t/data/map_hem/HEM13-HEM15.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= HEM13-HEM15.fa
  32 ALPHABET= ACGT
  33 Sequence name            Weight Length  Sequence name            Weight Length
  34 -------------            ------ ------  -------------            ------ ------
  35 SGD_Scer_YDR044W         1.0000   1000  MIT_Spar_c130_3912       1.0000   1000
  36 MIT_Sbay_c896_21290      1.0000   1000  WashU_Smik_Contig2283.3  1.0000   1000
  37 SGD_Scer_YOR176W         1.0000    727  MIT_Spar_c278_20970      1.0000    727
  38 MIT_Smik_c935_20455      1.0000    727  WashU_Skud_Contig2050.4  1.0000    727
  39 WashU_Sbay_Contig480.2   1.0000    727
  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 HEM13-HEM15.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=            7635    N=               9
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.304 C 0.196 G 0.196 T 0.304
  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 = 204   E-value = 7.1e-025
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  :9::4:::::1::::::7:1
  75 pos.-specific     C  ::4::::::4:::3:8:16:
  76 probability       G  a14a6:::a:9a4:::a2:9
  77 matrix            T  ::1::aaa:6::67a2::4:
  78
  79          bits    2.5 *  *    *  *    *
  80                  2.3 *  *    *  *    *
  81                  2.0 *  *    * **    *  *
  82                  1.8 *  *    * **    *  *
  83 Information      1.5 *  * **** **  ***  *
  84 content          1.3 ** * **** **  ***  *
  85 (32.6 bits)      1.0 ***************** **
  86                  0.8 ********************
  87                  0.5 ********************
  88                  0.3 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           GACGGTTTGTGGTTTCGACG
  92 consensus              G A    C  GC T GT
  93 sequence
  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_Skud_Contig2050.4      -    569  1.73e-12 CAATATTTTC GACGGTTTGTGGTTTCGACG CGCACTTTGA
 103 MIT_Spar_c278_20970          -    563  1.73e-12 CATTATTTTC GACGGTTTGTGGTTTCGACG CGCAATTCGA
 104 SGD_Scer_YOR176W             -    561  1.73e-12 CATTGTTTTC GACGGTTTGTGGTTTCGACG CGCAATGTGA
 105 WashU_Smik_Contig2283.3      +    624  1.50e-11 TGAACTTCTT GAGGATTTGCGGGTTCGGTG ATAAAAAATG
 106 MIT_Smik_c935_20455          -    547  2.58e-11 CATTATTTTC GACGGTTTGTGGTTTTGACG CGCAATTGGA
 107 WashU_Sbay_Contig480.2       -    574  3.01e-11 CGATATTTTT GATGGTTTGTGGTTTCGACG CGCACTTCGA
 108 SGD_Scer_YDR044W             +    623  6.31e-11 ACAAACTCCA GAGGATTTGCGGGCTTGATG ATAAAATGTA
 109 MIT_Spar_c130_3912           +    618  1.73e-10 CGAAACTCTA GAGGATTTGCAGGCTCGGTG ATAAAATGTA
 110 MIT_Sbay_c896_21290          +    622  5.29e-10 CGGAACTCTT GGGGATTTGCGGGCTCGCTA ATAAAAAGTG
 111 --------------------------------------------------------------------------------
 112
 113 --------------------------------------------------------------------------------
 114         Motif 1 block diagrams
 115 --------------------------------------------------------------------------------
 116 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 117 -------------            ----------------  -------------
 118 WashU_Skud_Contig2050.4           1.7e-12  568_[-1]_139
 119 MIT_Spar_c278_20970               1.7e-12  562_[-1]_145
 120 SGD_Scer_YOR176W                  1.7e-12  560_[-1]_147
 121 WashU_Smik_Contig2283.3           1.5e-11  623_[+1]_357
 122 MIT_Smik_c935_20455               2.6e-11  546_[-1]_161
 123 WashU_Sbay_Contig480.2              3e-11  573_[-1]_134
 124 SGD_Scer_YDR044W                  6.3e-11  622_[+1]_358
 125 MIT_Spar_c130_3912                1.7e-10  617_[+1]_363
 126 MIT_Sbay_c896_21290               5.3e-10  621_[+1]_359
 127 --------------------------------------------------------------------------------
 128
 129 --------------------------------------------------------------------------------
 130         Motif 1 in BLOCKS format
 131 --------------------------------------------------------------------------------
 132 BL   MOTIF 1 width=20 seqs=9
 133 WashU_Skud_Contig2050.4  (  569) GACGGTTTGTGGTTTCGACG  1
 134 MIT_Spar_c278_20970      (  563) GACGGTTTGTGGTTTCGACG  1
 135 SGD_Scer_YOR176W         (  561) GACGGTTTGTGGTTTCGACG  1
 136 WashU_Smik_Contig2283.3  (  624) GAGGATTTGCGGGTTCGGTG  1
 137 MIT_Smik_c935_20455      (  547) GACGGTTTGTGGTTTTGACG  1
 138 WashU_Sbay_Contig480.2   (  574) GATGGTTTGTGGTTTCGACG  1
 139 SGD_Scer_YDR044W         (  623) GAGGATTTGCGGGCTTGATG  1
 140 MIT_Spar_c130_3912       (  618) GAGGATTTGCAGGCTCGGTG  1
 141 MIT_Sbay_c896_21290      (  622) GGGGATTTGCGGGCTCGCTA  1
 142 //
 143
 144 --------------------------------------------------------------------------------
 145
 146 --------------------------------------------------------------------------------
