t/data/map_hem/HEM3-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= HEM3-HEM15.fa
  32 ALPHABET= ACGT
  33 Sequence name            Weight Length  Sequence name            Weight Length
  34 -------------            ------ ------  -------------            ------ ------
  35 SGD_Scer_YDL205C         1.0000    860  MIT_Spar_c429_3020       1.0000    860
  36 MIT_Smik_c193_2483       1.0000    860  MIT_Sbay_c841_3215       1.0000    860
  37 WashU_Skud_Contig1850.5  1.0000    860  SGD_Scer_YOR176W         1.0000    727
  38 MIT_Spar_c278_20970      1.0000    727  MIT_Smik_c935_20455      1.0000    727
  39 WashU_Skud_Contig2050.4  1.0000    727  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 HEM3-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=       10    maxsites=       10    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=            7935    N=              10
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.308 C 0.192 G 0.192 T 0.308
  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 =   19   sites =  10   llr = 215   E-value = 3.6e-028
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  1:aa6a:a::::55:a::a
  75 pos.-specific     C  16::::a::a5a::5:5a:
  76 probability       G  8:::::::a::::5::5::
  77 matrix            T  :4::4:::::5:5:5::::
  78
  79          bits    2.5       * ** *     *
  80                  2.3       * ** *     *
  81                  2.0       * ** *     *
  82                  1.8       * ** *     *
  83 Information      1.5 * ** ***** *   ****
  84 content          1.3 **** ***** *   ****
  85 (31.0 bits)      1.0 **** ******* ******
  86                  0.8 ************ ******
  87                  0.5 *******************
  88                  0.3 *******************
  89                  0.0 -------------------
  90
  91 Multilevel           GCAAAACAGCCCAACACCA
  92 consensus             T  T     T TGT G
  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_Contig1850.5      +    110  3.58e-11 TTTTCAAAAA GCAATACAGCCCTGTACCA TTCAAACACG
 103 MIT_Sbay_c841_3215           +    111  3.58e-11 TATTCAAAAC GCAATACAGCCCTGTACCA TTCAAATACG
 104 WashU_Sbay_Contig480.2       -    514  6.04e-11 AACAGGTGGA GCAAAACAGCTCAACAGCA GAACAAAAAA
 105 MIT_Spar_c278_20970          -    504  6.04e-11 GAACAGTGAA GCAAAACAGCTCAACAGCA GGGCAAAAAA
 106 SGD_Scer_YOR176W             -    502  6.04e-11 GAACAGTAAA GCAAAACAGCTCAACAGCA GGACAAAAAA
 107 MIT_Spar_c429_3020           +    110  1.14e-10 TATTCAAAAT GTAAAACAGCCCTGTACCA TGCAAACACG
 108 MIT_Smik_c193_2483           +    112  1.56e-10 TATTCAAAAA GTAATACAGCCCTGTACCA TTCAAACACG
 109 MIT_Smik_c935_20455          -    488  2.17e-10 GAACAATGAA GTAAAACAGCTCAACAGCA GAGCAAAAAA
 110 WashU_Skud_Contig2050.4      -    505  5.56e-10 AACAGATGGA ACAAAACAGCTCAACAGCA GAACAAAAAA
 111 SGD_Scer_YDL205C             +    110  5.89e-10 TATTCAAAAT CTAATACAGCCCTGTACCA TGCAAACACG
 112 --------------------------------------------------------------------------------
 113
 114 --------------------------------------------------------------------------------
 115         Motif 1 block diagrams
 116 --------------------------------------------------------------------------------
 117 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 118 -------------            ----------------  -------------
 119 WashU_Skud_Contig1850.5           3.6e-11  109_[+1]_732
 120 MIT_Sbay_c841_3215                3.6e-11  110_[+1]_731
 121 WashU_Sbay_Contig480.2              6e-11  513_[-1]_195
 122 MIT_Spar_c278_20970                 6e-11  503_[-1]_205
 123 SGD_Scer_YOR176W                    6e-11  501_[-1]_207
 124 MIT_Spar_c429_3020                1.1e-10  109_[+1]_732
 125 MIT_Smik_c193_2483                1.6e-10  111_[+1]_730
 126 MIT_Smik_c935_20455               2.2e-10  487_[-1]_221
 127 WashU_Skud_Contig2050.4           5.6e-10  504_[-1]_204
 128 SGD_Scer_YDL205C                  5.9e-10  109_[+1]_732
 129 --------------------------------------------------------------------------------
 130
 131 --------------------------------------------------------------------------------
 132         Motif 1 in BLOCKS format
 133 --------------------------------------------------------------------------------
 134 BL   MOTIF 1 width=19 seqs=10
 135 WashU_Skud_Contig1850.5  (  110) GCAATACAGCCCTGTACCA  1
 136 MIT_Sbay_c841_3215       (  111) GCAATACAGCCCTGTACCA  1
 137 WashU_Sbay_Contig480.2   (  514) GCAAAACAGCTCAACAGCA  1
 138 MIT_Spar_c278_20970      (  504) GCAAAACAGCTCAACAGCA  1
 139 SGD_Scer_YOR176W         (  502) GCAAAACAGCTCAACAGCA  1
 140 MIT_Spar_c429_3020       (  110) GTAAAACAGCCCTGTACCA  1
 141 MIT_Smik_c193_2483       (  112) GTAATACAGCCCTGTACCA  1
 142 MIT_Smik_c935_20455      (  488) GTAAAACAGCTCAACAGCA  1
 143 WashU_Skud_Contig2050.4  (  505) ACAAAACAGCTCAACAGCA  1
 144 SGD_Scer_YDL205C         (  110) CTAATACAGCCCTGTACCA  1
 145 //
 146
 147 --------------------------------------------------------------------------------
 148
 149 --------------------------------------------------------------------------------
