t/data/test-3.0-2.meme

   1 ********************************************************************************
   2 MEME - Motif discovery tool
   3 ********************************************************************************
   4 MEME version 3.0 (Release date: 2002/04/02 00:11:59)
   5
   6 For further information on how to interpret these results or to get
   7 a copy of the MEME software please access http://meme.sdsc.edu.
   8
   9 This file may be used as input to the MAST algorithm for searching
  10 sequence databases for matches to groups of motifs.  MAST is available
  11 for interactive use and downloading at http://meme.sdsc.edu.
  12 ********************************************************************************
  13
  14
  15 ********************************************************************************
  16 REFERENCE
  17 ********************************************************************************
  18 If you use this program in your research, please cite:
  19
  20 Timothy L. Bailey and Charles Elkan,
  21 "Fitting a mixture model by expectation maximization to discover
  22 motifs in biopolymers", Proceedings of the Second International
  23 Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
  24 AAAI Press, Menlo Park, California, 1994.
  25 ********************************************************************************
  26
  27
  28 ********************************************************************************
  29 TRAINING SET
  30 ********************************************************************************
  31 DATAFILE= test.fasta
  32 ALPHABET= ACGT
  33 Sequence name            Weight Length  Sequence name            Weight Length
  34 -------------            ------ ------  -------------            ------ ------
  35 68723                    1.0000   2000  16939                    1.0000   2001
  36 20754                    1.0000   2001  6707                     1.0000   2000
  37 20755                    1.0000   2000  6700                     1.0000   2002
  38 20760                    1.0000   2000  20761                    1.0000   2000
  39 20762                    1.0000   2000
  40 ********************************************************************************
  41
  42 ********************************************************************************
  43 COMMAND LINE SUMMARY
  44 ********************************************************************************
  45 This information can also be useful in the event you wish to report a
  46 problem with the MEME software.
  47
  48 command: meme test.fasta -dna -nostatus -nmotifs 2 -minsites 8 -maxw 20 -revcomp
  49
  50 model:  mod=         zoops    nmotifs=         2    evt=           inf
  51 object function=  E-value of product of p-values
  52 width:  minw=            8    maxw=           20    minic=        0.00
  53 width:  wg=             11    ws=              1    endgaps=       yes
  54 nsites: minsites=        8    maxsites=        9    wnsites=       0.8
  55 theta:  prob=            1    spmap=         uni    spfuzz=        0.5
  56 em:     prior=   dirichlet    b=            0.01    maxiter=        50
  57         distance=    1e-05
  58 data:   n=           18004    N=               9
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.295 C 0.205 G 0.205 T 0.295
  63 Background letter frequencies (from dataset with add-one prior applied):
  64 A 0.295 C 0.205 G 0.205 T 0.295
  65 ********************************************************************************
  66
  67
  68 ********************************************************************************
  69 MOTIF  1        width =   20   sites =   8   llr = 147   E-value = 1.3e-002
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  ::a1::931:6:348:1::1
  75 pos.-specific     C  aa:::8:11841:331:139
  76 probability       G  :::9::::63::84::3:8:
  77 matrix            T  ::::a3161::9:::969::
  78
  79          bits    2.3 **
  80                  2.1 **
  81                  1.8 *** *
  82                  1.6 *****              *
  83 Information      1.4 ******   * **  * ***
  84 content          1.1 *******  * ** ** ***
  85 (26.5 bits)      0.9 *******  **** ** ***
  86                  0.7 ******* ***** ******
  87                  0.5 ********************
  88                  0.2 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           CCAGTCATGCATGAATTTGC
  92 consensus                 T A GC AGC G C
  93 sequence                          C
  94
  95 --------------------------------------------------------------------------------
  96
  97 --------------------------------------------------------------------------------
  98         Motif 1 sites sorted by position p-value
  99 --------------------------------------------------------------------------------
 100 Sequence name            Strand  Start   P-value                    Site
 101 -------------            ------  ----- ---------            --------------------
