******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.4.1 (Release date: Sat Aug 21 19:23:23 2021 -0700) 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= /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_5_peaks/seqs-centered 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 /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_5_peaks/seqs-centered -oc /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_5_peaks/meme_out -mod zoops -nmotifs 10 -minw 6 -maxw 15 -bfile /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_5_peaks/background -dna -revcomp -nostatus model: mod= zoops nmotifs= 10 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + - width: minw= 6 maxw= 15 nsites: minsites= 2 maxsites= 10056 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= 1005600 N= 10056 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.195 C 0.305 G 0.305 T 0.195 Background letter frequencies (from file /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d1_LPS_TRIM1_5_peaks/background): A 0.193 C 0.307 G 0.307 T 0.193 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF WWTTTTTKTWTTTTT MEME-1 width = 15 sites = 1552 llr = 19117 E-value = 6.2e-350 ******************************************************************************** -------------------------------------------------------------------------------- Motif WWTTTTTKTWTTTTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 44111111:51::12 pos.-specific C :1::11:11:::::: probability G :1:11::4::1111: matrix T 548788948478988 bits 2.4 2.1 * 1.9 * 1.7 * * Relative 1.4 * * *** Entropy 1.2 * *** * ***** (17.8 bits) 0.9 * ***** ******* 0.7 * ***** ******* 0.5 ******* ******* 0.2 *************** 0.0 --------------- Multilevel TATTTTTGTATTTTT consensus AT T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTTTTTKTWTTTTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 864816 bayes= 11.2232 E= 6.2e-350 117 -350 -373 142 113 -194 -145 100 -50 -263 -309 201 -119 -287 -121 194 -107 -261 -233 205 -90 -199 -297 202 -172 -731 -1724 228 -49 -127 31 87 -302 -145 -437 214 140 -281 -285 107 -49 -290 -191 194 -342 -337 -112 207 -242 -889 -213 221 -95 -314 -233 206 -24 -328 -290 198 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTTTTTKTWTTTTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1552 E= 6.2e-350 0.434278 0.027062 0.023196 0.515464 0.421392 0.079897 0.112113 0.386598 0.136598 0.049613 0.036082 0.777706 0.084407 0.041881 0.132732 0.740979 0.092139 0.050258 0.061211 0.796392 0.103093 0.077320 0.039304 0.780284 0.058634 0.001933 0.000000 0.939433 0.137242 0.127577 0.381443 0.353737 0.023840 0.112758 0.014820 0.848582 0.507732 0.043814 0.042526 0.405928 0.137242 0.041237 0.081830 0.739691 0.018041 0.029639 0.141753 0.810567 0.036082 0.000644 0.070232 0.893041 0.099871 0.034794 0.061211 0.804124 0.163660 0.031572 0.041237 0.763531 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTTTTTKTWTTTTT MEME-1 regular expression -------------------------------------------------------------------------------- [TA][AT]TTTTT[GT]T[AT]TTTTT -------------------------------------------------------------------------------- Time 306.90 secs. ******************************************************************************** ******************************************************************************** MOTIF CCTGTARTCCMRGCT MEME-2 width = 15 sites = 1001 llr = 12752 E-value = 2.7e-181 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCTGTARTCCMRGCT MEME-2 Description -------------------------------------------------------------------------------- Simplified A :2:1:65:::46::3 pos.