 150         Motif 1 position-specific scoring matrix
 151 --------------------------------------------------------------------------------
 152 log-odds matrix: alength= 4 w= 19 n= 7755 bayes= 9.59712 E= 3.6e-028
 153   -169    -81    219   -997
 154   -997    177   -997     30
 155    162   -997   -997   -997
 156    162   -997   -997   -997
 157     89   -997   -997     30
 158    162   -997   -997   -997
 159   -997    251   -997   -997
 160    162   -997   -997   -997
 161   -997   -997    251   -997
 162   -997    251   -997   -997
 163   -997    151   -997     62
 164   -997    251   -997   -997
 165     62   -997   -997     62
 166     62   -997    151   -997
 167   -997    151   -997     62
 168    162   -997   -997   -997
 169   -997    151    151   -997
 170   -997    251   -997   -997
 171    162   -997   -997   -997
 172 --------------------------------------------------------------------------------
 173
 174 --------------------------------------------------------------------------------
 175         Motif 1 position-specific probability matrix
 176 --------------------------------------------------------------------------------
 177 letter-probability matrix: alength= 4 w= 19 nsites= 10 E= 3.6e-028
 178  0.100000  0.100000  0.800000  0.000000
 179  0.000000  0.600000  0.000000  0.400000
 180  1.000000  0.000000  0.000000  0.000000
 181  1.000000  0.000000  0.000000  0.000000
 182  0.600000  0.000000  0.000000  0.400000
 183  1.000000  0.000000  0.000000  0.000000
 184  0.000000  1.000000  0.000000  0.000000
 185  1.000000  0.000000  0.000000  0.000000
 186  0.000000  0.000000  1.000000  0.000000
 187  0.000000  1.000000  0.000000  0.000000
 188  0.000000  0.500000  0.000000  0.500000
 189  0.000000  1.000000  0.000000  0.000000
 190  0.500000  0.000000  0.000000  0.500000
 191  0.500000  0.000000  0.500000  0.000000
 192  0.000000  0.500000  0.000000  0.500000
 193  1.000000  0.000000  0.000000  0.000000
 194  0.000000  0.500000  0.500000  0.000000
 195  0.000000  1.000000  0.000000  0.000000
 196  1.000000  0.000000  0.000000  0.000000
 197 --------------------------------------------------------------------------------
 198
 199 --------------------------------------------------------------------------------
 200         Motif 1 regular expression
 201 --------------------------------------------------------------------------------
 202 G[CT]AA[AT]ACAGC[CT]C[AT][AG][CT]A[CG]CA
 203 --------------------------------------------------------------------------------
 204
 205
 206
 207
 208 Time  6.58 secs.
 209
 210 ********************************************************************************
 211
 212
 213 ********************************************************************************
 214 MOTIF  2        width =   20   sites =  10   llr = 204   E-value = 3.8e-022
 215 ********************************************************************************
 216 --------------------------------------------------------------------------------
 217         Motif 2 Description
 218 --------------------------------------------------------------------------------
 219 Simplified        A  :::::3::3a5a5:a:a78:
 220 pos.-specific     C  ::6:62:a::::55:a:::6
 221 probability       G  :a:a:55:7::::::::31:
 222 matrix            T  a:4:4:5:::5::5::::14
 223
 224          bits    2.5  * *   *       *
 225                  2.3  * *   *       *
 226                  2.0  * *   *       *
 227                  1.8  * *   *       *
 228 Information      1.5 ** *   * * *  ***
 229 content          1.3 *****  *** *  ***  *
 230 (29.5 bits)      1.0 ***** **** ******* *
 231                  0.8 ********** *********
 232                  0.5 ********************
 233                  0.3 ********************
 234                  0.0 --------------------
 235
 236 Multilevel           TGCGCGGCGAAAACACAAAC
 237 consensus              T TAT A T CT   G T
 238 sequence                  C
 239
 240 --------------------------------------------------------------------------------
 241
 242 --------------------------------------------------------------------------------
 243         Motif 2 sites sorted by position p-value
 244 --------------------------------------------------------------------------------
 245 Sequence name            Strand  Start   P-value                    Site
 246 -------------            ------  ----- ---------            --------------------
 247 WashU_Sbay_Contig480.2       +    570  1.49e-12 TCTTTCGAAG TGCGCGTCGAAACCACAAAC CATCAAAAAT
 248 WashU_Skud_Contig2050.4      +    565  1.49e-12 TCTTTCAAAG TGCGCGTCGAAACCACAAAC CGTCGAAAAT
 249 MIT_Spar_c278_20970          +    559  1.49e-12 TCTTTCGAAT TGCGCGTCGAAACCACAAAC CGTCGAAAAT
 250 SGD_Scer_YOR176W             +    557  1.49e-12 TCTTTCACAT TGCGCGTCGAAACCACAAAC CGTCGAAAAC
 251 MIT_Smik_c935_20455          +    543  3.24e-11 TCTCTCCAAT TGCGCGTCAAAACCACAAAC CGTCGAAAAT
 252 MIT_Smik_c193_2483           +    176  9.12e-10 AATCCAGCTA TGCGTAGCGATAATACAGAT GATTGTTTGA
 253 MIT_Sbay_c841_3215           +    175  1.46e-09 AATCAAGTTA TGTGCCGCGATAATACAATC TTTTGGCCTA
