******************************************************************************** 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_d0_TRIM1_0_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_d0_TRIM1_0_peaks/seqs-centered -oc /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d0_TRIM1_0_peaks/meme_out -mod zoops -nmotifs 10 -minw 6 -maxw 15 -bfile /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d0_TRIM1_0_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= 15721 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= 1572100 N= 15721 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.198 C 0.302 G 0.302 T 0.198 Background letter frequencies (from file /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d0_TRIM1_0_peaks/background): A 0.196 C 0.304 G 0.304 T 0.196 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF AMWAAAAAWAMAAAA MEME-1 width = 15 sites = 2232 llr = 25017 E-value = 3.1e-204 ******************************************************************************** -------------------------------------------------------------------------------- Motif AMWAAAAAWAMAAAA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 734787984738889 pos.-specific C :411:1:1::4111: probability G :111:1:111211:: matrix T 224:21115211111 bits 2.3 2.1 1.9 1.6 * * * Relative 1.4 * * * ** Entropy 1.2 * ** ** * **** (16.2 bits) 0.9 * ******* **** 0.7 * ******** **** 0.5 * ******** **** 0.2 *************** 0.0 --------------- Multilevel ACAAAAAATACAAAA consensus TAT A A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMWAAAAAWAMAAAA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1352006 bayes= 11.4073 E= 3.1e-204 189 -281 -782 21 67 45 -173 -11 113 -188 -208 109 193 -104 -153 -777 210 -682 -940 -32 184 -241 -138 -65 219 -740 -264 -184 194 -190 -251 -78 113 -391 -192 126 186 -488 -144 -26 69 38 -98 -54 196 -201 -235 -94 201 -181 -207 -188 209 -185 -940 -128 219 -350 -445 -161 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMWAAAAAWAMAAAA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 2232 E= 3.1e-204 0.728495 0.043459 0.001344 0.226703 0.311380 0.414427 0.091846 0.182348 0.429659 0.082437 0.071685 0.416219 0.746864 0.147401 0.104839 0.000896 0.840054 0.002688 0.000448 0.156810 0.700269 0.057348 0.116935 0.125448 0.894713 0.001792 0.048835 0.054659 0.750896 0.081541 0.053315 0.114247 0.429659 0.020161 0.080197 0.469982 0.713710 0.010305 0.112007 0.163978 0.316308 0.394265 0.154122 0.135305 0.762545 0.075269 0.059588 0.102599 0.787634 0.086918 0.072133 0.053315 0.834677 0.084229 0.000448 0.080645 0.895161 0.026882 0.013889 0.064068 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AMWAAAAAWAMAAAA MEME-1 regular expression -------------------------------------------------------------------------------- [AT][CA][AT]AAAAA[TA]A[CA]AAAA -------------------------------------------------------------------------------- Time 343.69 secs. ******************************************************************************** ******************************************************************************** MOTIF CCTGTAATCCCAGCW MEME-2 width = 15 sites = 652 llr = 11024 E-value = 1.5e-116 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCTGTAATCCCAGCW MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::1:a7::::a::5 pos.