t/data/test.meme

   1 ********************************************************************************
   2 MEME - Motif discovery tool
   3 ********************************************************************************
   4 MEME version 3.0 (Release date: 2001/03/05 14:24:28)
   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= D10Mit194.set.genbank.fasta.nref
  32 ALPHABET= ACGT
  33 Sequence name           Weight Length  Sequence name           Weight Length
  34 -------------           ------ ------  -------------           ------ ------
  35 20218                   1.0000   2000  10657                   1.0000   2000
  36 83796                   1.0000   2000  6603                    1.0000   2000
  37 ********************************************************************************
  38
  39 ********************************************************************************
  40 COMMAND LINE SUMMARY
  41 ********************************************************************************
  42 This information can also be useful in the event you wish to report a
  43 problem with the MEME software.
  44
  45 command: meme D10Mit194.set.genbank.fasta.nref -dna -print_fasta -nmotifs 3 -maxw 25
  46
  47 model:  mod=         zoops    nmotifs=         3    evt=           inf
  48 object function=  E-value of product of p-values
  49 width:  minw=            8    maxw=           25    minic=        0.00
  50 width:  wg=             11    ws=              1    endgaps=       yes
  51 nsites: minsites=        2    maxsites=        4    wnsites=       0.8
  52 theta:  prob=            1    spmap=         uni    spfuzz=        0.5
  53 em:     prior=   dirichlet    b=            0.01    maxiter=        50
  54         distance=    1e-05
  55 data:   n=            8000    N=               4
  56 strands: +
  57 sample: seed=            0    seqfrac=         1
  58 Letter frequencies in dataset:
  59 A 0.255 C 0.236 G 0.252 T 0.257
  60 Background letter frequencies (from dataset with add-one prior applied):
  61 A 0.255 C 0.236 G 0.252 T 0.257
  62 ********************************************************************************
  63
  64
  65 ********************************************************************************
  66 MOTIF  1        width =   25   sites =   4   llr = 106   E-value = 1.2e-002
  67 ********************************************************************************
  68 --------------------------------------------------------------------------------
  69         Motif 1 Description
  70 --------------------------------------------------------------------------------
  71 Simplified        A  :8:88aaa:53a8:::3:a::3::3
  72 pos.-specific     C  a3::3:::::3:::5a8a:8a5aa8
  73 probability       G  ::8:::::3:5::::::::3:::::
  74 matrix            T  ::33::::85::3a5::::::3:::
  75
  76          bits    2.1 *              * *  * **
  77                  1.9 *    ***   * * * ** * **
  78                  1.7 *    ***   * * * ** * **
  79                  1.5 *    ***   * * * ** * **
  80 Information      1.2 *********  *** ****** ***
  81 content          1.0 ********** ********** ***
  82 (38.1 bits)      0.8 ********** ********** ***
  83                  0.6 ********** **************
  84                  0.4 *************************
  85                  0.2 *************************
  86                  0.0 -------------------------
  87
  88 Multilevel           CAGAAAAATAGAATCCCCACCCCCC
  89 consensus             CTTC   GTA T T A  G A  A
  90 sequence                       C          T
  91
  92 --------------------------------------------------------------------------------
  93
  94 --------------------------------------------------------------------------------
  95         Motif 1 sites sorted by position p-value
  96 --------------------------------------------------------------------------------
  97 Sequence name             Start   P-value                      Site
  98 -------------             ----- ---------            -------------------------
  99 6603                       1311  2.59e-15 GGCGCATTGA CAGAAAAATTGAATTCCCACCCCCC AATGAGGAGG
 100 83796                      1284  2.59e-15 GGAGGATTGA CAGAAAAATTGAATTCCCACCCCCC AACGAGGAGG
