/test-data/meme/meme/meme_output_txt_1.txt
Plain Text | 325 lines | 288 code | 37 blank | 0 comment | 0 complexity | e10abfb51a2b5c00990e2dd4803152d0 MD5 | raw file
1******************************************************************************** 2MEME - Motif discovery tool 3******************************************************************************** 4MEME version 4.6.0 (Release date: Thu Jan 20 14:06:48 PST 2011) 5 6For further information on how to interpret these results or to get 7a copy of the MEME software please access http://meme.nbcr.net. 8 9This file may be used as input to the MAST algorithm for searching 10sequence databases for matches to groups of motifs. MAST is available 11for interactive use and downloading at http://meme.nbcr.net. 12******************************************************************************** 13 14 15******************************************************************************** 16REFERENCE 17******************************************************************************** 18If you use this program in your research, please cite: 19 20Timothy L. Bailey and Charles Elkan, 21"Fitting a mixture model by expectation maximization to discover 22motifs in biopolymers", Proceedings of the Second International 23Conference on Intelligent Systems for Molecular Biology, pp. 28-36, 24AAAI Press, Menlo Park, California, 1994. 25******************************************************************************** 26 27 28******************************************************************************** 29TRAINING SET 30******************************************************************************** 31DATAFILE= dataset_3.dat 32ALPHABET= ACDEFGHIKLMNPQRSTVWY 33Sequence name Weight Length Sequence name Weight Length 34------------- ------ ------ ------------- ------ ------ 35chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50 36chr21_28217753_28217803_ 1.0000 50 chr21_31710037_31710087_ 1.0000 50 37chr21_31744582_31744632_ 1.0000 50 chr21_31768316_31768366_ 1.0000 50 38chr21_31914206_31914256_ 1.0000 50 chr21_31933633_31933683_ 1.0000 50 39chr21_31962741_31962791_ 1.0000 50 chr21_31964683_31964733_ 1.0000 50 40chr21_31973364_31973414_ 1.0000 50 chr21_31992870_31992920_ 1.0000 50 41chr21_32185595_32185645_ 1.0000 50 chr21_32202076_32202126_ 1.0000 50 42chr21_32253899_32253949_ 1.0000 50 chr21_32410820_32410870_ 1.0000 50 43chr21_36411748_36411798_ 1.0000 50 chr21_37838750_37838800_ 1.0000 50 44chr21_45705687_45705737_ 1.0000 50 chr21_45971413_45971463_ 1.0000 50 45chr21_45978668_45978718_ 1.0000 50 chr21_45993530_45993580_ 1.0000 50 46chr21_46020421_46020471_ 1.0000 50 chr21_46031920_46031970_ 1.0000 50 47chr21_46046964_46047014_ 1.0000 50 chr21_46057197_46057247_ 1.0000 50 48chr21_46086869_46086919_ 1.0000 50 chr21_46102103_46102153_ 1.0000 50 49chr21_47517957_47518007_ 1.0000 50 chr21_47575506_47575556_ 1.0000 50 50******************************************************************************** 51 52******************************************************************************** 53COMMAND LINE SUMMARY 54******************************************************************************** 55This information can also be useful in the event you wish to report a 56problem with the MEME software. 57 58command: meme dataset_3.dat -o dataset_4_files -nostatus 59 60model: mod= zoops nmotifs= 1 evt= inf 61object function= E-value of product of p-values 62width: minw= 8 maxw= 50 minic= 0.00 63width: wg= 11 ws= 1 endgaps= yes 64nsites: minsites= 2 maxsites= 30 wnsites= 0.8 65theta: prob= 1 spmap= pam spfuzz= 120 66global: substring= yes branching= no wbranch= no 67em: prior= megap b= 7500 maxiter= 50 68 distance= 1e-05 69data: n= 1500 N= 30 70 71sample: seed= 0 seqfrac= 1 72Dirichlet mixture priors file: prior30.plib 73Letter frequencies in dataset: 74A 0.294 C 0.231 D 0.000 E 0.000 F 0.000 G 0.257 H 0.000 I 0.000 K 0.000 75L 0.000 M 0.000 N 0.000 P 0.000 Q 0.000 R 0.000 S 0.000 T 0.217 V 0.000 76W 0.000 Y 0.000 77Background letter frequencies (from dataset with add-one prior applied): 78A 0.291 C 0.229 D 0.001 E 0.001 F 0.001 G 0.255 