t/data/map_hem/HEM4-HEM13.meme.txt

   1 ********************************************************************************
   2 MEME - Motif discovery tool
   3 ********************************************************************************
   4 MEME version 3.5.4 (Release date:    )
   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.nbcr.net.
   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.nbcr.net.
  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= HEM4-HEM13.fa
  32 ALPHABET= ACGT
  33 Sequence name            Weight Length  Sequence name            Weight Length
  34 -------------            ------ ------  -------------            ------ ------
  35 SGD_Scer_YOR278W         1.0000    635  MIT_Spar_c261_21317      1.0000    635
  36 MIT_Smik_c492_20940      1.0000    635  WashU_Skud_Contig1682.4  1.0000    635
  37 WashU_Sbay_Contig635.57  1.0000    635  SGD_Scer_YDR044W         1.0000   1000
  38 MIT_Spar_c130_3912       1.0000   1000  MIT_Sbay_c896_21290      1.0000   1000
  39 WashU_Smik_Contig2283.3  1.0000   1000
  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 HEM4-HEM13.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4
  49
  50 model:  mod=          oops    nmotifs=         5    evt=           inf
  51 object function=  E-value of product of p-values
  52 width:  minw=            6    maxw=           20    minic=        0.00
  53 width:  wg=             11    ws=              1    endgaps=       yes
  54 nsites: minsites=        9    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=            7175    N=               9
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.306 C 0.194 G 0.194 T 0.306
  63 Background letter frequencies (from yeast.nc.1.freq):
  64 A 0.324 C 0.176 G 0.176 T 0.324
  65 ********************************************************************************
  66
  67
  68 ********************************************************************************
  69 MOTIF  1        width =   20   sites =   9   llr = 201   E-value = 6.7e-025
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  :::::63:::::86::61::
  75 pos.-specific     C  :61::4:::9:::2:a::::
  76 probability       G  a46:a::a:1::2:9:::9a
  77 matrix            T  ::3a::7:a:aa:21:491:
  78
  79          bits    2.5 *   *  *       *   *
  80                  2.3 *   *  *       *   *
  81                  2.0 *   *  * *    **  **
  82                  1.8 *   *  * *    **  **
  83 Information      1.5 ** **  *****  **  **
  84 content          1.3 ** **  *****  **  **
  85 (32.2 bits)      1.0 ** *** ****** ** ***
  86                  0.8 ************* ******
  87                  0.5 ********************
  88                  0.3 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           GCGTGATGTCTTAAGCATGG
  92 consensus             GT  CA     GC  T
  93 sequence                          T
  94
  95 --------------------------------------------------------------------------------
  96
  97 --------------------------------------------------------------------------------
  98         Motif 1 sites sorted by position p-value
  99 --------------------------------------------------------------------------------
 100 Sequence name            Strand  Start   P-value                    Site
 101 -------------            ------  ----- ---------            --------------------
 102 WashU_Sbay_Contig635.57      +    377  1.24e-12 ACATATGGAG GCGTGATGTCTTAAGCATGG TAATCCGGAA
 103 WashU_Skud_Contig1682.4      +    370  1.24e-12 ACATATGGAG GCGTGATGTCTTAAGCATGG TAATCCGGAA
 104 MIT_Smik_c492_20940          +    375  1.24e-12 ACATATGGAG GCGTGATGTCTTAAGCATGG TAATCCGGAA
 105 MIT_Spar_c261_21317          +    369  1.24e-12 ACATATGGAG GCGTGATGTCTTAAGCATGG TAATCCGGAA
 106 SGD_Scer_YOR278W             +    366  1.24e-12 ACATATGGAG GCGTGATGTCTTAAGCATGG TAATCCGGAA
 107 MIT_Spar_c130_3912           +    217  1.16e-10 TCAGCTCTTT GGTTGCAGTCTTGTGCTTGG TTCAAGCTGG
 108 WashU_Smik_Contig2283.3      +    213  3.08e-10 ACAGTTCGTT GGCTGCAGTGTTACGCTTGG TTGAAGCTGG
 109 SGD_Scer_YDR044W             +    225  4.42e-10 TCAGCGCTTT GGTTGCAGTCTTATGCTTTG TTCAAGCTGG
 110 MIT_Sbay_c896_21290          +    223  8.28e-10 ACAGCTCTTT GGTTGCTGTCTTGCTCTAGG TCCAAGCTGG
 111 --------------------------------------------------------------------------------
 112
 113 --------------------------------------------------------------------------------
 114         Motif 1 block diagrams
 115 --------------------------------------------------------------------------------
 116 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 117 -------------            ----------------  -------------
 118 WashU_Sbay_Contig635.57           1.2e-12  376_[+1]_239
 119 WashU_Skud_Contig1682.4           1.2e-12  369_[+1]_246
 120 MIT_Smik_c492_20940               1.2e-12  374_[+1]_241
 121 MIT_Spar_c261_21317               1.2e-12  368_[+1]_247
 122 SGD_Scer_YOR278W                  1.2e-12  365_[+1]_250
 123 MIT_Spar_c130_3912                1.2e-10  216_[+1]_764
 124 WashU_Smik_Contig2283.3           3.1e-10  212_[+1]_768
 125 SGD_Scer_YDR044W                  4.4e-10  224_[+1]_756
 126 MIT_Sbay_c896_21290               8.3e-10  222_[+1]_758
 127 --------------------------------------------------------------------------------
 128
 129 --------------------------------------------------------------------------------
 130         Motif 1 in BLOCKS format
