t/data/map_hem/HEM3-HEM12.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-HEM12.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_YDR047W         1.0000   1000
  38 MIT_Spar_c130_3923       1.0000   1000  MIT_Sbay_c896_21277      1.0000   1000
  39 WashU_Skud_Contig1362.1  1.0000    761
  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-HEM12.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=            8061    N=               9
  59 strands: + -
  60 sample: seed=            0    seqfrac=         1
  61 Letter frequencies in dataset:
  62 A 0.295 C 0.205 G 0.205 T 0.295
  63 Background letter frequencies (from 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 = 189   E-value = 1.1e-018
  70 ********************************************************************************
  71 --------------------------------------------------------------------------------
  72         Motif 1 Description
  73 --------------------------------------------------------------------------------
  74 Simplified        A  :784a4a4:::::4a::7::
  75 pos.-specific     C  4321:6::aaa4:::9a3::
  76 probability       G  1::::::6::::a::::::7
  77 matrix            T  4::4:::::::6:6:1::a3
  78
  79          bits    2.5         *** *   *
  80                  2.3         *** *   *
  81                  2.0         *** *  **
  82                  1.8         *** *  **
  83 Information      1.5     * * *** * *** *
  84 content          1.3     * * *** * *** **
  85 (30.3 bits)      1.0  ** ********* ******
  86                  0.8 *** ****************
  87                  0.5 *** ****************
  88                  0.3 ********************
  89                  0.0 --------------------
  90
  91 Multilevel           CAAAACAGCCCTGTACCATG
  92 consensus            TCCT A A   C A   C T
  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 MIT_Spar_c429_3020           +    111  1.67e-11 ATTCAAAATG TAAAACAGCCCTGTACCATG CAAACACGAG
 103 SGD_Scer_YDL205C             +    111  1.67e-11 ATTCAAAATC TAATACAGCCCTGTACCATG CAAACACGAG
 104 WashU_Skud_Contig1850.5      +    111  5.77e-11 TTTCAAAAAG CAATACAGCCCTGTACCATT CAAACACGAA
 105 MIT_Sbay_c841_3215           +    112  5.77e-11 ATTCAAAACG CAATACAGCCCTGTACCATT CAAATACGAA
 106 MIT_Smik_c193_2483           +    113  1.63e-10 ATTCAAAAAG TAATACAGCCCTGTACCATT CAAACACGAG
 107 MIT_Sbay_c896_21277          +    206  2.60e-10 TTCCATGGCG TCAAAAAACCCCGAACCCTG TATAAACGAG
 108 MIT_Spar_c130_3923           +    235  4.70e-10 TCTCTCCTGC CACCAAAACCCCGAACCCTG TCCCGTATAT
 109 SGD_Scer_YDR047W             +    238  7.68e-10 CTCTCCTGCC GCCAAAAACCCCGAACCCTG TCCTGTATAT
 110 WashU_Skud_Contig1362.1      +    201  9.83e-10 TTTCCTGCTG CCAAAAAACCCCGAATCATG TAGAAGCGAG
 111 --------------------------------------------------------------------------------
 112
 113 --------------------------------------------------------------------------------
 114         Motif 1 block diagrams
 115 --------------------------------------------------------------------------------
 116 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 117 -------------            ----------------  -------------
 118 MIT_Spar_c429_3020                1.7e-11  110_[+1]_730
 119 SGD_Scer_YDL205C                  1.7e-11  110_[+1]_730
 120 WashU_Skud_Contig1850.5           5.8e-11  110_[+1]_730
 121 MIT_Sbay_c841_3215                5.8e-11  111_[+1]_729
 122 MIT_Smik_c193_2483                1.6e-10  112_[+1]_728
 123 MIT_Sbay_c896_21277               2.6e-10  205_[+1]_775
 124 MIT_Spar_c130_3923                4.7e-10  234_[+1]_746
 125 SGD_Scer_YDR047W                  7.7e-10  237_[+1]_743
 126 WashU_Skud_Contig1362.1           9.8e-10  200_[+1]_541
 127 --------------------------------------------------------------------------------
 128
 129 --------------------------------------------------------------------------------
 130         Motif 1 in BLOCKS format
 131 --------------------------------------------------------------------------------
 132 BL   MOTIF 1 width=20 seqs=9
 133 MIT_Spar_c429_3020       (  111) TAAAACAGCCCTGTACCATG  1
 134 SGD_Scer_YDL205C         (  111) TAATACAGCCCTGTACCATG  1
 135 WashU_Skud_Contig1850.5  (  111) CAATACAGCCCTGTACCATT  1
 136 MIT_Sbay_c841_3215       (  112) CAATACAGCCCTGTACCATT  1