H 0.001 I 0.001 K 0.001 79L 0.001 M 0.001 N 0.001 P 0.001 Q 0.001 R 0.001 S 0.001 T 0.215 V 0.001 80W 0.001 Y 0.001 81******************************************************************************** 82 83 84******************************************************************************** 85MOTIF 1 width = 11 sites = 25 llr = 239 E-value = 2.4e-011 86******************************************************************************** 87-------------------------------------------------------------------------------- 88 Motif 1 Description 89-------------------------------------------------------------------------------- 90Simplified A 2323:a:a8a8 91pos.-specific C ::3:::::::: 92probability D ::::::::::: 93matrix E ::::::::::: 94 F ::::::::::: 95 G 7746::::::1 96 H ::::::::::: 97 I ::::::::::: 98 K ::::::::::: 99 L ::::::::::: 100 M ::::::::::: 101 N ::::::::::: 102 P ::::::::::: 103 Q ::::::::::: 104 R ::::::::::: 105 S ::::::::::: 106 T 1:2:a:a:2:: 107 V ::::::::::: 108 W ::::::::::: 109 Y ::::::::::: 110 111 bits 10.6 112 9.5 113 8.5 114 7.4 115Relative 6.3 116Entropy 5.3 117(13.8 bits) 4.2 118 3.2 119 2.1 * ** 120 1.1 ** ******** 121 0.0 ----------- 122 123Multilevel GGGGTATAAAA 124consensus AACA T 125sequence 126 127 128-------------------------------------------------------------------------------- 129 130-------------------------------------------------------------------------------- 131 Motif 1 sites sorted by position p-value 132-------------------------------------------------------------------------------- 133Sequence name Start P-value Site 134------------- ----- --------- ----------- 135chr21_46046964_46047014_ 13 1.06e-06 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC 136chr21_46057197_46057247_ 37 3.41e-06 ACAGGCCCTG GGCATATAAAA GCC 137chr21_45971413_45971463_ 10 3.41e-06 CAGGCCCTG GGCATATAAAA GCCCCAGCAG 138chr21_31964683_31964733_ 14 3.41e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC 139chr21_45993530_45993580_ 8 4.00e-06 CCAAGGA GGAGTATAAAA GCCCCACAAA 140chr21_32202076_32202126_ 14 5.01e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC 141chr21_46031920_46031970_ 16 6.06e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC 142chr21_32410820_32410870_ 22 8.67e-06 AATCACTGAG GATGTATAAAA GTCCCAGGGA 143chr21_32185595_32185645_ 19 8.67e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT 144chr21_31992870_31992920_ 17 8.67e-06 CACTATTGAA GATGTATAAAA TTTCATTTGC 145chr21_46020421_46020471_ 3 1.21e-05 GA GACATATAAAA GCCAACATCC 146chr21_47517957_47518007_ 33 1.59e-05 CCGGCGGGGC GGGGTATAAAG GGGGCGG 147chr21_45978668_45978718_ 5 1.59e-05 CAGA GGGGTATAAAG GTTCCGACCA 148chr21_31914206_31914256_ 16 1.68e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG 149chr21_32253899_32253949_ 20 2.03e-05 CACCAGCAAG GATATATAAAA GCTCAGGAGT 150chr21_31744582_31744632_ 13 3.06e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC 151chr21_19617074_19617124_ 40 3.06e-05 CCTCGGGACG TGGGTATATAA 152chr21_45705687_45705737_ 38 3.82e-05 CGTGGTCGCG GGGGTATAACA GC 153chr21_31768316_31768366_ 1 3.82e-05 . AACGTATATAA ATGGTCCTGT 154chr21_47575506_47575556_ 31 4.02e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG 155chr21_26934381_26934431_ 28 5.52e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG 156chr21_31710037_31710087_ 15 5.94e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC 157chr21_36411748_36411798_ 23 6.78e-05 AGTTTCAGTT GGCATCTAAAA ATTATATAAC 158chr21_31933633_31933683_ 3 2.08e-04 TC AGAGTATATAT AAATGTTCCT 159chr21_31962741_31962791_ 14 4.05e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC 160-------------------------------------------------------------------------------- 161 162-------------------------------------------------------------------------------- 163 Motif 1 block diagrams 164-------------------------------------------------------------------------------- 165SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM 166------------- ---------------- ------------- 167chr21_46046964_46047014_ 1.1e-06 12_[1]_27 168chr21_46057197_46057247_ 3.4e-06 36_[1]_3 169chr21_45971413_45971463_ 3.4e-06 9_[1]_30 