******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.3.3 (Release date: Sun Feb 7 15:39:52 2021 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** 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 ******************************************************************************** PRIMARY SEQUENCES= MergedChipseq_peaks.fa CONTROL SEQUENCES= --none-- ALPHABET= ACGT ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme MergedChipseq_peaks.fa -oc meme_output -dna -nmotifs 5 model: mod= zoops nmotifs= 5 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 8 maxw= 50 nsites: minsites= 2 maxsites= 64559 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 28693739 N= 64559 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.293 C 0.207 G 0.207 T 0.293 Background letter frequencies (from file dataset with add-one prior applied): A 0.293 C 0.207 G 0.207 T 0.293 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TCCCMSCACYTYGGSMKSCYRARGYGSKRGGATYACWKGMGBBMRSSASY MEME-1 width = 50 sites = 1110 llr = 38077 E-value = 5.4e-065 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCCCMSCACYTYGGSMKSCYRARGYGSKRGGATYACWKGMGBBMRSSASY MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::161:52:::21:6::::5a41:3::422a::7:41:63:1441:9:: pos.-specific C :996348:76:4::43:496::::4:3:2::::5:91::3:444:33:43 probability G :::1:6:2::::896:66::5:69:766388:::2:14916231556:52 matrix T 9112::22:496::::4::4::::6::41:::95:145:11421::::15 bits 2.3 2.0 1.8 * * * * * * 1.6 ** * * * * * * * Relative 1.4 *** * * * * * * **** * * Entropy 1.1 *** * * *** ** * * * **** * * * (49.5 bits) 0.9 *** ** ******* ******** *** **** * * * ** 0.7 *** *** ******************** ******* ** * ***** 0.5 ******* ******************** ******* ***** ******* 0.2 ************************************************** 0.0 -------------------------------------------------- Multilevel TCCCAGCACCTTGGGAGGCCGAGGTGGGAGGATTACTTGAGTCCGGGAGT consensus CC GAT C CCTC TA A CACTG CG AG CACGAACC CC sequence T GT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCMSCACYTYGGSMKSCYRARGYGSKRGGATYACWKGMGBBMRSSASY MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 50 n= 25529809 bayes= 16.7304 E= 5.4e-065 -382 -206 -414 165 -1676 215 -376 -218 -1676 211 -439 -155 -98 143 -63 -86 106 75 -309 -395 -200 77 143 -435 -395 194 -326 -82 78 -320 21 -32 -38 177 -314 -262 -554 144 -484 54 -576 -238 -526 169 -426 76 -352 107 -59 -332 186 -326 -234 -426 214 -426 -270 78 153 -676 107 69 -352 -314 -402 -484 156 31 -734 78 156 -326 -454 217 -384 -282 -349 148 -414 39 68 -359 125 -389 172 -503 -309 -602 45 -426 151 -734 -246 -467 218 -1676 -334 91 -345 94 8 -452 171 -676 -282 73 147 -289 -299 -452 151 31 38 -40 71 -125 -94 -526 200 -426 -96 -375 198 -426 172 -426 -309 -676 -602 -238 -484 169 -454 114 -280 77 127 -280 23 -382 -602 215 -452 -208 39 -84 -189 60 -206 -352 84 88 -256 -438 217 -554 93 45 -131 -192 0 -298 154 -190 -376 84 10 40 -167 79 74 -53 38 111 -162 -146 60 -375 135 -465 -146 76 134 -389 -273 76 149 -370 164 -338 -235 -339 -310 79 131 -166 -292 38 -31 84 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCMSCACYTYGGSMKSCYRARGYGSKRGGATYACWKGMGBBMRSSASY MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 50 nsites= 1110 E= 5.4e-065 0.020721 0.049550 0.011712 0.918018 0.000000 0.919820 0.015315 0.064865 0.000000 0.890090 0.009910 0.100000 0.148649 0.555856 0.134234 0.161261 0.609910 0.346847 0.024324 0.018919 0.072973 0.353153 0.559459 0.014414 0.018919 0.792793 0.021622 0.166667 0.503604 0.022523 0.239640 0.234234 0.224324 0.704505 0.023423 0.047748 0.006306 