-specific C 87:::1:2996::9: probability G :::9::41:::49:: matrix T 21a:a3:611::::7 bits 2.4 * 2.1 * * 1.9 * * 1.7 * * Relative 1.4 * * * * Entropy 1.2 *** ** **** (18.4 bits) 0.9 * *** * ** **** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel CCTGTAATCCCAGCT consensus T TGC AG A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGTARTCCMRGCT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 864816 bayes= 11.4803 E= 2.7e-181 -442 133 -509 12 -17 126 -356 -153 -1661 -568 -1661 237 -122 -568 156 -559 -459 -380 -1661 233 159 -132 -291 40 148 -480 54 -659 -1661 -32 -120 169 -1661 158 -509 -146 -342 159 -594 -192 101 89 -1661 -213 168 -1661 31 -1661 -255 -409 161 -389 -242 158 -480 -246 54 -568 -494 187 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGTARTCCMRGCT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1001 E= 2.7e-181 0.008991 0.772228 0.008991 0.209790 0.171828 0.735265 0.025974 0.066933 0.000000 0.005994 0.000000 0.994006 0.082917 0.005994 0.907093 0.003996 0.007992 0.021978 0.000000 0.970030 0.582418 0.122877 0.040959 0.253746 0.539461 0.010989 0.447552 0.001998 0.000000 0.245754 0.133866 0.620380 0.000000 0.921079 0.008991 0.069930 0.017982 0.926074 0.004995 0.050949 0.388611 0.567433 0.000000 0.043956 0.618382 0.000000 0.381618 0.000000 0.032967 0.017982 0.936064 0.012987 0.035964 0.918082 0.010989 0.034965 0.279720 0.005994 0.009990 0.704296 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGTARTCCMRGCT MEME-2 regular expression -------------------------------------------------------------------------------- [CT]CTGT[AT][AG][TC]CC[CA][AG]GC[TA] -------------------------------------------------------------------------------- Time 548.94 secs. ******************************************************************************** ******************************************************************************** MOTIF CCTCAGCCTCCCRAR MEME-3 width = 15 sites = 670 llr = 9488 E-value = 1.1e-157 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCTCAGCCTCCCRAR MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::61::::::695 pos.-specific C 99:81:aa:a98::: probability G ::::39::::::415 matrix T 11a21:::a:12::: bits 2.4 * 2.1 * * 1.9 * * 1.7 * * * Relative 1.4 ** ****** * Entropy 1.2 **** ****** * (20.4 bits) 0.9 **** ********** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel CCTCAGCCTCCCAAG consensus G G A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCAGCCTCCCRAR MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 864816 bayes= 12.1888 E= 1.1e-157 -384 157 -451 -169 -1603 159 -488 -162 -421 -488 -668 234 -1603 143 -488 -26 160 -210 -10 -180 -143 -1603 160 -1603 -1603 166 -1603 -255 -1603 164 -1603 -226 -1603 -536 -1603 236 -701 163 -1603 -211 -1603 163 -1603 -193 -301 132 -436 3 162 -323 23 -384 215 -1603 -107 -1603 122 -468 81 -1603 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCAGCCTCCCRAR MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 670 E= 1.1e-157 0.013433 0.913433 0.013433 0.059701 0.000000 0.926866 0.010448 0.062687 0.010448 0.010448 0.002985 0.976119 0.000000 0.828358 0.010448 0.161194 0.586567 0.071642 0.286567 0.055224 0.071642 0.000000 0.928358 0.000000 0.000000 0.967164 0.000000 0.032836 0.000000 0.959701 0.000000 0.040299 0.000000 0.007463 0.000000 0.992537 0.001493 0.953731 0.000000 0.044776 0.000000 0.949254 0.000000 0.050746 0.023881 0.764179 0.014925 0.197015 0.594030 0.032836 0.359701 0.013433 0.853731 0.000000 0.146269 0.000000 0.450746 0.011940 0.537313 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCAGCCTCCCRAR MEME-3 regular expression -------------------------------------------------------------------------------- CCTC[AG]GCCTCCC[AG]A[GA] -------------------------------------------------------------------------------- Time 787.01 secs. ******************************************************************************** ******************************************************************************** MOTIF TAGAGAYRGGGTTTC MEME-4 width = 15 sites = 425 llr = 6397 E-value = 5.2e-115 ******************************************************************************** -------------------------------------------------------------------------------- Motif TAGAGAYRGGGTTTC MEME-4 Description -------------------------------------------------------------------------------- Simplified A :7:a:9:4121:::: pos.