 147         Motif 1 position-specific scoring matrix
 148 --------------------------------------------------------------------------------
 149 log-odds matrix: alength= 4 w= 20 n= 7464 bayes= 9.69407 E= 7.1e-025
 150   -982   -982    251   -982
 151    145   -982    -66   -982
 152   -982    134    134   -154
 153   -982   -982    251   -982
 154     45   -982    166   -982
 155   -982   -982   -982    162
 156   -982   -982   -982    162
 157   -982   -982   -982    162
 158   -982   -982    251   -982
 159   -982    134   -982     78
 160   -154   -982    234   -982
 161   -982   -982    251   -982
 162   -982   -982    134     78
 163   -982     92   -982    104
 164   -982   -982   -982    162
 165   -982    215   -982    -55
 166   -982   -982    251   -982
 167    104    -66     34   -982
 168   -982    166   -982     45
 169   -154   -982    234   -982
 170 --------------------------------------------------------------------------------
 171
 172 --------------------------------------------------------------------------------
 173         Motif 1 position-specific probability matrix
 174 --------------------------------------------------------------------------------
 175 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 7.1e-025
 176  0.000000  0.000000  1.000000  0.000000
 177  0.888889  0.000000  0.111111  0.000000
 178  0.000000  0.444444  0.444444  0.111111
 179  0.000000  0.000000  1.000000  0.000000
 180  0.444444  0.000000  0.555556  0.000000
 181  0.000000  0.000000  0.000000  1.000000
 182  0.000000  0.000000  0.000000  1.000000
 183  0.000000  0.000000  0.000000  1.000000
 184  0.000000  0.000000  1.000000  0.000000
 185  0.000000  0.444444  0.000000  0.555556
 186  0.111111  0.000000  0.888889  0.000000
 187  0.000000  0.000000  1.000000  0.000000
 188  0.000000  0.000000  0.444444  0.555556
 189  0.000000  0.333333  0.000000  0.666667
 190  0.000000  0.000000  0.000000  1.000000
 191  0.000000  0.777778  0.000000  0.222222
 192  0.000000  0.000000  1.000000  0.000000
 193  0.666667  0.111111  0.222222  0.000000
 194  0.000000  0.555556  0.000000  0.444444
 195  0.111111  0.000000  0.888889  0.000000
 196 --------------------------------------------------------------------------------
 197
 198 --------------------------------------------------------------------------------
 199         Motif 1 regular expression
 200 --------------------------------------------------------------------------------
 201 GA[CG]G[GA]TTTG[TC]GG[TG][TC]T[CT]G[AG][CT]G
 202 --------------------------------------------------------------------------------
 203
 204
 205
 206
 207 Time  5.96 secs.
 208
 209 ********************************************************************************
 210
 211
 212 ********************************************************************************
 213 MOTIF  2        width =   20   sites =   9   llr = 177   E-value = 5.1e-015
 214 ********************************************************************************
 215 --------------------------------------------------------------------------------
 216         Motif 2 Description
 217 --------------------------------------------------------------------------------
 218 Simplified        A  :::::39::::::3:1::::
 219 pos.-specific     C  8::1:1::9111::::9168
 220 probability       G  ::a:161a1:6::::4::::
 221 matrix            T  2a:99::::939a7a41942
 222
 223          bits    2.5   *    *
 224                  2.3   *    *
 225                  2.0   *    **       *
 226                  1.8   *    **       *
 227 Information      1.5 ***    **   * * *  *
 228 content          1.3 ***** **** ** * ** *
 229 (28.4 bits)      1.0 ***** **** ** * ****
 230                  0.8 *************** ****
 231                  0.5 ********************
 232                  0.3 ********************
 233                  0.0 --------------------
 234
 235 Multilevel           CTGTTGAGCTGTTTTGCTCC
 236 consensus            T    A    T  A T  TT
 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_Contig480.2       +    516  3.60e-13 TTTTGTTCTG CTGTTGAGCTGTTTTGCTCC ACCTGTTCAA
 247 MIT_Spar_c278_20970          +    506  2.05e-12 TTTTGCCCTG CTGTTGAGCTGTTTTGCTTC ACTGTTCAAC
 248 WashU_Skud_Contig2050.4      +    507  5.04e-11 TTTTGTTCTG CTGTTGAGCTGTTTTGTTCC ATCTGTTCAA
 249 SGD_Scer_YOR176W             +    504  5.04e-11 TTTTGTCCTG CTGTTGAGCTGTTTTGCTTT ACTGTTCAAC
 250 MIT_Smik_c935_20455          +    490  5.99e-11 TTTTGCTCTG CTGTTGAGCTGTTTTACTTC ATTGTTCAAC
 251 WashU_Smik_Contig2283.3      -     88  7.45e-10 ATTGTCTCAC CTGTTAAGCTTTTATTCCCC GTGTTTTCTT
 252 MIT_Spar_c130_3912           -     91  1.12e-09 TTGTCTTTCT TTGTTAAGCTTTTATTCTCC AGCTTTTTTT
 253 SGD_Scer_YDR044W             -     94  1.12e-09 TTGTCTTTCT TTGTTAAGCTTTTATTCTCC GGGTTTTCTT