-specific C 99::::::999::9: probability G :::9::3:::::a:: matrix T :1a:a::a111:::5 bits 2.3 * 2.1 * ** * * 1.9 * ** * * 1.6 * ** * * Relative 1.4 *** ********** Entropy 1.2 *************** (24.4 bits) 0.9 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel CCTGTAATCCCAGCA consensus G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGTAATCCCAGCW MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1352006 bayes= 13.0811 E= 1.5e-116 -368 162 -531 -224 -600 163 -763 -187 -468 -763 -463 232 -124 -504 158 -1599 -468 -1599 -431 232 228 -1599 -272 -1599 192 -1599 -24 -1599 -1599 -446 -1599 233 -700 164 -1599 -191 -468 161 -663 -171 -541 163 -1599 -175 231 -1599 -482 -368 -204 -1599 165 -1599 -354 164 -363 -441 135 -417 -1599 130 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGTAATCCCAGCW MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 652 E= 1.5e-116 0.015337 0.935583 0.007669 0.041411 0.003067 0.941718 0.001534 0.053681 0.007669 0.001534 0.012270 0.978528 0.082822 0.009202 0.907975 0.000000 0.007669 0.000000 0.015337 0.976994 0.953988 0.000000 0.046012 0.000000 0.742331 0.000000 0.257669 0.000000 0.000000 0.013804 0.000000 0.986196 0.001534 0.946319 0.000000 0.052147 0.007669 0.929448 0.003067 0.059816 0.004601 0.937117 0.000000 0.058282 0.973926 0.000000 0.010736 0.015337 0.047546 0.000000 0.952454 0.000000 0.016871 0.949387 0.024540 0.009202 0.500000 0.016871 0.000000 0.483129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTGTAATCCCAGCW MEME-2 regular expression -------------------------------------------------------------------------------- CCTGTA[AG]TCCCAGC[AT] -------------------------------------------------------------------------------- Time 606.82 secs. ******************************************************************************** ******************************************************************************** MOTIF GGAGGCBGMGGCRGG MEME-3 width = 15 sites = 2518 llr = 23672 E-value = 5.2e-111 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGAGGCBGMGGCRGG MEME-3 Description -------------------------------------------------------------------------------- Simplified A 116111:161:1311 pos.-specific C 1:3::93:3::7113 probability G 891991491991597 matrix T ::::::3::::21:: bits 2.3 2.1 1.9 1.6 Relative 1.4 * Entropy 1.2 * ** * ** (13.6 bits) 0.9 ** *** * ** * 0.7 ****** **** * 0.5 ****** ***** ** 0.2 *************** 0.0 --------------- Multilevel GGAGGCGGAGGCGGG consensus C T C A C sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGCBGMGGCRGG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1352006 bayes= 11.1228 E= 5.2e-111 -157 -217 144 -230 -195 -343 160 -1794 163 -24 -119 -1794 -121 -380 154 -478 -134 -799 160 -1794 -177 152 -238 -404 -330 -20 36 73 -85 -799 154 -514 149 16 -206 -244 -190 -406 161 -536 -251 -380 159 -284 -187 121 -184 -32 67 -133 76 -194 -184 -178 150 -1794 -124 -22 111 -1794 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGCBGMGGCRGG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 2518 E= 5.2e-111 0.065925 0.067514 0.826847 0.039714 0.050834 0.028197 0.920969 0.000000 0.608817 0.257744 0.133439 0.000000 0.084988 0.021843 0.886021 0.007149 0.077442 0.001191 0.921366 0.000000 0.057585 0.872121 0.058380 0.011914 0.019857 0.265290 0.388801 0.326052 0.108817 0.001191 0.884432 0.005560 0.551231 0.339952 0.072677 0.036140 0.052423 0.018268 0.924543 0.004766 0.034551 0.021843 0.916203 0.027403 0.053614 0.704130 0.084988 0.157268 0.312550 0.121128 0.515091 0.051231 0.054805 0.088165 0.857029 0.000000 0.083002 0.261319 0.655679 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGAGGCBGMGGCRGG MEME-3 regular expression -------------------------------------------------------------------------------- GG[AC]GGC[GTC]G[AC]GGC[GA]G[GC] -------------------------------------------------------------------------------- Time 866.31 secs. ******************************************************************************** ******************************************************************************** MOTIF CCAGCCTGGSCAACA MEME-4 width = 15 sites = 514 llr = 8256 E-value = 7.3e-102 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCAGCCTGGSCAACA MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::a:::::11:8a:a pos.