******************************************************************************** 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/MemeChipOutput/GRCh38-107_AZ_exp1_d0_TRIM1_1_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/MemeChipOutput/GRCh38-107_AZ_exp1_d0_TRIM1_1_peaks/seqs-centered -oc /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d0_TRIM1_1_peaks/meme_out -mod zoops -nmotifs 10 -minw 5 -maxw 20 -bfile /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d0_TRIM1_1_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= 5 maxw= 20 nsites: minsites= 2 maxsites= 14321 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= 1432100 N= 14321 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.191 C 0.309 G 0.309 T 0.191 Background letter frequencies (from file /scratch/jngalang/MotifAnalysis/MemeChipOutput/GRCh38-107_AZ_exp1_d0_TRIM1_1_peaks/background): A 0.188 C 0.312 G 0.312 T 0.188 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF TWWTTTTTKTWTTTTTWKTW MEME-1 width = 20 sites = 1347 llr = 21525 E-value = 2.7e-328 ******************************************************************************** -------------------------------------------------------------------------------- Motif TWWTTTTTKTWTTTTTWKTW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2541111:11511:1:4225 pos.-specific C 111:1:1:111::111::11 probability G :111:11:5:1:::111411 matrix T 74488889483899895473 bits 2.4 2.2 1.9 * ** 1.7 * *** Relative 1.4 ** * * *** * Entropy 1.2 ***** * ***** (23.1 bits) 1.0 * ***** * ****** * 0.7 ** ***** ******** ** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TAATTTTTGTATTTTTTGTA consensus ATT T T AT T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TWWTTTTTKTWTTTTTWKTW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1160001 bayes= 12.0379 E= 2.7e-328 19 -172 -299 179 131 -215 -188 102 123 -158 -173 94 -70 -502 -168 205 -147 -206 -291 212 -69 -639 -259 214 -106 -210 -204 202 -698 -291 -274 228 -82 -216 57 94 -80 -206 -639 212 144 -251 -163 83 -36 -591 -526 216 -121 -613 -771 228 -640 -239 -613 231 -81 -259 -190 201 -698 -187 -236 218 121 -351 -245 136 -28 -274 52 90 -22 -255 -141 183 147 -261 -153 77 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TWWTTTTTKTWTTTTTWKTW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 1347 E= 2.7e-328 0.214551 0.095026 0.039347 0.651076 0.464736 0.070527 0.084633 0.380104 0.441722 0.104677 0.094284 0.359317 0.115813 0.009651 0.097253 0.777283 0.067558 0.074981 0.041574 0.815887 0.116555 0.003712 0.051967 0.827765 0.089829 0.072754 0.075724 0.761693 0.001485 0.041574 0.046771 0.910171 0.106162 0.069785 0.464736 0.359317 0.107647 0.074981 0.003712 0.813660 0.510022 0.054937 0.100965 0.334076 0.146251 0.005197 0.008166 0.840386 0.080921 0.004454 0.001485 0.913140 0.002227 0.059391 0.004454 0.933927 0.106904 0.051967 0.083890 0.757238 0.001485 0.085375 0.060876 0.852264 0.433556 0.027468 0.057164 0.481811 0.154417 0.046771 0.448404 0.350408 0.161099 0.053452 0.117298 0.668151 0.521158 0.051225 0.108389 0.319228 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TWWTTTTTKTWTTTTTWKTW MEME-1 regular expression -------------------------------------------------------------------------------- [TA][AT][AT]TTTTT[GT]T[AT]TTTTT[TA][GT]T[AT] -------------------------------------------------------------------------------- Time 418.47 secs. ******************************************************************************** ******************************************************************************** MOTIF TAATCCCAGCWMYTTGGGAG MEME-2 width = 20 sites = 601 llr = 12870 E-value = 1.2e-207 ******************************************************************************** -------------------------------------------------------------------------------- Motif TAATCCCAGCWMYTTGGGAG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :a8::::a::54:::2::a: pos.