 131 --------------------------------------------------------------------------------
 132 BL   MOTIF 1 width=20 seqs=9
 133 WashU_Sbay_Contig635.57  (  377) GCGTGATGTCTTAAGCATGG  1
 134 WashU_Skud_Contig1682.4  (  370) GCGTGATGTCTTAAGCATGG  1
 135 MIT_Smik_c492_20940      (  375) GCGTGATGTCTTAAGCATGG  1
 136 MIT_Spar_c261_21317      (  369) GCGTGATGTCTTAAGCATGG  1
 137 SGD_Scer_YOR278W         (  366) GCGTGATGTCTTAAGCATGG  1
 138 MIT_Spar_c130_3912       (  217) GGTTGCAGTCTTGTGCTTGG  1
 139 WashU_Smik_Contig2283.3  (  213) GGCTGCAGTGTTACGCTTGG  1
 140 SGD_Scer_YDR044W         (  225) GGTTGCAGTCTTATGCTTTG  1
 141 MIT_Sbay_c896_21290      (  223) GGTTGCTGTCTTGCTCTAGG  1
 142 //
 143
 144 --------------------------------------------------------------------------------
 145
 146 --------------------------------------------------------------------------------
 147         Motif 1 position-specific scoring matrix
 148 --------------------------------------------------------------------------------
 149 log-odds matrix: alength= 4 w= 20 n= 7004 bayes= 9.60218 E= 6.7e-025
 150   -982   -982    251   -982
 151   -982    166    134   -982
 152   -982    -66    166      4
 153   -982   -982   -982    162
 154   -982   -982    251   -982
 155     78    134   -982   -982
 156      4   -982   -982    104
 157   -982   -982    251   -982
 158   -982   -982   -982    162
 159   -982    234    -66   -982
 160   -982   -982   -982    162
 161   -982   -982   -982    162
 162    126   -982     34   -982
 163     78     34   -982    -55
 164   -982   -982    234   -154
 165   -982    251   -982   -982
 166     78   -982   -982     45
 167   -154   -982   -982    145
 168   -982   -982    234   -154
 169   -982   -982    251   -982
 170 --------------------------------------------------------------------------------
 171
 172 --------------------------------------------------------------------------------
 173         Motif 1 position-specific probability matrix
 174 --------------------------------------------------------------------------------
 175 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.7e-025
 176  0.000000  0.000000  1.000000  0.000000
 177  0.000000  0.555556  0.444444  0.000000
 178  0.000000  0.111111  0.555556  0.333333
 179  0.000000  0.000000  0.000000  1.000000
 180  0.000000  0.000000  1.000000  0.000000
 181  0.555556  0.444444  0.000000  0.000000
 182  0.333333  0.000000  0.000000  0.666667
 183  0.000000  0.000000  1.000000  0.000000
 184  0.000000  0.000000  0.000000  1.000000
 185  0.000000  0.888889  0.111111  0.000000
 186  0.000000  0.000000  0.000000  1.000000
 187  0.000000  0.000000  0.000000  1.000000
 188  0.777778  0.000000  0.222222  0.000000
 189  0.555556  0.222222  0.000000  0.222222
 190  0.000000  0.000000  0.888889  0.111111
 191  0.000000  1.000000  0.000000  0.000000
 192  0.555556  0.000000  0.000000  0.444444
 193  0.111111  0.000000  0.000000  0.888889
 194  0.000000  0.000000  0.888889  0.111111
 195  0.000000  0.000000  1.000000  0.000000
 196 --------------------------------------------------------------------------------
 197
 198 --------------------------------------------------------------------------------
 199         Motif 1 regular expression
 200 --------------------------------------------------------------------------------
 201 G[CG][GT]TG[AC][TA]GTCTT[AG][ACT]GC[AT]TGG
 202 --------------------------------------------------------------------------------
 203
 204
 205
 206
 207 Time  5.38 secs.
 208
 209 ********************************************************************************
 210
 211
 212 ********************************************************************************
 213 MOTIF  2        width =   20   sites =   9   llr = 197   E-value = 4.1e-023
 214 ********************************************************************************
 215 --------------------------------------------------------------------------------
 216         Motif 2 Description
 217 --------------------------------------------------------------------------------
 218 Simplified        A  1::367a:::::::7a:4a:
 219 pos.-specific     C  :646::::::6::::::::1
 220 probability       G  9461::::6a4:aa3:a::9
 221 matrix            T  ::::43:a4::a:::::6::
 222
 223          bits    2.5          *  **  *
 224                  2.3          *  **  *
 225                  2.0 *        *  **  *  *
 226                  1.8 *        *  **  *  *
 227 Information      1.5 ***   ** ***** ** **
 228 content          1.3 ***   ** ***** ** **
 229 (31.6 bits)      1.0 ***   *********** **
 230                  0.8 ********************
 231                  0.5 ********************
 232                  0.3 ********************
 233                  0.0 --------------------
 234
 235 Multilevel           GCGCAAATGGCTGGAAGTAG
 236 consensus             GCATT  T G   G  A
 237 sequence
 238
 239 --------------------------------------------------------------------------------
 240
 241 --------------------------------------------------------------------------------
 242         Motif 2 sites sorted by position p-value
 243 --------------------------------------------------------------------------------
 244 Sequence name            Strand  Start   P-value                    Site
 245 -------------            ------  ----- ---------            --------------------
 246 WashU_Sbay_Contig635.57      -    338  1.95e-13 TCTATGTCAA GCGCAAATGGCTGGAAGTAG ACCAATTTCT