0.560360 0.007207 0.426126 0.005405 0.039640 0.005405 0.949550 0.015315 0.350450 0.018018 0.616216 0.194595 0.020721 0.754054 0.030631 0.057658 0.010811 0.916216 0.015315 0.045045 0.355856 0.596396 0.002703 0.616216 0.332432 0.018018 0.033333 0.018018 0.007207 0.610811 0.363964 0.001802 0.355856 0.611712 0.030631 0.012613 0.931532 0.014414 0.041441 0.026126 0.577477 0.011712 0.384685 0.469369 0.017117 0.493694 0.019820 0.964865 0.006306 0.024324 0.004505 0.399099 0.010811 0.588288 0.001802 0.053153 0.008108 0.938739 0.000000 0.028829 0.388288 0.018919 0.563964 0.309009 0.009009 0.679279 0.002703 0.041441 0.343243 0.575676 0.039640 0.036937 0.009009 0.590991 0.363063 0.381982 0.156757 0.337838 0.123423 0.152252 0.005405 0.827027 0.015315 0.150450 0.015315 0.818919 0.015315 0.962162 0.010811 0.024324 0.002703 0.004505 0.039640 0.007207 0.948649 0.012613 0.456757 0.029730 0.500901 0.707207 0.029730 0.242342 0.020721 0.004505 0.917117 0.009009 0.069369 0.384685 0.115315 0.055856 0.444144 0.070270 0.018018 0.372072 0.539640 0.049550 0.009910 0.934234 0.006306 0.556757 0.281982 0.083784 0.077477 0.293694 0.026126 0.601802 0.078378 0.021622 0.369369 0.221622 0.387387 0.091892 0.357658 0.346847 0.203604 0.381081 0.445045 0.067568 0.106306 0.444144 0.015315 0.528829 0.011712 0.106306 0.349550 0.524324 0.019820 0.044144 0.349550 0.583784 0.022523 0.911712 0.019820 0.040541 0.027928 0.034234 0.358559 0.514414 0.092793 0.038739 0.269369 0.167568 0.524324 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCMSCACYTYGGSMKSCYRARGYGSKRGGATYACWKGMGBBMRSSASY MEME-1 regular expression -------------------------------------------------------------------------------- TCCC[AC][GC]C[AGT][CA][CT]T[TC]GG[GC][AC][GT][GC]C[CT][GA]A[GA]G[TC][GA][GC][GT][AG]GGAT[TC][AG]C[TA][TG]G[AC][GA][TCG][CGT][CA][GA][GC][GC]A[GC][TC] -------------------------------------------------------------------------------- Time 404.62 secs. ******************************************************************************** ******************************************************************************** MOTIF HAAAMAAAAMAAAWAAAMAAAAAAAWRM MEME-2 width = 28 sites = 15393 llr = 147572 E-value = 4.0e-040 ******************************************************************************** -------------------------------------------------------------------------------- Motif HAAAMAAAAMAAAWAAAMAAAAAAAWRM MEME-2 Description -------------------------------------------------------------------------------- Simplified A 4766466a74978568758665655554 pos.-specific C 2::1311:141:112213:112111113 probability G 2:321:2:3::1111:211222222121 matrix T 2311231::2:1:31::211:2121322 bits 2.3 2.0 1.8 * 1.6 * Relative 1.4 * Entropy 1.1 * * * (13.8 bits) 0.9 * * * * * 0.7 * ** *** ** * 0.5 *** ******** *** * * * 0.2 *************************** 0.0 ---------------------------- Multilevel AAAAAAAAAAAAAAAAAAAAAAAAAAAA consensus CTGGCT GC T C G GTGC sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HAAAMAAAAMAAAWAAAMAAAAAAAWRM MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 28 n= 26950107 bayes= 13.0718 E= 4.0e-040 32 21 -22 -43 118 -963 -362 12 104 -297 34 -141 100 -104 24 -212 60 48 -134 -66 107 -92 -314 -22 110 -72 -43 -164 177 -2055 -2055 -2055 116 -153 40 -2055 61 78 -304 -77 159 -118 -2055 -347 135 -273 -78 -154 141 -86 -110 -441 79 -48 -175 -5 106 -32 -55 -181 148 -19 -2055 -2055 126 -94 -13 -2055 70 33 -111 -79 137 -905 -67 -141 101 -50 -26 -170 101 -60 12 -260 75 -31 -44 -65 110 -131 -42 -113 85 -70 -13 -91 81 -84 26 -128 68 -79 -76 -2 73 -88 26 -92 52 49 -134 -50 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HAAAMAAAAMAAAWAAAMAAAAAAAWRM MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 28 nsites= 15393 E= 4.0e-040 0.364711 0.239719 0.177418 0.218151 0.663159 0.000260 0.016891 0.319691 0.600143 0.026376 0.262977 0.110505 0.587085 0.100630 0.244981 0.067303 0.445267 0.287533 0.081985 0.185214 0.615410 0.108946 0.023517 0.252128 0.626584 0.125577 0.153446 0.094394 1.000000 0.000000 0.000000 0.000000 0.655168 0.071656 0.273176 0.000000 0.448061 0.354902 0.025141 0.171896 0.882609 0.090950 0.000000 0.026441 0.747288 0.031248 0.120574 0.100890 0.775482 0.114078 0.096602 0.013837 0.506399 0.148574 0.061392 0.283635 0.608718 0.165595 0.141818 0.083869 0.819139 0.180861 0.000000 0.000000 0.702787 0.107711 0.189502 0.000000 0.474436 0.260638 0.095823 0.169103 0.759436 0.000390 0.129799 0.110375 0.590528 0.146560 0.172546 0.090366 0.589814 0.136621 0.225037 0.048529 0.494056 0.166959 0.152212 0.186773 0.628208 0.083090 0.154811 0.133892 0.526928 0.127655 0.189437 0.155980 0.514974 0.115832 0.248555 0.120639 0.469954 0.119145 0.122523 0.288378 0.484116 0.112454 0.248814 0.154616 0.421230 0.289677 0.081920 0.207172 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HAAAMAAAAMAAAWAAAMAAAAAAAWRM MEME-2 regular expression -------------------------------------------------------------------------------- [ACT][AT][AG][AG][AC][AT]AA[AG][AC]AAA[AT]AAA[AC]AA[AG]AAA[AG][AT][AG][ACT] -------------------------------------------------------------------------------- Time 802.73 secs. ******************************************************************************** ******************************************************************************** MOTIF GCTCACTGCAVCCTCYRCCTCCYRGGYTCMAGYGATYCTCCYRCCYCAG MEME-3 width = 49 sites = 973 llr = 22286 E-value = 1.1e-027 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCTCACTGCAVCCTCYRCCTCCYRGGYTCMAGYGATYCTCCYRCCYCAG MEME-3 Description -------------------------------------------------------------------------------- Simplified A 1:::6:11163::1:1321:1:1311:::66:12511:1:112:::15: pos.-specific C 2838372283278274267378512253942252224726752763723 probability G 6111:2161142112242:1111576111:27252212121:4212:26 matrix T 11611161:11116121:261131:136::1131154161141225211 bits 2.3 2.0 1.8 1.6 * Relative 1.4 * * Entropy 1.1 * * * * * * * (33.0 bits) 0.9 * * * * ** * * ** * ** * * * * * * 0.7 **** * ** ** * ** ** ****** * * ** ** * * 0.5 ****** *** **** ************* *** ** *** **** * 0.2 ************************************************* 0.0 ------------------------------------------------- Multilevel GCTCACTGCAGCCTCCGCCTCCCGGGCTCAAGCGATCCTCCCGCCTCAG consensus C CG C CA C TA C TA CTC C TACCT C TA C GC sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCTCACTGCAVCCTCYRCCTCCYRGGYTCMAGYGATYCTCCYRCCYCAG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 49 n= 25594368 bayes= 16.9814 E= 1.1e-027 -191 -10 157 -139 -330 190 -100 -162 -557 36 -83 106 -1657 191 -51 -195 108 36 -433 -146 -273 169 14 -225 -130 -9 -75 94 -137 -4 159 -220 -237 193 -77 -303 100 35 -121 -220 23 -10 82 -160 -269 170 -14 -162 -315 192 -149 -140 -237 1 -90 109 -657 173 -21 -117 -127 107 0 -30 11 -8 97 -183 -84 155 -8 -303 -151 181 -665 -80 -263 44 -93 94 -227 176 -81 -127 -257 189 -128 -154 -193 133 -89 -1 -5 -63 133 -223 -160 -35 182 -535 -154 11 159 -246 -615 135 -50 13 -583 53 -126 105 -657 208 -86 -499 108 84 -533 -535 92 -28 -23 -159 -407 -7 177 -189 -211 119 -19 -7 -34 -27 129 -170 88 -4 -13 -201 -209 2 -14 86 -176 106 -103 38 -340 172 -22 -135 -194 21 -71 93 -283 164 -10 -126 -169 174 -58 -183 -127 115 -407 47 -28 -4 106 -121 -535 168 -27 -87 -260 163 -74 -66 -583 52 -28 85 -232 180 -220 -73 71 -18 6 -126 -483 50 162 -227 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCTCACTGCAVCCTCYRCCTCCYRGGYTCMAGYGATYCTCCYRCCYCAG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 49 nsites= 973 E= 1.1e-027 0.078109 0.193217 0.616650 0.112025 0.029805 0.770812 0.103803 0.095581 0.006166 0.265159 0.116136 0.612539 0.000000 0.778006 0.145940 0.076053 0.617677 0.265159 0.010277 0.106886 0.044193 0.665982 0.228160 0.061665 0.119219 0.194245 0.123330 0.563207 0.113052 0.200411 0.622816 0.063720 0.056526 0.786228 0.121274 0.035971 0.583762 0.263104 0.089414 0.063720 0.344296 0.192189 0.366906 0.096608 0.045221 0.671120 0.188078 0.095581 0.032888 0.782117 0.073998 0.110997 0.056526 0.207605 0.110997 0.624872 0.003083 0.687564 0.178828 0.130524 0.121274 0.432682 0.207605 0.238438 0.316547 0.195272 0.405961 0.082220 0.163412 0.604317 0.196300 0.035971 0.102775 0.726619 0.002055 0.168551 0.047276 0.280576 0.108941 0.563207 0.060637 0.699897 0.118191 0.121274 0.049332 0.764645 0.085303 0.100719 0.077081 0.519013 0.112025 0.291881 0.282631 0.133607 0.521069 0.062693 0.096608 0.162384 0.733813 0.007194 0.100719 0.223022 0.622816 0.053443 0.004111 0.528263 0.146968 0.320658 0.005139 0.299075 0.086331 0.609455 0.003083 0.873587 0.114080 0.009250 0.618705 0.368962 0.005139 0.007194 0.554985 0.170606 0.176773 0.097636 0.017472 0.197328 0.706064 0.079137 0.067831 0.471737 0.181912 0.278520 0.231244 0.171634 0.506680 0.090442 0.537513 0.200411 0.189106 0.072970 0.068859 0.209661 0.188078 0.533402 0.086331 0.430627 0.101747 0.381295 0.027749 0.679342 0.177801 0.115108 0.076053 0.238438 0.126413 0.559096 0.041110 0.643371 0.193217 0.122302 0.090442 0.688592 0.138746 0.082220 0.121274 0.459404 0.012333 0.406989 0.240493 0.200411 0.432682 0.126413 0.007194 0.660843 0.171634 0.160329 0.048304 0.641316 0.124358 0.186023 0.005139 0.297020 0.170606 0.527235 0.058582 0.719424 0.045221 0.176773 0.478931 0.182939 0.215827 0.122302 0.010277 0.291881 0.637205 0.060637 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCTCACTGCAVCCTCYRCCTCCYRGGYTCMAGYGATYCTCCYRCCYCAG MEME-3 regular expression -------------------------------------------------------------------------------- GC[TC]C[AC][CG]T[GC]C[AC][GA]CC[TC]C[CTG][GA]CC[TC]CC[CT][GA]G[GC][CT][TC]C[AC]AG[CT][GA][AC][TC][CT]C[TC]CC[CT][GAC]CC[TC]C[AG][GC] -------------------------------------------------------------------------------- Time 1193.24 secs. ******************************************************************************** ******************************************************************************** MOTIF GGBKGSRGKGAGCYRRGRKSRBGCCRSYGSACTCCAGSCTGGGSVRSAGR MEME-4 width = 50 sites = 1933 llr = 36039 E-value = 2.7e-022 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGBKGSRGKGAGCYRRGRKSRBGCCRSYGSACTCCAGSCTGGGSVRSAGR MEME-4 Description -------------------------------------------------------------------------------- Simplified A :211:1611151113314113:2114111:5111:611111111341523 pos.