-specific C ::::999::a:54:3::::: probability G ::2:::::9::::::8aa:a matrix T a::a::1:::5:5a7::::: bits 2.4 * * * 2.2 ** * * * * 1.9 ** * * * * 1.7 ** * * * * Relative 1.4 ****** *** * **** Entropy 1.2 *********** * **** (30.9 bits) 1.0 *********** ******** 0.7 ******************** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TAATCCCAGCACTTTGGGAG consensus TAC C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAATCCCAGCWMYTTGGGAG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1160001 bayes= 12.9577 E= 1.2e-207 -1588 -355 -423 235 236 -597 -346 -1588 210 -755 -73 -523 -582 -597 -655 240 -682 160 -597 -196 -1588 160 -497 -212 -401 155 -1588 -136 240 -755 -497 -1588 -212 -755 160 -450 -423 162 -555 -282 148 -497 -523 128 124 66 -409 -201 -582 50 -497 153 -682 -323 -555 235 -350 -6 -438 183 -25 -523 140 -450 -217 -597 161 -582 -257 -597 162 -582 240 -1588 -655 -450 -236 -655 162 -1588 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAATCCCAGCWMYTTGGGAG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 601 E= 1.2e-207 0.000000 0.026622 0.016639 0.956739 0.966722 0.004992 0.028286 0.000000 0.805324 0.001664 0.188020 0.004992 0.003328 0.004992 0.003328 0.988353 0.001664 0.945092 0.004992 0.048253 0.000000 0.946755 0.009983 0.043261 0.011647 0.915141 0.000000 0.073211 0.988353 0.001664 0.009983 0.000000 0.043261 0.001664 0.946755 0.008319 0.009983 0.956739 0.006656 0.026622 0.524126 0.009983 0.008319 0.457571 0.442596 0.492512 0.018303 0.046589 0.003328 0.442596 0.009983 0.544093 0.001664 0.033278 0.006656 0.958403 0.016639 0.299501 0.014975 0.668885 0.158070 0.008319 0.825291 0.008319 0.041597 0.004992 0.950083 0.003328 0.031614 0.004992 0.960067 0.003328 0.988353 0.000000 0.003328 0.008319 0.036606 0.003328 0.960067 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAATCCCAGCWMYTTGGGAG MEME-2 regular expression -------------------------------------------------------------------------------- TAATCCCAGC[AT][CA][TC]T[TC]GGGAG -------------------------------------------------------------------------------- Time 769.90 secs. ******************************************************************************** ******************************************************************************** MOTIF TCRCYATGTTGSCCAGGCTG MEME-3 width = 20 sites = 571 llr = 11020 E-value = 7.2e-168 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCRCYATGTTGSCCAGGCTG MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::6::6:1::2:::a::1:: pos.-specific C :8:963:::2:59a:::9:: probability G ::4::1:9::85:::aa::a matrix T a21:4:a:a8::1:::::a: bits 2.4 * * 2.2 * * * * * 1.9 * * * * * 1.7 * * * * * Relative 1.4 * * * ** **** ** Entropy 1.2 * * **** ******** (27.8 bits) 1.0 ***** ***** ******** 0.7 *********** ******** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TCACCATGTTGGCCAGGCTG consensus TG TC C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCRCYATGTTGSCCAGGCTG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1160001 bayes= 12.7757 E= 7.2e-168 -1580 -416 -648 238 -416 127 -431 22 162 -516 17 -157 -394 160 -467 -266 -374 88 -747 112 167 -20 -186 -204 -516 -302 -747 235 -125 -548 152 -342 -516 -648 -648 239 -416 -70 -467 206 -2 -589 135 -374 -250 54 64 -284 -1580 148 -516 -66 -416 161 -648 -257 238 -589 -431 -574 -242 -747 161 -474 -394 -648 165 -516 -107 150 -747 -274 -516 -1580 -1580 241 -235 -747 162 -674 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCRCYATGTTGSCCAGGCTG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 571 E= 7.2e-168 0.000000 0.017513 0.003503 0.978984 0.010508 0.754816 0.015762 0.218914 0.577933 0.008757 0.350263 0.063047 0.012259 0.945709 0.012259 0.029772 0.014011 