 254 MIT_Sbay_c896_21290          -    335  3.38e-07 TTCACACAGG CTGCGCGGGCCCTTTTCTTT TTAAACGAGT
 255 --------------------------------------------------------------------------------
 256
 257 --------------------------------------------------------------------------------
 258         Motif 2 block diagrams
 259 --------------------------------------------------------------------------------
 260 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 261 -------------            ----------------  -------------
 262 WashU_Sbay_Contig480.2            3.6e-13  515_[+2]_192
 263 MIT_Spar_c278_20970                 2e-12  505_[+2]_202
 264 WashU_Skud_Contig2050.4             5e-11  506_[+2]_201
 265 SGD_Scer_YOR176W                    5e-11  503_[+2]_204
 266 MIT_Smik_c935_20455                 6e-11  489_[+2]_218
 267 WashU_Smik_Contig2283.3           7.5e-10  87_[-2]_893
 268 MIT_Spar_c130_3912                1.1e-09  90_[-2]_890
 269 SGD_Scer_YDR044W                  1.1e-09  93_[-2]_887
 270 MIT_Sbay_c896_21290               3.4e-07  334_[-2]_646
 271 --------------------------------------------------------------------------------
 272
 273 --------------------------------------------------------------------------------
 274         Motif 2 in BLOCKS format
 275 --------------------------------------------------------------------------------
 276 BL   MOTIF 2 width=20 seqs=9
 277 WashU_Sbay_Contig480.2   (  516) CTGTTGAGCTGTTTTGCTCC  1
 278 MIT_Spar_c278_20970      (  506) CTGTTGAGCTGTTTTGCTTC  1
 279 WashU_Skud_Contig2050.4  (  507) CTGTTGAGCTGTTTTGTTCC  1
 280 SGD_Scer_YOR176W         (  504) CTGTTGAGCTGTTTTGCTTT  1
 281 MIT_Smik_c935_20455      (  490) CTGTTGAGCTGTTTTACTTC  1
 282 WashU_Smik_Contig2283.3  (   88) CTGTTAAGCTTTTATTCCCC  1
 283 MIT_Spar_c130_3912       (   91) TTGTTAAGCTTTTATTCTCC  1
 284 SGD_Scer_YDR044W         (   94) TTGTTAAGCTTTTATTCTCC  1
 285 MIT_Sbay_c896_21290      (  335) CTGCGCGGGCCCTTTTCTTT  1
 286 //
 287
 288 --------------------------------------------------------------------------------
 289
 290 --------------------------------------------------------------------------------
 291         Motif 2 position-specific scoring matrix
 292 --------------------------------------------------------------------------------
 293 log-odds matrix: alength= 4 w= 20 n= 7464 bayes= 9.69407 E= 5.1e-015
 294   -982    215   -982    -55
 295   -982   -982   -982    162
 296   -982   -982    251   -982
 297   -982    -66   -982    145
 298   -982   -982    -66    145
 299      4    -66    166   -982
 300    145   -982    -66   -982
 301   -982   -982    251   -982
 302   -982    234    -66   -982
 303   -982    -66   -982    145
 304   -982    -66    166      4
 305   -982    -66   -982    145
 306   -982   -982   -982    162
 307      4   -982   -982    104
 308   -982   -982   -982    162
 309   -154   -982    134     45
 310   -982    234   -982   -154
 311   -982    -66   -982    145
 312   -982    166   -982     45
 313   -982    215   -982    -55
 314 --------------------------------------------------------------------------------
 315
 316 --------------------------------------------------------------------------------
 317         Motif 2 position-specific probability matrix
 318 --------------------------------------------------------------------------------
 319 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.1e-015
 320  0.000000  0.777778  0.000000  0.222222
 321  0.000000  0.000000  0.000000  1.000000
 322  0.000000  0.000000  1.000000  0.000000
 323  0.000000  0.111111  0.000000  0.888889
 324  0.000000  0.000000  0.111111  0.888889
 325  0.333333  0.111111  0.555556  0.000000
 326  0.888889  0.000000  0.111111  0.000000
 327  0.000000  0.000000  1.000000  0.000000
 328  0.000000  0.888889  0.111111  0.000000
 329  0.000000  0.111111  0.000000  0.888889
 330  0.000000  0.111111  0.555556  0.333333
 331  0.000000  0.111111  0.000000  0.888889
 332  0.000000  0.000000  0.000000  1.000000
 333  0.333333  0.000000  0.000000  0.666667
 334  0.000000  0.000000  0.000000  1.000000
 335  0.111111  0.000000  0.444444  0.444444
 336  0.000000  0.888889  0.000000  0.111111
 337  0.000000  0.111111  0.000000  0.888889
 338  0.000000  0.555556  0.000000  0.444444
 339  0.000000  0.777778  0.000000  0.222222
 340 --------------------------------------------------------------------------------
 341
 342 --------------------------------------------------------------------------------
 343         Motif 2 regular expression
 344 --------------------------------------------------------------------------------
 345 [CT]TGTT[GA]AGCT[GT]TT[TA]T[GT]CT[CT][CT]
 346 --------------------------------------------------------------------------------
