV NS V V S V S S V -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------------- RAM1_YEAST 206 7.64e-45 NGGFKTCLEV GEVDTRGIYCALSIATLLNILTEELTEGVLNYLKNCQNYEGGFGSCPHVD EAHGGYTFCA BET2_YEAST 132 2.21e-44 EDGSFQGDRF GEVDTRFVYTALSALSILGELTSEVVDPAVDFVLKCYNFDGGFGLCPNAE SHAAQAFTCL PFTB_RAT 197 9.48e-44 PDGSFLMHVG GEVDVRSAYCAASVASLTNIITPDLFEGTAEWIARCQNWEGGIGGVPGME AHGGYTFCGL RATRABGERB 139 7.21e-43 EDGSFAGDIW GEIDTRFSFCAVATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSE SHAGQIYCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RAM1_YEAST 7.6e-45 205_[2]_176 BET2_YEAST 2.2e-44 131_[2]_144 PFTB_RAT 9.5e-44 196_[2]_191 RATRABGERB 7.2e-43 138_[2]_143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=50 seqs=4 RAM1_YEAST ( 206) GEVDTRGIYCALSIATLLNILTEELTEGVLNYLKNCQNYEGGFGSCPHVD 1 BET2_YEAST ( 132) GEVDTRFVYTALSALSILGELTSEVVDPAVDFVLKCYNFDGGFGLCPNAE 1 PFTB_RAT ( 197) GEVDVRSAYCAASVASLTNIITPDLFEGTAEWIARCQNWEGGIGGVPGME 1 RATRABGERB ( 139) GEIDTRFSFCAVATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSE 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 50 n= 1655 bayes= 8.68912 E= 3.0e-023 -165 -415 -275 -320 -437 357 -340 -421 -287 -500 -342 -176 -350 -340 -266 -250 -303 -363 -396 -415 -442 -645 -223 399 -599 -520 -471 -509 -487 -630 -510 -362 -572 -338 -491 -526 -476 -516 -600 -596 -98 -256 -394 -342 -247 -404 -344 180 -326 -163 -103 -310 -322 -339 -289 -332 -129 351 -404 -376 -284 -454 382 -85 -412 -363 -277 -384 -340 -456 -344 -31 -409 -310 -329 -318 -321 -356 -422 -387 -121 -256 -326 -305 -265 -323 -292 -83 -227 -245 -109 -119 -289 -219 -221 -24 378 115 -343 -326 -306 -368 -437 -411 -452 -402 -217 -378 -90 -415 -331 -260 -321 -206 446 -361 -321 -428 -326 -417 -66 -257 -244 -224 350 72 -203 -170 -197 -200 -125 -127 -244 -200 -208 59 -119 -147 -219 -23 182 -195 -311 -236 -154 -242 -233 180 -201 -115 -22 -184 -249 -198 -188 32 -58 228 -258 -213 -187 -297 -324 -280 228 -349 -24 -205 -252 -219 -138 -200 -287 -237 -214 -236 -222 -195 -49 382 -296 467 -526 -472 -462 -492 -480 -378 -486 -482 -347 -416 -481 -468 -424 -411 -157 -396 -560 -536 371 -182 -357 -300 -306 -169 -341 -248 -290 -310 -185 -250 -322 -289 -268 -82 -137 -109 -358 -366 119 -233 -374 -285 -118 -312 -264 47 -244 193 25 -230 -274 -222 -221 -222 -106 173 -256 -217 142 -219 -303 -293 -331 -199 -305 -306 -245 -366 -226 -124 -238 -249 -229 301 73 -227 -380 -347 111 -213 -338 -267 -161 -298 -252 189 -231 -113 -26 -209 -264 -227 -211 -196 120 270 -275 -233 259 -224 -344 -260 -147 -238 -277 -39 -227 171 -12 -220 -266 -220 -217 -153 -116 -32 -281 -245 93 -234 -294 -285 -314 -241 -288 -281 -218 -349 -203 -102 -246 -233 -207 285 201 -233 -363 -326 -245 -336 -480 -383 -115 -454 -354 139 -342 263 46 -346 -347 -281 -291 -370 -226 -49 -299 -288 -194 -312 -414 -322 -124 -387 -308 -29 -274 263 38 -281 -309 -241 -241 -293 87 -63 -287 -264 -141 -376 -97 -179 -386 281 -185 -383 -173 -442 -313 305 -275 -189 -203 -140 -170 -328 -397 -334 -82 -326 -111 136 -229 -237 -132 261 156 -158 -68 -60 -196 -23 -13 -134 -77 -18 -293 -219 -245 -336 -480 -383 -115 -454 -354 139 -342 263 46 -346 -347 -281 -291 -370 -226 -49 -299 -288 -134 -297 92 -131 -320 -254 -214 -222 -153 -341 -166 -23 -256 -148 -177 -16 373 -179 -364 -325 137 -302 -94 129 -252 -186 -116 -210 -15 -245 -121 -29 250 -17 -51 86 -44 -151 -305 -222 -169 -511 124 338 -420 -318 -248 41 -132 -381 -258 -134 -277 -82 -202 -240 -201 -275 -458 -377 -111 -245 -320 -237 -111 -308 -228 49 -190 206 34 143 -258 -180 -179 -214 -100 141 -243 -198 -59 -213 -340 -268 112 -307 -239 55 -233 -110 -24 -211 -258 -227 -207 -209 128 310 -259 -187 -336 -637 -54 391 -576 -454 -405 -474 -330 -561 -438 -286 -451 -232 -397 -421 -381 -448 -584 -549 -107 -370 -172 -143 -346 295 -201 -307 85 -354 -222 -72 146 -133 -106 -161 -160 -256 -353 -312 306 -172 -317 -246 -227 -175 -274 -95 -221 -210 -98 -198 -270 -220 -211 -77 126 145 -306 -285 87 -241 -377 -309 -156 -337 -288 258 -267 47 -7 -242 -299 -260 -248 -248 -108 225 -284 -237 -163 -477 192 300 -414 -242 -195 -360 -121 -400 -276 178 -261 -82 -190 -180 -173 -303 -448 -351 -270 -333 -401 -366 354 -411 -109 -232 -331 -221 -171 -259 -345 -298 -287 -305 -291 -236 281 249 -151 -282 -416 -364 -199 -410 -363 269 -327 38 -37 -303 -351 -331 -311 -327 -153 277 -356 -312 118 -262 -196 -98 -150 -238 -145 -54 142 174 -5 -88 -189 -59 -32 -137 -71 -50 -249 -190 -66 -338 -106 -35 -268 -193 -78 -221 202 -247 -117 212 -174 10 214 95 -44 -176 -286 -212 -342 470 -541 -484 -478 -541 -493 -402 -509 -504 -364 -441 -506 -489 -439 -468 -353 -440 -577 -557 -129 -315 -242 -93 -123 -301 -27 -160 -95 -186 185 -112 -233 377 -88 -188 -131 -147 -213 114 -311 -404 -210 -357 -366 -334 -119 -305 -267 -430 -299 467 -340 -239 -285 -181 -207 -339 -357 -357 -270 -333 -401 -366 354 -411 -109 -232 -331 -221 -171 -259 -345 -298 -287 -305 -291 -236 281 249 -174 -522 290 267 -451 -307 -250 -366 -150 -412 -290 -72 -281 -86 -235 -244 -221 -304 -472 -397 -165 -415 -275 -320 -437 357 -340 -421 -287 -500 -342 -176 -350 -340 -266 -250 -303 -363 -396 -415 -165 -415 -275 -320 -437 357 -340 -421 -287 -500 -342 -176 -350 -340 -266 -250 -303 -363 -396 -415 -275 -315 -447 -411 418 -450 -363 4 -394 -140 -113 -352 -359 -394 -382 -330 -312 -166 -206 -69 -165 -415 -275 -320 -437 357 -340 -421 -287 -500 -342 -176 -350 -340 -266 -250 -303 -363 -396 -415 73 179 -246 -184 -158 114 -193 -72 -145 46 -45 -113 -198 -142 -147 124 -21 -41 -251 -186 -111 404 -355 -270 -226 -316 -263 -96 -170 -204 -102 -219 -297 -212 88 -227 -134 89 -323 -268 -127 -394 -309 -269 -358 -315 -298 -323 -233 -345 -280 -253 437 -228 -238 -216 -198 -274 -431 -407 -140 -387 -91 -154 -357 290 174 -359 -138 -409 -276 195 -263 -153 -165 -138 -161 -310 -373 -291 236 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0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.250000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GE[VI]D[TV]R[FGS][AISV][YF][CT]A[LAV][SA][AITV][AL][SAT][LI][LT][GN][IEK][LI][TD][AEPS][EDI][LNV][VFT][ED][GKP][ATV][AILV][EDN][FWY][VIL][LAK][KNRS]C[QMY]N[FWY][DE]GG[FI]G[CGLS][CRV]P[GHN][AMSV][ED] -------------------------------------------------------------------------------- Time 5.70 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RAM1_YEAST 8.29e-64 205_[2(7.64e-45)]_36_[1(4.70e-27)]_108 PFTB_RAT 8.01e-65 133_[1(5.68e-09)]_31_[2(9.48e-44)]_35_[1(3.49e-29)]_30_[1(6.10e-07)]_62 BET2_YEAST 1.87e-70 31_[2(1.42e-05)]_50_[2(2.21e-44)]_37_[1(6.27e-34)]_17_[1(9.32e-07)]_26 RATRABGERB 1.33e-67 42_[2(3.11e-09)]_46_[2(7.21e-43)]_34_[1(1.37e-32)]_17_[1(2.11e-07)]_28 CAL1_YEAST 1.63e-25 212_[2(4.52e-06)]_8_[1(5.14e-27)]_20_[1(5.21e-05)]_22 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 2 reached. ******************************************************************************** CPU: tlb-sayonara.imb.uq.edu.au ********************************************************************************