-specific C a9::aa:::58::9: probability G :::9:::a94:2::: matrix T :1:1::a:::2::1: bits 2.3 * * * 2.1 * * * * 1.9 * * * * 1.6 * ** * * Relative 1.4 ******** ** * Entropy 1.2 ********* **** (23.2 bits) 0.9 ********* ***** 0.7 ********* ***** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel CCAGCCTGGCCAACA consensus G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAGCCTGGSCAACA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1352006 bayes= 13.362 E= 7.3e-102 -1565 167 -1565 -249 -1565 164 -1565 -185 235 -728 -1565 -1565 -1565 -1565 159 -123 -507 165 -1565 -233 -385 166 -570 -307 -665 -1565 -1565 235 -1565 -496 170 -1565 -82 -1565 154 -466 -180 64 55 -296 -407 136 -429 -3 201 -496 -60 -1565 233 -1565 -448 -1565 -1565 160 -383 -170 232 -383 -1565 -1565 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAGCCTGGSCAACA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 514 E= 7.3e-102 0.000000 0.964981 0.000000 0.035019 0.000000 0.945525 0.000000 0.054475 0.998054 0.001946 0.000000 0.000000 0.000000 0.000000 0.916342 0.083658 0.005837 0.955253 0.000000 0.038911 0.013619 0.957198 0.005837 0.023346 0.001946 0.000000 0.000000 0.998054 0.000000 0.009728 0.990272 0.000000 0.110895 0.000000 0.881323 0.007782 0.056420 0.472763 0.445525 0.025292 0.011673 0.780156 0.015564 0.192607 0.789883 0.009728 0.200389 0.000000 0.986381 0.000000 0.013619 0.000000 0.000000 0.918288 0.021401 0.060311 0.978599 0.021401 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAGCCTGGSCAACA MEME-4 regular expression -------------------------------------------------------------------------------- CCAGCCTGG[CG]C[AG]ACA -------------------------------------------------------------------------------- Time 1124.66 secs. ******************************************************************************** ******************************************************************************** MOTIF AGGTCAGGAGTTCGA MEME-5 width = 15 sites = 379 llr = 6028 E-value = 1.6e-076 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGGTCAGGAGTTCGA MEME-5 Description -------------------------------------------------------------------------------- Simplified A a::::a1:a:1::2a pos.-specific C ::239:::::::6:: probability G :a7:::9a:a::17: matrix T :::71:::::8a3:: bits 2.3 * * * 2.1 * * * * 1.9 * * * * * 1.6 * * * * * Relative 1.4 ** ********* * Entropy 1.2 ** ********* * (22.9 bits) 0.9 ** ********* ** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel AGGTCAGGAGTTCGA consensus CC TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGTCAGGAGTTCGA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1352006 bayes= 13.7026 E= 1.6e-076 234 -1521 -1521 -522 -463 -385 165 -341 -422 -31 126 -363 -1521 -17 -1521 190 -422 162 -684 -197 228 -526 -315 -522 -163 -684 160 -389 -231 -585 165 -1521 231 -1521 -385 -621 -263 -452 165 -1521 -60 -352 -268 202 -1521 -1521 -1521 235 -363 108 -245 54 26 -326 126 -522 234 -684 -1521 -621 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGTCAGGAGTTCGA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 379 E= 1.6e-076 0.994723 0.000000 0.000000 0.005277 0.007916 0.021108 0.952507 0.018470 0.010554 0.245383 0.728232 0.015831 0.000000 0.269129 0.000000 0.730871 0.010554 0.936675 0.002639 0.050132 0.952507 0.007916 0.034301 0.005277 0.063325 0.002639 0.920844 0.013193 0.039578 0.005277 0.955145 0.000000 0.976253 0.000000 0.021108 0.002639 0.031662 0.013193 0.955145 0.000000 0.129288 0.026385 0.047493 0.796834 0.000000 0.000000 0.000000 1.000000 0.015831 0.643799 0.055409 0.284960 0.234828 0.031662 0.728232 0.005277 0.994723 0.002639 0.000000 0.002639 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGTCAGGAGTTCGA MEME-5 regular expression -------------------------------------------------------------------------------- AG[GC][TC]CAGGAGTT[CT][GA]A -------------------------------------------------------------------------------- Time 1386.68 secs. ******************************************************************************** ******************************************************************************** MOTIF GTGAAACCCYRTCTC MEME-6 width = 15 sites = 427 llr = 6627 E-value = 1.6e-060 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTGAAACCCYRTCTC MEME-6 Description -------------------------------------------------------------------------------- Simplified A :12a7a::::4:::: pos.-specific C :3::::9897::a:9 probability G a:8:3:::::6:::: matrix T :6:::::213:a:a: bits 2.3 * * * 2.1 * * * * 1.9 * * * * 1.6 * * *** Relative 1.4 * * ** *** Entropy 1.2 * ***** * **** (22.4 bits) 0.9 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GTGAAACCCCGTCTC consensus C G T TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGAAACCCYRTCTC MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1352006 bayes= 13.2727 E= 1.6e-060 -239 -1538 165 -480 -158 -2 -1538 169 -14 -470 142 -1538 235 -1538 -1538 -639 188 -543 -16 -1538 234 -701 -543 -1538 -439 164 -1538 -222 -407 136 -1538 10 -407 156 -1538 -110 -380 110 -701 75 85 -1538 109 -1538 -480 -602 -1538 233 -1538 172 -1538 -1538 -1538 -443 -602 232 -480 161 -343 -248 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGAAACCCYRTCTC MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 427 E= 1.6e-060 0.037471 0.000000 0.955504 0.007026 0.065574 0.299766 0.000000 0.634660 0.177986 0.011710 0.810304 0.000000 0.997658 0.000000 0.000000 0.002342 0.721311 0.007026 0.271663 0.000000 0.990632 0.002342 0.007026 0.000000 0.009368 0.948478 0.000000 0.042155 0.011710 0.777518 0.000000 0.210773 0.011710 0.896956 0.000000 0.091335 0.014052 0.653396 0.002342 0.330211 0.353630 0.000000 0.646370 0.000000 0.007026 0.004684 0.000000 0.988290 0.000000 1.000000 0.000000 0.000000 0.000000 0.014052 0.004684 0.981265 0.007026 0.929742 0.028103 0.035129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGAAACCCYRTCTC MEME-6 regular expression -------------------------------------------------------------------------------- G[TC]GA[AG]AC[CT]C[CT][GA]TCTC -------------------------------------------------------------------------------- Time 1632.82 secs. ******************************************************************************** ******************************************************************************** MOTIF GCCACCAYGCCYRGC MEME-7 width = 15 sites = 590 llr = 7955 E-value = 1.2e-051 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCCACCAYGCCYRGC MEME-7 Description -------------------------------------------------------------------------------- Simplified A 2::a::7:3:::4:: pos.-specific C :aa:a8:6:9a6::a probability G 8:::::3:7:::6a: matrix T :::::2:3:1:3::: bits 2.3 * 2.1 * 1.9 * 1.6 ** Relative 1.4 **** ** ** Entropy 1.2 ***** * ** ** (19.5 bits) 0.9 ******* ******* 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GCCACCACGCCCGGC consensus GTA TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCACCAYGCCYRGC MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1352006 bayes= 12.9639 E= 1.2e-051 -3 -1585 141 -1585 -1585 166 -1585 -227 -1585 172 -1585 -1585 233 -1585 -516 -585 -1585 167 -516 -315 -353 141 -548 -23 179 -1585 8 -1585 -277 101 -390 78 58 -468 117 -405 -453 161 -490 -190 -1585 166 -1585 -233 -340 110 -1585 76 97 -1585 97 -340 -240 -490 165 -1585 -385 166 -1585 -295 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCACCAYGCCYRGC MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 590 E= 1.2e-051 0.191525 0.000000 0.808475 0.000000 0.000000 0.959322 0.000000 