 347
 348
 349
 350
 351 Time 11.78 secs.
 352
 353 ********************************************************************************
 354
 355
 356 ********************************************************************************
 357 MOTIF  3        width =   19   sites =   9   llr = 177   E-value = 3.0e-016
 358 ********************************************************************************
 359 --------------------------------------------------------------------------------
 360         Motif 3 Description
 361 --------------------------------------------------------------------------------
 362 Simplified        A  :::3:1:1::2::::1::3
 363 pos.-specific     C  1:a7::a:a:149:46167
 364 probability       G  :4:::::9:a:2:::::::
 365 matrix            T  96::a9::::731a6394:
 366
 367          bits    2.5   *   * **
 368                  2.3   *   * **
 369                  2.0   *   ****  *
 370                  1.8   *   ****  *
 371 Information      1.5   * * ****  **
 372 content          1.3 * *** ****  **  * *
 373 (28.4 bits)      1.0 **********  *** ***
 374                  0.8 ********** ********
 375                  0.5 *******************
 376                  0.3 *******************
 377                  0.0 -------------------
 378
 379 Multilevel           TTCCTTCGCGTCCTTCTCC
 380 consensus             G A      AT  CT TA
 381 sequence                        G
 382
 383 --------------------------------------------------------------------------------
 384
 385 --------------------------------------------------------------------------------
 386         Motif 3 sites sorted by position p-value
 387 --------------------------------------------------------------------------------
 388 Sequence name            Strand  Start   P-value                   Site
 389 -------------            ------  ----- ---------            -------------------
 390 MIT_Spar_c278_20970          +    156  5.34e-12 ACTAAAAGTA TTCCTTCGCGTCCTCCTTC TTCAATCCCA
 391 SGD_Scer_YOR176W             +    154  5.34e-12 ACCAAAAGTA TTCCTTCGCGTCCTCCTTC TTCAATCCCA
 392 WashU_Skud_Contig2050.4      +    160  9.86e-12 AAAAGAAGTA TTCCTTCGCGTGCTTCTCC TTTCTGTGTC
 393 MIT_Smik_c935_20455          +    151  6.97e-11 GACCAAAAGA CTCCTTCGCGTCCTCCTTC TTCAAGTCTC
 394 WashU_Smik_Contig2283.3      -    660  1.04e-09 CCGTAATTGT TGCATTCGCGTTCTTTTCA ACAATACATT
 395 MIT_Spar_c130_3912           -    652  1.04e-09 CCACAATCGT TGCATTCGCGTTCTTTTCA ACAATACATT
 396 SGD_Scer_YDR044W             -    657  2.59e-09 CCGTAATTGT TGCATTCGCGATCTTTTCA ACAATACATT
 397 WashU_Sbay_Contig480.2       +    204  3.78e-09 AAAAGAAGTA TTCCTACGCGAGCTCCCTC TTCAAGTGCC
 398 MIT_Sbay_c896_21290          -    440  1.61e-08 GTTCAGGGAG TGCCTTCACGCCTTTATCC CCTGGTATTC
 399 --------------------------------------------------------------------------------
 400
 401 --------------------------------------------------------------------------------
 402         Motif 3 block diagrams
 403 --------------------------------------------------------------------------------
 404 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 405 -------------            ----------------  -------------
 406 MIT_Spar_c278_20970               5.3e-12  155_[+3]_553
 407 SGD_Scer_YOR176W                  5.3e-12  153_[+3]_555
 408 WashU_Skud_Contig2050.4           9.9e-12  159_[+3]_549
 409 MIT_Smik_c935_20455                 7e-11  150_[+3]_558
 410 WashU_Smik_Contig2283.3             1e-09  659_[-3]_322
 411 MIT_Spar_c130_3912                  1e-09  651_[-3]_330
 412 SGD_Scer_YDR044W                  2.6e-09  656_[-3]_325
 413 WashU_Sbay_Contig480.2            3.8e-09  203_[+3]_505
 414 MIT_Sbay_c896_21290               1.6e-08  439_[-3]_542
 415 --------------------------------------------------------------------------------
 416
 417 --------------------------------------------------------------------------------
 418         Motif 3 in BLOCKS format
 419 --------------------------------------------------------------------------------
 420 BL   MOTIF 3 width=19 seqs=9
 421 MIT_Spar_c278_20970      (  156) TTCCTTCGCGTCCTCCTTC  1
 422 SGD_Scer_YOR176W         (  154) TTCCTTCGCGTCCTCCTTC  1
 423 WashU_Skud_Contig2050.4  (  160) TTCCTTCGCGTGCTTCTCC  1
 424 MIT_Smik_c935_20455      (  151) CTCCTTCGCGTCCTCCTTC  1
 425 WashU_Smik_Contig2283.3  (  660) TGCATTCGCGTTCTTTTCA  1
 426 MIT_Spar_c130_3912       (  652) TGCATTCGCGTTCTTTTCA  1
 427 SGD_Scer_YDR044W         (  657) TGCATTCGCGATCTTTTCA  1
 428 WashU_Sbay_Contig480.2   (  204) TTCCTACGCGAGCTCCCTC  1
 429 MIT_Sbay_c896_21290      (  440) TGCCTTCACGCCTTTATCC  1
 430 //
 431
 432 --------------------------------------------------------------------------------
 433
 434 --------------------------------------------------------------------------------
 435         Motif 3 position-specific scoring matrix
 436 --------------------------------------------------------------------------------