 137 MIT_Smik_c193_2483       (  113) TAATACAGCCCTGTACCATT  1
 138 MIT_Sbay_c896_21277      (  206) TCAAAAAACCCCGAACCCTG  1
 139 MIT_Spar_c130_3923       (  235) CACCAAAACCCCGAACCCTG  1
 140 SGD_Scer_YDR047W         (  238) GCCAAAAACCCCGAACCCTG  1
 141 WashU_Skud_Contig1362.1  (  201) CCAAAAAACCCCGAATCATG  1
 142 //
 143
 144 --------------------------------------------------------------------------------
 145
 146 --------------------------------------------------------------------------------
 147         Motif 1 position-specific scoring matrix
 148 --------------------------------------------------------------------------------
 149 log-odds matrix: alength= 4 w= 20 n= 7890 bayes= 9.77424 E= 1.1e-018
 150   -982    134    -66     45
 151    104     92   -982   -982
 152    126     34   -982   -982
 153     45    -66   -982     45
 154    162   -982   -982   -982
 155     45    166   -982   -982
 156    162   -982   -982   -982
 157     45   -982    166   -982
 158   -982    251   -982   -982
 159   -982    251   -982   -982
 160   -982    251   -982   -982
 161   -982    134   -982     78
 162   -982   -982    251   -982
 163     45   -982   -982     78
 164    162   -982   -982   -982
 165   -982    234   -982   -154
 166   -982    251   -982   -982
 167    104     92   -982   -982
 168   -982   -982   -982    162
 169   -982   -982    192      4
 170 --------------------------------------------------------------------------------
 171
 172 --------------------------------------------------------------------------------
 173         Motif 1 position-specific probability matrix
 174 --------------------------------------------------------------------------------
 175 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.1e-018
 176  0.000000  0.444444  0.111111  0.444444
 177  0.666667  0.333333  0.000000  0.000000
 178  0.777778  0.222222  0.000000  0.000000
 179  0.444444  0.111111  0.000000  0.444444
 180  1.000000  0.000000  0.000000  0.000000
 181  0.444444  0.555556  0.000000  0.000000
 182  1.000000  0.000000  0.000000  0.000000
 183  0.444444  0.000000  0.555556  0.000000
 184  0.000000  1.000000  0.000000  0.000000
 185  0.000000  1.000000  0.000000  0.000000
 186  0.000000  1.000000  0.000000  0.000000
 187  0.000000  0.444444  0.000000  0.555556
 188  0.000000  0.000000  1.000000  0.000000
 189  0.444444  0.000000  0.000000  0.555556
 190  1.000000  0.000000  0.000000  0.000000
 191  0.000000  0.888889  0.000000  0.111111
 192  0.000000  1.000000  0.000000  0.000000
 193  0.666667  0.333333  0.000000  0.000000
 194  0.000000  0.000000  0.000000  1.000000
 195  0.000000  0.000000  0.666667  0.333333
 196 --------------------------------------------------------------------------------
 197
 198 --------------------------------------------------------------------------------
 199         Motif 1 regular expression
 200 --------------------------------------------------------------------------------
 201 [CT][AC][AC][AT]A[CA]A[GA]CCC[TC]G[TA]ACC[AC]T[GT]
 202 --------------------------------------------------------------------------------
 203
 204
 205
 206
 207 Time  6.92 secs.
 208
 209 ********************************************************************************
 210
 211
 212 ********************************************************************************
 213 MOTIF  2        width =   20   sites =   9   llr = 187   E-value = 6.5e-018
 214 ********************************************************************************
 215 --------------------------------------------------------------------------------
 216         Motif 2 Description
 217 --------------------------------------------------------------------------------
 218 Simplified        A  ::::1:11::4::a:3:a::
 219 pos.-specific     C  68441:6:a::7a:::4:46
 220 probability       G  ::::8a:9::61::676:63
 221 matrix            T  4266::3::a:2::4::::1
 222
 223          bits    2.5      *  *   *
 224                  2.3      *  *   *
 225                  2.0      * **   *
 226                  1.8      * **   *
 227 Information      1.5  *  ** ***  **  ***
 228 content          1.3  *  ** ***  ** ****
 229 (30.0 bits)      1.0 ****** *************
 230                  0.8 ********************