0.576182 0.001751 0.408056 0.597198 0.271454 0.085814 0.045534 0.005254 0.038529 0.001751 0.954466 0.078809 0.007005 0.896673 0.017513 0.005254 0.003503 0.003503 0.987741 0.010508 0.192644 0.012259 0.784588 0.185639 0.005254 0.795096 0.014011 0.033275 0.455342 0.485114 0.026270 0.000000 0.872154 0.008757 0.119089 0.010508 0.954466 0.003503 0.031524 0.975482 0.005254 0.015762 0.003503 0.035026 0.001751 0.956217 0.007005 0.012259 0.003503 0.978984 0.005254 0.089317 0.880911 0.001751 0.028021 0.005254 0.000000 0.000000 0.994746 0.036778 0.001751 0.959720 0.001751 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCRCYATGTTGSCCAGGCTG MEME-3 regular expression -------------------------------------------------------------------------------- T[CT][AG]C[CT][AC]TGTTG[GC]CCAGGCTG -------------------------------------------------------------------------------- Time 1119.69 secs. ******************************************************************************** ******************************************************************************** MOTIF CAGGCRYGHGCCACYRCRCC MEME-4 width = 20 sites = 832 llr = 12569 E-value = 6.1e-147 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAGGCRYGHGCCACYRCRCC MEME-4 Description -------------------------------------------------------------------------------- Simplified A :92:23:142::a::5:4:: pos.-specific C 9:::6:423:aa:96:7:97 probability G :17a:5:7:8:::::5:6:: matrix T 1:::226:3::::13:3::2 bits 2.4 * 2.2 * 1.9 * 1.7 * * Relative 1.4 * * **** * Entropy 1.2 * * **** * (21.8 bits) 1.0 ** * * ***** * ** 0.7 **** ** *********** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel CAGGCGTGAGCCACCACGCC consensus A AAC C TGTA T sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGCRYGHGCCACYRCRCC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1160001 bayes= 12.075 E= 6.1e-147 -448 147 -421 -76 221 -602 -131 -1634 17 -521 126 -243 -270 -570 163 -1634 20 90 -521 3 67 -421 61 15 -1634 31 -456 167 -37 -102 117 -1634 103 5 -470 58 -1 -602 136 -470 -1634 165 -1634 -304 -1634 164 -1634 -270 241 -1634 -1634 -529 -1634 158 -570 -167 -370 100 -456 88 150 -643 58 -1634 -320 113 -485 60 108 -456 86 -304 -1634 160 -485 -212 -359 123 -485 35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGCRYGHGCCACYRCRCC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 832 E= 6.1e-147 0.008413 0.864183 0.016827 0.110577 0.868990 0.004808 0.126202 0.000000 0.211538 0.008413 0.745192 0.034856 0.028846 0.006010 0.965144 0.000000 0.216346 0.584135 0.008413 0.191106 0.299279 0.016827 0.475962 0.207933 0.000000 0.388221 0.013221 0.598558 0.145433 0.153846 0.700721 0.000000 0.383413 0.323317 0.012019 0.281250 0.186298 0.004808 0.801683 0.007212 0.000000 0.977163 0.000000 0.022837 0.000000 0.971154 0.000000 0.028846 0.995192 0.000000 0.000000 0.004808 0.000000 0.935096 0.006010 0.058894 0.014423 0.626202 0.013221 0.346154 0.530048 0.003606 0.466346 0.000000 0.020433 0.683894 0.010817 0.284856 0.397837 0.013221 0.566106 0.022837 0.000000 0.945913 0.010817 0.043269 0.015625 0.734375 0.010817 0.239183 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGGCRYGHGCCACYRCRCC MEME-4 regular expression -------------------------------------------------------------------------------- CA[GA]G[CA][GAT][TC]G[ACT]GCCAC[CT][AG][CT][GA]C[CT] -------------------------------------------------------------------------------- Time 1466.54 secs. ******************************************************************************** ******************************************************************************** MOTIF ATCRCTTGARSYCAGGAGKT MEME-5 width = 20 sites = 417 llr = 8375 E-value = 2.7e-109 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATCRCTTGARSYCAGGAGKT MEME-5 Description -------------------------------------------------------------------------------- Simplified A a::6::::a4:::7::a::: pos.