 247 WashU_Skud_Contig1682.4      -    331  1.95e-13 TCTATGTAAA GCGCAAATGGCTGGAAGTAG ACCAATCTCT
 248 MIT_Smik_c492_20940          -    336  1.95e-13 TCTATATAAA GCGCAAATGGCTGGAAGTAG ACAAATTTCT
 249 MIT_Spar_c261_21317          -    330  1.95e-13 TCTATATAAA GCGCAAATGGCTGGAAGTAG ACCAATTTTT
 250 SGD_Scer_YOR278W             -    327  1.95e-13 TCTATATAAA GCGCAAATGGCTGGAAGTAG ACCAATTTTT
 251 MIT_Sbay_c896_21290          +    253  1.81e-10 TCCAAGCTGG GGCATAATTGGTGGGAGAAG CCAGAAAATG
 252 WashU_Smik_Contig2283.3      +    243  2.62e-10 TTGAAGCTGG GGCATTATTGGTGGAAGAAG CCAGAAAAGA
 253 MIT_Spar_c130_3912           +    247  2.73e-10 TTCAAGCTGG GGCATTATTGGTGGGAGAAG CCAGAAAAGG
 254 SGD_Scer_YDR044W             +    255  1.92e-09 TTCAAGCTGG AGCGTTATTGGTGGGAGAAC CAGAAAAGGC
 255 --------------------------------------------------------------------------------
 256
 257 --------------------------------------------------------------------------------
 258         Motif 2 block diagrams
 259 --------------------------------------------------------------------------------
 260 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 261 -------------            ----------------  -------------
 262 WashU_Sbay_Contig635.57           1.9e-13  337_[-2]_278
 263 WashU_Skud_Contig1682.4           1.9e-13  330_[-2]_285
 264 MIT_Smik_c492_20940               1.9e-13  335_[-2]_280
 265 MIT_Spar_c261_21317               1.9e-13  329_[-2]_286
 266 SGD_Scer_YOR278W                  1.9e-13  326_[-2]_289
 267 MIT_Sbay_c896_21290               1.8e-10  252_[+2]_728
 268 WashU_Smik_Contig2283.3           2.6e-10  242_[+2]_738
 269 MIT_Spar_c130_3912                2.7e-10  246_[+2]_734
 270 SGD_Scer_YDR044W                  1.9e-09  254_[+2]_726
 271 --------------------------------------------------------------------------------
 272
 273 --------------------------------------------------------------------------------
 274         Motif 2 in BLOCKS format
 275 --------------------------------------------------------------------------------
 276 BL   MOTIF 2 width=20 seqs=9
 277 WashU_Sbay_Contig635.57  (  338) GCGCAAATGGCTGGAAGTAG  1
 278 WashU_Skud_Contig1682.4  (  331) GCGCAAATGGCTGGAAGTAG  1
 279 MIT_Smik_c492_20940      (  336) GCGCAAATGGCTGGAAGTAG  1
 280 MIT_Spar_c261_21317      (  330) GCGCAAATGGCTGGAAGTAG  1
 281 SGD_Scer_YOR278W         (  327) GCGCAAATGGCTGGAAGTAG  1
 282 MIT_Sbay_c896_21290      (  253) GGCATAATTGGTGGGAGAAG  1
 283 WashU_Smik_Contig2283.3  (  243) GGCATTATTGGTGGAAGAAG  1
 284 MIT_Spar_c130_3912       (  247) GGCATTATTGGTGGGAGAAG  1
 285 SGD_Scer_YDR044W         (  255) AGCGTTATTGGTGGGAGAAC  1
 286 //
 287
 288 --------------------------------------------------------------------------------
 289
 290 --------------------------------------------------------------------------------
 291         Motif 2 position-specific scoring matrix
 292 --------------------------------------------------------------------------------
 293 log-odds matrix: alength= 4 w= 20 n= 7004 bayes= 9.60218 E= 4.1e-023
 294   -154   -982    234   -982
 295   -982    166    134   -982
 296   -982    134    166   -982
 297      4    166    -66   -982
 298     78   -982   -982     45
 299    104   -982   -982      4
 300    162   -982   -982   -982
 301   -982   -982   -982    162
 302   -982   -982    166     45
 303   -982   -982    251   -982
 304   -982    166    134   -982
 305   -982   -982   -982    162
 306   -982   -982    251   -982
 307   -982   -982    251   -982
 308    104   -982     92   -982
 309    162   -982   -982   -982
 310   -982   -982    251   -982
 311     45   -982   -982     78
 312    162   -982   -982   -982
 313   -982    -66    234   -982
 314 --------------------------------------------------------------------------------
 315
 316 --------------------------------------------------------------------------------
 317         Motif 2 position-specific probability matrix
 318 --------------------------------------------------------------------------------
 319 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 4.1e-023
 320  0.111111  0.000000  0.888889  0.000000
 321  0.000000  0.555556  0.444444  0.000000
 322  0.000000  0.444444  0.555556  0.000000
 323  0.333333  0.555556  0.111111  0.000000
 324  0.555556  0.000000  0.000000  0.444444
 325  0.666667  0.000000  0.000000  0.333333
 326  1.000000  0.000000  0.000000  0.000000
 327  0.000000  0.000000  0.000000  1.000000
 328  0.000000  0.000000  0.555556  0.444444
 329  0.000000  0.000000  1.000000  0.000000
 330  0.000000  0.555556  0.444444  0.000000
 331  0.000000  0.000000  0.000000  1.000000
 332  0.000000  0.000000  1.000000  0.000000
 333  0.000000  0.000000  1.000000  0.000000
 334  0.666667  0.000000  0.333333  0.000000
 335  1.000000  0.000000  0.000000  0.000000
 336  0.000000  0.000000  1.000000  0.000000
 337  0.444444  0.000000  0.000000  0.555556
 338  1.000000  0.000000  0.000000  0.000000
 339  0.000000  0.111111  0.888889  0.000000
 340 --------------------------------------------------------------------------------
 341
 342 --------------------------------------------------------------------------------
 343         Motif 2 regular expression
 344 --------------------------------------------------------------------------------
 345 G[CG][GC][CA][AT][AT]AT[GT]G[CG]TGG[AG]AG[TA]AG
 346 --------------------------------------------------------------------------------