 437 log-odds matrix: alength= 4 w= 19 n= 7473 bayes= 9.69581 E= 3.0e-016
 438   -982    -66   -982    145
 439   -982   -982    134     78
 440   -982    251   -982   -982
 441      4    192   -982   -982
 442   -982   -982   -982    162
 443   -154   -982   -982    145
 444   -982    251   -982   -982
 445   -154   -982    234   -982
 446   -982    251   -982   -982
 447   -982   -982    251   -982
 448    -55    -66   -982    104
 449   -982    134     34      4
 450   -982    234   -982   -154
 451   -982   -982   -982    162
 452   -982    134   -982     78
 453   -154    166   -982      4
 454   -982    -66   -982    145
 455   -982    166   -982     45
 456      4    192   -982   -982
 457 --------------------------------------------------------------------------------
 458
 459 --------------------------------------------------------------------------------
 460         Motif 3 position-specific probability matrix
 461 --------------------------------------------------------------------------------
 462 letter-probability matrix: alength= 4 w= 19 nsites= 9 E= 3.0e-016
 463  0.000000  0.111111  0.000000  0.888889
 464  0.000000  0.000000  0.444444  0.555556
 465  0.000000  1.000000  0.000000  0.000000
 466  0.333333  0.666667  0.000000  0.000000
 467  0.000000  0.000000  0.000000  1.000000
 468  0.111111  0.000000  0.000000  0.888889
 469  0.000000  1.000000  0.000000  0.000000
 470  0.111111  0.000000  0.888889  0.000000
 471  0.000000  1.000000  0.000000  0.000000
 472  0.000000  0.000000  1.000000  0.000000
 473  0.222222  0.111111  0.000000  0.666667
 474  0.000000  0.444444  0.222222  0.333333
 475  0.000000  0.888889  0.000000  0.111111
 476  0.000000  0.000000  0.000000  1.000000
 477  0.000000  0.444444  0.000000  0.555556
 478  0.111111  0.555556  0.000000  0.333333
 479  0.000000  0.111111  0.000000  0.888889
 480  0.000000  0.555556  0.000000  0.444444
 481  0.333333  0.666667  0.000000  0.000000
 482 --------------------------------------------------------------------------------
 483
 484 --------------------------------------------------------------------------------
 485         Motif 3 regular expression
 486 --------------------------------------------------------------------------------
 487 T[TG]C[CA]TTCGCG[TA][CTG]CT[TC][CT]T[CT][CA]
 488 --------------------------------------------------------------------------------
 489
 490
 491
 492
 493 Time 17.43 secs.
 494
 495 ********************************************************************************
 496
 497
 498 ********************************************************************************
 499 MOTIF  4        width =   20   sites =   9   llr = 171   E-value = 3.0e-012
 500 ********************************************************************************
 501 --------------------------------------------------------------------------------
 502         Motif 4 Description
 503 --------------------------------------------------------------------------------
 504 Simplified        A  1a6aa:a8::32:a44:7aa
 505 pos.-specific     C  :::::6::1::19::6:3::
 506 probability       G  9:4::::::a71::::1:::
 507 matrix            T  :::::4:29::61:6:9:::
 508
 509          bits    2.5          *
 510                  2.3          *
 511                  2.0 *        *  *
 512                  1.8 *        *  *
 513 Information      1.5 ** ** *  *  **    **
 514 content          1.3 ** ** * *** **  * **
 515 (27.4 bits)      1.0 ******* *** ** *****
 516                  0.8 *********** ********
 517                  0.5 *********** ********
 518                  0.3 ********************
 519                  0.0 --------------------
 520
 521 Multilevel           GAAAACAATGGTCATCTAAA
 522 consensus              G  T T  AA  AA C
 523 sequence
 524
 525 --------------------------------------------------------------------------------
 526
 527 --------------------------------------------------------------------------------
 528         Motif 4 sites sorted by position p-value
 529 --------------------------------------------------------------------------------
 530 Sequence name            Strand  Start   P-value                    Site
 531 -------------            ------  ----- ---------            --------------------
 532 SGD_Scer_YOR176W             +    581  1.12e-11 ACAAACCGTC GAAAACAATGGTCATCTAAA TAAAGGGTTC
 533 WashU_Smik_Contig2283.3      +    166  4.85e-11 TTTTCAAAAA GAGAACAATGGTCAAATAAA GGTTTATCTA
 534 MIT_Spar_c278_20970          +    583  8.09e-11 ACAAACCGTC GAAAATAATGGTCATCTAAA TAAAGGGTTC
 535 MIT_Spar_c130_3912           +    170  3.22e-10 TTTTCGAAAC GAGAACAATGGACAAATCAA GCTTTATCTA
 536 MIT_Smik_c935_20455          +    567  6.16e-10 ACAAACCGTC GAAAATAATGATCATCTAAA TAAAAGAGTT
 537 SGD_Scer_YDR044W             +    174  1.95e-09 CTTTCGAAAC GAGAACAATGGGCAAAGCAA GCTTTATCTT
