******************************************************************************** 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 oops -protein -nostatus -nmotifs 2 -minw 8 model: mod= oops 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= 5 maxsites= 5 wnsites= 0.8 theta: prob= 1 spmap= pam spfuzz= 120 global: substring= yes branching= no wbranch= no em: prior= dmix b= 0 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= 8.44294 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 0.000000 0.000000 0.000000 0.000000 0.200000 0.200000 0.200000 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 0.000000 0.000000 0.000000 0.000000 0.200000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 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 0.200000 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 0.600000 0.000000 0.000000 0.000000 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 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 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 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 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 0.000000 0.000000 0.600000 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 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 0.200000 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 0.200000 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 0.000000 0.400000 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 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.400000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 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 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 0.400000 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 0.000000 0.000000 1.000000 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 0.200000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 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 0.200000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 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 1.24 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 22 sites = 5 llr = 230 E-value = 4.4e-013 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::::2:::2::::2:2::::: pos.-specific C 82:2:::::::::::::::::: probability D ::4:::::::8:2:22:a:::: matrix E ::244::::::::422:::::: F ::::::::4:::::::::44:: G ::::::8a:::::6:::::::: H :::::::::::::::2::::a: I ::::::::2::::::::::::: K ::2222::::24::2::::::: L ::::2:::42::::::::2::: M :::::::::::::::2:::::: N :::::::::::2::2::::::: P ::::2:2:::::8:::::2::: Q :82::2:::::::::::::::: R :::::::::2:4::::2::::: S :::::::::4:::::22::::2 T 2::2:4:::::::::::::::8 V ::::::::::::::::4:2::: W :::::::::::::::::::::: Y :::::::::::::::::::6:: bits 5.8 5.2 * 4.6 * 4.0 ** * * * Relative 3.5 ** ** * * * *** Entropy 2.9 ** ** **** * *** (66.3 bits) 2.3 ********* **** ******* 1.7 ********************** 1.2 ********************** 0.6 ********************** 0.0 ---------------------- Multilevel CQDEETGGFSDKPGADVDFYHT consensus TCECKAP LAKRDEDEA LF S sequence KKLK IL N EHR P QTPQ R KMS V NS -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------------- RATRABGERB 270 7.25e-24 REKLRSFILA CQDEETGGFADRPGDMVDPFHT LFGIAGLSLL BET2_YEAST 266 1.18e-21 YEKLTEFILK CQDEKKGGISDRPENEVDVFHT VFGVAGLSLM RAM1_YEAST 343 3.34e-21 HALRDYILYC CQEKEQPGLRDKPGAHSDFYHT NYCLLGLAVA PFTB_RAT 342 3.38e-19 QQALQEYILM CCQCPAGGLLDKPGKSRDFYHT CYCLSGLSIA CAL1_YEAST 321 4.81e-14 ELVTNYLLDR TQKTLTGGFSKNDEEDADLYHS CLGSAALALI -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RATRABGERB 7.2e-24 269_[2]_40 BET2_YEAST 1.2e-21 265_[2]_38 RAM1_YEAST 3.3e-21 342_[2]_67 PFTB_RAT 3.4e-19 341_[2]_74 CAL1_YEAST 4.8e-14 320_[2]_34 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=22 seqs=5 RATRABGERB ( 270) CQDEETGGFADRPGDMVDPFHT 1 BET2_YEAST ( 266) CQDEKKGGISDRPENEVDVFHT 1 RAM1_YEAST ( 343) CQEKEQPGLRDKPGAHSDFYHT 1 PFTB_RAT ( 342) CCQCPAGGLLDKPGKSRDFYHT 1 CAL1_YEAST ( 321) TQKTLTGGFSKNDEEDADLYHS 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 22 n= 1795 bayes= 8.48382 E= 4.4e-013 -317 468 -536 -480 -473 -515 -489 -393 -502 -496 -358 -431 -496 -481 -434 -439 -202 -421 -572 -551 -201 -28 -352 -110 -388 -392 -45 -323 -218 -293 -130 -177 -280 435 -152 -273 -235 -303 -327 -386 -101 -461 226 200 -366 -252 -171 -296 142 -325 -195 -63 -210 179 -106 -160 -127 -232 -399 -310 -39 127 -86 197 -232 -186 -81 -180 159 -220 -89 1 -155 14 6 -70 148 -136 -275 -194 -54 -354 -66 215 -262 -208 -104 -209 154 -4 -113 -26 160 9 -17 -97 -59 -161 -303 -220 109 -318 -107 -17 -246 -198 -89 -192 159 -232 -97 -10 -164 171 12 -63 240 -146 -282 -207 -155 -406 -271 -314 -437 348 -337 -418 -283 -497 -338 -171 32 -333 -265 -240 -290 -356 -399 -415 -176 -427 -286 -332 -447 358 -350 -433 -298 -511 -353 -188 -360 -351 -277 -261 -315 -375 -406 -425 -253 -339 -527 -442 287 -470 -372 161 -402 180 36 -379 -390 -333 -355 -390 -242 -73 -270 -215 145 -250 -160 -77 -208 -199 -130 -136 -22 -8 -77 -48 -178 -48 140 187 10 -98 -272 -203 -261 -452 373 -63 -408 -335 -255 -377 -56 -443 -329 -19 -380 -253 -275 -283 -285 -345 -421 -376 -190 -410 -273 -160 -401 -304 -150 -302 299 -322 -201 170 -285 -45 295 -221 -166 -272 -344 -309 -106 -385 26 -217 -346 -298 -272 -305 -205 -329 -260 -201 420 -198 -216 -191 -175 -255 -429 -395 -148 -419 -141 170 -426 310 -269 -390 -187 -446 -308 -100 -301 -180 -220 -209 -227 -325 -415 -386 110 -357 131 152 -267 -184 -93 -229 149 -257 -123 190 -164 6 -33 -82 -53 -176 -307 -218 -36 -329 116 133 -230 -179 182 -199 27 -230 211 15 -150 22 -11 73 -33 -150 -277 -173 155 -224 -224 -142 -204 -219 -182 -47 -94 -184 -75 -118 -213 -113 114 44 -57 264 -287 -237 -291 -459 383 -92 -417 -370 -283 -390 -349 -461 -350 -37 -416 -318 -335 -325 -328 -362 -427 -393 -142 -249 -385 -310 340 -341 -256 -34 -271 38 -12 -245 90 -255 -251 -241 -141 97 -205 -69 -229 -329 -362 -321 283 -383 -55 -236 -290 -245 -169 -229 -322 -266 -248 -273 -258 -228 -63 367 -334 -407 -306 -333 -257 -386 482 -415 -346 -379 -261 -89 -344 -90 -175 -295 -273 -364 -300 -124 -145 -275 -320 -331 -332 -339 -304 -212 -239 -361 -157 -102 -300 -226 -230 94 393 -169 -371 -379 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 22 nsites= 5 E= 4.4e-013 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 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 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.200000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.200000 0.200000 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 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.400000 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 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 0.400000 0.000000 0.000000 0.200000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 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 0.200000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.200000 0.000000 0.000000 0.400000 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 0.000000 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 0.600000 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 0.200000 0.000000 0.200000 0.200000 0.000000 0.000000 0.000000 0.000000 0.200000 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 0.200000 0.200000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.200000 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 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.200000 0.000000 0.400000 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 0.400000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT][QC][DEKQ][ECKT][EKLP][TAKQ][GP]G[FLI][SALR][DK][KRN][PD][GE][ADEKN][DEHMS][VARS]D[FLPV][YF]H[TS] -------------------------------------------------------------------------------- Time 2.20 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- RAM1_YEAST 2.49e-40 291_[1(4.70e-27)]_19_[2(3.34e-21)]_67 PFTB_RAT 1.93e-40 133_[1(5.68e-09)]_19_[1(4.88e-05)]_16_[1(4.55e-09)]_17_[1(3.49e-29)]_28_[2(3.38e-19)]_74 BET2_YEAST 7.54e-48 66_[2(1.77e-05)]_31_[1(4.36e-09)]_16_[1(7.32e-08)]_19_[1(6.27e-34)]_15_[2(1.18e-21)]_38 RATRABGERB 1.07e-48 126_[1(2.13e-09)]_16_[1(4.63e-06)]_16_[1(1.37e-32)]_15_[2(7.25e-24)]_40 CAL1_YEAST 2.44e-33 270_[1(5.14e-27)]_18_[2(4.81e-14)]_34 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 2 reached. ******************************************************************************** CPU: tlb-sayonara.imb.uq.edu.au ********************************************************************************