-specific C ::8:a3::::568::::::2 probability G :::4:::a:64::3aa:a4: matrix T :a2::7a::::42:::::68 bits 2.4 * * 2.2 ** * * * 1.9 ** * * * 1.7 ** * * ** Relative 1.4 ** ***** **** * Entropy 1.2 ** ***** ***** * (29.0 bits) 1.0 ** ******* ********* 0.7 ********** ********* 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel ATCACTTGAGCCCAGGAGTT consensus G C AGT G GC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCRCTTGARSYCAGGAGKT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1160001 bayes= 13.7093 E= 2.7e-109 239 -444 -1535 -1535 -1535 -294 -1535 235 -297 128 -356 1 163 -385 26 -312 -1535 163 -702 -248 -1535 -28 -702 198 -1535 -1535 -1535 241 -283 -1535 164 -1535 238 -1535 -385 -629 103 -444 94 -529 -529 74 50 -248 -1535 90 -1535 115 -329 140 -1535 -25 194 -1535 -31 -283 -259 -602 163 -1535 -1535 -356 164 -1535 236 -1535 -312 -1535 -1535 -1535 168 -1535 -629 -332 34 160 -1535 -35 -1535 201 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCRCTTGARSYCAGGAGKT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 417 E= 2.7e-109 0.985612 0.014388 0.000000 0.000000 0.000000 0.040767 0.000000 0.959233 0.023981 0.760192 0.026379 0.189448 0.582734 0.021583 0.374101 0.021583 0.000000 0.964029 0.002398 0.033573 0.000000 0.256595 0.002398 0.741007 0.000000 0.000000 0.000000 1.000000 0.026379 0.000000 0.973621 0.000000 0.976019 0.000000 0.021583 0.002398 0.383693 0.014388 0.597122 0.004796 0.004796 0.520384 0.441247 0.033573 0.000000 0.582734 0.000000 0.417266 0.019185 0.822542 0.000000 0.158273 0.721823 0.000000 0.251799 0.026379 0.031175 0.004796 0.964029 0.000000 0.000000 0.026379 0.973621 0.000000 0.964029 0.000000 0.035971 0.000000 0.000000 0.000000 1.000000 0.000000 0.002398 0.031175 0.395683 0.570743 0.000000 0.244604 0.000000 0.755396 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCRCTTGARSYCAGGAGKT MEME-5 regular expression -------------------------------------------------------------------------------- ATC[AG]C[TC]TGA[GA][CG][CT]C[AG]GGAG[TG][TC] -------------------------------------------------------------------------------- Time 1810.00 secs. ******************************************************************************** ******************************************************************************** MOTIF CSCCGCCSCCGCCSCSSCCC MEME-6 width = 20 sites = 2113 llr = 18873 E-value = 4.6e-056 ******************************************************************************** -------------------------------------------------------------------------------- Motif CSCCGCCSCCGCCSCSSCCC MEME-6 Description -------------------------------------------------------------------------------- Simplified A :::21::::11::::11::1 pos.-specific C 8586277697:995944877 probability G 25236224127113145122 matrix T :::::11:::2::2:1111: bits 2.4 2.2 1.9 1.7 Relative 1.4 Entropy 1.2 * * * (12.9 bits) 1.0 * * ** * 0.7 *** ** *** * * 0.5 ************* * *** 0.2 ******************** 0.0 -------------------- Multilevel CCCCGCCCCCGCCCCCGCCC consensus G GC G G GC GG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSCCGCCSCCGCCSCSSCCC MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1160001 bayes= 11.257 E= 4.6e-056 -246 137 -98 -1769 -605 78 56 -1769 -342 132 -88 -242 -15 86 -25 -1769 -88 -55 104 -216 -438 116 -70 -92 -263 124 -81 -177 -382 88 39 -1769 -1769 152 -186 -335 -114 120 -92 -246 -66 -1769 119 -17 -411 146 -171 -244 -1769 155 -188 -705 -302 69 -14 2 -1769 148 -128 -1769 -104 50 32 -129 -104 18 58 -111 -254 136 -146 -188 -244 115 -57 -157 -188 116 -40 -382 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSCCGCCSCCGCCSCSSCCC MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 2113 E= 4.6e-056 0.034075 0.807383 0.158542 0.000000 0.002840 