 231                  0.5 ********************
 232                  0.3 ********************
 233                  0.0 --------------------
 234
 235 Multilevel           CCTTGGCGCTGCCAGGGAGC
 236 consensus            TTCC  T   AT  TAC CG
 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 SGD_Scer_YDL205C             +    489  3.06e-13 ACATCTTTAC CCCCGGTGCTGCCAGGGAGC AAAATAATTA
 247 MIT_Spar_c429_3020           +    493  9.57e-12 GACATCTTAC CCCCGGTGCTGTCAGGGAGC AAAAAAATGA
 248 MIT_Sbay_c841_3215           +    503  2.31e-11 CCCTCCCCCT TCTCCGCGCTGCCAGGGACC AGGCAAGGGC
 249 MIT_Sbay_c896_21277          -    239  1.64e-10 TATCTGCCTT TTCTGGCGCTACCATGCAGC TTCCTCGTTT
 250 MIT_Spar_c130_3923           -    287  2.77e-10 TTATTCGCTA TCTTGGCGCTACCATACACG ATTTTTTTTC
 251 WashU_Skud_Contig1850.5      +    494  5.55e-10 ACATCTTCAC CTTCGGAGCTGGCAGGGAGC AAGGGACTCT
 252 WashU_Skud_Contig1362.1      -    246  6.00e-10 TGCCCGTTTT CCTTGGCGCTACCATACACT TCCTCTGTTT
 253 SGD_Scer_YDR047W             -    289  1.18e-09 TTATCCGCCA TCTTGGCGCTATCATACACG ATCTTTTTCA
 254 MIT_Smik_c193_2483           +    493  1.25e-09 TTCATCTTAC CCCTAGTACTGCCAGGGAGG AACTAAACCT
 255 --------------------------------------------------------------------------------
 256
 257 --------------------------------------------------------------------------------
 258         Motif 2 block diagrams
 259 --------------------------------------------------------------------------------
 260 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 261 -------------            ----------------  -------------
 262 SGD_Scer_YDL205C                  3.1e-13  488_[+2]_352
 263 MIT_Spar_c429_3020                9.6e-12  492_[+2]_348
 264 MIT_Sbay_c841_3215                2.3e-11  502_[+2]_338
 265 MIT_Sbay_c896_21277               1.6e-10  238_[-2]_742
 266 MIT_Spar_c130_3923                2.8e-10  286_[-2]_694
 267 WashU_Skud_Contig1850.5           5.6e-10  493_[+2]_347
 268 WashU_Skud_Contig1362.1             6e-10  245_[-2]_496
 269 SGD_Scer_YDR047W                  1.2e-09  288_[-2]_692
 270 MIT_Smik_c193_2483                1.3e-09  492_[+2]_348
 271 --------------------------------------------------------------------------------
 272
 273 --------------------------------------------------------------------------------
 274         Motif 2 in BLOCKS format
 275 --------------------------------------------------------------------------------
 276 BL   MOTIF 2 width=20 seqs=9
 277 SGD_Scer_YDL205C         (  489) CCCCGGTGCTGCCAGGGAGC  1
 278 MIT_Spar_c429_3020       (  493) CCCCGGTGCTGTCAGGGAGC  1
 279 MIT_Sbay_c841_3215       (  503) TCTCCGCGCTGCCAGGGACC  1
 280 MIT_Sbay_c896_21277      (  239) TTCTGGCGCTACCATGCAGC  1
 281 MIT_Spar_c130_3923       (  287) TCTTGGCGCTACCATACACG  1
 282 WashU_Skud_Contig1850.5  (  494) CTTCGGAGCTGGCAGGGAGC  1
 283 WashU_Skud_Contig1362.1  (  246) CCTTGGCGCTACCATACACT  1
 284 SGD_Scer_YDR047W         (  289) TCTTGGCGCTATCATACACG  1
 285 MIT_Smik_c193_2483       (  493) CCCTAGTACTGCCAGGGAGG  1
 286 //
 287
 288 --------------------------------------------------------------------------------
 289
 290 --------------------------------------------------------------------------------
 291         Motif 2 position-specific scoring matrix
 292 --------------------------------------------------------------------------------
 293 log-odds matrix: alength= 4 w= 20 n= 7890 bayes= 9.77424 E= 6.5e-018
 294   -982    166   -982     45
 295   -982    215   -982    -55
 296   -982    134   -982     78
 297   -982    134   -982     78
 298   -154    -66    215   -982
 299   -982   -982    251   -982
 300   -154    166   -982      4
 301   -154   -982    234   -982
 302   -982    251   -982   -982
 303   -982   -982   -982    162
 304     45   -982    166   -982
 305   -982    192    -66    -55
 306   -982    251   -982   -982
 307    162   -982   -982   -982
 308   -982   -982    166     45
 309      4   -982    192   -982
 310   -982    134    166   -982
 311    162   -982   -982   -982
 312   -982    134    166   -982
 313   -982    166     92   -154
 314 --------------------------------------------------------------------------------
 315
 316 --------------------------------------------------------------------------------