-specific C 222116:21122751122242326626316262671156221143252:1 probability G 76337337372721547233445212316422222184326673433265 matrix T 1134111:5111:322:141131121:42:::51:11:15111212:111 bits 2.3 2.0 1.8 1.6 Relative 1.4 Entropy 1.1 * * (26.9 bits) 0.9 * * * * ** * * * * * * 0.7 * **** * ** * * * * * * *** *** * * 0.5 ** **** * ** * * **** * ** * ** *** *** * ** 0.2 ************************* ******************* **** 0.0 -------------------------------------------------- Multilevel GGGTGCAGTGAGCCGGGATCGGGCCACTGCACTCCAGCCTGGGCGACAGG consensus TG GG G G GTAACGGGACCG GGCTGCG G GG GAGGCAA sequence C C C T G C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGBKGSRGKGAGCYRRGRKSRBGCCRSYGSACTCCAGSCTGGGSVRSAGR MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 50 n= 25529809 bayes= 15.9991 E= 2.7e-022 -482 -46 177 -114 -78 -14 147 -211 -157 21 72 14 -133 -53 67 48 -482 -47 178 -116 -238 144 61 -214 93 -764 70 -150 -152 -14 177 -756 -104 -88 47 65 -186 -101 183 -187 71 0 9 -165 -195 -9 171 -249 -180 166 11 -286 -116 127 -97 -15 -16 -103 123 -96 -2 -79 107 -89 -166 15 171 -715 58 -1 26 -145 -114 -45 55 49 -173 104 73 -104 24 -33 92 -157 -682 60 95 -5 -61 -3 139 -222 -206 148 10 -117 -180 153 -51 -76 53 -17 24 -98 -186 146 60 -304 -144 70 -81 58 -99 -180 150 -50 -290 143 93 -498 79 20 4 -275 -125 160 23 -569 -115 -6 -8 69 -130 147 -13 -131 -1756 183 4 -258 104 -61 -55 -126 -143 -193 188 -194 -157 128 77 -267 -212 157 31 -222 -118 -40 -15 85 -164 -20 161 -167 -129 -64 159 -122 -120 -83 176 -242 -117 106 35 -74 -1 32 86 -199 48 -24 29 -83 -107 139 58 -498 69 18 -2 -171 -26 -464 157 -117 22 -149 136 -243 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGBKGSRGKGAGCYRRGRKSRBGCCRSYGSACTCCAGSCTGGGSVRSAGR MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 50 nsites= 1933 E= 2.7e-022 0.010347 0.150543 0.706156 0.132954 0.170202 0.187274 0.574754 0.067770 0.098810 0.238489 0.340404 0.322297 0.116399 0.142783 0.330574 0.410243 0.010347 0.148991 0.709778 0.130885 0.056389 0.560269 0.316606 0.066736 0.558200 0.001035 0.336782 0.103983 0.102431 0.187274 0.708743 0.001552 0.142266 0.112261 0.286601 0.458872 0.080704 0.102949 0.736161 0.080186 0.479565 0.206415 0.220383 0.093637 0.076048 0.194516 0.677186 0.052250 0.084325 0.651319 0.224004 0.040352 0.131402 0.497672 0.106053 0.264873 0.261252 0.101397 0.486808 0.150543 0.288153 0.119503 0.433523 0.158820 0.092602 0.228660 0.676668 0.002069 0.438696 0.205380 0.248836 0.107087 0.132954 0.151061 0.302638 0.413347 0.088464 0.424211 0.344542 0.142783 0.345577 0.164511 0.391102 0.098810 0.002587 0.313502 0.399897 0.284014 0.191412 0.202276 0.543197 0.063114 0.070357 0.577858 0.221417 0.130367 0.083808 0.596999 0.145887 0.173306 0.423176 0.183135 0.245215 0.148474 0.080704 0.569064 0.314537 0.035696 0.108122 0.336265 0.118469 0.437144 0.146922 0.059493 0.585618 0.207967 0.039317 0.557682 0.393689 0.009312 0.504915 0.237972 0.213658 0.043456 0.123125 0.627522 0.243663 0.005691 0.131919 0.197620 0.196586 0.473875 0.118986 0.573720 0.188826 0.118469 0.000000 0.737196 0.213658 0.049146 0.601138 0.135023 0.141231 0.122607 0.108639 0.054320 0.760476 0.076565 0.098810 0.501811 0.353337 0.046042 0.067253 0.613037 0.256596 0.063114 0.129333 0.156751 0.186239 0.527677 0.093637 0.180548 0.633730 0.092085 0.120021 0.132437 0.621831 0.125711 0.127781 0.116399 0.700983 0.054837 0.129850 0.431454 0.263321 0.175375 0.291257 0.258148 0.376617 0.073978 0.407139 0.175375 0.252457 0.165028 0.139679 0.541645 0.309364 0.009312 0.472323 0.234351 0.203828 0.089498 0.244180 0.008277 0.617175 0.130367 0.341956 0.073461 0.530264 0.054320 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGBKGSRGKGAGCYRRGRKSRBGCCRSYGSACTCCAGSCTGGGSVRSAGR MEME-4 regular expression -------------------------------------------------------------------------------- GG[GTC][TG]G[CG][AG]G[TG]G[AGC]G[CG][CT][GA][GA][GC][AGC][TG][CG][GA][GCT][GC][CG]C[AG][CG][TC][GT][CG][ACG][CG]TC[CG]AG[CG][CG]TGGG[CG][GAC][AG][CG][ACG][GA][GA] -------------------------------------------------------------------------------- Time 