 101 20218                       938  6.34e-12 TTTTTGGTAA CCTTAAAATAAAATCCCCACCACCA CTTTTAAAAA
 102 10657                      1685  8.70e-12 GGCCCGCGCG CAGACAAAGACATTCCACAGCTCCC GCCCCCTCCA
 103 --------------------------------------------------------------------------------
 104
 105 --------------------------------------------------------------------------------
 106         Motif 1 block diagrams
 107 --------------------------------------------------------------------------------
 108 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 109 -------------            ----------------  -------------
 110 6603                              2.6e-15  1310_[1]_665
 111 83796                             2.6e-15  1283_[1]_692
 112 20218                             6.3e-12  937_[1]_1038
 113 10657                             8.7e-12  1684_[1]_291
 114 --------------------------------------------------------------------------------
 115
 116 --------------------------------------------------------------------------------
 117         Motif 1 in FASTA format
 118 --------------------------------------------------------------------------------
 119 >6603                     pos 1311
 120 CAGAAAAATTGAATTCCCACCCCCC
 121 >83796                    pos 1284
 122 CAGAAAAATTGAATTCCCACCCCCC
 123 >20218                    pos  938
 124 CCTTAAAATAAAATCCCCACCACCA
 125 >10657                    pos 1685
 126 CAGACAAAGACATTCCACAGCTCCC
 127 --------------------------------------------------------------------------------
 128
 129 --------------------------------------------------------------------------------
 130         Motif 1 position-specific scoring matrix
 131 --------------------------------------------------------------------------------
 132 log-odds matrix: alength= 4 w= 25 n= 7904 bayes= 11.6849 E= 1.2e-002
 133   -865    208   -865   -865
 134    156      8   -865   -865
 135   -865   -865    157     -4
 136    156   -865   -865     -4
 137    156      8   -865   -865
 138    197   -865   -865   -865
 139    197   -865   -865   -865
 140    197   -865   -865   -865
 141   -865   -865     -1    154
 142     97   -865   -865     96
 143     -3      8     99   -865
 144    197   -865   -865   -865
 145    156   -865   -865     -4
 146   -865   -865   -865    196
 147   -865    108   -865     96
 148   -865    208   -865   -865
 149     -3    166   -865   -865
 150   -865    208   -865   -865
 151    197   -865   -865   -865
 152   -865    166     -1   -865
 153   -865    208   -865   -865
 154     -3    108   -865     -4
 155   -865    208   -865   -865
 156   -865    208   -865   -865
 157     -3    166   -865   -865
 158 --------------------------------------------------------------------------------
 159
 160 --------------------------------------------------------------------------------
 161         Motif 1 position-specific probability matrix
 162 --------------------------------------------------------------------------------
 163 letter-probability matrix: alength= 4 w= 25 n= 7904 E= 1.2e-002
 164  0.000635  0.998096  0.000629  0.000640
 165  0.748765  0.249966  0.000629  0.000640
 166  0.000635  0.000589  0.748759  0.250017
 167  0.748765  0.000589  0.000629  0.250017
 168  0.748765  0.249966  0.000629  0.000640
 169  0.998141  0.000589  0.000629  0.000640
 170  0.998141  0.000589  0.000629  0.000640
 171  0.998141  0.000589  0.000629  0.000640
 172  0.000635  0.000589  0.250006  0.748770
 173  0.499388  0.000589  0.000629  0.499393
 174  0.250012  0.249966  0.499382  0.000640
 175  0.998141  0.000589  0.000629  0.000640
 176  0.748765  0.000589  0.000629  0.250017
 177  0.000635  0.000589  0.000629  0.998147
 178  0.000635  0.499343  0.000629  0.499393
 179  0.000635  0.998096  0.000629  0.000640
 180  0.250012  0.748719  0.000629  0.000640
 181  0.000635  0.998096  0.000629  0.000640
 182  0.998141  0.000589  0.000629  0.000640
 183  0.000635  0.748719  0.250006  0.000640
 184  0.000635  0.998096  0.000629  0.000640
 185  0.250012  0.499343  0.000629  0.250017
 186  0.000635  0.998096  0.000629  0.000640
 187  0.000635  0.998096  0.000629  0.000640
 188  0.250012  0.748719  0.000629  0.000640
 189 --------------------------------------------------------------------------------