-specific C 1:::::6:::::3:8 probability G ::9:9::6989:::: matrix T 92::::4::::a7a2 bits 2.4 * * 2.1 * * * 1.9 * * * * * 1.7 * * * * * Relative 1.4 * ** * * * Entropy 1.2 ****** * **** (21.7 bits) 0.9 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel TAGAGACGGGGTTTC consensus T TA A C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGAGAYRGGGTTTC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 864816 bayes= 12.6322 E= 5.2e-115 -436 -222 -1538 226 193 -702 -264 15 -255 -371 162 -635 237 -1538 -1538 -1538 -227 -403 159 -355 227 -371 -312 -403 -635 95 -403 99 94 -444 99 -536 -100 -702 151 -304 34 -702 129 -1538 -127 -702 155 -319 -1538 -344 -422 231 -436 7 -1538 179 -1538 -702 -702 237 -477 134 -1538 17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGAGAYRGGGTTTC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 425 E= 5.2e-115 0.009412 0.065882 0.000000 0.924706 0.734118 0.002353 0.049412 0.214118 0.032941 0.023529 0.941176 0.002353 1.000000 0.000000 0.000000 0.000000 0.040000 0.018824 0.924706 0.016471 0.929412 0.023529 0.035294 0.011765 0.002353 0.595294 0.018824 0.383529 0.369412 0.014118 0.611765 0.004706 0.096471 0.002353 0.877647 0.023529 0.244706 0.002353 0.752941 0.000000 0.080000 0.002353 0.896471 0.021176 0.000000 0.028235 0.016471 0.955294 0.009412 0.322353 0.000000 0.668235 0.000000 0.002353 0.002353 0.995294 0.007059 0.776471 0.000000 0.216471 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAGAGAYRGGGTTTC MEME-4 regular expression -------------------------------------------------------------------------------- T[AT]GAGA[CT][GA]G[GA]GT[TC]T[CT] -------------------------------------------------------------------------------- Time 1022.54 secs. ******************************************************************************** ******************************************************************************** MOTIF GCYRGGCRTGGTGGC MEME-5 width = 15 sites = 448 llr = 6087 E-value = 9.3e-091 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCYRGGCRTGGTGGC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::3:::4:2::::: pos.-specific C :a6:::7:3:::::8 probability G 9::7aa:6:89:aa: matrix T ::4:::3:7::a::2 bits 2.4 2.1 * 1.9 * 1.7 ** * * Relative 1.4 ** ** **** Entropy 1.2 ** ** * ***** (19.6 bits) 0.9 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GCCGGGCGTGGTGGC consensus TA TAC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCYRGGCRTGGTGGC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 864816 bayes= 12.5843 E= 9.3e-091 -311 -510 162 -297 -443 163 -1545 -226 -1545 104 -610 92 81 -1545 111 -1545 -1545 -1545 170 -1545 -1545 -1545 170 -1545 -297 121 -510 41 100 -1545 95 -311 -1545 7 -610 181 -30 -410 141 -411 -211 -410 161 -1545 -1545 -378 -452 232 -253 -710 165 -1545 -285 -1545 166 -1545 -485 139 -1545 -4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCYRGGCRTGGTGGC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 448 E= 9.3e-091 0.022321 0.008929 0.944196 0.024554 0.008929 0.950893 0.000000 0.040179 0.000000 0.631696 0.004464 0.363839 0.337054 0.000000 0.662946 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.024554 0.709821 0.008929 0.256696 0.386161 0.000000 0.591518 0.022321 0.000000 0.321429 0.004464 0.674107 0.156250 0.017857 0.814732 0.011161 0.044643 0.017857 0.937500 0.000000 0.000000 0.022321 0.013393 0.964286 0.033482 