 254 WashU_Skud_Contig1850.5      +    173  3.07e-09 AATCAATCTA TGTGTCGCGATAATACAAGT GATTGATTGG
 255 MIT_Spar_c429_3020           +    174  3.52e-09 ATCCAAGCTA TGTGTAGCAATAATACAGAT GATTGATTGG
 256 SGD_Scer_YDL205C             +    174  3.52e-09 ATTCAGGCTA TGTGTAGCAATAATACAGAT AGTTAGTAGC
 257 --------------------------------------------------------------------------------
 258
 259 --------------------------------------------------------------------------------
 260         Motif 2 block diagrams
 261 --------------------------------------------------------------------------------
 262 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 263 -------------            ----------------  -------------
 264 WashU_Sbay_Contig480.2            1.5e-12  569_[+2]_138
 265 WashU_Skud_Contig2050.4           1.5e-12  564_[+2]_143
 266 MIT_Spar_c278_20970               1.5e-12  558_[+2]_149
 267 SGD_Scer_YOR176W                  1.5e-12  556_[+2]_151
 268 MIT_Smik_c935_20455               3.2e-11  542_[+2]_165
 269 MIT_Smik_c193_2483                9.1e-10  175_[+2]_665
 270 MIT_Sbay_c841_3215                1.5e-09  174_[+2]_666
 271 WashU_Skud_Contig1850.5           3.1e-09  172_[+2]_668
 272 MIT_Spar_c429_3020                3.5e-09  173_[+2]_667
 273 SGD_Scer_YDL205C                  3.5e-09  173_[+2]_667
 274 --------------------------------------------------------------------------------
 275
 276 --------------------------------------------------------------------------------
 277         Motif 2 in BLOCKS format
 278 --------------------------------------------------------------------------------
 279 BL   MOTIF 2 width=20 seqs=10
 280 WashU_Sbay_Contig480.2   (  570) TGCGCGTCGAAACCACAAAC  1
 281 WashU_Skud_Contig2050.4  (  565) TGCGCGTCGAAACCACAAAC  1
 282 MIT_Spar_c278_20970      (  559) TGCGCGTCGAAACCACAAAC  1
 283 SGD_Scer_YOR176W         (  557) TGCGCGTCGAAACCACAAAC  1
 284 MIT_Smik_c935_20455      (  543) TGCGCGTCAAAACCACAAAC  1
 285 MIT_Smik_c193_2483       (  176) TGCGTAGCGATAATACAGAT  1
 286 MIT_Sbay_c841_3215       (  175) TGTGCCGCGATAATACAATC  1
 287 WashU_Skud_Contig1850.5  (  173) TGTGTCGCGATAATACAAGT  1
 288 MIT_Spar_c429_3020       (  174) TGTGTAGCAATAATACAGAT  1
 289 SGD_Scer_YDL205C         (  174) TGTGTAGCAATAATACAGAT  1
 290 //
 291
 292 --------------------------------------------------------------------------------
 293
 294 --------------------------------------------------------------------------------
 295         Motif 2 position-specific scoring matrix
 296 --------------------------------------------------------------------------------
 297 log-odds matrix: alength= 4 w= 20 n= 7745 bayes= 9.59526 E= 3.8e-022
 298   -997   -997   -997    162
 299   -997   -997    251   -997
 300   -997    177   -997     30
 301   -997   -997    251   -997
 302   -997    177   -997     30
 303    -11     19    151   -997
 304   -997   -997    151     62
 305   -997    251   -997   -997
 306    -11   -997    199   -997
 307    162   -997   -997   -997
 308     62   -997   -997     62
 309    162   -997   -997   -997
 310     62    151   -997   -997
 311   -997    151   -997     62
 312    162   -997   -997   -997
 313   -997    251   -997   -997
 314    162   -997   -997   -997
 315    111   -997     77   -997
 316    130   -997    -81   -169
 317   -997    177   -997     30
 318 --------------------------------------------------------------------------------
 319
 320 --------------------------------------------------------------------------------
 321         Motif 2 position-specific probability matrix
 322 --------------------------------------------------------------------------------
 323 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 3.8e-022
 324  0.000000  0.000000  0.000000  1.000000
 325  0.000000  0.000000  1.000000  0.000000
 326  0.000000  0.600000  0.000000  0.400000
 327  0.000000  0.000000  1.000000  0.000000
 328  0.000000  0.600000  0.000000  0.400000
 329  0.300000  0.200000  0.500000  0.000000
 330  0.000000  0.000000  0.500000  0.500000
 331  0.000000  1.000000  0.000000  0.000000
 332  0.300000  0.000000  0.700000  0.000000
 333  1.000000  0.000000  0.000000  0.000000
 334  0.500000  0.000000  0.000000  0.500000
 335  1.000000  0.000000  0.000000  0.000000
 336  0.500000  0.500000  0.000000  0.000000
 337  0.000000  0.500000  0.000000  0.500000
 338  1.000000  0.000000  0.000000  0.000000
 339  0.000000  1.000000  0.000000  0.000000
 340  1.000000  0.000000  0.000000  0.000000
 341  0.700000  0.000000  0.300000  0.000000
 342  0.800000  0.000000  0.100000  0.100000
 343  0.000000  0.600000  0.000000  0.400000
 344 --------------------------------------------------------------------------------
 345
 346 --------------------------------------------------------------------------------
 347         Motif 2 regular expression
 348 --------------------------------------------------------------------------------
 349 TG[CT]G[CT][GAC][GT]C[GA]A[AT]A[AC][CT]ACA[AG]A[CT]
 350 --------------------------------------------------------------------------------