 317         Motif 2 position-specific probability matrix
 318 --------------------------------------------------------------------------------
 319 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 6.5e-018
 320  0.000000  0.555556  0.000000  0.444444
 321  0.000000  0.777778  0.000000  0.222222
 322  0.000000  0.444444  0.000000  0.555556
 323  0.000000  0.444444  0.000000  0.555556
 324  0.111111  0.111111  0.777778  0.000000
 325  0.000000  0.000000  1.000000  0.000000
 326  0.111111  0.555556  0.000000  0.333333
 327  0.111111  0.000000  0.888889  0.000000
 328  0.000000  1.000000  0.000000  0.000000
 329  0.000000  0.000000  0.000000  1.000000
 330  0.444444  0.000000  0.555556  0.000000
 331  0.000000  0.666667  0.111111  0.222222
 332  0.000000  1.000000  0.000000  0.000000
 333  1.000000  0.000000  0.000000  0.000000
 334  0.000000  0.000000  0.555556  0.444444
 335  0.333333  0.000000  0.666667  0.000000
 336  0.000000  0.444444  0.555556  0.000000
 337  1.000000  0.000000  0.000000  0.000000
 338  0.000000  0.444444  0.555556  0.000000
 339  0.000000  0.555556  0.333333  0.111111
 340 --------------------------------------------------------------------------------
 341
 342 --------------------------------------------------------------------------------
 343         Motif 2 regular expression
 344 --------------------------------------------------------------------------------
 345 [CT][CT][TC][TC]GG[CT]GCT[GA][CT]CA[GT][GA][GC]A[GC][CG]
 346 --------------------------------------------------------------------------------
 347
 348
 349
 350
 351 Time 13.49 secs.
 352
 353 ********************************************************************************
 354
 355
 356 ********************************************************************************
 357 MOTIF  3        width =   20   sites =   9   llr = 183   E-value = 1.9e-017
 358 ********************************************************************************
 359 --------------------------------------------------------------------------------
 360         Motif 3 Description
 361 --------------------------------------------------------------------------------
 362 Simplified        A  :1::6:1::162::1:a:71
 363 pos.-specific     C  :2::3a:1:22::a29::::
 364 probability       G  a6:a1:9::::87:6::::8
 365 matrix            T  :1a::::9a72:3:11:a31
 366
 367          bits    2.5 *  * *       *
 368                  2.3 *  * *       *
 369                  2.0 *  * **      * *
 370                  1.8 *  * **      * *
 371 Information      1.5 * ** ** *  * * ***
 372 content          1.3 * ** ****  *** *** *
 373 (29.4 bits)      1.0 * ** ****  *** *** *
 374                  0.8 *********  *********
 375                  0.5 ********************
 376                  0.3 ********************
 377                  0.0 --------------------
 378
 379 Multilevel           GGTGACGTTTAGGCGCATAG
 380 consensus             C  C    CCAT C   T
 381 sequence                       T
 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_Skud_Contig1850.5      +    681  3.00e-13 AAAGTTGGAA GGTGACGTTTAGGCGCATAG GCAATCTCCC
 391 MIT_Spar_c429_3020           +    674  3.00e-13 GAGGTTAGAG GGTGACGTTTAGGCGCATAG GCAACCTCCC
 392 SGD_Scer_YDL205C             +    673  3.00e-13 AAGGTTAGAC GGTGACGTTTAGGCGCATAG GCAATCTCCC
 393 MIT_Sbay_c841_3215           +    700  3.16e-11 AACATTAGAG GGTGACGTTTTAGCGCATAG GCAATCTCCC
 394 MIT_Smik_c193_2483           +    674  1.45e-10 AAGGTCAGAG GATGACGTTTAAGCGCATAG GCAATCTCCC
 395 MIT_Spar_c130_3923           +    713  2.43e-10 ACTCTAAAAT GCTGCCGTTCCGTCCCATTG AGTTTTATTT
 396 SGD_Scer_YDR047W             +    713  2.43e-10 GTTAAAAAAT GCTGCCGTTCCGTCCCATTG AGTTTTATTT
 397 WashU_Skud_Contig1362.1      +    703  2.69e-08 TCGATCGAAC GTTGCCGTTTAGTCTTATTT TCCTTTCCGT
 398 MIT_Sbay_c896_21277          -    969  4.38e-08 GGGGGCTAGT GGTGGCACTATGGCACATAA AAGCCGTGCA
 399 --------------------------------------------------------------------------------
 400
 401 --------------------------------------------------------------------------------
 402         Motif 3 block diagrams
 403 --------------------------------------------------------------------------------
 404 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 405 -------------            ----------------  -------------