1580.18 secs. ******************************************************************************** ******************************************************************************** MOTIF WGGCCRGGCRCRGTGGCTCAYGCCTGTA MEME-5 width = 28 sites = 221 llr = 7317 E-value = 4.2e-019 ******************************************************************************** -------------------------------------------------------------------------------- Motif WGGCCRGGCRCRGTGGCTCAYGCCTGTA MEME-5 Description -------------------------------------------------------------------------------- Simplified A 41:::4:::6:4:::::::a:2:::1:a pos.-specific C :::a7:::a:8:::::a:a:6:aa:::: probability G 29a::6aa:4:5a:aa:::::8:::9:: matrix T 4:::3:::::2::a:::a::3:::a:a: bits 2.3 * * * * * 2.0 ** *** * *** * ** * 1.8 *** *** * ***** **** * 1.6 *** *** * ******** ****** Relative 1.4 *** *** * ******** ******* Entropy 1.1 ******** * **************** (47.8 bits) 0.9 *************************** 0.7 *************************** 0.5 **************************** 0.2 **************************** 0.0 ---------------------------- Multilevel AGGCCGGGCACGGTGGCTCACGCCTGTA consensus T TA G A TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WGGCCRGGCRCRGTGGCTCAYGCCTGTA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 28 n= 26950107 bayes= 19.117 E= 4.2e-019 51 -1443 -19 46 -156 -1443 212 -1443 -1443 -393 225 -1443 -1443 223 -1443 -321 -1443 177 -452 -4 31 -1443 162 -1443 -256 -1443 220 -1443 -1443 -1443 227 -1443 -369 223 -452 -1443 93 -451 107 -1443 -1443 199 -1443 -73 60 -1443 134 -321 -1443 -1443 227 -1443 -601 -451 -452 174 -369 -1443 223 -601 -1443 -1443 227 -1443 -1443 223 -1443 -321 -1443 -1443 -551 176 -1443 226 -452 -1443 176 -451 -1443 -1443 -501 165 -1443 23 -23 -1443 186 -1443 -1443 221 -1443 -270 -501 224 -393 -1443 -1443 -1443 -1443 177 -243 -1443 219 -1443 -1443 -319 -1443 174 177 -1443 -1443 -1443 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WGGCCRGGCRCRGTGGCTCAYGCCTGTA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 28 nsites= 221 E= 4.2e-019 0.416290 0.000000 0.180995 0.402715 0.099548 0.000000 0.900452 0.000000 0.000000 0.013575 0.986425 0.000000 0.000000 0.968326 0.000000 0.031674 0.000000 0.705882 0.009050 0.285068 0.361991 0.000000 0.638009 0.000000 0.049774 0.000000 0.950226 0.000000 0.000000 0.000000 1.000000 0.000000 0.022624 0.968326 0.009050 0.000000 0.556561 0.009050 0.434389 0.000000 0.000000 0.823529 0.000000 0.176471 0.443439 0.000000 0.524887 0.031674 0.000000 0.000000 1.000000 0.000000 0.004525 0.009050 0.009050 0.977376 0.022624 0.000000 0.972851 0.004525 0.000000 0.000000 1.000000 0.000000 0.000000 0.968326 0.000000 0.031674 0.000000 0.000000 0.004525 0.995475 0.000000 0.990950 0.009050 0.000000 0.990950 0.009050 0.000000 0.000000 0.009050 0.647059 0.000000 0.343891 0.248869 0.000000 0.751131 0.000000 0.000000 0.954751 0.000000 0.045249 0.009050 0.977376 0.013575 0.000000 0.000000 0.000000 0.000000 1.000000 0.054299 0.000000 0.945701 0.000000 0.000000 0.022624 0.000000 0.977376 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WGGCCRGGCRCRGTGGCTCAYGCCTGTA MEME-5 regular expression -------------------------------------------------------------------------------- [AT]GGC[CT][GA]GGC[AG]C[GA]GTGGCTCA[CT][GA]CCTGTA -------------------------------------------------------------------------------- Time 1959.68 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: regmedhpc3 ********************************************************************************