 351
 352
 353
 354
 355 Time 12.80 secs.
 356
 357 ********************************************************************************
 358
 359
 360 ********************************************************************************
 361 MOTIF  3        width =   20   sites =  10   llr = 199   E-value = 1.7e-020
 362 ********************************************************************************
 363 --------------------------------------------------------------------------------
 364         Motif 3 Description
 365 --------------------------------------------------------------------------------
 366 Simplified        A  ::5:::a6a:9a91:1::::
 367 pos.-specific     C  1a::5::::::::14::195
 368 probability       G  ::5:::::::::18681:::
 369 matrix            T  9::a5a:4:a1::::19915
 370
 371          bits    2.5  *
 372                  2.3  *
 373                  2.0  *                *
 374                  1.8  *                *
 375 Information      1.5  * * ** ** * ***  *
 376 content          1.3 ** * ** ***********
 377 (28.6 bits)      1.0 ******* ************
 378                  0.8 ********************
 379                  0.5 ********************
 380                  0.3 ********************
 381                  0.0 --------------------
 382
 383 Multilevel           TCATCTAAATAAAGGGTTCC
 384 consensus              G T  T      C    T
 385 sequence
 386
 387 --------------------------------------------------------------------------------
 388
 389 --------------------------------------------------------------------------------
 390         Motif 3 sites sorted by position p-value
 391 --------------------------------------------------------------------------------
 392 Sequence name            Strand  Start   P-value                    Site
 393 -------------            ------  ----- ---------            --------------------
 394 WashU_Skud_Contig2050.4      +    600  3.79e-11 AAAATATTGA TCATCTAAATAAAGGGTTCT TATTTGCACA
 395 MIT_Spar_c278_20970          +    594  3.79e-11 AAAATAATGG TCATCTAAATAAAGGGTTCT TATTTGAACA
 396 SGD_Scer_YOR176W             +    592  3.79e-11 AAAACAATGG TCATCTAAATAAAGGGTTCT TATTAAACAG
 397 WashU_Skud_Contig1850.5      +    205  4.47e-11 TTGATTGGTG TCGTTTATATAAAGCGTTCC TTCAATTTTT
 398 MIT_Spar_c429_3020           +    206  4.47e-11 TTGATTGGCG TCGTTTATATAAAGCGTTCC TTCATTTTTT
 399 SGD_Scer_YDL205C             +    205  4.47e-11 GTTAGTAGCC TCGTTTATATAAAGCGTTCC TTTACTTTTT
 400 WashU_Sbay_Contig480.2       +    605  2.26e-10 AAAATATCGA CCATCTAAATAAAGGGTTCT TGTTTGAATA
 401 MIT_Smik_c193_2483           +    208  5.94e-10 TTGTTTGATG TCGTTTATATTAAGCGTTCC TTCAGTTTTT
 402 MIT_Sbay_c841_3215           +    207  2.13e-08 TTGGCCTATA TCGTTTAAATAAGCGTTCCT TTAATTTTTC
 403 MIT_Smik_c935_20455          +    578  3.47e-08 AAAATAATGA TCATCTAAATAAAAGAGTTC ACGTTTTCAC
 404 --------------------------------------------------------------------------------
 405
 406 --------------------------------------------------------------------------------
 407         Motif 3 block diagrams
 408 --------------------------------------------------------------------------------
 409 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 410 -------------            ----------------  -------------
 411 WashU_Skud_Contig2050.4           3.8e-11  599_[+3]_108
 412 MIT_Spar_c278_20970               3.8e-11  593_[+3]_114
 413 SGD_Scer_YOR176W                  3.8e-11  591_[+3]_116
 414 WashU_Skud_Contig1850.5           4.5e-11  204_[+3]_636
 415 MIT_Spar_c429_3020                4.5e-11  205_[+3]_635
 416 SGD_Scer_YDL205C                  4.5e-11  204_[+3]_636
 417 WashU_Sbay_Contig480.2            2.3e-10  604_[+3]_103
 418 MIT_Smik_c193_2483                5.9e-10  207_[+3]_633
 419 MIT_Sbay_c841_3215                2.1e-08  206_[+3]_634
 420 MIT_Smik_c935_20455               3.5e-08  577_[+3]_130
 421 --------------------------------------------------------------------------------
 422
 423 --------------------------------------------------------------------------------
 424         Motif 3 in BLOCKS format
 425 --------------------------------------------------------------------------------
 426 BL   MOTIF 3 width=20 seqs=10
 427 WashU_Skud_Contig2050.4  (  600) TCATCTAAATAAAGGGTTCT  1
 428 MIT_Spar_c278_20970      (  594) TCATCTAAATAAAGGGTTCT  1
 429 SGD_Scer_YOR176W         (  592) TCATCTAAATAAAGGGTTCT  1
 430 WashU_Skud_Contig1850.5  (  205) TCGTTTATATAAAGCGTTCC  1
 431 MIT_Spar_c429_3020       (  206) TCGTTTATATAAAGCGTTCC  1
 432 SGD_Scer_YDL205C         (  205) TCGTTTATATAAAGCGTTCC  1
 433 WashU_Sbay_Contig480.2   (  605) CCATCTAAATAAAGGGTTCT  1
 434 MIT_Smik_c193_2483       (  208) TCGTTTATATTAAGCGTTCC  1
 435 MIT_Sbay_c841_3215       (  207) TCGTTTAAATAAGCGTTCCT  1
 436 MIT_Smik_c935_20455      (  578) TCATCTAAATAAAAGAGTTC  1
 437 //
 438
 439 --------------------------------------------------------------------------------
 440
 441 --------------------------------------------------------------------------------
 442         Motif 3 position-specific scoring matrix