 190
 191
 192
 193
 194
 195 Time 38.44 secs.
 196
 197 ********************************************************************************
 198
 199
 200 ********************************************************************************
 201 MOTIF  2        width =   25   sites =   4   llr = 101   E-value = 4.5e-001
 202 ********************************************************************************
 203 --------------------------------------------------------------------------------
 204         Motif 2 Description
 205 --------------------------------------------------------------------------------
 206 Simplified        A  ::::a::383:5:3:::a33:83:a
 207 pos.-specific     C  a3a8:3a33:a::5::8::::383:
 208 probability       G  ::::::::::::::::3:38a::8:
 209 matrix            T  :8:3:8:5:8:5a3aa::5::::::
 210
 211          bits    2.1 * *   *   *         *
 212                  1.9 * * * *   * * ** *  *   *
 213                  1.7 * * * *   * * ** *  *   *
 214                  1.5 * * * *   * * ** *  *   *
 215 Information      1.2 ******* *** * **** ******
 216 content          1.0 ******* ***** **** ******
 217 (36.6 bits)      0.8 ******* ***** **** ******
 218                  0.6 ******* ********** ******
 219                  0.4 *************************
 220                  0.2 *************************
 221                  0.0 -------------------------
 222
 223 Multilevel           CTCCATCTATCATCTTCATGGACGA
 224 consensus             C T C ACA T A  G AA CAC
 225 sequence                    C     T    G
 226
 227 --------------------------------------------------------------------------------
 228
 229 --------------------------------------------------------------------------------
 230         Motif 2 sites sorted by position p-value
 231 --------------------------------------------------------------------------------
 232 Sequence name             Start   P-value                      Site
 233 -------------             ----- ---------            -------------------------
 234 6603                       1000  1.62e-15 CGGGAACATG CTCCATCTATCATCTTCATGGACGA AATCGACTCC
 235 83796                       978  4.69e-15 CGAGAACATG CTCCATCCATCATCTTCATGGACGA GATTGACTCT
 236 20218                      1545  1.69e-11 TAGCTTCTCT CCCCATCAATCTTATTCAGAGCCCA CCCCTCCCCC
 237 10657                      1075  3.40e-11 AGGATCTGGT CTCTACCTCACTTTTTGAAGGAAGA AACACTTAAT
 238 --------------------------------------------------------------------------------
 239
 240 --------------------------------------------------------------------------------
 241         Motif 2 block diagrams
 242 --------------------------------------------------------------------------------
 243 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 244 -------------            ----------------  -------------
 245 6603                              1.6e-15  999_[2]_976
 246 83796                             4.7e-15  977_[2]_998
 247 20218                             1.7e-11  1544_[2]_431
 248 10657                             3.4e-11  1074_[2]_901
 249 --------------------------------------------------------------------------------
 250
 251 --------------------------------------------------------------------------------
 252         Motif 2 in FASTA format
 253 --------------------------------------------------------------------------------
 254 >6603                     pos 1000
 255 CTCCATCTATCATCTTCATGGACGA
 256 >83796                    pos  978
 257 CTCCATCCATCATCTTCATGGACGA
 258 >20218                    pos 1545
 259 CCCCATCAATCTTATTCAGAGCCCA
 260 >10657                    pos 1075
 261 CTCTACCTCACTTTTTGAAGGAAGA
 262 --------------------------------------------------------------------------------
 263
 264 --------------------------------------------------------------------------------
 265         Motif 2 position-specific scoring matrix
 266 --------------------------------------------------------------------------------
 267 log-odds matrix: alength= 4 w= 25 n= 7904 bayes= 10.9476 E= 4.5e-001
 268   -865    208   -865   -865
 269   -865      8   -865    154
 270   -865    208   -865   -865
 271   -865    166   -865     -4
 272    197   -865   -865   -865
 273   -865      8   -865    154
 274   -865    208   -865   -865
 275     -3      8   -865     96
 276    156      8   -865   -865
 277     -3   -865   -865    154
 278   -865    208   -865   -865
 279     97   -865   -865     96
 280   -865   -865   -865    196
 281     -3    108   -865     -4
 282   -865   -865   -865    196
 283   -865   -865   -865    196
 284   -865    166     -1   -865
 285    197   -865   -865   -865
 286     -3   -865     -1     96
 287     -3   -865    157   -865
 288   -865   -865    198   -865
 289    156      8   -865   -865
 290     -3    166   -865   -865