0.002232 0.964286 0.000000 0.026786 0.000000 0.973214 0.000000 0.006696 0.805804 0.000000 0.187500 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCYRGGCRTGGTGGC MEME-5 regular expression -------------------------------------------------------------------------------- GC[CT][GA]GG[CT][GA][TC]GGTGGC -------------------------------------------------------------------------------- Time 1255.80 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCGGSGGCGGSGGC MEME-6 width = 15 sites = 1180 llr = 11009 E-value = 6.4e-066 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCGGSGGCGGSGGC MEME-6 Description -------------------------------------------------------------------------------- Simplified A ::11::11:1::11: pos.-specific C 1:82:6::9216127 probability G 9a:79499:794873 matrix T ::1:::::11::1:: bits 2.4 2.1 1.9 1.7 * Relative 1.4 * * Entropy 1.2 ** * *** * (13.5 bits) 0.9 *** * *** * 0.7 *** * *** *** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GGCGGCGGCGGCGGC consensus G G CG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGSGGCGGSGGC MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 864816 bayes= 11.3189 E= 6.4e-066 -1685 -104 147 -1685 -425 -750 169 -1685 -105 141 -325 -176 -59 -103 118 -292 -231 -275 158 -1685 -351 87 32 -237 -174 -398 157 -437 -101 -433 150 -337 -266 154 -592 -147 -179 -72 116 -144 -1685 -241 162 -1685 -344 92 39 -1685 -166 -201 140 -190 -135 -46 110 -225 -308 109 -7 -258 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGSGGCGGSGGC MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1180 E= 6.4e-066 0.000000 0.149153 0.850847 0.000000 0.010169 0.001695 0.988136 0.000000 0.093220 0.817797 0.032203 0.056780 0.127966 0.150000 0.696610 0.025424 0.038983 0.045763 0.915254 0.000000 0.016949 0.562712 0.383051 0.037288 0.057627 0.019492 0.913559 0.009322 0.095763 0.015254 0.870339 0.018644 0.030508 0.894915 0.005085 0.069492 0.055932 0.186441 0.686441 0.071186 0.000000 0.057627 0.942373 0.000000 0.017797 0.580508 0.401695 0.000000 0.061017 0.076271 0.811017 0.051695 0.075424 0.223729 0.660169 0.040678 0.022881 0.651695 0.293220 0.032203 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGSGGCGGSGGC MEME-6 regular expression -------------------------------------------------------------------------------- GGCGG[CG]GGCGG[CG]G[GC][CG] -------------------------------------------------------------------------------- Time 1488.32 secs. ******************************************************************************** ******************************************************************************** MOTIF CTYRGCTCACTGCAA MEME-7 width = 15 sites = 208 llr = 3566 E-value = 7.0e-066 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTYRGCTCACTGCAA MEME-7 Description -------------------------------------------------------------------------------- Simplified A :1:3::::a::1:a8 pos.-specific C a:6::a:a:a1:a:: probability G :::69::::::9::2 matrix T :94:::a:::9:::: bits 2.4 * 2.1 * * * 1.9 * * * * * 1.7 * ***** ** Relative 1.4 ** *********** Entropy 1.2 ** *********** (24.7 bits) 0.9 *** *********** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel CTCGGCTCACTGCAA consensus TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTYRGCTCACTGCAA MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 864816 bayes= 13.6515 E= 7.0e-066 -1434 166 -1434 -274 -80 -1434 -1434 220 -1434 105 -1434 92 82 -441 101 -300 -200 -1434 162 -532 -1434 164 -400 -300 -1434 -1434 -1434 237 -1434 170 -1434 -1434 234 -1434 -367 -1434 -1434 170 -1434 -1434 -1434 -230 -1434 228 -133 -1434 159 -1434 -532 170 -1434 -1434 235 -1434 -400 -1434 207 -500 -79 -1434 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTYRGCTCACTGCAA MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 208 E= 7.0e-066 