 443 --------------------------------------------------------------------------------
 444 log-odds matrix: alength= 4 w= 20 n= 7745 bayes= 9.59526 E= 1.7e-020
 445   -997    -81   -997    147
 446   -997    251   -997   -997
 447     62   -997    151   -997
 448   -997   -997   -997    162
 449   -997    151   -997     62
 450   -997   -997   -997    162
 451    162   -997   -997   -997
 452     89   -997   -997     30
 453    162   -997   -997   -997
 454   -997   -997   -997    162
 455    147   -997   -997   -169
 456    162   -997   -997   -997
 457    147   -997    -81   -997
 458   -169    -81    219   -997
 459   -997    119    177   -997
 460   -169   -997    219   -169
 461   -997   -997    -81    147
 462   -997    -81   -997    147
 463   -997    236   -997   -169
 464   -997    151   -997     62
 465 --------------------------------------------------------------------------------
 466
 467 --------------------------------------------------------------------------------
 468         Motif 3 position-specific probability matrix
 469 --------------------------------------------------------------------------------
 470 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 1.7e-020
 471  0.000000  0.100000  0.000000  0.900000
 472  0.000000  1.000000  0.000000  0.000000
 473  0.500000  0.000000  0.500000  0.000000
 474  0.000000  0.000000  0.000000  1.000000
 475  0.000000  0.500000  0.000000  0.500000
 476  0.000000  0.000000  0.000000  1.000000
 477  1.000000  0.000000  0.000000  0.000000
 478  0.600000  0.000000  0.000000  0.400000
 479  1.000000  0.000000  0.000000  0.000000
 480  0.000000  0.000000  0.000000  1.000000
 481  0.900000  0.000000  0.000000  0.100000
 482  1.000000  0.000000  0.000000  0.000000
 483  0.900000  0.000000  0.100000  0.000000
 484  0.100000  0.100000  0.800000  0.000000
 485  0.000000  0.400000  0.600000  0.000000
 486  0.100000  0.000000  0.800000  0.100000
 487  0.000000  0.000000  0.100000  0.900000
 488  0.000000  0.100000  0.000000  0.900000
 489  0.000000  0.900000  0.000000  0.100000
 490  0.000000  0.500000  0.000000  0.500000
 491 --------------------------------------------------------------------------------
 492
 493 --------------------------------------------------------------------------------
 494         Motif 3 regular expression
 495 --------------------------------------------------------------------------------
 496 TC[AG]T[CT]TA[AT]ATAAAG[GC]GTTC[CT]
 497 --------------------------------------------------------------------------------
 498
 499
 500
 501
 502 Time 19.05 secs.
 503
 504 ********************************************************************************
 505
 506
 507 ********************************************************************************
 508 MOTIF  4        width =   20   sites =  10   llr = 191   E-value = 6.7e-018
 509 ********************************************************************************
 510 --------------------------------------------------------------------------------
 511         Motif 4 Description
 512 --------------------------------------------------------------------------------
 513 Simplified        A  :975::45:a7::911:::9
 514 pos.-specific     C  a1::76147::::169::::
 515 probability       G  ::311:412:3:a:::::a1
 516 matrix            T  :::4241:1::a::3:aa::
 517
 518          bits    2.5 *           *     *
 519                  2.3 *           *     *
 520                  2.0 *           *  *  *
 521                  1.8 *           *  *  *
 522 Information      1.5 *        * **  ****
 523 content          1.3 **  **  ** *** *****
 524 (27.6 bits)      1.0 *** **  ****** *****
 525                  0.8 *** ** *************
 526                  0.5 *** ** *************
 527                  0.3 ********************
 528                  0.0 --------------------
 529
 530 Multilevel           CAAACCAACAATGACCTTGA
 531 consensus              GTTTGCG G   T
 532 sequence
 533
 534 --------------------------------------------------------------------------------
 535
 536 --------------------------------------------------------------------------------
 537         Motif 4 sites sorted by position p-value
 538 --------------------------------------------------------------------------------
 539 Sequence name            Strand  Start   P-value                    Site
 540 -------------            ------  ----- ---------            --------------------
 541 MIT_Sbay_c841_3215           +    145  1.51e-11 ATACGAACGC CAATCTGCCAATGACCTTGA AATCAAGTTA
 542 MIT_Spar_c429_3020           +    144  1.51e-11 ACACGAGCCT CAATCTGCCAATGACCTTGA ATCCAAGCTA
 543 SGD_Scer_YDL205C             +    144  1.51e-11 ACACGAGCGT CAATCTGCCAATGACCTTGA ATTCAGGCTA
 544 MIT_Spar_c278_20970          +    123  1.17e-10 TGCTTGGTGC CAAACCAAGAGTGACCTTGA CCGACTAAAA
 545 SGD_Scer_YOR176W             +    121  4.51e-10 TGTTTGGTGT CAAGCCAAGAGTGACCTTGA CCGACCAAAA
 546 MIT_Smik_c935_20455          +    119  1.09e-09 CTTTAATGAT CAGACCAACAGTGATCTTGG CCGACCAAAA
 547 WashU_Skud_Contig2050.4      +    124  2.63e-09 GTTTAATAAT CAGACCAACAATGATATTGA CCGACCAAAA