0.040678 0.000000 1.000000 0.000000 0.000000 0.988136 0.000000 0.008475 0.003390 0.000000 0.969492 0.008475 0.022034 0.016949 0.808475 0.006780 0.167797 0.679661 0.000000 0.320339 0.000000 0.028814 0.613559 0.020339 0.337288 0.293220 0.011864 0.683051 0.011864 0.008475 0.928814 0.010169 0.052542 0.000000 0.961017 0.000000 0.038983 0.018644 0.649153 0.000000 0.332203 0.384746 0.000000 0.596610 0.018644 0.037288 0.010169 0.952542 0.000000 0.013559 0.961017 0.000000 0.025424 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCACCAYGCCYRGC MEME-7 regular expression -------------------------------------------------------------------------------- GCCACC[AG][CT][GA]CC[CT][GA]GC -------------------------------------------------------------------------------- Time 1863.50 secs. ******************************************************************************** ******************************************************************************** MOTIF GGTTCAAGYGATTCT MEME-8 width = 15 sites = 246 llr = 4160 E-value = 4.0e-029 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGTTCAAGYGATTCT MEME-8 Description -------------------------------------------------------------------------------- Simplified A 11:::a9::2a:::: pos.-specific C ::2:a:::61::2a: probability G 99::::1a:7::::: matrix T ::8a::::3::a8:9 bits 2.3 * * 2.1 * * ** 1.9 * * ** * 1.6 * *** ** ** Relative 1.4 * ****** ***** Entropy 1.2 ******** ***** (24.4 bits) 0.9 ********* ***** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GGTTCAAGCGATTCT consensus C TA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTTCAAGYGATTCT MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1352006 bayes= 14.5696 E= 4.0e-029 -134 -1459 160 -1459 -169 -522 160 -401 -559 -58 -1459 201 -1459 -1459 -1459 235 -1459 167 -622 -279 231 -422 -622 -559 215 -290 -205 -359 -559 -1459 171 -559 -1459 106 -390 82 19 -252 124 -459 231 -1459 -342 -1459 -1459 -1459 -1459 235 -1459 -64 -622 203 -459 169 -464 -1459 -301 -342 -622 227 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTTCAAGYGATTCT MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 246 E= 4.0e-029 0.077236 0.000000 0.922764 0.000000 0.060976 0.008130 0.918699 0.012195 0.004065 0.203252 0.000000 0.792683 0.000000 0.000000 0.000000 1.000000 0.000000 0.967480 0.004065 0.028455 0.975610 0.016260 0.004065 0.004065 0.869919 0.040650 0.073171 0.016260 0.004065 0.000000 0.991870 0.004065 0.000000 0.634146 0.020325 0.345528 0.223577 0.052846 0.715447 0.008130 0.971545 0.000000 0.028455 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.195122 0.004065 0.800813 0.008130 0.979675 0.012195 0.000000 0.024390 0.028455 0.004065 0.943089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTTCAAGYGATTCT MEME-8 regular expression -------------------------------------------------------------------------------- GG[TC]TCAAG[CT][GA]ATTCT -------------------------------------------------------------------------------- Time 2092.12 secs. ******************************************************************************** ******************************************************************************** MOTIF GCTCACTGCAACCTC MEME-9 width = 15 sites = 162 llr = 2838 E-value = 1.5e-026 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCTCACTGCAACCTC MEME-9 Description -------------------------------------------------------------------------------- Simplified A ::::a::::a9:::: pos.