 347
 348
 349
 350
 351 Time 10.47 secs.
 352
 353 ********************************************************************************
 354
 355
 356 ********************************************************************************
 357 MOTIF  3        width =   20   sites =   9   llr = 184   E-value = 6.0e-018
 358 ********************************************************************************
 359 --------------------------------------------------------------------------------
 360         Motif 3 Description
 361 --------------------------------------------------------------------------------
 362 Simplified        A  :21199:a::71:::6:::9
 363 pos.-specific     C  98:3::::193:::::::4:
 364 probability       G  1:961:a::1:94:13::6:
 365 matrix            T  :::::1::9:::6a91aa:1
 366
 367          bits    2.5       *
 368                  2.3       *
 369                  2.0 * *   *  * *
 370                  1.8 * *   *  * *
 371 Information      1.5 ***   ** * * *  ***
 372 content          1.3 *** * **** * ** ***
 373 (29.5 bits)      1.0 *************** ****
 374                  0.8 *************** ****
 375                  0.5 ********************
 376                  0.3 ********************
 377                  0.0 --------------------
 378
 379 Multilevel           CCGGAAGATCAGTTTATTGA
 380 consensus             A C      C G  G  C
 381 sequence
 382
 383 --------------------------------------------------------------------------------
 384
 385 --------------------------------------------------------------------------------
 386         Motif 3 sites sorted by position p-value
 387 --------------------------------------------------------------------------------
 388 Sequence name            Strand  Start   P-value                    Site
 389 -------------            ------  ----- ---------            --------------------
 390 WashU_Sbay_Contig635.57      +    401  5.77e-12 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGCTC
 391 WashU_Skud_Contig1682.4      +    394  5.77e-12 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
 392 MIT_Smik_c492_20940          +    399  5.77e-12 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
 393 MIT_Spar_c261_21317          +    393  5.77e-12 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTC
 394 SGD_Scer_YOR278W             +    390  5.77e-12 GCATGGTAAT CCGGAAGATCAGTTTATTGA ATGATGGTTT
 395 MIT_Spar_c130_3912           +    763  1.18e-11 AGAAAAATGA CCGCAAGATCCGGTTGTTCA TAACTTTCTA
 396 SGD_Scer_YDR044W             +    767  1.43e-10 AGAAAAATGA CCGCAAGATCCGGTTGTTCT CAACCTTCTA
 397 MIT_Sbay_c896_21290          +    781  2.40e-08 GAAGGGGGTG CAAAGTGATCCGGTTGTTCA TATTTCTTCA
 398 WashU_Smik_Contig2283.3      -    359  1.26e-07 TGGGTGGGAA GAGCAAGACGAAGTGTTTCA CGGCGGGGCC
 399 --------------------------------------------------------------------------------
 400
 401 --------------------------------------------------------------------------------
 402         Motif 3 block diagrams
 403 --------------------------------------------------------------------------------
 404 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 405 -------------            ----------------  -------------
 406 WashU_Sbay_Contig635.57           5.8e-12  400_[+3]_215
 407 WashU_Skud_Contig1682.4           5.8e-12  393_[+3]_222
 408 MIT_Smik_c492_20940               5.8e-12  398_[+3]_217
 409 MIT_Spar_c261_21317               5.8e-12  392_[+3]_223
 410 SGD_Scer_YOR278W                  5.8e-12  389_[+3]_226
 411 MIT_Spar_c130_3912                1.2e-11  762_[+3]_218
 412 SGD_Scer_YDR044W                  1.4e-10  766_[+3]_214
 413 MIT_Sbay_c896_21290               2.4e-08  780_[+3]_200
 414 WashU_Smik_Contig2283.3           1.3e-07  358_[-3]_622
 415 --------------------------------------------------------------------------------
 416
 417 --------------------------------------------------------------------------------
 418         Motif 3 in BLOCKS format
 419 --------------------------------------------------------------------------------
 420 BL   MOTIF 3 width=20 seqs=9
 421 WashU_Sbay_Contig635.57  (  401) CCGGAAGATCAGTTTATTGA  1
 422 WashU_Skud_Contig1682.4  (  394) CCGGAAGATCAGTTTATTGA  1
 423 MIT_Smik_c492_20940      (  399) CCGGAAGATCAGTTTATTGA  1
 424 MIT_Spar_c261_21317      (  393) CCGGAAGATCAGTTTATTGA  1
 425 SGD_Scer_YOR278W         (  390) CCGGAAGATCAGTTTATTGA  1
 426 MIT_Spar_c130_3912       (  763) CCGCAAGATCCGGTTGTTCA  1
 427 SGD_Scer_YDR044W         (  767) CCGCAAGATCCGGTTGTTCT  1
 428 MIT_Sbay_c896_21290      (  781) CAAAGTGATCCGGTTGTTCA  1
 429 WashU_Smik_Contig2283.3  (  359) GAGCAAGACGAAGTGTTTCA  1
 430 //
 431
 432 --------------------------------------------------------------------------------
 433
 434 --------------------------------------------------------------------------------
 435         Motif 3 position-specific scoring matrix
 436 --------------------------------------------------------------------------------