 548 MIT_Smik_c193_2483           +    146  3.28e-09 ACACGAGCGC CAATTTGCCAATGAACTTGA AATCCAGCTA
 549 WashU_Skud_Contig1850.5      +    143  8.39e-09 AACACGAACG CCAATCTGCAATGACCTTGA AATCAATCTA
 550 WashU_Sbay_Contig480.2       +    168  3.20e-08 GTTTAGTAAG CAGAGCCATAATGCTCTTGA CCGACCAAAA
 551 --------------------------------------------------------------------------------
 552
 553 --------------------------------------------------------------------------------
 554         Motif 4 block diagrams
 555 --------------------------------------------------------------------------------
 556 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 557 -------------            ----------------  -------------
 558 MIT_Sbay_c841_3215                1.5e-11  144_[+4]_696
 559 MIT_Spar_c429_3020                1.5e-11  143_[+4]_697
 560 SGD_Scer_YDL205C                  1.5e-11  143_[+4]_697
 561 MIT_Spar_c278_20970               1.2e-10  122_[+4]_585
 562 SGD_Scer_YOR176W                  4.5e-10  120_[+4]_587
 563 MIT_Smik_c935_20455               1.1e-09  118_[+4]_589
 564 WashU_Skud_Contig2050.4           2.6e-09  123_[+4]_584
 565 MIT_Smik_c193_2483                3.3e-09  145_[+4]_695
 566 WashU_Skud_Contig1850.5           8.4e-09  142_[+4]_698
 567 WashU_Sbay_Contig480.2            3.2e-08  167_[+4]_540
 568 --------------------------------------------------------------------------------
 569
 570 --------------------------------------------------------------------------------
 571         Motif 4 in BLOCKS format
 572 --------------------------------------------------------------------------------
 573 BL   MOTIF 4 width=20 seqs=10
 574 MIT_Sbay_c841_3215       (  145) CAATCTGCCAATGACCTTGA  1
 575 MIT_Spar_c429_3020       (  144) CAATCTGCCAATGACCTTGA  1
 576 SGD_Scer_YDL205C         (  144) CAATCTGCCAATGACCTTGA  1
 577 MIT_Spar_c278_20970      (  123) CAAACCAAGAGTGACCTTGA  1
 578 SGD_Scer_YOR176W         (  121) CAAGCCAAGAGTGACCTTGA  1
 579 MIT_Smik_c935_20455      (  119) CAGACCAACAGTGATCTTGG  1
 580 WashU_Skud_Contig2050.4  (  124) CAGACCAACAATGATATTGA  1
 581 MIT_Smik_c193_2483       (  146) CAATTTGCCAATGAACTTGA  1
 582 WashU_Skud_Contig1850.5  (  143) CCAATCTGCAATGACCTTGA  1
 583 WashU_Sbay_Contig480.2   (  168) CAGAGCCATAATGCTCTTGA  1
 584 //
 585
 586 --------------------------------------------------------------------------------
 587
 588 --------------------------------------------------------------------------------
 589         Motif 4 position-specific scoring matrix
 590 --------------------------------------------------------------------------------
 591 log-odds matrix: alength= 4 w= 20 n= 7745 bayes= 9.59526 E= 6.7e-018
 592   -997    251   -997   -997
 593    147    -81   -997   -997
 594    111   -997     77   -997
 595     62   -997    -81     30
 596   -997    199    -81    -70
 597   -997    177   -997     30
 598     30    -81    119   -169
 599     62    119    -81   -997
 600   -997    199     19   -169
 601    162   -997   -997   -997
 602    111   -997     77   -997
 603   -997   -997   -997    162
 604   -997   -997    251   -997
 605    147    -81   -997   -997
 606   -169    177   -997    -11
 607   -169    236   -997   -997
 608   -997   -997   -997    162
 609   -997   -997   -997    162
 610   -997   -997    251   -997
 611    147   -997    -81   -997
 612 --------------------------------------------------------------------------------
 613
 614 --------------------------------------------------------------------------------
 615         Motif 4 position-specific probability matrix
 616 --------------------------------------------------------------------------------
 617 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 6.7e-018
 618  0.000000  1.000000  0.000000  0.000000
 619  0.900000  0.100000  0.000000  0.000000
 620  0.700000  0.000000  0.300000  0.000000
 621  0.500000  0.000000  0.100000  0.400000
 622  0.000000  0.700000  0.100000  0.200000
 623  0.000000  0.600000  0.000000  0.400000
 624  0.400000  0.100000  0.400000  0.100000
 625  0.500000  0.400000  0.100000  0.000000
 626  0.000000  0.700000  0.200000  0.100000
 627  1.000000  0.000000  0.000000  0.000000
 628  0.700000  0.000000  0.300000  0.000000
 629  0.000000  0.000000  0.000000  1.000000
 630  0.000000  0.000000  1.000000  0.000000
 631  0.900000  0.100000  0.000000  0.000000
 632  0.100000  0.600000  0.000000  0.300000
 633  0.100000  0.900000  0.000000  0.000000
 634  0.000000  0.000000  0.000000  1.000000
 635  0.000000  0.000000  0.000000  1.000000
 636  0.000000  0.000000  1.000000  0.000000
 637  0.900000  0.000000  0.100000  0.000000
 638 --------------------------------------------------------------------------------
 639
 640 --------------------------------------------------------------------------------
 641         Motif 4 regular expression
 642 --------------------------------------------------------------------------------
 643 CA[AG][AT][CT][CT][AG][AC][CG]A[AG]TGA[CT]CTTGA
 644 --------------------------------------------------------------------------------