-specific C :9:a:a1:a::89:a probability G a::::::9::11::: matrix T ::a:::9:::::1a: bits 2.3 * * * 2.1 * * * * 1.9 * * * * 1.6 * * * * ** ** Relative 1.4 *********** *** Entropy 1.2 *********** *** (25.3 bits) 0.9 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GCTCACTGCAACCTC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCTCACTGCAACCTC MEME-9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1352006 bayes= 14.5086 E= 1.5e-026 -499 -1398 171 -1398 -499 164 -462 -240 -1398 -1398 -562 234 -1398 166 -1398 -218 232 -403 -1398 -1398 -1398 167 -562 -299 -267 -216 -562 219 -199 -562 164 -1398 -1398 166 -1398 -240 234 -562 -1398 -1398 212 -1398 -104 -1398 -218 144 -192 -199 -1398 161 -562 -153 -1398 -1398 -1398 235 -1398 170 -462 -1398 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCTCACTGCAACCTC MEME-9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 162 E= 1.5e-026 0.006173 0.000000 0.993827 0.000000 0.006173 0.944444 0.012346 0.037037 0.000000 0.000000 0.006173 0.993827 0.000000 0.956790 0.000000 0.043210 0.981481 0.018519 0.000000 0.000000 0.000000 0.969136 0.006173 0.024691 0.030864 0.067901 0.006173 0.895062 0.049383 0.006173 0.944444 0.000000 0.000000 0.962963 0.000000 0.037037 0.993827 0.006173 0.000000 0.000000 0.851852 0.000000 0.148148 0.000000 0.043210 0.827160 0.080247 0.049383 0.000000 0.925926 0.006173 0.067901 0.000000 0.000000 0.000000 1.000000 0.000000 0.987654 0.012346 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCTCACTGCAACCTC MEME-9 regular expression -------------------------------------------------------------------------------- GCTCACTGCAACCTC -------------------------------------------------------------------------------- Time 2318.77 secs. ******************************************************************************** ******************************************************************************** MOTIF ATCRYGCCACTGCAC MEME-10 width = 15 sites = 165 llr = 2727 E-value = 2.8e-013 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATCRYGCCACTGCAC MEME-10 Description -------------------------------------------------------------------------------- Simplified A a::3:3::a::::a: pos.-specific C ::7:6:aa:8::9:a probability G ::17:7:::::a::: matrix T :a2:4::::2a:1:: bits 2.3 * 2.1 ** * * * 1.9 ** * * * 1.6 ** *** * ** Relative 1.4 ** *** ** ** Entropy 1.2 ** ********* (23.8 bits) 0.9 ** ************ 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel ATCGCGCCACTGCAC consensus TATA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCRYGCCACTGCAC MEME-10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1352006 bayes= 15.0665 E= 2.8e-013 232 -1401 -406 -1401 -1401 -1401 -564 234 -1401 124 -219 15 82 -1401 111 -1401 -1401 105 -1401 91 38 -1401 127 -402 -1401 172 -1401 -1401 -1401 172 -1401 -1401 231 -1401 -332 -1401 -1401 143 -1401 -11 -1401 -332 -1401 231 -302 -564 167 -1401 -402 158 -1401 -132 232 -1401 -406 -1401 -1401 172 -1401 -1401 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCRYGCCACTGCAC MEME-10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 165 E= 2.8e-013 0.981818 0.000000 0.018182 0.000000 0.000000 0.000000 0.006061 0.993939 0.000000 0.715152 0.066667 0.218182 0.345455 0.000000 0.654545 0.000000 0.000000 0.630303 0.000000 0.369697 0.254545 0.000000 0.733333 0.012121 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.969697 0.000000 0.030303 0.000000 0.000000 0.818182 0.000000 0.181818 0.000000 0.030303 0.000000 0.969697 0.024242 0.006061 0.969697 0.000000 0.012121 0.909091 0.000000 0.078788 0.981818 0.000000 0.018182 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCRYGCCACTGCAC MEME-10 regular expression -------------------------------------------------------------------------------- AT[CT][GA][CT][GA]CCACTGCAC -------------------------------------------------------------------------------- Time 2551.64 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (10) found. ******************************************************************************** CPU: cn45 ********************************************************************************