 437 log-odds matrix: alength= 4 w= 20 n= 7004 bayes= 9.60218 E= 6.0e-018
 438   -982    234    -66   -982
 439    -55    215   -982   -982
 440   -154   -982    234   -982
 441   -154     92    166   -982
 442    145   -982    -66   -982
 443    145   -982   -982   -154
 444   -982   -982    251   -982
 445    162   -982   -982   -982
 446   -982    -66   -982    145
 447   -982    234    -66   -982
 448    104     92   -982   -982
 449   -154   -982    234   -982
 450   -982   -982    134     78
 451   -982   -982   -982    162
 452   -982   -982    -66    145
 453     78   -982     92   -154
 454   -982   -982   -982    162
 455   -982   -982   -982    162
 456   -982    134    166   -982
 457    145   -982   -982   -154
 458 --------------------------------------------------------------------------------
 459
 460 --------------------------------------------------------------------------------
 461         Motif 3 position-specific probability matrix
 462 --------------------------------------------------------------------------------
 463 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.0e-018
 464  0.000000  0.888889  0.111111  0.000000
 465  0.222222  0.777778  0.000000  0.000000
 466  0.111111  0.000000  0.888889  0.000000
 467  0.111111  0.333333  0.555556  0.000000
 468  0.888889  0.000000  0.111111  0.000000
 469  0.888889  0.000000  0.000000  0.111111
 470  0.000000  0.000000  1.000000  0.000000
 471  1.000000  0.000000  0.000000  0.000000
 472  0.000000  0.111111  0.000000  0.888889
 473  0.000000  0.888889  0.111111  0.000000
 474  0.666667  0.333333  0.000000  0.000000
 475  0.111111  0.000000  0.888889  0.000000
 476  0.000000  0.000000  0.444444  0.555556
 477  0.000000  0.000000  0.000000  1.000000
 478  0.000000  0.000000  0.111111  0.888889
 479  0.555556  0.000000  0.333333  0.111111
 480  0.000000  0.000000  0.000000  1.000000
 481  0.000000  0.000000  0.000000  1.000000
 482  0.000000  0.444444  0.555556  0.000000
 483  0.888889  0.000000  0.000000  0.111111
 484 --------------------------------------------------------------------------------
 485
 486 --------------------------------------------------------------------------------
 487         Motif 3 regular expression
 488 --------------------------------------------------------------------------------
 489 C[CA]G[GC]AAGATC[AC]G[TG]TT[AG]TT[GC]A
 490 --------------------------------------------------------------------------------
 491
 492
 493
 494
 495 Time 15.56 secs.
 496
 497 ********************************************************************************
 498
 499
 500 ********************************************************************************
 501 MOTIF  4        width =   20   sites =   9   llr = 185   E-value = 1.4e-017
 502 ********************************************************************************
 503 --------------------------------------------------------------------------------
 504         Motif 4 Description
 505 --------------------------------------------------------------------------------
 506 Simplified        A  1:a91a81:6aa6::2a::6
 507 pos.-specific     C  :9::3::::3::::a::::4
 508 probability       G  ::::::24a1::4a:::8a:
 509 matrix            T  91:16::4:::::::8:2::
 510
 511          bits    2.5         *    **   *
 512                  2.3         *    **   *
 513                  2.0  *      *    **   *
 514                  1.8  *      *    **   *
 515 Information      1.5  **  *  * ** ** ***
 516 content          1.3  **  *  * ** ** ***
 517 (29.7 bits)      1.0 **** ** * ***** ****
 518                  0.8 **** ** ************
 519                  0.5 ********************
 520                  0.3 ********************
 521                  0.0 --------------------
 522
 523 Multilevel           TCAATAAGGAAAAGCTAGGA
 524 consensus                C GT C  G  A T C
 525 sequence
 526
 527 --------------------------------------------------------------------------------
 528
 529 --------------------------------------------------------------------------------
 530         Motif 4 sites sorted by position p-value
 531 --------------------------------------------------------------------------------
 532 Sequence name            Strand  Start   P-value                    Site
 533 -------------            ------  ----- ---------            --------------------
 534 WashU_Skud_Contig1682.4      +    296  5.02e-11 GGATTAGATT TCAATAATGAAAAGCTAGGA ATAAAAGAGA
 535 MIT_Smik_c492_20940          +    301  5.02e-11 GGATTAGATT TCAATAATGAAAAGCTAGGA ACAAAAGAAA
 536 MIT_Spar_c261_21317          +    296  5.02e-11 GGATTAGATT TCAATAATGAAAAGCTAGGA ACAGAAAAAT
 537 SGD_Scer_YOR278W             +    292  5.02e-11 GGATTAGATT TCAATAATGAAAAGCTAGGA ACAAAAAAAA
 538 MIT_Sbay_c896_21290          +    699  6.10e-11 GAGGAAAATA TCAACAAGGCAAGGCTATGC CTTTCGAAGA
 539 MIT_Spar_c130_3912           +    693  6.60e-11 GAGAGAAATA TCAACAGGGCAAGGCAAGGC TATGCTCTTT