 102 20761                        +   1879  6.50e-13 TCTGATTAAG CCAGTCATGCATGGATTTGC ATTTTGGTTG
 103 20760                        +   1875  6.50e-13 CCCAGTCACG CCAGTCATGCATGGATTTGC ATTTTGATTG
 104 6700                         +   1100  2.27e-10 CCTGCTCATG CCAGTCATGGATAAATTTGC ATCTGGCTTA
 105 20755                        +   1478  5.08e-10 CCCTGTCAGG CCAGTTATGGATGAATGTGC ACTTAANNNN
 106 6707                         +   1431  6.11e-09 TCACACAGAT CCAGTCAATCCTGCCTGTCC ATCTCAATGA
 107 20762                        +   1878  1.89e-08 CCTGGTTAGG CCAGTTAAACACAGATTTGC ATTTTGGTTA
 108 16939                        -    914  2.01e-08 ACTTTTCCTT CCAATCATGCCTGCCCTTGA ACCCTATTGG
 109 20754                        +   1175  6.73e-08 GCTCACCTTG CCAGTCTCCCCTGAATACCC TACATGCCCT
 110 --------------------------------------------------------------------------------
 111
 112 --------------------------------------------------------------------------------
 113         Motif 1 block diagrams
 114 --------------------------------------------------------------------------------
 115 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 116 -------------            ----------------  -------------
 117 20761                             6.5e-13  1878_[+1]_102
 118 20760                             6.5e-13  1874_[+1]_106
 119 6700                              2.3e-10  1099_[+1]_883
 120 20755                             5.1e-10  1477_[+1]_503
 121 6707                              6.1e-09  1430_[+1]_550
 122 20762                             1.9e-08  1877_[+1]_103
 123 16939                               2e-08  913_[-1]_1068
 124 20754                             6.7e-08  1174_[+1]_807
 125 --------------------------------------------------------------------------------
 126
 127 --------------------------------------------------------------------------------
 128         Motif 1 in BLOCKS format
 129 --------------------------------------------------------------------------------
 130 BL   MOTIF 1 width=20 seqs=8
 131 20761                    ( 1879) CCAGTCATGCATGGATTTGC  1
 132 20760                    ( 1875) CCAGTCATGCATGGATTTGC  1
 133 6700                     ( 1100) CCAGTCATGGATAAATTTGC  1
 134 20755                    ( 1478) CCAGTTATGGATGAATGTGC  1
 135 6707                     ( 1431) CCAGTCAATCCTGCCTGTCC  1
 136 20762                    ( 1878) CCAGTTAAACACAGATTTGC  1
 137 16939                    (  914) CCAATCATGCCTGCCCTTGA  1
 138 20754                    ( 1175) CCAGTCTCCCCTGAATACCC  1
 139 //
 140
 141 --------------------------------------------------------------------------------
 142
 143 --------------------------------------------------------------------------------
 144         Motif 1 position-specific scoring matrix
 145 --------------------------------------------------------------------------------
 146 log-odds matrix: alength= 4 w= 20 n= 17833 bayes= 11.1216 E= 1.3e-002
 147   -965    229   -965   -965
 148   -965    229   -965   -965
 149    176   -965   -965   -965
 150   -124   -965    210   -965
 151   -965   -965   -965    176
 152   -965    187   -965    -24
 153    157   -965   -965   -124
 154    -24    -71   -965    108
 155   -124    -71    161   -124
 156   -965    187     29   -965
 157    108     87   -965   -965
 158   -965    -71   -965    157
 159    -24   -965    187   -965
 160     34     29     87   -965
 161    134     29   -965   -965
 162   -965    -71   -965    157
 163   -124   -965     29    108
 164   -965    -71   -965    157
 165   -965     29    187   -965
 166   -124    210   -965   -965
 167 --------------------------------------------------------------------------------
 168
 169 --------------------------------------------------------------------------------
 170         Motif 1 position-specific probability matrix
 171 --------------------------------------------------------------------------------
 172 letter-probability matrix: alength= 4 w= 20 n= 17833 E= 1.3e-002
 173  0.000369  0.999007  0.000255  0.000369
 174  0.000369  0.999007  0.000255  0.000369
 175  0.999120  0.000255  0.000255  0.000369
 176  0.125213  0.000255  0.874163  0.000369
 177  0.000369  0.000255  0.000255  0.999120
 178  0.000369  0.749319  0.000255  0.250057
 179  0.874276  0.000255  0.000255  0.125213
 180  0.250057  0.125099  0.000255  0.624589
 181  0.125213  0.125099  0.624475  0.125213
 182  0.000369  0.749319  0.249943  0.000369
 183  0.624589  0.374787  0.000255  0.000369
 184  0.000369  0.125099  0.000255  0.874276
 185  0.250057  0.000255  0.749319  0.000369
 186  0.374901  0.249943  0.374787  0.000369
 187  0.749432  0.249943  0.000255  0.000369
 188  0.000369  0.125099  0.000255  0.874276
 189  0.125213  0.000255  0.249943  0.624589
 190  0.000369  0.125099  0.000255  0.874276
 191  0.000369  0.249943  0.749319  0.000369
 192  0.125213  0.874163  0.000255  0.000369
 193 --------------------------------------------------------------------------------