 645
 646
 647
 648
 649 Time 25.42 secs.
 650
 651 ********************************************************************************
 652
 653
 654 ********************************************************************************
 655 MOTIF  5        width =   20   sites =  10   llr = 190   E-value = 6.6e-017
 656 ********************************************************************************
 657 --------------------------------------------------------------------------------
 658         Motif 5 Description
 659 --------------------------------------------------------------------------------
 660 Simplified        A  219a56:::::19aa::15:
 661 pos.-specific     C  ::1:541:1a11::::1::6
 662 probability       G  :9::::::8::81::::1::
 663 matrix            T  8:::::9a1:9::::a9854
 664
 665          bits    2.5          *
 666                  2.3          *
 667                  2.0  *       *
 668                  1.8  *       *
 669 Information      1.5  * *   *** * ***
 670 content          1.3  ***  ***********  *
 671 (27.4 bits)      1.0 *****************  *
 672                  0.8 ****************** *
 673                  0.5 ********************
 674                  0.3 ********************
 675                  0.0 --------------------
 676
 677 Multilevel           TGAAAATTGCTGAAATTTAC
 678 consensus            A   CC            TT
 679 sequence
 680
 681 --------------------------------------------------------------------------------
 682
 683 --------------------------------------------------------------------------------
 684         Motif 5 sites sorted by position p-value
 685 --------------------------------------------------------------------------------
 686 Sequence name            Strand  Start   P-value                    Site
 687 -------------            ------  ----- ---------            --------------------
 688 WashU_Skud_Contig1850.5      +    282  3.68e-11 TTTTCACTTT TGAAAATTGCTGAAATTTTC GTAGCAAAAA
 689 MIT_Sbay_c841_3215           +    280  3.68e-11 TTTTTTCACT TGAAAATTGCTGAAATTTTC GTAGCTGAAA
 690 MIT_Smik_c193_2483           +    285  3.68e-11 TTTTCACTTT TGAAAATTGCTGAAATTTTC GTAACAAAAA
 691 SGD_Scer_YOR176W             +    415  1.86e-10 GTAAAGCTGT TGAACCTTCCTGAAATTTAC TTCTAAAATT
 692 MIT_Spar_c429_3020           +    282  3.08e-10 TTTTCACTTT TGAAAACTGCTGAAATTTTC GTAGCAAAAA
 693 SGD_Scer_YDL205C             +    281  3.80e-09 TTTTCACTTT AAAAAATTGCTGAAATTTTC GTAGCCAAAA
 694 WashU_Skud_Contig2050.4      +    417  5.20e-09 TGCAAAATGT TGAACCTTTCCGAAATTTAT TGCCAGAAAC
 695 MIT_Spar_c278_20970          +    418  5.20e-09 GTAAAGCTGT TGAACCTTGCTAAAATCTAT TACTATAATT
 696 WashU_Sbay_Contig480.2       +    453  9.34e-09 CAGAGTTGGT TGAACCTTGCTCGAATTGAT AGCTCAAAGT
 697 MIT_Smik_c935_20455          +    419  1.01e-08 AATATGCCAA AGCACATTGCTGAAATTAAT CAGTAAAGCT
 698 --------------------------------------------------------------------------------
 699
 700 --------------------------------------------------------------------------------
 701         Motif 5 block diagrams
 702 --------------------------------------------------------------------------------
 703 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 704 -------------            ----------------  -------------
 705 WashU_Skud_Contig1850.5           3.7e-11  281_[+5]_559
 706 MIT_Sbay_c841_3215                3.7e-11  279_[+5]_561
 707 MIT_Smik_c193_2483                3.7e-11  284_[+5]_556
 708 SGD_Scer_YOR176W                  1.9e-10  414_[+5]_293
 709 MIT_Spar_c429_3020                3.1e-10  281_[+5]_559
 710 SGD_Scer_YDL205C                  3.8e-09  280_[+5]_560
 711 WashU_Skud_Contig2050.4           5.2e-09  416_[+5]_291
 712 MIT_Spar_c278_20970               5.2e-09  417_[+5]_290
 713 WashU_Sbay_Contig480.2            9.3e-09  452_[+5]_255
 714 MIT_Smik_c935_20455                 1e-08  418_[+5]_289
 715 --------------------------------------------------------------------------------
 716
 717 --------------------------------------------------------------------------------
 718         Motif 5 in BLOCKS format
 719 --------------------------------------------------------------------------------
 720 BL   MOTIF 5 width=20 seqs=10
 721 WashU_Skud_Contig1850.5  (  282) TGAAAATTGCTGAAATTTTC  1
 722 MIT_Sbay_c841_3215       (  280) TGAAAATTGCTGAAATTTTC  1
 723 MIT_Smik_c193_2483       (  285) TGAAAATTGCTGAAATTTTC  1
 724 SGD_Scer_YOR176W         (  415) TGAACCTTCCTGAAATTTAC  1
 725 MIT_Spar_c429_3020       (  282) TGAAAACTGCTGAAATTTTC  1
 726 SGD_Scer_YDL205C         (  281) AAAAAATTGCTGAAATTTTC  1
 727 WashU_Skud_Contig2050.4  (  417) TGAACCTTTCCGAAATTTAT  1
 728 MIT_Spar_c278_20970      (  418) TGAACCTTGCTAAAATCTAT  1
 729 WashU_Sbay_Contig480.2   (  453) TGAACCTTGCTCGAATTGAT  1
 730 MIT_Smik_c935_20455      (  419) AGCACATTGCTGAAATTAAT  1
 731 //
 732
 733 --------------------------------------------------------------------------------
 734
 735 --------------------------------------------------------------------------------
 736         Motif 5 position-specific scoring matrix
 737 --------------------------------------------------------------------------------
 738 log-odds matrix: alength= 4 w= 20 n= 7745 bayes= 9.59526 E= 6.6e-017