0.000000 0.971154 0.000000 0.028846 0.110577 0.000000 0.000000 0.889423 0.000000 0.634615 0.000000 0.365385 0.341346 0.014423 0.620192 0.024038 0.048077 0.000000 0.947115 0.004808 0.000000 0.956731 0.019231 0.024038 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.975962 0.000000 0.024038 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.062500 0.000000 0.937500 0.076923 0.000000 0.923077 0.000000 0.004808 0.995192 0.000000 0.000000 0.980769 0.000000 0.019231 0.000000 0.812500 0.009615 0.177885 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTYRGCTCACTGCAA MEME-7 regular expression -------------------------------------------------------------------------------- CT[CT][GA]GCTCACTGCAA -------------------------------------------------------------------------------- Time 1713.18 secs. ******************************************************************************** ******************************************************************************** MOTIF TCAAGYGATYCTCCY MEME-8 width = 15 sites = 515 llr = 7128 E-value = 2.0e-062 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCAAGYGATYCTCCY MEME-8 Description -------------------------------------------------------------------------------- Simplified A ::97::2a:::2::: pos.-specific C 1a:1:41::68:994 probability G :::2a:7::::2::: matrix T 9:1::6::a416::6 bits 2.4 2.1 ** 1.9 * * ** 1.7 * * ** Relative 1.4 *** * ** * Entropy 1.2 *** * ** ** (20.0 bits) 0.9 ***** ******** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel TCAAGTGATCCTCCT consensus CA T C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCAAGYGATYCTCCY MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 864816 bayes= 12.0394 E= 2.0e-062 -1565 -188 -572 224 -463 167 -1565 -363 226 -1565 -630 -139 181 -155 -68 -283 -224 -1565 164 -1565 -263 31 -314 152 20 -255 123 -505 235 -1565 -430 -663 -1565 -413 -472 233 -505 86 -1565 118 -317 143 -498 -44 1 -1565 -63 166 -363 160 -630 -205 -346 159 -498 -205 -293 19 -450 166 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCAAGYGATYCTCCY MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 515 E= 2.0e-062 0.000000 0.083495 0.005825 0.910680 0.007767 0.976699 0.000000 0.015534 0.922330 0.000000 0.003883 0.073786 0.675728 0.104854 0.192233 0.027184 0.040777 0.000000 0.959223 0.000000 0.031068 0.380583 0.034951 0.553398 0.221359 0.052427 0.720388 0.005825 0.982524 0.000000 0.015534 0.001942 0.000000 0.017476 0.011650 0.970874 0.005825 0.557282 0.000000 0.436893 0.021359 0.827184 0.009709 0.141748 0.194175 0.000000 0.198058 0.607767 0.015534 0.933981 0.003883 0.046602 0.017476 0.926214 0.009709 0.046602 0.025243 0.351456 0.013592 0.609709 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCAAGYGATYCTCCY MEME-8 regular expression -------------------------------------------------------------------------------- TCAAG[TC][GA]AT[CT]CTCC[TC] -------------------------------------------------------------------------------- Time 1936.10 secs. ******************************************************************************** ******************************************************************************** MOTIF GGTCTCGAACTCCTG MEME-9 width = 15 sites = 310 llr = 4936 E-value = 7.8e-062 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGTCTCGAACTCCTG MEME-9 Description -------------------------------------------------------------------------------- Simplified A 11::::3a8:::::1 pos.