 194
 195
 196
 197
 198
 199 Time 75.70 secs.
 200
 201 ********************************************************************************
 202
 203
 204 ********************************************************************************
 205 MOTIF  2        width =   15   sites =   8   llr = 117   E-value = 1.2e+003
 206 ********************************************************************************
 207 --------------------------------------------------------------------------------
 208         Motif 2 Description
 209 --------------------------------------------------------------------------------
 210 Simplified        A  :1a39:::::18:::
 211 pos.-specific     C  ::::1:::8a:::::
 212 probability       G  96:3::1:::::4::
 213 matrix            T  13:5:a9a3:936aa
 214
 215          bits    2.3          *
 216                  2.1          *
 217                  1.8   *  * * *   **
 218                  1.6 * *  * * *   **
 219 Information      1.4 * * ******   **
 220 content          1.1 * * *******  **
 221 (21.0 bits)      0.9 * * ***********
 222                  0.7 *** ***********
 223                  0.5 ***************
 224                  0.2 ***************
 225                  0.0 ---------------
 226
 227 Multilevel           GGATATTTCCTATTT
 228 consensus             T A    T  TG
 229 sequence                G
 230
 231 --------------------------------------------------------------------------------
 232
 233 --------------------------------------------------------------------------------
 234         Motif 2 sites sorted by position p-value
 235 --------------------------------------------------------------------------------
 236 Sequence name            Strand  Start   P-value                 Site
 237 -------------            ------  ----- ---------            ---------------
 238 20762                        +   1845  2.62e-09 TCCAGGAACA GGATATTTCCTATTT TTGAGAGTCC
 239 6700                         +   1068  2.62e-09 TTTCAGAACA GGATATTTCCTATTT TGAGTATCCT
 240 20755                        +   1445  2.84e-08 GCCAAGGGTG GGATATTTTCTATTT TGTAGAGTCC
 241 20754                        -    664  5.62e-08 TTTCTTAGAA GGAAATTTCCTTGTT CTCTTTCTAT
 242 20761                        +    670  1.06e-07 GAAGAAAAAG GAAGATTTCCTAGTT AACAATTCAA
 243 68723                        -   1925  5.26e-07 TTGCTTTCTT TGAGATGTCCTAGTT CACTCCTAAA
 244 20760                        -    651  5.56e-07 TTTAAACTTG GTAAATTTTCTTTTT CTTCACATTT
 245 16939                        -   1616  6.78e-07 TAGTTCAGTT GTATCTTTCCAATTT TGATGTTTGG
 246 --------------------------------------------------------------------------------
 247
 248 --------------------------------------------------------------------------------
 249         Motif 2 block diagrams
 250 --------------------------------------------------------------------------------
 251 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 252 -------------            ----------------  -------------
 253 20762                             2.6e-09  1844_[+2]_141
 254 6700                              2.6e-09  1067_[+2]_920
 255 20755                             2.8e-08  1444_[+2]_541
 256 20754                             5.6e-08  663_[-2]_1323
 257 20761                             1.1e-07  669_[+2]_1316
 258 68723                             5.3e-07  1924_[-2]_61
 259 20760                             5.6e-07  650_[-2]_1335
 260 16939                             6.8e-07  1615_[-2]_371
 261 --------------------------------------------------------------------------------
 262
 263 --------------------------------------------------------------------------------
 264         Motif 2 in BLOCKS format
 265 --------------------------------------------------------------------------------
 266 BL   MOTIF 2 width=15 seqs=8
 267 20762                    ( 1845) GGATATTTCCTATTT  1
 268 6700                     ( 1068) GGATATTTCCTATTT  1
 269 20755                    ( 1445) GGATATTTTCTATTT  1
 270 20754                    (  664) GGAAATTTCCTTGTT  1
 271 20761                    (  670) GAAGATTTCCTAGTT  1
 272 68723                    ( 1925) TGAGATGTCCTAGTT  1
 273 20760                    (  651) GTAAATTTTCTTTTT  1
 274 16939                    ( 1616) GTATCTTTCCAATTT  1
 275 //
 276
 277 --------------------------------------------------------------------------------
 278
 279 --------------------------------------------------------------------------------
 280         Motif 2 position-specific scoring matrix
 281 --------------------------------------------------------------------------------
 282 log-odds matrix: alength= 4 w= 15 n= 17878 bayes= 11.1253 E= 1.2e+003
 283   -965   -965    210   -124
 284   -124   -965    161    -24
 285    176   -965   -965   -965
 286    -24   -965     29     76
 287    157    -71   -965   -965
 288   -965   -965   -965    176
 289   -965   -965    -71    157
 290   -965   -965   -965    176
 291   -965    187   -965    -24
 292   -965    229   -965   -965
 293   -124   -965   -965    157
 294    134   -965   -965    -24
 295   -965   -965     87    108
 296   -965   -965   -965    176
 297   -965   -965   -965    176
 298 --------------------------------------------------------------------------------
 299
 300 --------------------------------------------------------------------------------
 301         Motif 2 position-specific probability matrix
 302 --------------------------------------------------------------------------------
 303 letter-probability matrix: alength= 4 w= 15 n= 17878 E= 1.2e+003
 304  0.000369  0.000255  0.874163  0.125213
 305  0.125213  0.000255  0.624475  0.250057
 306  0.999120  0.000255  0.000255  0.000369
 307  0.250057  0.000255  0.249943  0.499745
 308  0.874276  0.125099  0.000255  0.000369
 309  0.000369  0.000255  0.000255  0.999120
 310  0.000369  0.000255  0.125099  0.874276
 311  0.000369  0.000255  0.000255  0.999120
 312  0.000369  0.749319  0.000255  0.250057
 313  0.000369  0.999007  0.000255  0.000369
 314  0.125213  0.000255  0.000255  0.874276
 315  0.749432  0.000255  0.000255  0.250057
 316  0.000369  0.000255  0.374787  0.624589
 317  0.000369  0.000255  0.000255  0.999120
 318  0.000369  0.000255  0.000255  0.999120
 319 --------------------------------------------------------------------------------