 406 WashU_Skud_Contig1850.5             3e-13  680_[+3]_160
 407 MIT_Spar_c429_3020                  3e-13  673_[+3]_167
 408 SGD_Scer_YDL205C                    3e-13  672_[+3]_168
 409 MIT_Sbay_c841_3215                3.2e-11  699_[+3]_141
 410 MIT_Smik_c193_2483                1.5e-10  673_[+3]_167
 411 MIT_Spar_c130_3923                2.4e-10  712_[+3]_268
 412 SGD_Scer_YDR047W                  2.4e-10  712_[+3]_268
 413 WashU_Skud_Contig1362.1           2.7e-08  702_[+3]_39
 414 MIT_Sbay_c896_21277               4.4e-08  968_[-3]_12
 415 --------------------------------------------------------------------------------
 416
 417 --------------------------------------------------------------------------------
 418         Motif 3 in BLOCKS format
 419 --------------------------------------------------------------------------------
 420 BL   MOTIF 3 width=20 seqs=9
 421 WashU_Skud_Contig1850.5  (  681) GGTGACGTTTAGGCGCATAG  1
 422 MIT_Spar_c429_3020       (  674) GGTGACGTTTAGGCGCATAG  1
 423 SGD_Scer_YDL205C         (  673) GGTGACGTTTAGGCGCATAG  1
 424 MIT_Sbay_c841_3215       (  700) GGTGACGTTTTAGCGCATAG  1
 425 MIT_Smik_c193_2483       (  674) GATGACGTTTAAGCGCATAG  1
 426 MIT_Spar_c130_3923       (  713) GCTGCCGTTCCGTCCCATTG  1
 427 SGD_Scer_YDR047W         (  713) GCTGCCGTTCCGTCCCATTG  1
 428 WashU_Skud_Contig1362.1  (  703) GTTGCCGTTTAGTCTTATTT  1
 429 MIT_Sbay_c896_21277      (  969) GGTGGCACTATGGCACATAA  1
 430 //
 431
 432 --------------------------------------------------------------------------------
 433
 434 --------------------------------------------------------------------------------
 435         Motif 3 position-specific scoring matrix
 436 --------------------------------------------------------------------------------
 437 log-odds matrix: alength= 4 w= 20 n= 7890 bayes= 9.77424 E= 1.9e-017
 438   -982   -982    251   -982
 439   -154     34    166   -154
 440   -982   -982   -982    162
 441   -982   -982    251   -982
 442     78     92    -66   -982
 443   -982    251   -982   -982
 444   -154   -982    234   -982
 445   -982    -66   -982    145
 446   -982   -982   -982    162
 447   -154     34   -982    104
 448     78     34   -982    -55
 449    -55   -982    215   -982
 450   -982   -982    192      4
 451   -982    251   -982   -982
 452   -154     34    166   -154
 453   -982    234   -982   -154
 454    162   -982   -982   -982
 455   -982   -982   -982    162
 456    104   -982   -982      4
 457   -154   -982    215   -154
 458 --------------------------------------------------------------------------------
 459
 460 --------------------------------------------------------------------------------
 461         Motif 3 position-specific probability matrix
 462 --------------------------------------------------------------------------------
 463 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 1.9e-017
 464  0.000000  0.000000  1.000000  0.000000
 465  0.111111  0.222222  0.555556  0.111111
 466  0.000000  0.000000  0.000000  1.000000
 467  0.000000  0.000000  1.000000  0.000000
 468  0.555556  0.333333  0.111111  0.000000
 469  0.000000  1.000000  0.000000  0.000000
 470  0.111111  0.000000  0.888889  0.000000
 471  0.000000  0.111111  0.000000  0.888889
 472  0.000000  0.000000  0.000000  1.000000
 473  0.111111  0.222222  0.000000  0.666667
 474  0.555556  0.222222  0.000000  0.222222
 475  0.222222  0.000000  0.777778  0.000000
 476  0.000000  0.000000  0.666667  0.333333
 477  0.000000  1.000000  0.000000  0.000000
 478  0.111111  0.222222  0.555556  0.111111
 479  0.000000  0.888889  0.000000  0.111111
 480  1.000000  0.000000  0.000000  0.000000
 481  0.000000  0.000000  0.000000  1.000000
 482  0.666667  0.000000  0.000000  0.333333
 483  0.111111  0.000000  0.777778  0.111111
 484 --------------------------------------------------------------------------------
 485
 486 --------------------------------------------------------------------------------
 487         Motif 3 regular expression
 488 --------------------------------------------------------------------------------
 489 G[GC]TG[AC]CGTT[TC][ACT][GA][GT]C[GC]CAT[AT]G
 490 --------------------------------------------------------------------------------