170chr21_31964683_31964733_ 3.4e-06 13_[1]_26 171chr21_45993530_45993580_ 4e-06 7_[1]_32 172chr21_32202076_32202126_ 5e-06 13_[1]_26 173chr21_46031920_46031970_ 6.1e-06 15_[1]_24 174chr21_32410820_32410870_ 8.7e-06 21_[1]_18 175chr21_32185595_32185645_ 8.7e-06 18_[1]_21 176chr21_31992870_31992920_ 8.7e-06 16_[1]_23 177chr21_46020421_46020471_ 1.2e-05 2_[1]_37 178chr21_47517957_47518007_ 1.6e-05 32_[1]_7 179chr21_45978668_45978718_ 1.6e-05 4_[1]_35 180chr21_31914206_31914256_ 1.7e-05 15_[1]_24 181chr21_32253899_32253949_ 2e-05 19_[1]_20 182chr21_31744582_31744632_ 3.1e-05 12_[1]_27 183chr21_19617074_19617124_ 3.1e-05 39_[1] 184chr21_45705687_45705737_ 3.8e-05 37_[1]_2 185chr21_31768316_31768366_ 3.8e-05 [1]_39 186chr21_47575506_47575556_ 4e-05 30_[1]_9 187chr21_26934381_26934431_ 5.5e-05 27_[1]_12 188chr21_31710037_31710087_ 5.9e-05 14_[1]_25 189chr21_36411748_36411798_ 6.8e-05 22_[1]_17 190chr21_31933633_31933683_ 0.00021 2_[1]_37 191chr21_31962741_31962791_ 0.0004 13_[1]_26 192-------------------------------------------------------------------------------- 193 194-------------------------------------------------------------------------------- 195 Motif 1 in BLOCKS format 196-------------------------------------------------------------------------------- 197BL MOTIF 1 width=11 seqs=25 198chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1 199chr21_46057197_46057247_ ( 37) GGCATATAAAA 1 200chr21_45971413_45971463_ ( 10) GGCATATAAAA 1 201chr21_31964683_31964733_ ( 14) GGCATATAAAA 1 202chr21_45993530_45993580_ ( 8) GGAGTATAAAA 1 203chr21_32202076_32202126_ ( 14) GAGGTATAAAA 1 204chr21_46031920_46031970_ ( 16) AGGGTATAAAA 1 205chr21_32410820_32410870_ ( 22) GATGTATAAAA 1 206chr21_32185595_32185645_ ( 19) GGGATATATAA 1 207chr21_31992870_31992920_ ( 17) GATGTATAAAA 1 208chr21_46020421_46020471_ ( 3) GACATATAAAA 1 209chr21_47517957_47518007_ ( 33) GGGGTATAAAG 1 210chr21_45978668_45978718_ ( 5) GGGGTATAAAG 1 211chr21_31914206_31914256_ ( 16) AGAGTATAAAA 1 212chr21_32253899_32253949_ ( 20) GATATATAAAA 1 213chr21_31744582_31744632_ ( 13) AGCATATATAA 1 214chr21_19617074_19617124_ ( 40) TGGGTATATAA 1 215chr21_45705687_45705737_ ( 38) GGGGTATAACA 1 216chr21_31768316_31768366_ ( 1) AACGTATATAA 1 217chr21_47575506_47575556_ ( 31) AGCGTATAAAG 1 218chr21_26934381_26934431_ ( 28) GAGTTATAAAA 1 219chr21_31710037_31710087_ ( 15) TGAGTATATAA 1 220chr21_36411748_36411798_ ( 23) GGCATCTAAAA 1 221chr21_31933633_31933683_ ( 3) AGAGTATATAT 1 222chr21_31962741_31962791_ ( 14) GTTGGATAAAA 1 223// 224 225-------------------------------------------------------------------------------- 226 227-------------------------------------------------------------------------------- 228 Motif 1 position-specific scoring matrix 229-------------------------------------------------------------------------------- 230log-odds matrix: alength= 20 w= 11 n= 1200 bayes= 5.33554 E= 2.4e-011 231 -32 -680 91 77 7 138 -20 55 64 107 11 150 142 72 87 396 -148 221 -140 -36 232 -11 -680 89 76 7 137 -21 55 63 107 10 149 141 71 87 396 -239 220 -140 -36 233 -79 41 4 21 -7 44 -62 42 -5 99 0 99 138 52 42 399 -46 223 -173 -68 234 11 -677 48 47 -2 127 -43 46 27 101 3 124 138 60 62 397 -235 220 -160 -55 235 -596 -820 12 -21 -53 -267 -74 37 16 44 -37 98 31 9 19 319 212 127 -193 -95 236 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8 237 -838 -990 -89 -149 -151 -841 -161 -117 -113 -66 -209 -68 -69 -129 -91 111 221 -55 -255 -173 238 176 -858 -79 -103 -115 -717 -148 -95 -108 -17 -162 -61 -12 -95 -69 193 -737 52 -240 -153 239 134 -686 0 16 -12 -553 -68 44 -8 96 -9 88 124 41 36 384 11 216 -177 -71 240 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8 241 147 -614 89 129 93 -121 12 160 113 217 108 144 144 111 125 447 -241 332 -81 22 242-------------------------------------------------------------------------------- 243 244-------------------------------------------------------------------------------- 245 Motif 1 position-specific probability matrix 246-------------------------------------------------------------------------------- 247letter-probability matrix: alength= 20 w= 11 nsites= 25 E= 2.4e-011 