0.537151 0.460009 0.000000 0.017511 0.777567 0.169901 0.035021 0.169427 0.567913 0.262660 0.000000 0.102224 0.213914 0.641742 0.042120 0.008992 0.699953 0.191671 0.099385 0.030289 0.736867 0.177946 0.054898 0.013251 0.576432 0.410317 0.000000 0.000000 0.895409 0.086133 0.018457 0.085187 0.715570 0.165168 0.034075 0.118788 0.000000 0.714150 0.167061 0.010885 0.858968 0.095599 0.034548 0.000000 0.913867 0.084714 0.001420 0.023190 0.503549 0.282537 0.190724 0.000000 0.871273 0.128727 0.000000 0.091339 0.442026 0.389967 0.076668 0.091339 0.353999 0.467582 0.087080 0.032182 0.803597 0.113109 0.051112 0.034548 0.692381 0.209655 0.063417 0.051112 0.698533 0.237104 0.013251 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CSCCGCCSCCGCCSCSSCCC MEME-6 regular expression -------------------------------------------------------------------------------- C[CG]C[CG][GC]CC[CG]CCGCC[CG]C[CG][GC]C[CG][CG] -------------------------------------------------------------------------------- Time 2150.94 secs. ******************************************************************************** ******************************************************************************** MOTIF WWDWDDWWWDDWWABWTDAW MEME-7 width = 20 sites = 712 llr = 7149 E-value = 3.5e-029 ******************************************************************************** -------------------------------------------------------------------------------- Motif WWDWDDWWWDDWWABWTDAW MEME-7 Description -------------------------------------------------------------------------------- Simplified A 43333345643355:5:465 pos.-specific C ::2::112:2:2:23::::1 probability G :121432::23:213:331: matrix T 65353334434432457334 bits 2.4 2.2 1.9 1.7 Relative 1.4 * * * Entropy 1.2 * * ** (14.5 bits) 1.0 * * * ** ** 0.7 ** * ** ** ** ** 0.5 ** * ** **** ***** 0.2 ******************** 0.0 -------------------- Multilevel TTTTGTAAAATTAATATAAA consensus AAAAAATTTTGAT CTGGTT sequence G TG GACG G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWDWDDWWWDDWWABWTDAW MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1160001 bayes= 12.9596 E= 3.5e-029 121 -1612 -1612 159 62 -371 -107 152 64 -96 -47 78 87 -679 -115 145 74 -275 28 48 60 -147 -26 87 110 -112 -85 58 129 -82 -1612 96 172 -679 -1612 101 91 -101 -57 58 66 -1612 14 94 88 -59 -1612 125 133 -1612 -47 69 153 -93 -151 -3 -260 -1 -17 102 143 -1612 -463 135 -1612 -1612 -11 192 115 -499 -5 54 172 -1612 -151 52 136 -124 -1612 104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWDWDDWWWDDWWABWTDAW MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 712 E= 3.5e-029 0.435393 0.000000 0.000000 0.564607 0.287921 0.023876 0.148876 0.539326 0.292135 0.160112 0.224719 0.323034 0.342697 0.002809 0.140449 0.514045 0.314607 0.046348 0.377809 0.261236 0.285112 0.112360 0.259831 0.342697 0.403090 0.143258 0.172753 0.280899 0.457865 0.176966 0.000000 0.365169 0.619382 0.002809 0.000000 0.377809 0.353933 0.154494 0.210674 0.280899 0.296348 0.000000 0.344101 0.359551 0.345506 0.207865 0.000000 0.446629 0.473315 0.000000 0.224719 0.301966 0.542135 0.164326 0.109551 0.183989 0.030899 0.308989 0.278090 0.382022 0.507022 0.000000 0.012640 0.480337 0.000000 0.000000 0.289326 0.710674 0.415730 0.009831 0.301966 0.272472 0.620787 0.000000 0.109551 0.269663 0.483146 0.132022 0.000000 0.384831 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWDWDDWWWDDWWABWTDAW MEME-7 regular expression -------------------------------------------------------------------------------- [TA][TA][TAG][TA][GAT][TAG][AT][AT][AT][ATG][TGA][TAC][ATG]A[TCG][AT][TG][AGT][AT][AT] -------------------------------------------------------------------------------- Time 2477.48 secs. ******************************************************************************** ******************************************************************************** MOTIF AARDAAAKDYAGASAAGAAA MEME-8 width = 20 sites = 349 llr = 3610 E-value = 9.3e-022 ******************************************************************************** -------------------------------------------------------------------------------- Motif AARDAAAKDYAGASAAGAAA MEME-8 Description -------------------------------------------------------------------------------- Simplified A 8664578221728187:676 pos.