 491
 492
 493
 494
 495 Time 20.03 secs.
 496
 497 ********************************************************************************
 498
 499
 500 ********************************************************************************
 501 MOTIF  4        width =   15   sites =   9   llr = 142   E-value = 2.9e-008
 502 ********************************************************************************
 503 --------------------------------------------------------------------------------
 504         Motif 4 Description
 505 --------------------------------------------------------------------------------
 506 Simplified        A  ::::9:::::8::::
 507 pos.-specific     C  a8:::11:89:899:
 508 probability       G  :::::1:::::11:2
 509 matrix            T  :2aa189a2121:18
 510
 511          bits    2.5 *
 512                  2.3 *
 513                  2.0 *        *  **
 514                  1.8 *        *  **
 515 Information      1.5 ****   *** ***
 516 content          1.3 ****  **** ***
 517 (22.8 bits)      1.0 ***** **** ****
 518                  0.8 ***************
 519                  0.5 ***************
 520                  0.3 ***************
 521                  0.0 ---------------
 522
 523 Multilevel           CCTTATTTCCACCCT
 524 consensus             T      T T   G
 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_Contig1850.5      +    723  6.31e-10 TATTGTTCAC CCTTATTTCCACCCT CAAAGGATAA
 535 MIT_Sbay_c841_3215           +    742  6.31e-10 TATTGTTCAC CCTTATTTCCACCCT CAAACGACAA
 536 MIT_Smik_c193_2483           +    716  6.31e-10 TATTATTCAC CCTTATTTCCACCCT CAAACGATAA
 537 MIT_Spar_c429_3020           +    716  6.31e-10 TATTGTTCAC CCTTATTTCCACCCT CAAACGATAA
 538 SGD_Scer_YDL205C             +    715  6.31e-10 TATTGTTCAC CCTTATTTCCACCCT CAAACGATAA
 539 MIT_Spar_c130_3923           -    332  8.79e-08 AACAACATAT CCTTAGCTTCACCCT GCCAATACTG
 540 MIT_Sbay_c896_21277          +    178  6.08e-07 AAAATTGTTT CTTTATTTTTTCCCT CTTTTCCATG
 541 SGD_Scer_YDR047W             -    467  1.01e-06 GAAAAAACTT CTTTACTTCCATGCG CGCGTTTTTG
 542 WashU_Skud_Contig1362.1      +    186  1.07e-06 AATTTTTTGG CCTTTTTTCCTGCTG CCAAAAAACC
 543 --------------------------------------------------------------------------------
 544
 545 --------------------------------------------------------------------------------
 546         Motif 4 block diagrams
 547 --------------------------------------------------------------------------------
 548 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 549 -------------            ----------------  -------------
 550 WashU_Skud_Contig1850.5           6.3e-10  722_[+4]_123
 551 MIT_Sbay_c841_3215                6.3e-10  741_[+4]_104
 552 MIT_Smik_c193_2483                6.3e-10  715_[+4]_130
 553 MIT_Spar_c429_3020                6.3e-10  715_[+4]_130
 554 SGD_Scer_YDL205C                  6.3e-10  714_[+4]_131
 555 MIT_Spar_c130_3923                8.8e-08  331_[-4]_654
 556 MIT_Sbay_c896_21277               6.1e-07  177_[+4]_808
 557 SGD_Scer_YDR047W                    1e-06  466_[-4]_519
 558 WashU_Skud_Contig1362.1           1.1e-06  185_[+4]_561
 559 --------------------------------------------------------------------------------
 560
 561 --------------------------------------------------------------------------------
 562         Motif 4 in BLOCKS format
 563 --------------------------------------------------------------------------------
 564 BL   MOTIF 4 width=15 seqs=9
 565 WashU_Skud_Contig1850.5  (  723) CCTTATTTCCACCCT  1
 566 MIT_Sbay_c841_3215       (  742) CCTTATTTCCACCCT  1
 567 MIT_Smik_c193_2483       (  716) CCTTATTTCCACCCT  1
 568 MIT_Spar_c429_3020       (  716) CCTTATTTCCACCCT  1
 569 SGD_Scer_YDL205C         (  715) CCTTATTTCCACCCT  1
 570 MIT_Spar_c130_3923       (  332) CCTTAGCTTCACCCT  1
 571 MIT_Sbay_c896_21277      (  178) CTTTATTTTTTCCCT  1
 572 SGD_Scer_YDR047W         (  467) CTTTACTTCCATGCG  1
 573 WashU_Skud_Contig1362.1  (  186) CCTTTTTTCCTGCTG  1
 574 //
 575
 576 --------------------------------------------------------------------------------
 577
 578 --------------------------------------------------------------------------------
 579         Motif 4 position-specific scoring matrix
 580 --------------------------------------------------------------------------------
 581 log-odds matrix: alength= 4 w= 15 n= 7935 bayes= 9.78245 E= 2.9e-008
 582   -982    251   -982   -982
 583   -982    215   -982    -55
 584   -982   -982   -982    162
 585   -982   -982   -982    162
 586    145   -982   -982   -154