 540 WashU_Smik_Contig2283.3      +    701  1.34e-09 GAGAAAAATA TTAACAAGGGAAGGCAAGGC TATGTTCTAT
 541 WashU_Sbay_Contig635.57      +    304  1.34e-09 GGATTAGATT TCATTAAAGAAAAGCTAGGA ACAAAGAAAT
 542 SGD_Scer_YDR044W             +    701  2.68e-09 AGAAATATCA ACAAAAGGGCAAGGCTATGC CTTCTGGAAA
 543 --------------------------------------------------------------------------------
 544
 545 --------------------------------------------------------------------------------
 546         Motif 4 block diagrams
 547 --------------------------------------------------------------------------------
 548 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 549 -------------            ----------------  -------------
 550 WashU_Skud_Contig1682.4             5e-11  295_[+4]_320
 551 MIT_Smik_c492_20940                 5e-11  300_[+4]_315
 552 MIT_Spar_c261_21317                 5e-11  295_[+4]_320
 553 SGD_Scer_YOR278W                    5e-11  291_[+4]_324
 554 MIT_Sbay_c896_21290               6.1e-11  698_[+4]_282
 555 MIT_Spar_c130_3912                6.6e-11  692_[+4]_288
 556 WashU_Smik_Contig2283.3           1.3e-09  700_[+4]_280
 557 WashU_Sbay_Contig635.57           1.3e-09  303_[+4]_312
 558 SGD_Scer_YDR044W                  2.7e-09  700_[+4]_280
 559 --------------------------------------------------------------------------------
 560
 561 --------------------------------------------------------------------------------
 562         Motif 4 in BLOCKS format
 563 --------------------------------------------------------------------------------
 564 BL   MOTIF 4 width=20 seqs=9
 565 WashU_Skud_Contig1682.4  (  296) TCAATAATGAAAAGCTAGGA  1
 566 MIT_Smik_c492_20940      (  301) TCAATAATGAAAAGCTAGGA  1
 567 MIT_Spar_c261_21317      (  296) TCAATAATGAAAAGCTAGGA  1
 568 SGD_Scer_YOR278W         (  292) TCAATAATGAAAAGCTAGGA  1
 569 MIT_Sbay_c896_21290      (  699) TCAACAAGGCAAGGCTATGC  1
 570 MIT_Spar_c130_3912       (  693) TCAACAGGGCAAGGCAAGGC  1
 571 WashU_Smik_Contig2283.3  (  701) TTAACAAGGGAAGGCAAGGC  1
 572 WashU_Sbay_Contig635.57  (  304) TCATTAAAGAAAAGCTAGGA  1
 573 SGD_Scer_YDR044W         (  701) ACAAAAGGGCAAGGCTATGC  1
 574 //
 575
 576 --------------------------------------------------------------------------------
 577
 578 --------------------------------------------------------------------------------
 579         Motif 4 position-specific scoring matrix
 580 --------------------------------------------------------------------------------
 581 log-odds matrix: alength= 4 w= 20 n= 7004 bayes= 9.60218 E= 1.4e-017
 582   -154   -982   -982    145
 583   -982    234   -982   -154
 584    162   -982   -982   -982
 585    145   -982   -982   -154
 586   -154     92   -982     78
 587    162   -982   -982   -982
 588    126   -982     34   -982
 589   -154   -982    134     45
 590   -982   -982    251   -982
 591     78     92    -66   -982
 592    162   -982   -982   -982
 593    162   -982   -982   -982
 594     78   -982    134   -982
 595   -982   -982    251   -982
 596   -982    251   -982   -982
 597    -55   -982   -982    126
 598    162   -982   -982   -982
 599   -982   -982    215    -55
 600   -982   -982    251   -982
 601     78    134   -982   -982
 602 --------------------------------------------------------------------------------
 603
 604 --------------------------------------------------------------------------------
 605         Motif 4 position-specific probability matrix
 606 --------------------------------------------------------------------------------
 607 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.4e-017
 608  0.111111  0.000000  0.000000  0.888889
 609  0.000000  0.888889  0.000000  0.111111
 610  1.000000  0.000000  0.000000  0.000000
 611  0.888889  0.000000  0.000000  0.111111
 612  0.111111  0.333333  0.000000  0.555556
 613  1.000000  0.000000  0.000000  0.000000
 614  0.777778  0.000000  0.222222  0.000000
 615  0.111111  0.000000  0.444444  0.444444
 616  0.000000  0.000000  1.000000  0.000000
 617  0.555556  0.333333  0.111111  0.000000
 618  1.000000  0.000000  0.000000  0.000000
 619  1.000000  0.000000  0.000000  0.000000
 620  0.555556  0.000000  0.444444  0.000000
 621  0.000000  0.000000  1.000000  0.000000
 622  0.000000  1.000000  0.000000  0.000000
 623  0.222222  0.000000  0.000000  0.777778
 624  1.000000  0.000000  0.000000  0.000000
 625  0.000000  0.000000  0.777778  0.222222
 626  0.000000  0.000000  1.000000  0.000000
 627  0.555556  0.444444  0.000000  0.000000
 628 --------------------------------------------------------------------------------
 629
 630 --------------------------------------------------------------------------------
 631         Motif 4 regular expression
 632 --------------------------------------------------------------------------------
 633 TCAA[TC]A[AG][GT]G[AC]AA[AG]GC[TA]A[GT]G[AC]
 634 --------------------------------------------------------------------------------