 291   -865      8    157   -865
 292    197   -865   -865   -865
 293 --------------------------------------------------------------------------------
 294
 295 --------------------------------------------------------------------------------
 296         Motif 2 position-specific probability matrix
 297 --------------------------------------------------------------------------------
 298 letter-probability matrix: alength= 4 w= 25 n= 7904 E= 4.5e-001
 299  0.000635  0.998096  0.000629  0.000640
 300  0.000635  0.249966  0.000629  0.748770
 301  0.000635  0.998096  0.000629  0.000640
 302  0.000635  0.748719  0.000629  0.250017
 303  0.998141  0.000589  0.000629  0.000640
 304  0.000635  0.249966  0.000629  0.748770
 305  0.000635  0.998096  0.000629  0.000640
 306  0.250012  0.249966  0.000629  0.499393
 307  0.748765  0.249966  0.000629  0.000640
 308  0.250012  0.000589  0.000629  0.748770
 309  0.000635  0.998096  0.000629  0.000640
 310  0.499388  0.000589  0.000629  0.499393
 311  0.000635  0.000589  0.000629  0.998147
 312  0.250012  0.499343  0.000629  0.250017
 313  0.000635  0.000589  0.000629  0.998147
 314  0.000635  0.000589  0.000629  0.998147
 315  0.000635  0.748719  0.250006  0.000640
 316  0.998141  0.000589  0.000629  0.000640
 317  0.250012  0.000589  0.250006  0.499393
 318  0.250012  0.000589  0.748759  0.000640
 319  0.000635  0.000589  0.998135  0.000640
 320  0.748765  0.249966  0.000629  0.000640
 321  0.250012  0.748719  0.000629  0.000640
 322  0.000635  0.249966  0.748759  0.000640
 323  0.998141  0.000589  0.000629  0.000640
 324 --------------------------------------------------------------------------------
 325
 326
 327
 328
 329
 330 Time 78.29 secs.
 331
 332 ********************************************************************************
 333
 334
 335 ********************************************************************************
 336 MOTIF  3        width =   21   sites =   4   llr = 88   E-value = 4.8e-001
 337 ********************************************************************************
 338 --------------------------------------------------------------------------------
 339         Motif 3 Description
 340 --------------------------------------------------------------------------------
 341 Simplified        A  :::58:::::3::::33::::
 342 pos.-specific     C  8:833::8:8:a:8a8:a5a8
 343 probability       G  3::::::3:::::3:::::::
 344 matrix            T  :a33:aa:a38:a:::8:5:3
 345
 346          bits    2.1            *  *  * *
 347                  1.9  *   ** *  ** *  * *
 348                  1.7  *   ** *  ** *  * *
 349                  1.5  *   ** *  ** *  * *
 350 Information      1.2 *** ************** **
 351 content          1.0 *** *****************
 352 (31.8 bits)      0.8 *** *****************
 353                  0.6 *** *****************
 354                  0.4 *********************
 355                  0.2 *********************
 356                  0.0 ---------------------
 357
 358 Multilevel           CTCAATTCTCTCTCCCTCCCC
 359 consensus            G TCC  G TA  G AA T T
 360 sequence                T
 361
 362 --------------------------------------------------------------------------------
 363
 364 --------------------------------------------------------------------------------
 365         Motif 3 sites sorted by position p-value
 366 --------------------------------------------------------------------------------
 367 Sequence name             Start   P-value                    Site
 368 -------------             ----- ---------            ---------------------
 369 10657                      1511  1.45e-13 CCCAGGCGGT CTCAATTCTCTCTCCCTCCCC TTTCCGTGAC
 370 83796                      1801  7.40e-12 TGTATATGCA CTCTCTTCTCTCTCCCTCTCC AGGTCATGCA
 371 6603                       1811  1.22e-10 GTAACTTAAT GTTCATTCTCTCTCCCACCCC TAGGTCATGC
 372 20218                       606  7.57e-10 CCCAGGCCAG CTCAATTGTTACTGCATCTCT AGGATTGGAA
 373 --------------------------------------------------------------------------------
 374
 375 --------------------------------------------------------------------------------
 376         Motif 3 block diagrams
 377 --------------------------------------------------------------------------------
 378 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 379 -------------            ----------------  -------------
 380 10657                             1.5e-13  1510_[3]_469
 381 83796                             7.4e-12  1800_[3]_179
 382 6603                              1.2e-10  1810_[3]_169
 383 20218                             7.6e-10  605_[3]_1374
 384 --------------------------------------------------------------------------------
 385
 386 --------------------------------------------------------------------------------
 387         Motif 3 in FASTA format