 587   -982    -66    -66    126
 588   -982    -66   -982    145
 589   -982   -982   -982    162
 590   -982    215   -982    -55
 591   -982    234   -982   -154
 592    126   -982   -982    -55
 593   -982    215    -66   -154
 594   -982    234    -66   -982
 595   -982    234   -982   -154
 596   -982   -982     34    126
 597 --------------------------------------------------------------------------------
 598
 599 --------------------------------------------------------------------------------
 600         Motif 4 position-specific probability matrix
 601 --------------------------------------------------------------------------------
 602 letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 2.9e-008
 603  0.000000  1.000000  0.000000  0.000000
 604  0.000000  0.777778  0.000000  0.222222
 605  0.000000  0.000000  0.000000  1.000000
 606  0.000000  0.000000  0.000000  1.000000
 607  0.888889  0.000000  0.000000  0.111111
 608  0.000000  0.111111  0.111111  0.777778
 609  0.000000  0.111111  0.000000  0.888889
 610  0.000000  0.000000  0.000000  1.000000
 611  0.000000  0.777778  0.000000  0.222222
 612  0.000000  0.888889  0.000000  0.111111
 613  0.777778  0.000000  0.000000  0.222222
 614  0.000000  0.777778  0.111111  0.111111
 615  0.000000  0.888889  0.111111  0.000000
 616  0.000000  0.888889  0.000000  0.111111
 617  0.000000  0.000000  0.222222  0.777778
 618 --------------------------------------------------------------------------------
 619
 620 --------------------------------------------------------------------------------
 621         Motif 4 regular expression
 622 --------------------------------------------------------------------------------
 623 C[CT]TTATTT[CT]C[AT]CCC[TG]
 624 --------------------------------------------------------------------------------
 625
 626
 627
 628
 629 Time 26.29 secs.
 630
 631 ********************************************************************************
 632
 633
 634 ********************************************************************************
 635 MOTIF  5        width =   20   sites =   9   llr = 161   E-value = 2.9e-008
 636 ********************************************************************************
 637 --------------------------------------------------------------------------------
 638         Motif 5 Description
 639 --------------------------------------------------------------------------------
 640 Simplified        A  2:6197:7:::::::22:a6
 641 pos.-specific     C  :8211:6:11:9:1:::6:3
 642 probability       G  8228:2:3:6:196:88::1
 643 matrix            T  :::::14:93a:13a::4::
 644
 645          bits    2.5
 646                  2.3
 647                  2.0            **
 648                  1.8  *         **
 649 Information      1.5 ** *      *** *** *
 650 content          1.3 ** **   * *** *** *
 651 (25.9 bits)      1.0 ** ** *** *** *****
 652                  0.8 ** ** **************
 653                  0.5 ********************
 654                  0.3 ********************
 655                  0.0 --------------------
 656
 657 Multilevel           GCAGAACATGTCGGTGGCAA
 658 consensus            AGC  GTG T   T AAT C
 659 sequence               G
 660
 661 --------------------------------------------------------------------------------
 662
 663 --------------------------------------------------------------------------------
 664         Motif 5 sites sorted by position p-value
 665 --------------------------------------------------------------------------------
 666 Sequence name            Strand  Start   P-value                    Site
 667 -------------            ------  ----- ---------            --------------------
 668 SGD_Scer_YDL205C             +    561  1.62e-11 AAGGGTAGCA GCAGAATGTGTCGGTGGTAC CGGTGTGATA
 669 MIT_Spar_c130_3923           +    171  4.79e-11 GACAAAAAGG GCAGAACATTTCGTTGGCAA AATTTAAACT
 670 SGD_Scer_YDR047W             +    174  1.01e-10 GATGAAAATG GCAGAACATTTCGCTGGCAA AATTAAAACT
 671 WashU_Skud_Contig1850.5      +    566  1.81e-09 AAGGATAGCA ACGGAATGTGTCGGTGGTAG CGGATGTGGC
 672 MIT_Smik_c193_2483           +    563  3.96e-09 AAGGGTAGCG ACGGCGTATGTCGGTGGTAC CGGATATGGC
 673 WashU_Skud_Contig1362.1      +    138  5.96e-09 CATACGAAAG GCAGAACACCTCGTTGACAA AACTGAAACT
 674 MIT_Sbay_c841_3215           +    572  1.26e-08 CGAGGGTCGC GGCCAATGTGTCGGTAGTAC CGGATGGGGC
 675 MIT_Sbay_c896_21277          +    144  3.29e-08 GACACGAATA GGAAAGCATTTCGTTGACAA AAATAAAATT
 676 MIT_Spar_c429_3020           +    786  4.67e-08 GGATTGAAAA GCCGATCATGTGTGTAGCAA TAGTAGTAGT