 739    -70   -997   -997    130
 740   -169   -997    236   -997
 741    147    -81   -997   -997
 742    162   -997   -997   -997
 743     62    151   -997   -997
 744     89    119   -997   -997
 745   -997    -81   -997    147
 746   -997   -997   -997    162
 747   -997    -81    219   -169
 748   -997    251   -997   -997
 749   -997    -81   -997    147
 750   -169    -81    219   -997
 751    147   -997    -81   -997
 752    162   -997   -997   -997
 753    162   -997   -997   -997
 754   -997   -997   -997    162
 755   -997    -81   -997    147
 756   -169   -997    -81    130
 757     62   -997   -997     62
 758   -997    177   -997     30
 759 --------------------------------------------------------------------------------
 760
 761 --------------------------------------------------------------------------------
 762         Motif 5 position-specific probability matrix
 763 --------------------------------------------------------------------------------
 764 letter-probability matrix: alength= 4 w= 20 nsites= 10 E= 6.6e-017
 765  0.200000  0.000000  0.000000  0.800000
 766  0.100000  0.000000  0.900000  0.000000
 767  0.900000  0.100000  0.000000  0.000000
 768  1.000000  0.000000  0.000000  0.000000
 769  0.500000  0.500000  0.000000  0.000000
 770  0.600000  0.400000  0.000000  0.000000
 771  0.000000  0.100000  0.000000  0.900000
 772  0.000000  0.000000  0.000000  1.000000
 773  0.000000  0.100000  0.800000  0.100000
 774  0.000000  1.000000  0.000000  0.000000
 775  0.000000  0.100000  0.000000  0.900000
 776  0.100000  0.100000  0.800000  0.000000
 777  0.900000  0.000000  0.100000  0.000000
 778  1.000000  0.000000  0.000000  0.000000
 779  1.000000  0.000000  0.000000  0.000000
 780  0.000000  0.000000  0.000000  1.000000
 781  0.000000  0.100000  0.000000  0.900000
 782  0.100000  0.000000  0.100000  0.800000
 783  0.500000  0.000000  0.000000  0.500000
 784  0.000000  0.600000  0.000000  0.400000
 785 --------------------------------------------------------------------------------
 786
 787 --------------------------------------------------------------------------------
 788         Motif 5 regular expression
 789 --------------------------------------------------------------------------------
 790 [TA]GAA[AC][AC]TTGCTGAAATTT[AT][CT]
 791 --------------------------------------------------------------------------------
 792
 793
 794
 795
 796 Time 31.23 secs.
 797
 798 ********************************************************************************
 799
 800
 801 ********************************************************************************
 802 SUMMARY OF MOTIFS
 803 ********************************************************************************
 804
 805 --------------------------------------------------------------------------------
 806         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 807 --------------------------------------------------------------------------------
 808 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 809 -------------            ----------------  -------------
 810 SGD_Scer_YDL205C                 8.36e-26  109_[+1(5.89e-10)]_15_[+4(1.51e-11)]_10_[+2(3.52e-09)]_11_[+3(4.47e-11)]_56_[+5(3.80e-09)]_560
 811 MIT_Spar_c429_3020               1.64e-27  109_[+1(1.14e-10)]_15_[+4(1.51e-11)]_10_[+2(3.52e-09)]_12_[+3(4.47e-11)]_56_[+5(3.08e-10)]_494_[+2(3.35e-05)]_22_[+5(2.99e-05)]_3
 812 MIT_Smik_c193_2483               1.55e-25  111_[+1(1.56e-10)]_15_[+4(3.28e-09)]_10_[+2(9.12e-10)]_12_[+3(5.94e-10)]_57_[+5(3.68e-11)]_556
 813 MIT_Sbay_c841_3215               1.09e-26  110_[+1(3.58e-11)]_15_[+4(1.51e-11)]_10_[+2(1.46e-09)]_12_[+3(2.13e-08)]_53_[+5(3.68e-11)]_561
 814 WashU_Skud_Contig1850.5          2.56e-26  109_[+1(3.58e-11)]_14_[+4(8.39e-09)]_10_[+2(3.07e-09)]_12_[+3(4.47e-11)]_57_[+5(3.68e-11)]_559
 815 SGD_Scer_YOR176W                 3.30e-30  120_[+4(4.51e-10)]_274_[+5(1.86e-10)]_67_[-1(6.04e-11)]_36_[+2(1.49e-12)]_15_[+3(3.79e-11)]_116
 816 MIT_Spar_c278_20970              2.16e-29  122_[+4(1.17e-10)]_239_[+5(6.19e-05)]_16_[+5(5.20e-09)]_66_[-1(6.04e-11)]_36_[+2(1.49e-12)]_15_[+3(3.79e-11)]_114
 817 MIT_Smik_c935_20455              1.31e-23  118_[+4(1.09e-09)]_280_[+5(1.01e-08)]_49_[-1(2.17e-10)]_36_[+2(3.24e-11)]_15_[+3(3.47e-08)]_130
 818 WashU_Skud_Contig2050.4          3.42e-27  123_[+4(2.63e-09)]_235_[+1(5.68e-05)]_19_[+5(5.20e-09)]_68_[-1(5.56e-10)]_12_[+1(5.97e-05)]_10_[+2(1.49e-12)]_15_[+3(3.79e-11)]_108
 819 WashU_Sbay_Contig480.2           4.20e-26  167_[+4(3.20e-08)]_265_[+5(9.34e-09)]_41_[-1(6.04e-11)]_37_[+2(1.49e-12)]_15_[+3(2.26e-10)]_103
 820 --------------------------------------------------------------------------------
 821
 822 ********************************************************************************
 823
 824
 825 ********************************************************************************
 826 Stopped because nmotifs = 5 reached.
 827 ********************************************************************************
 828
 829 CPU: dhn02990.mrc-dunn.cam.ac.uk
 830
 831 ********************************************************************************