 538 WashU_Skud_Contig2050.4      +    589  2.29e-09 ACAAACCGTC GAAAATATTGATCATCTAAA TAAAGGGTTC
 539 MIT_Sbay_c896_21290          +    176  4.95e-09 TTCTCGAAGG GAGAACAATGGATAAATCAA AGCTTATCTA
 540 WashU_Sbay_Contig480.2       +    594  3.59e-08 ACAAACCATC AAAAATATCGACCATCTAAA TAAAGGGTTC
 541 --------------------------------------------------------------------------------
 542
 543 --------------------------------------------------------------------------------
 544         Motif 4 block diagrams
 545 --------------------------------------------------------------------------------
 546 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 547 -------------            ----------------  -------------
 548 SGD_Scer_YOR176W                  1.1e-11  580_[+4]_127
 549 WashU_Smik_Contig2283.3           4.8e-11  165_[+4]_815
 550 MIT_Spar_c278_20970               8.1e-11  582_[+4]_125
 551 MIT_Spar_c130_3912                3.2e-10  169_[+4]_811
 552 MIT_Smik_c935_20455               6.2e-10  566_[+4]_141
 553 SGD_Scer_YDR044W                    2e-09  173_[+4]_807
 554 WashU_Skud_Contig2050.4           2.3e-09  588_[+4]_119
 555 MIT_Sbay_c896_21290                 5e-09  175_[+4]_805
 556 WashU_Sbay_Contig480.2            3.6e-08  593_[+4]_114
 557 --------------------------------------------------------------------------------
 558
 559 --------------------------------------------------------------------------------
 560         Motif 4 in BLOCKS format
 561 --------------------------------------------------------------------------------
 562 BL   MOTIF 4 width=20 seqs=9
 563 SGD_Scer_YOR176W         (  581) GAAAACAATGGTCATCTAAA  1
 564 WashU_Smik_Contig2283.3  (  166) GAGAACAATGGTCAAATAAA  1
 565 MIT_Spar_c278_20970      (  583) GAAAATAATGGTCATCTAAA  1
 566 MIT_Spar_c130_3912       (  170) GAGAACAATGGACAAATCAA  1
 567 MIT_Smik_c935_20455      (  567) GAAAATAATGATCATCTAAA  1
 568 SGD_Scer_YDR044W         (  174) GAGAACAATGGGCAAAGCAA  1
 569 WashU_Skud_Contig2050.4  (  589) GAAAATATTGATCATCTAAA  1
 570 MIT_Sbay_c896_21290      (  176) GAGAACAATGGATAAATCAA  1
 571 WashU_Sbay_Contig480.2   (  594) AAAAATATCGACCATCTAAA  1
 572 //
 573
 574 --------------------------------------------------------------------------------
 575
 576 --------------------------------------------------------------------------------
 577         Motif 4 position-specific scoring matrix
 578 --------------------------------------------------------------------------------
 579 log-odds matrix: alength= 4 w= 20 n= 7464 bayes= 9.69407 E= 3.0e-012
 580   -154   -982    234   -982
 581    162   -982   -982   -982
 582     78   -982    134   -982
 583    162   -982   -982   -982
 584    162   -982   -982   -982
 585   -982    166   -982     45
 586    162   -982   -982   -982
 587    126   -982   -982    -55
 588   -982    -66   -982    145
 589   -982   -982    251   -982
 590      4   -982    192   -982
 591    -55    -66    -66     78
 592   -982    234   -982   -154
 593    162   -982   -982   -982
 594     45   -982   -982     78
 595     45    166   -982   -982
 596   -982   -982    -66    145
 597    104     92   -982   -982
 598    162   -982   -982   -982
 599    162   -982   -982   -982
 600 --------------------------------------------------------------------------------
 601
 602 --------------------------------------------------------------------------------
 603         Motif 4 position-specific probability matrix
 604 --------------------------------------------------------------------------------
 605 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.0e-012
 606  0.111111  0.000000  0.888889  0.000000
 607  1.000000  0.000000  0.000000  0.000000
 608  0.555556  0.000000  0.444444  0.000000
 609  1.000000  0.000000  0.000000  0.000000
 610  1.000000  0.000000  0.000000  0.000000
 611  0.000000  0.555556  0.000000  0.444444
 612  1.000000  0.000000  0.000000  0.000000
 613  0.777778  0.000000  0.000000  0.222222
 614  0.000000  0.111111  0.000000  0.888889
 615  0.000000  0.000000  1.000000  0.000000
 616  0.333333  0.000000  0.666667  0.000000
 617  0.222222  0.111111  0.111111  0.555556
 618  0.000000  0.888889  0.000000  0.111111
 619  1.000000  0.000000  0.000000  0.000000
 620  0.444444  0.000000  0.000000  0.555556
 621  0.444444  0.555556  0.000000  0.000000
 622  0.000000  0.000000  0.111111  0.888889
 623  0.666667  0.333333  0.000000  0.000000
 624  1.000000  0.000000  0.000000  0.000000
 625  1.000000  0.000000  0.000000  0.000000
 626 --------------------------------------------------------------------------------
 627
 628 --------------------------------------------------------------------------------
 629         Motif 4 regular expression
 630 --------------------------------------------------------------------------------
 631 GA[AG]AA[CT]A[AT]TG[GA][TA]CA[TA][CA]T[AC]AA
 632 --------------------------------------------------------------------------------