 635
 636
 637
 638
 639 Time 20.51 secs.
 640
 641 ********************************************************************************
 642
 643
 644 ********************************************************************************
 645 MOTIF  5        width =   20   sites =   9   llr = 178   E-value = 2.4e-015
 646 ********************************************************************************
 647 --------------------------------------------------------------------------------
 648         Motif 5 Description
 649 --------------------------------------------------------------------------------
 650 Simplified        A  61372:::::1:::aaa74:
 651 pos.-specific     C  4:::1a:6:9:::1::::::
 652 probability       G  :9137:a:6::7:9::::::
 653 matrix            T  ::6::::44193a::::36a
 654
 655          bits    2.5      **
 656                  2.3      **
 657                  2.0  *   **  *   *
 658                  1.8  *   **  *   *
 659 Information      1.5  *   **  *  *****  *
 660 content          1.3  *   **  * ******  *
 661 (28.5 bits)      1.0 ** **************  *
 662                  0.8 ** *****************
 663                  0.5 ** *****************
 664                  0.3 ********************
 665                  0.0 --------------------
 666
 667 Multilevel           AGTAGCGCGCTGTGAAAATT
 668 consensus            C AGA  TT  T     TA
 669 sequence
 670
 671 --------------------------------------------------------------------------------
 672
 673 --------------------------------------------------------------------------------
 674         Motif 5 sites sorted by position p-value
 675 --------------------------------------------------------------------------------
 676 Sequence name            Strand  Start   P-value                    Site
 677 -------------            ------  ----- ---------            --------------------
 678 MIT_Spar_c261_21317          +    517  7.89e-12 CGCCGCATCA AGAAGCGCGCTGTGAAAATT TTTCGTTTTT
 679 SGD_Scer_YOR278W             +    499  2.23e-11 CGCCGCACCA AGGAGCGCGCTGTGAAAATT TTTCGCTTTA
 680 WashU_Skud_Contig1682.4      +    512  4.09e-10 TCGCAGCGTC AGTGGCGCGTTGTGAAAAAT TTTCACTTTT
 681 MIT_Spar_c130_3912           +    283  4.88e-10 AAGGCGAAAG CGTAGCGTTCTTTGAAATTT GGATTCTGTT
 682 SGD_Scer_YDR044W             +    290  4.88e-10 AAGGCGAAAG CGTAGCGTTCTTTGAAATTT GGCTTCTGTT
 683 MIT_Sbay_c896_21290          +    289  5.32e-10 AATGCGAAAG CGTACCGTTCTGTGAAAAAT GGCTTCGGTT
 684 MIT_Smik_c492_20940          +    516  1.70e-09 CATTGTGATA AGAGACGCGCAGTGAAAAAT TTTCGCTTTT
 685 WashU_Sbay_Contig635.57      +    525  2.83e-09 TCATCGCGGA AAAGACGCGCTGTGAAAAAT TTTCTCTTTT
 686 WashU_Smik_Contig2283.3      +    284  3.02e-09 GAAAGAGTAG CGTAGCGTTCTTTCAAATTT TGGTTTCGGG
 687 --------------------------------------------------------------------------------
 688
 689 --------------------------------------------------------------------------------
 690         Motif 5 block diagrams
 691 --------------------------------------------------------------------------------
 692 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 693 -------------            ----------------  -------------
 694 MIT_Spar_c261_21317               7.9e-12  516_[+5]_99
 695 SGD_Scer_YOR278W                  2.2e-11  498_[+5]_117
 696 WashU_Skud_Contig1682.4           4.1e-10  511_[+5]_104
 697 MIT_Spar_c130_3912                4.9e-10  282_[+5]_698
 698 SGD_Scer_YDR044W                  4.9e-10  289_[+5]_691
 699 MIT_Sbay_c896_21290               5.3e-10  288_[+5]_692
 700 MIT_Smik_c492_20940               1.7e-09  515_[+5]_100
 701 WashU_Sbay_Contig635.57           2.8e-09  524_[+5]_91
 702 WashU_Smik_Contig2283.3             3e-09  283_[+5]_697
 703 --------------------------------------------------------------------------------
 704
 705 --------------------------------------------------------------------------------
 706         Motif 5 in BLOCKS format
 707 --------------------------------------------------------------------------------
 708 BL   MOTIF 5 width=20 seqs=9
 709 MIT_Spar_c261_21317      (  517) AGAAGCGCGCTGTGAAAATT  1
 710 SGD_Scer_YOR278W         (  499) AGGAGCGCGCTGTGAAAATT  1
 711 WashU_Skud_Contig1682.4  (  512) AGTGGCGCGTTGTGAAAAAT  1
 712 MIT_Spar_c130_3912       (  283) CGTAGCGTTCTTTGAAATTT  1
 713 SGD_Scer_YDR044W         (  290) CGTAGCGTTCTTTGAAATTT  1
 714 MIT_Sbay_c896_21290      (  289) CGTACCGTTCTGTGAAAAAT  1
 715 MIT_Smik_c492_20940      (  516) AGAGACGCGCAGTGAAAAAT  1
 716 WashU_Sbay_Contig635.57  (  525) AAAGACGCGCTGTGAAAAAT  1
 717 WashU_Smik_Contig2283.3  (  284) CGTAGCGTTCTTTCAAATTT  1
 718 //
 719
 720 --------------------------------------------------------------------------------
 721
 722 --------------------------------------------------------------------------------
 723         Motif 5 position-specific scoring matrix
 724 --------------------------------------------------------------------------------
 725 log-odds matrix: alength= 4 w= 20 n= 7004 bayes= 9.60218 E= 2.4e-015