248 0.240000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.080000 0.000000 0.000000 0.000000 249 0.280000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 250 0.160000 0.320000 0.000000 0.000000 0.000000 0.360000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.160000 0.000000 0.000000 0.000000 251 0.320000 0.000000 0.000000 0.000000 0.000000 0.640000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 252 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.960000 0.000000 0.000000 0.000000 253 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 254 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 255 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 256 0.760000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.240000 0.000000 0.000000 0.000000 257 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 258 0.840000 0.000000 0.000000 0.000000 0.000000 0.120000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 259-------------------------------------------------------------------------------- 260 261-------------------------------------------------------------------------------- 262 Motif 1 regular expression 263-------------------------------------------------------------------------------- 264[GA][GA][GC][GA]TATA[AT]AA 265-------------------------------------------------------------------------------- 266 267 268 269 270Time 2.13 secs. 271 272******************************************************************************** 273 274 275******************************************************************************** 276SUMMARY OF MOTIFS 277******************************************************************************** 278 279-------------------------------------------------------------------------------- 280 Combined block diagrams: non-overlapping sites with p-value < 0.0001 281-------------------------------------------------------------------------------- 282SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM 283------------- ---------------- ------------- 284chr21_19617074_19617124_ 1.22e-03 39_[1(3.06e-05)] 285chr21_26934381_26934431_ 2.21e-03 27_[1(5.52e-05)]_12 286chr21_28217753_28217803_ 7.29e-01 50 287chr21_31710037_31710087_ 2.37e-03 14_[1(5.94e-05)]_25 288chr21_31744582_31744632_ 1.22e-03 12_[1(3.06e-05)]_27 289chr21_31768316_31768366_ 1.53e-03 [1(3.82e-05)]_39 290chr21_31914206_31914256_ 6.70e-04 15_[1(1.68e-05)]_24 291chr21_31933633_31933683_ 1.81e-03 4_[1(4.54e-05)]_35 292chr21_31962741_31962791_ 1.61e-02 50 293chr21_31964683_31964733_ 1.36e-04 13_[1(3.41e-06)]_26 294chr21_31973364_31973414_ 1.99e-01 50 295chr21_31992870_31992920_ 3.47e-04 16_[1(8.67e-06)]_23 296chr21_32185595_32185645_ 3.47e-04 18_[1(8.67e-06)]_21 297chr21_32202076_32202126_ 2.01e-04 13_[1(5.01e-06)]_26 298chr21_32253899_32253949_ 8.11e-04 19_[1(2.03e-05)]_20 299chr21_32410820_32410870_ 3.47e-04 21_[1(8.67e-06)]_18 300chr21_36411748_36411798_ 2.71e-03 22_[1(6.78e-05)]_17 301chr21_37838750_37838800_ 8.23e-02 50 302chr21_45705687_45705737_ 1.53e-03 37_[1(3.82e-05)]_2 303chr21_45971413_45971463_ 1.36e-04 9_[1(3.41e-06)]_30 304chr21_45978668_45978718_ 6.37e-04 4_[1(1.59e-05)]_35 305chr21_45993530_45993580_ 1.60e-04 7_[1(4.00e-06)]_32 306chr21_46020421_46020471_ 4.83e-04 2_[1(1.21e-05)]_37 307chr21_46031920_46031970_ 2.43e-04 15_[1(6.06e-06)]_24 308chr21_46046964_46047014_ 4.26e-05 12_[1(1.06e-06)]_27 309chr21_46057197_46057247_ 1.36e-04 36_[1(3.41e-06)]_3 310chr21_46086869_46086919_ 4.30e-02 50 311chr21_46102103_46102153_ 4.30e-02 50 312chr21_47517957_47518007_ 6.37e-04 32_[1(1.59e-05)]_7 313chr21_47575506_47575556_ 1.61e-03 30_[1(4.02e-05)]_9 314-------------------------------------------------------------------------------- 315 316******************************************************************************** 317 318 319******************************************************************************** 320Stopped because nmotifs = 1 reached. 321******************************************************************************** 322 323CPU: scofield 324 325********************************************************************************