 633
 634
 635
 636
 637 Time 23.00 secs.
 638
 639 ********************************************************************************
 640
 641
 642 ********************************************************************************
 643 MOTIF  5        width =   15   sites =   9   llr = 147   E-value = 3.6e-010
 644 ********************************************************************************
 645 --------------------------------------------------------------------------------
 646         Motif 5 Description
 647 --------------------------------------------------------------------------------
 648 Simplified        A  1:::4:::a::aa69
 649 pos.-specific     C  8::4:9a4:a9::::
 650 probability       G  1::61::6:::::::
 651 matrix            T  :aa:41::::1::41
 652
 653          bits    2.5       *  *
 654                  2.3       *  *
 655                  2.0      **  **
 656                  1.8      **  **
 657 Information      1.5 **** ********
 658 content          1.3 **** ********
 659 (23.5 bits)      1.0 **** ******** *
 660                  0.8 **** **********
 661                  0.5 **** **********
 662                  0.3 ***************
 663                  0.0 ---------------
 664
 665 Multilevel           CTTGACCGACCAAAA
 666 consensus               CT  C     T
 667 sequence
 668
 669 --------------------------------------------------------------------------------
 670
 671 --------------------------------------------------------------------------------
 672         Motif 5 sites sorted by position p-value
 673 --------------------------------------------------------------------------------
 674 Sequence name            Strand  Start   P-value                 Site
 675 -------------            ------  ----- ---------            ---------------
 676 WashU_Sbay_Contig480.2       +    183  1.26e-09 CCATAATGCT CTTGACCGACCAAAA GAAGTATTCC
 677 SGD_Scer_YOR176W             +    136  1.26e-09 CAAGAGTGAC CTTGACCGACCAAAA GTATTCCTTC
 678 MIT_Spar_c130_3912           -    252  1.01e-08 CCTTTTCTGG CTTCTCCCACCAATA ATGCCCCAGC
 679 MIT_Smik_c935_20455          +    134  1.04e-08 CAACAGTGAT CTTGGCCGACCAAAA GACTCCTTCG
 680 WashU_Skud_Contig2050.4      +    139  3.41e-08 CAACAATGAT ATTGACCGACCAAAA GAAGTATTCC
 681 SGD_Scer_YDR044W             -    260  3.41e-08 GCCTTTTCTG GTTCTCCCACCAATA ACGCTCCAGC
 682 MIT_Sbay_c896_21290          -    258  3.54e-08 CATTTTCTGG CTTCTCCCACCAATT ATGCCCCAGC
 683 MIT_Spar_c278_20970          +    138  4.50e-08 CAAGAGTGAC CTTGACCGACTAAAA GTATTCCTTC
 684 WashU_Smik_Contig2283.3      -    248  9.48e-08 TCTTTTCTGG CTTCTTCCACCAATA ATGCCCCAGC
 685 --------------------------------------------------------------------------------
 686
 687 --------------------------------------------------------------------------------
 688         Motif 5 block diagrams
 689 --------------------------------------------------------------------------------
 690 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 691 -------------            ----------------  -------------
 692 WashU_Sbay_Contig480.2            1.3e-09  182_[+5]_530
 693 SGD_Scer_YOR176W                  1.3e-09  135_[+5]_577
 694 MIT_Spar_c130_3912                  1e-08  251_[-5]_734
 695 MIT_Smik_c935_20455                 1e-08  133_[+5]_579
 696 WashU_Skud_Contig2050.4           3.4e-08  138_[+5]_574
 697 SGD_Scer_YDR044W                  3.4e-08  259_[-5]_726
 698 MIT_Sbay_c896_21290               3.5e-08  257_[-5]_728
 699 MIT_Spar_c278_20970               4.5e-08  137_[+5]_575
 700 WashU_Smik_Contig2283.3           9.5e-08  247_[-5]_738
 701 --------------------------------------------------------------------------------
 702
 703 --------------------------------------------------------------------------------
 704         Motif 5 in BLOCKS format
 705 --------------------------------------------------------------------------------
 706 BL   MOTIF 5 width=15 seqs=9
 707 WashU_Sbay_Contig480.2   (  183) CTTGACCGACCAAAA  1
 708 SGD_Scer_YOR176W         (  136) CTTGACCGACCAAAA  1
 709 MIT_Spar_c130_3912       (  252) CTTCTCCCACCAATA  1
 710 MIT_Smik_c935_20455      (  134) CTTGGCCGACCAAAA  1
 711 WashU_Skud_Contig2050.4  (  139) ATTGACCGACCAAAA  1
 712 SGD_Scer_YDR044W         (  260) GTTCTCCCACCAATA  1
 713 MIT_Sbay_c896_21290      (  258) CTTCTCCCACCAATT  1
 714 MIT_Spar_c278_20970      (  138) CTTGACCGACTAAAA  1
 715 WashU_Smik_Contig2283.3  (  248) CTTCTTCCACCAATA  1
 716 //
 717
 718 --------------------------------------------------------------------------------
 719
 720 --------------------------------------------------------------------------------
 721         Motif 5 position-specific scoring matrix
 722 --------------------------------------------------------------------------------
 723 log-odds matrix: alength= 4 w= 15 n= 7509 bayes= 9.70275 E= 3.6e-010