 726     78    134   -982   -982
 727   -154   -982    234   -982
 728      4   -982    -66     78
 729    104   -982     92   -982
 730    -55    -66    192   -982
 731   -982    251   -982   -982
 732   -982   -982    251   -982
 733   -982    166   -982     45
 734   -982   -982    166     45
 735   -982    234   -982   -154
 736   -154   -982   -982    145
 737   -982   -982    192      4
 738   -982   -982   -982    162
 739   -982    -66    234   -982
 740    162   -982   -982   -982
 741    162   -982   -982   -982
 742    162   -982   -982   -982
 743    104   -982   -982      4
 744     45   -982   -982     78
 745   -982   -982   -982    162
 746 --------------------------------------------------------------------------------
 747
 748 --------------------------------------------------------------------------------
 749         Motif 5 position-specific probability matrix
 750 --------------------------------------------------------------------------------
 751 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.4e-015
 752  0.555556  0.444444  0.000000  0.000000
 753  0.111111  0.000000  0.888889  0.000000
 754  0.333333  0.000000  0.111111  0.555556
 755  0.666667  0.000000  0.333333  0.000000
 756  0.222222  0.111111  0.666667  0.000000
 757  0.000000  1.000000  0.000000  0.000000
 758  0.000000  0.000000  1.000000  0.000000
 759  0.000000  0.555556  0.000000  0.444444
 760  0.000000  0.000000  0.555556  0.444444
 761  0.000000  0.888889  0.000000  0.111111
 762  0.111111  0.000000  0.000000  0.888889
 763  0.000000  0.000000  0.666667  0.333333
 764  0.000000  0.000000  0.000000  1.000000
 765  0.000000  0.111111  0.888889  0.000000
 766  1.000000  0.000000  0.000000  0.000000
 767  1.000000  0.000000  0.000000  0.000000
 768  1.000000  0.000000  0.000000  0.000000
 769  0.666667  0.000000  0.000000  0.333333
 770  0.444444  0.000000  0.000000  0.555556
 771  0.000000  0.000000  0.000000  1.000000
 772 --------------------------------------------------------------------------------
 773
 774 --------------------------------------------------------------------------------
 775         Motif 5 regular expression
 776 --------------------------------------------------------------------------------
 777 [AC]G[TA][AG][GA]CG[CT][GT]CT[GT]TGAAA[AT][TA]T
 778 --------------------------------------------------------------------------------
 779
 780
 781
 782
 783 Time 25.34 secs.
 784
 785 ********************************************************************************
 786
 787
 788 ********************************************************************************
 789 SUMMARY OF MOTIFS
 790 ********************************************************************************
 791
 792 --------------------------------------------------------------------------------
 793         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 794 --------------------------------------------------------------------------------
 795 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 796 -------------            ----------------  -------------
 797 SGD_Scer_YOR278W                 1.58e-35  291_[+4(5.02e-11)]_15_[-2(1.95e-13)]_19_[+1(1.24e-12)]_4_[+3(5.77e-12)]_89_[+5(2.23e-11)]_117
 798 MIT_Spar_c261_21317              5.85e-36  260_[+4(4.80e-06)]_15_[+4(5.02e-11)]_14_[-2(1.95e-13)]_19_[+1(1.24e-12)]_4_[+3(5.77e-12)]_104_[+5(7.89e-12)]_99
 799 MIT_Smik_c492_20940              1.00e-33  265_[+4(4.99e-05)]_15_[+4(5.02e-11)]_15_[-2(1.95e-13)]_19_[+1(1.24e-12)]_4_[+3(5.77e-12)]_97_[+5(1.70e-09)]_16_[+1(5.40e-05)]_64
 800 WashU_Skud_Contig1682.4          2.57e-34  295_[+4(5.02e-11)]_15_[-2(1.95e-13)]_19_[+1(1.24e-12)]_4_[+3(5.77e-12)]_98_[+5(4.09e-10)]_104
 801 WashU_Sbay_Contig635.57          3.77e-32  303_[+4(1.34e-09)]_14_[-2(1.95e-13)]_19_[+1(1.24e-12)]_4_[+3(5.77e-12)]_104_[+5(2.83e-09)]_91
 802 SGD_Scer_YDR044W                 4.25e-24  106_[+4(5.44e-05)]_98_[+1(4.42e-10)]_10_[+2(1.92e-09)]_15_[+5(4.88e-10)]_391_[+4(2.68e-09)]_46_[+3(1.43e-10)]_142_[+5(4.10e-05)]_52
 803 MIT_Spar_c130_3912               5.41e-28  103_[+4(5.44e-05)]_93_[+1(1.16e-10)]_10_[+2(2.73e-10)]_16_[+5(4.88e-10)]_390_[+4(6.60e-11)]_50_[+3(1.18e-11)]_218
 804 MIT_Sbay_c896_21290              3.19e-24  222_[+1(8.28e-10)]_10_[+2(1.81e-10)]_16_[+5(5.32e-10)]_390_[+4(6.10e-11)]_62_[+3(2.40e-08)]_200
 805 WashU_Smik_Contig2283.3          7.85e-22  212_[+1(3.08e-10)]_10_[+2(2.62e-10)]_21_[+5(3.02e-09)]_55_[-3(1.26e-07)]_322_[+4(1.34e-09)]_280
 806 --------------------------------------------------------------------------------
 807
 808 ********************************************************************************
 809
 810
 811 ********************************************************************************
 812 Stopped because nmotifs = 5 reached.
 813 ********************************************************************************
 814
 815 CPU: dhn02990.mrc-dunn.cam.ac.uk
 816
 817 ********************************************************************************