 388 --------------------------------------------------------------------------------
 389 >10657                    pos 1511
 390 CTCAATTCTCTCTCCCTCCCC
 391 >83796                    pos 1801
 392 CTCTCTTCTCTCTCCCTCTCC
 393 >6603                     pos 1811
 394 GTTCATTCTCTCTCCCACCCC
 395 >20218                    pos  606
 396 CTCAATTGTTACTGCATCTCT
 397 --------------------------------------------------------------------------------
 398
 399 --------------------------------------------------------------------------------
 400         Motif 3 position-specific scoring matrix
 401 --------------------------------------------------------------------------------
 402 log-odds matrix: alength= 4 w= 21 n= 7920 bayes= 10.9506 E= 4.8e-001
 403   -865    166     -1   -865
 404   -865   -865   -865    196
 405   -865    166   -865     -4
 406     97      8   -865     -4
 407    156      8   -865   -865
 408   -865   -865   -865    196
 409   -865   -865   -865    196
 410   -865    166     -1   -865
 411   -865   -865   -865    196
 412   -865    166   -865     -4
 413     -3   -865   -865    154
 414   -865    208   -865   -865
 415   -865   -865   -865    196
 416   -865    166     -1   -865
 417   -865    208   -865   -865
 418     -3    166   -865   -865
 419     -3   -865   -865    154
 420   -865    208   -865   -865
 421   -865    108   -865     96
 422   -865    208   -865   -865
 423   -865    166   -865     -4
 424 --------------------------------------------------------------------------------
 425
 426 --------------------------------------------------------------------------------
 427         Motif 3 position-specific probability matrix
 428 --------------------------------------------------------------------------------
 429 letter-probability matrix: alength= 4 w= 21 n= 7920 E= 4.8e-001
 430  0.000635  0.748719  0.250006  0.000640
 431  0.000635  0.000589  0.000629  0.998147
 432  0.000635  0.748719  0.000629  0.250017
 433  0.499388  0.249966  0.000629  0.250017
 434  0.748765  0.249966  0.000629  0.000640
 435  0.000635  0.000589  0.000629  0.998147
 436  0.000635  0.000589  0.000629  0.998147
 437  0.000635  0.748719  0.250006  0.000640
 438  0.000635  0.000589  0.000629  0.998147
 439  0.000635  0.748719  0.000629  0.250017
 440  0.250012  0.000589  0.000629  0.748770
 441  0.000635  0.998096  0.000629  0.000640
 442  0.000635  0.000589  0.000629  0.998147
 443  0.000635  0.748719  0.250006  0.000640
 444  0.000635  0.998096  0.000629  0.000640
 445  0.250012  0.748719  0.000629  0.000640
 446  0.250012  0.000589  0.000629  0.748770
 447  0.000635  0.998096  0.000629  0.000640
 448  0.000635  0.499343  0.000629  0.499393
 449  0.000635  0.998096  0.000629  0.000640
 450  0.000635  0.748719  0.000629  0.250017
 451 --------------------------------------------------------------------------------
 452
 453
 454
 455
 456
 457 Time 117.82 secs.
 458
 459 ********************************************************************************
 460
 461
 462 ********************************************************************************
 463 SUMMARY OF MOTIFS
 464 ********************************************************************************
 465
 466 --------------------------------------------------------------------------------
 467         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 468 --------------------------------------------------------------------------------
 469 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 470 -------------            ----------------  -------------
 471 20218                            7.77e-19  605_[3(7.57e-10)]_311_[1(6.34e-12)]_582_[2(1.69e-11)]_431
 472 10657                            5.46e-22  1_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_7_[1(6.00e-08)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_5_[1(1.18e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_4_[1(1.29e-07)]_332_[2(3.40e-11)]_383_[3(7.75e-07)]_7_[3(1.45e-13)]_56_[3(3.47e-05)]_76_[1(8.70e-12)]_291
 473 83796                            1.73e-27  977_[2(4.69e-15)]_281_[1(2.59e-15)]_492_[3(7.40e-12)]_179
 474 6603                             9.32e-27  597_[1(1.75e-07)]_[1(1.75e-07)]_[1(1.75e-07)]_327_[2(1.62e-15)]_286_[1(2.59e-15)]_475_[3(1.22e-10)]_169
 475 --------------------------------------------------------------------------------
 476
 477 ********************************************************************************
 478
 479
 480 ********************************************************************************
 481 Stopped because nmotifs = 3 reached.
 482 ********************************************************************************
 483
 484 CPU: hydra-1.lsd.ornl.gov
 485
 486 ********************************************************************************