 320
 321
 322
 323
 324
 325 Time 152.20 secs.
 326
 327 ********************************************************************************
 328
 329
 330 ********************************************************************************
 331 SUMMARY OF MOTIFS
 332 ********************************************************************************
 333
 334 --------------------------------------------------------------------------------
 335         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 336 --------------------------------------------------------------------------------
 337 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 338 -------------            ----------------  -------------
 339 68723                            2.83e-04  473_[-1(8.43e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_35_[-1(3.15e-06)]_[+1(1.38e-05)]_9_[-1(7.89e-05)]_63_[-1(2.97e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_26_[+2(4.37e-06)]_46_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_6_[-1(7.97e-06)]_24_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_1_[-2(5.92e-05)]_279_[-1(8.43e-06)]_[+1(1.38e-05)]_[+2(5.60e-05)]_157_[-2(5.26e-07)]_61
 340 16939                            3.50e-06  913_[-1(2.01e-08)]_682_[-2(6.78e-07)]_205_[+1(5.80e-05)]_146
 341 20754                            1.05e-06  39_[-2(1.78e-05)]_4_[+1(4.78e-06)]_564_[-2(7.42e-05)]_6_[-2(5.62e-08)]_146_[+2(3.98e-05)]_335_[+1(6.73e-08)]_93_[+1(5.54e-05)]_694
 342 6707                             2.26e-05  173_[+1(4.46e-05)]_655_[-2(5.60e-05)]_3_[+1(3.06e-06)]_12_[+1(4.78e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.93e-05)]_181_[-1(3.26e-05)]_251_[+1(6.11e-09)]_329_[+1(6.34e-05)]_201
 343 20755                            5.26e-09  160_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_3_[+1(6.41e-06)]_219_[-1(4.80e-05)]_962_[+2(2.84e-08)]_18_[+1(5.08e-10)]_6_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_14_[+1(7.97e-06)]_83
 344 6700                             2.48e-10  48_[+1(7.97e-06)]_267_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_129_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_3_[+1(4.41e-06)]_280_[+2(2.62e-09)]_17_[+1(2.27e-10)]_101_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+2(7.29e-05)]_[+1(6.41e-06)]_604_[-1(8.43e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_3
 345 20760                            1.53e-10  259_[-1(6.20e-05)]_339_[-2(3.17e-05)]_17_[-2(5.56e-07)]_436_[-2(4.06e-05)]_7_[+1(2.95e-07)]_6_[-1(1.12e-05)]_705_[+1(6.50e-13)]_106
 346 20761                            3.10e-11  397_[-2(1.10e-06)]_257_[+2(1.06e-07)]_382_[-2(5.60e-05)]_[+2(7.29e-05)]_[-1(3.24e-06)]_[+1(1.38e-05)]_[+1(1.38e-05)]_722_[+1(6.50e-13)]_102
 347 20762                            1.72e-08  134_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_[+1(1.38e-05)]_92_[+2(9.22e-05)]_517_[+1(7.97e-06)]_7_[-1(4.78e-06)]_439_[+2(2.62e-09)]_18_[+1(1.89e-08)]_103
 348 --------------------------------------------------------------------------------
 349
 350 ********************************************************************************
 351
 352
 353 ********************************************************************************
 354 Stopped because nmotifs = 2 reached.
 355 ********************************************************************************
 356
 357 CPU: crick
 358
 359 ********************************************************************************