-specific C :2:11211:5:2:31121:: probability G 123321:34215:5116222 matrix T 1:122:14422221:222:2 bits 2.4 2.2 1.9 1.7 Relative 1.4 * * Entropy 1.2 * * * * * * (14.9 bits) 1.0 * ** * * * ** 0.7 *** ** * * * ** *** 0.5 *** *** * * * ****** 0.2 ********* * * ****** 0.0 -------------------- Multilevel AAAAAAATTCAGAGAAGAAA consensus GGGC GGT A C C G sequence T AG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARDAAAKDYAGASAAGAAA MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1160001 bayes= 13.5697 E= 9.3e-022 210 -418 -186 -103 177 -81 -77 -1509 157 -1509 5 -64 94 -172 9 18 138 -152 -58 5 182 -54 -138 -1509 201 -138 -1509 -61 5 -186 4 108 27 -1509 20 115 -99 55 -58 36 190 -477 -152 -6 14 -93 58 -20 203 -318 -1509 7 -33 -23 66 -103 205 -128 -177 -1509 179 -196 -172 -10 -1509 -32 92 -23 165 -218 -96 -3 198 -268 -77 -286 173 -1509 -58 -18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARDAAAKDYAGASAAGAAA MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 349 E= 9.3e-022 0.805158 0.017192 0.085960 0.091691 0.638968 0.177650 0.183381 0.000000 0.555874 0.000000 0.323782 0.120344 0.361032 0.094556 0.332378 0.212034 0.487106 0.108883 0.209169 0.194842 0.664756 0.214900 0.120344 0.000000 0.756447 0.120344 0.000000 0.123209 0.194842 0.085960 0.320917 0.398281 0.226361 0.000000 0.358166 0.415473 0.094556 0.455587 0.209169 0.240688 0.699140 0.011461 0.108883 0.180516 0.206304 0.163324 0.467049 0.163324 0.767908 0.034384 0.000000 0.197708 0.148997 0.266476 0.492837 0.091691 0.779370 0.128940 0.091691 0.000000 0.650430 0.080229 0.094556 0.174785 0.000000 0.249284 0.590258 0.160458 0.587393 0.068768 0.160458 0.183381 0.742120 0.048711 0.183381 0.025788 0.624642 0.000000 0.209169 0.166189 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARDAAAKDYAGASAAGAAA MEME-8 regular expression -------------------------------------------------------------------------------- AA[AG][AGT][AG][AC]A[TG][TGA][CTG]A[GA]A[GC]AA[GC]AA[AG] -------------------------------------------------------------------------------- Time 2798.78 secs. ******************************************************************************** ******************************************************************************** MOTIF GCYGAGGCRGGAGRATCRCT MEME-9 width = 20 sites = 407 llr = 6416 E-value = 1.6e-020 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCYGAGGCRGGAGRATCRCT MEME-9 Description -------------------------------------------------------------------------------- Simplified A 1::2a:1:5::6149::5:1 pos.-specific C :a4::::7:::2:::17:82 probability G 9::8:99:499:86::24:3 matrix T ::6::::2:::2:::92:15 bits 2.4 2.2 * 1.9 * ** 1.7 * ** Relative 1.4 * * ** Entropy 1.2 ** *** ** ** (22.7 bits) 1.0 *********** **** * 0.7 **************** ** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GCTGAGGCAGGAGGATCACT consensus C TG C A G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCYGAGGCRGGAGRATCRCT MEME-9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1160001 bayes= 13.6894 E= 1.6e-020 -186 -540 155 -267 -525 163 -540 -326 -345 23 -599 170 -13 -353 135 -467 237 -599 -440 -467 -217 -399 158 -467 -140 -698 155 -393 -309 124 -540 30 149 -499 52 -367 -256 -367 153 -226 -209 -540 159 -426 159 -48 -467 8 -53 -418 143 -426 111 -1531 92 -525 229 -267 -329 -625 -345 -229 -599 228 -467 112 -99 -28 154 -299 36 -393 -280 143 -382 -76 -173 -92 -32 149 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCYGAGGCRGGAGRATCRCT MEME-9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 407 E= 1.6e-020 0.051597 0.007371 0.911548 0.029484 0.004914 0.968059 0.007371 0.019656 0.017199 0.366093 0.004914 0.611794 0.171990 0.027027 0.793612 0.007371 0.972973 0.004914 0.014742 0.007371 0.041769 0.019656 0.931204 0.007371 0.071253 0.002457 0.914005 0.012285 0.022113 0.739558 0.007371 0.230958 0.528256 0.009828 0.447174 0.014742 0.031941 0.024570 0.904177 0.039312 0.044226 0.007371 0.938575 0.009828 0.565111 0.223587 0.012285 0.199017 0.130221 0.017199 0.842752 0.009828 0.405405 0.000000 0.589681 0.004914 0.916462 0.049140 0.031941 0.002457 0.017199 0.063882 0.004914 0.914005 0.007371 0.680590 0.157248 0.154791 0.547912 0.039312 0.400491 0.012285 0.027027 0.840295 0.022113 0.110565 0.056511 0.164619 0.250614 0.528256 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCYGAGGCRGGAGRATCRCT MEME-9 regular expression -------------------------------------------------------------------------------- GC[TC]GAGG[CT][AG]GG[AC]G[GA]ATC[AG]C[TG] -------------------------------------------------------------------------------- Time 3114.89 secs. ******************************************************************************** ******************************************************************************** MOTIF GCTCACTGCAACCTCY MEME-10 width = 16 sites = 235 llr = 4127 E-value = 4.0e-014 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCTCACTGCAACCTCY MEME-10 Description -------------------------------------------------------------------------------- Simplified A ::::9::::a8::::1 pos.-specific C :9:91a::a::89:96 probability G a::::::a::11:::: matrix T ::a:::9:::::1a13 bits 2.4 * 2.2 * * * 1.9 * * * * * 1.7 * * **** * Relative 1.4 * ********* *** Entropy 1.2 *********** *** (25.3 bits) 1.0 *************** 0.7 *************** 0.5 **************** 0.2 **************** 0.0 ---------------- Multilevel GCTCACTGCAACCTCC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCTCACTGCAACCTCY MEME-10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 1217285 bayes= 14.4764 E= 4.0e-014 -266 -1452 164 -1452 -388 158 -619 -200 -1452 -1452 -1452 241 -1452 160 -619 -200 232 -239 -1452 -546 -1452 162 -420 -288 -288 -303 -619 231 -446 -619 166 -1452 -1452 167 -1452 -546 239 -1452 -420 -1452 210 -420 -107 -266 -200 142 -144 -1452 -546 159 -619 -188 -546 -420 -1452 238 -1452 159 -1452 -166 -107 91 -387 69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCTCACTGCAACCTCY MEME-10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 235 E= 4.0e-014 0.029787 0.000000 0.970213 0.000000 0.012766 0.936170 0.004255 0.046809 0.000000 0.000000 0.000000 1.000000 0.000000 0.948936 0.004255 0.046809 0.936170 0.059574 0.000000 0.004255 0.000000 0.957447 0.017021 0.025532 0.025532 0.038298 0.004255 0.931915 0.008511 0.004255 0.987234 0.000000 0.000000 0.995745 0.000000 0.004255 0.982979 0.000000 0.017021 0.000000 0.804255 0.017021 0.148936 0.029787 0.046809 0.838298 0.114894 0.000000 0.004255 0.940426 0.004255 0.051064 0.004255 0.017021 0.000000 0.978723 0.000000 0.940426 0.000000 0.059574 0.089362 0.587234 0.021277 0.302128 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCTCACTGCAACCTCY MEME-10 regular expression -------------------------------------------------------------------------------- GCTCACTGCAACCTC[CT] -------------------------------------------------------------------------------- Time 3430.18 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (10) found. ******************************************************************************** CPU: cn45 ********************************************************************************