-specific C ::1a:7:::9:991: probability G 99::::7:::::::9 matrix T ::9:a3::219:19: bits 2.4 * 2.1 * * 1.9 * * * * * 1.7 * * * * * Relative 1.4 **** ******** Entropy 1.2 ***** ******** (23.0 bits) 0.9 ****** ******** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GGTCTCGAACTCCTG consensus TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTCTCGAACTCCTG MEME-9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 864816 bayes= 12.8991 E= 7.8e-062 -126 -1492 156 -390 -190 -1492 163 -1492 -1492 -218 -1492 227 -490 164 -557 -273 -1492 -399 -657 234 -432 115 -1492 67 64 -340 109 -358 236 -1492 -457 -1492 202 -399 -399 -9 -1492 163 -1492 -190 -332 -311 -399 226 -1492 161 -457 -200 -1492 161 -657 -165 -390 -257 -1492 228 -144 -1492 159 -490 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTCTCGAACTCCTG MEME-9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 310 E= 7.8e-062 0.080645 0.000000 0.906452 0.012903 0.051613 0.000000 0.948387 0.000000 0.000000 0.067742 0.000000 0.932258 0.006452 0.958065 0.006452 0.029032 0.000000 0.019355 0.003226 0.977419 0.009677 0.683871 0.000000 0.306452 0.300000 0.029032 0.654839 0.016129 0.987097 0.000000 0.012903 0.000000 0.780645 0.019355 0.019355 0.180645 0.000000 0.948387 0.000000 0.051613 0.019355 0.035484 0.019355 0.925806 0.000000 0.938710 0.012903 0.048387 0.000000 0.935484 0.003226 0.061290 0.012903 0.051613 0.000000 0.935484 0.070968 0.000000 0.922581 0.006452 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTCTCGAACTCCTG MEME-9 regular expression -------------------------------------------------------------------------------- GGTCT[CT][GA]AACTCCTG -------------------------------------------------------------------------------- Time 2157.96 secs. ******************************************************************************** ******************************************************************************** MOTIF GGAGTGCAGTGGCRC MEME-10 width = 15 sites = 207 llr = 3266 E-value = 5.8e-048 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGAGTGCAGTGGCRC MEME-10 Description -------------------------------------------------------------------------------- Simplified A 1:a1:1:a2::::5: pos.-specific C ::::::a:::::7:7 probability G 9a:9:9::8:aa:5: matrix T ::::a::::a::3:3 bits 2.4 * 2.1 * * * * 1.9 * * * * 1.7 * * ** * * Relative 1.4 ******* *** Entropy 1.2 ************ (22.8 bits) 0.9 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GGAGTGCAGTGGCGC consensus TAT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGTGCAGTGGCRC MEME-10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 864816 bayes= 13.1889 E= 5.8e-048 -123 -599 157 -1434 -332 -340 163 -1434 232 -1434 -340 -432 -151 -499 159 -1434 -1434 -1434 -1434 237 -173 -1434 162 -1434 -1434 167 -1434 -300 231 -440 -340 -1434 -11 -1434 140 -432 -1434 -282 -1434 231 -232 -1434 165 -1434 -1434 -1434 170 -1434 -332 117 -1434 59 127 -1434 80 -1434 -1434 124 -499 46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGTGCAGTGGCRC MEME-10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 207 E= 5.8e-048 0.082126 0.004831 0.913043 0.000000 0.019324 0.028986 0.951691 0.000000 0.961353 0.000000 0.028986 0.009662 0.067633 0.009662 0.922705 0.000000 0.000000 0.000000 0.000000 1.000000 0.057971 0.000000 0.942029 0.000000 0.000000 0.975845 0.000000 0.024155 0.956522 0.014493 0.028986 0.000000 0.178744 0.000000 0.811594 0.009662 0.000000 0.043478 0.000000 0.956522 0.038647 0.000000 0.961353 0.000000 0.000000 0.000000 1.000000 0.000000 0.019324 0.690821 0.000000 0.289855 0.463768 0.000000 0.536232 0.000000 0.000000 0.724638 0.009662 0.265700 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGTGCAGTGGCRC MEME-10 regular expression -------------------------------------------------------------------------------- GGAGTGCAGTGG[CT][GA][CT] -------------------------------------------------------------------------------- Time 2378.66 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (10) found. ******************************************************************************** CPU: cn45 ********************************************************************************