 724   -154    215    -66   -982
 725   -982   -982   -982    162
 726   -982   -982   -982    162
 727   -982    134    166   -982
 728     45   -982    -66     45
 729   -982    234   -982   -154
 730   -982    251   -982   -982
 731   -982    134    166   -982
 732    162   -982   -982   -982
 733   -982    251   -982   -982
 734   -982    234   -982   -154
 735    162   -982   -982   -982
 736    162   -982   -982   -982
 737     78   -982   -982     45
 738    145   -982   -982   -154
 739 --------------------------------------------------------------------------------
 740
 741 --------------------------------------------------------------------------------
 742         Motif 5 position-specific probability matrix
 743 --------------------------------------------------------------------------------
 744 letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 3.6e-010
 745  0.111111  0.777778  0.111111  0.000000
 746  0.000000  0.000000  0.000000  1.000000
 747  0.000000  0.000000  0.000000  1.000000
 748  0.000000  0.444444  0.555556  0.000000
 749  0.444444  0.000000  0.111111  0.444444
 750  0.000000  0.888889  0.000000  0.111111
 751  0.000000  1.000000  0.000000  0.000000
 752  0.000000  0.444444  0.555556  0.000000
 753  1.000000  0.000000  0.000000  0.000000
 754  0.000000  1.000000  0.000000  0.000000
 755  0.000000  0.888889  0.000000  0.111111
 756  1.000000  0.000000  0.000000  0.000000
 757  1.000000  0.000000  0.000000  0.000000
 758  0.555556  0.000000  0.000000  0.444444
 759  0.888889  0.000000  0.000000  0.111111
 760 --------------------------------------------------------------------------------
 761
 762 --------------------------------------------------------------------------------
 763         Motif 5 regular expression
 764 --------------------------------------------------------------------------------
 765 CTT[GC][AT]CC[GC]ACCAA[AT]A
 766 --------------------------------------------------------------------------------
 767
 768
 769
 770
 771 Time 28.58 secs.
 772
 773 ********************************************************************************
 774
 775
 776 ********************************************************************************
 777 SUMMARY OF MOTIFS
 778 ********************************************************************************
 779
 780 --------------------------------------------------------------------------------
 781         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 782 --------------------------------------------------------------------------------
 783 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 784 -------------            ----------------  -------------
 785 SGD_Scer_YDR044W                 2.52e-22  93_[-2(1.12e-09)]_60_[+4(1.95e-09)]_66_[-5(3.41e-08)]_165_[-3(5.96e-05)]_164_[+1(6.31e-11)]_14_[-3(2.59e-09)]_325
 786 MIT_Spar_c130_3912               1.62e-23  90_[-2(1.12e-09)]_59_[+4(3.22e-10)]_62_[-5(1.01e-08)]_61_[-2(1.77e-05)]_85_[-3(5.96e-05)]_166_[+1(1.73e-10)]_14_[-3(1.04e-09)]_330
 787 MIT_Sbay_c896_21290              5.08e-18  94_[-2(2.30e-05)]_61_[+4(4.95e-09)]_62_[-5(3.54e-08)]_62_[-2(3.38e-07)]_31_[-3(3.05e-05)]_35_[-3(1.61e-08)]_163_[+1(5.29e-10)]_82_[-2(1.56e-05)]_257
 788 WashU_Smik_Contig2283.3          1.53e-24  7_[+1(1.86e-05)]_60_[-2(7.45e-10)]_58_[+4(4.85e-11)]_62_[-5(9.48e-08)]_336_[-3(6.30e-05)]_6_[+1(1.50e-11)]_16_[-3(1.04e-09)]_204_[-3(4.16e-06)]_99
 789 SGD_Scer_YOR176W                 9.09e-32  135_[+5(1.26e-09)]_3_[+3(5.34e-12)]_20_[-2(9.24e-05)]_269_[+2(2.71e-05)]_2_[+2(5.04e-11)]_37_[-1(1.73e-12)]_[+4(1.12e-11)]_55_[-1(7.71e-05)]_52
 790 MIT_Spar_c278_20970              8.55e-31  137_[+5(4.50e-08)]_3_[+3(5.34e-12)]_309_[+2(4.04e-05)]_2_[+2(2.05e-12)]_37_[-1(1.73e-12)]_[+4(8.09e-11)]_125
 791 MIT_Smik_c935_20455              5.42e-27  133_[+5(1.04e-08)]_2_[+3(6.97e-11)]_298_[+2(5.34e-05)]_2_[+2(5.99e-11)]_37_[-1(2.58e-11)]_[+4(6.16e-10)]_141
 792 WashU_Skud_Contig2050.4          5.92e-28  138_[+5(3.41e-08)]_6_[+3(9.86e-12)]_305_[+2(1.26e-05)]_3_[+2(5.04e-11)]_6_[-2(3.42e-05)]_16_[-1(1.73e-12)]_[+4(2.29e-09)]_119
 793 WashU_Sbay_Contig480.2           1.38e-26  182_[+5(1.26e-09)]_6_[+3(3.78e-09)]_270_[+2(7.91e-05)]_3_[+2(3.60e-13)]_38_[-1(3.01e-11)]_[+4(3.59e-08)]_114
 794 --------------------------------------------------------------------------------
 795
 796 ********************************************************************************
 797
 798
 799 ********************************************************************************
 800 Stopped because nmotifs = 5 reached.
 801 ********************************************************************************
 802
 803 CPU: dhn02990.mrc-dunn.cam.ac.uk
 804
 805 ********************************************************************************