 677 --------------------------------------------------------------------------------
 678
 679 --------------------------------------------------------------------------------
 680         Motif 5 block diagrams
 681 --------------------------------------------------------------------------------
 682 SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
 683 -------------            ----------------  -------------
 684 SGD_Scer_YDL205C                  1.6e-11  560_[+5]_280
 685 MIT_Spar_c130_3923                4.8e-11  170_[+5]_810
 686 SGD_Scer_YDR047W                    1e-10  173_[+5]_807
 687 WashU_Skud_Contig1850.5           1.8e-09  565_[+5]_275
 688 MIT_Smik_c193_2483                  4e-09  562_[+5]_278
 689 WashU_Skud_Contig1362.1             6e-09  137_[+5]_604
 690 MIT_Sbay_c841_3215                1.3e-08  571_[+5]_269
 691 MIT_Sbay_c896_21277               3.3e-08  143_[+5]_837
 692 MIT_Spar_c429_3020                4.7e-08  785_[+5]_55
 693 --------------------------------------------------------------------------------
 694
 695 --------------------------------------------------------------------------------
 696         Motif 5 in BLOCKS format
 697 --------------------------------------------------------------------------------
 698 BL   MOTIF 5 width=20 seqs=9
 699 SGD_Scer_YDL205C         (  561) GCAGAATGTGTCGGTGGTAC  1
 700 MIT_Spar_c130_3923       (  171) GCAGAACATTTCGTTGGCAA  1
 701 SGD_Scer_YDR047W         (  174) GCAGAACATTTCGCTGGCAA  1
 702 WashU_Skud_Contig1850.5  (  566) ACGGAATGTGTCGGTGGTAG  1
 703 MIT_Smik_c193_2483       (  563) ACGGCGTATGTCGGTGGTAC  1
 704 WashU_Skud_Contig1362.1  (  138) GCAGAACACCTCGTTGACAA  1
 705 MIT_Sbay_c841_3215       (  572) GGCCAATGTGTCGGTAGTAC  1
 706 MIT_Sbay_c896_21277      (  144) GGAAAGCATTTCGTTGACAA  1
 707 MIT_Spar_c429_3020       (  786) GCCGATCATGTGTGTAGCAA  1
 708 //
 709
 710 --------------------------------------------------------------------------------
 711
 712 --------------------------------------------------------------------------------
 713         Motif 5 position-specific scoring matrix
 714 --------------------------------------------------------------------------------
 715 log-odds matrix: alength= 4 w= 20 n= 7890 bayes= 9.77424 E= 2.9e-008
 716    -55   -982    215   -982
 717   -982    215     34   -982
 718     78     34     34   -982
 719   -154    -66    215   -982
 720    145    -66   -982   -982
 721    104   -982     34   -154
 722   -982    166   -982     45
 723    104   -982     92   -982
 724   -982    -66   -982    145
 725   -982    -66    166      4
 726   -982   -982   -982    162
 727   -982    234    -66   -982
 728   -982   -982    234   -154
 729   -982    -66    166      4
 730   -982   -982   -982    162
 731    -55   -982    215   -982
 732    -55   -982    215   -982
 733   -982    166   -982     45
 734    162   -982   -982   -982
 735     78     92    -66   -982
 736 --------------------------------------------------------------------------------
 737
 738 --------------------------------------------------------------------------------
 739         Motif 5 position-specific probability matrix
 740 --------------------------------------------------------------------------------
 741 letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.9e-008
 742  0.222222  0.000000  0.777778  0.000000
 743  0.000000  0.777778  0.222222  0.000000
 744  0.555556  0.222222  0.222222  0.000000
 745  0.111111  0.111111  0.777778  0.000000
 746  0.888889  0.111111  0.000000  0.000000
 747  0.666667  0.000000  0.222222  0.111111
 748  0.000000  0.555556  0.000000  0.444444
 749  0.666667  0.000000  0.333333  0.000000
 750  0.000000  0.111111  0.000000  0.888889
 751  0.000000  0.111111  0.555556  0.333333
 752  0.000000  0.000000  0.000000  1.000000
 753  0.000000  0.888889  0.111111  0.000000
 754  0.000000  0.000000  0.888889  0.111111
 755  0.000000  0.111111  0.555556  0.333333
 756  0.000000  0.000000  0.000000  1.000000
 757  0.222222  0.000000  0.777778  0.000000
 758  0.222222  0.000000  0.777778  0.000000
 759  0.000000  0.555556  0.000000  0.444444
 760  1.000000  0.000000  0.000000  0.000000
 761  0.555556  0.333333  0.111111  0.000000
 762 --------------------------------------------------------------------------------
 763
 764 --------------------------------------------------------------------------------
 765         Motif 5 regular expression
 766 --------------------------------------------------------------------------------
 767 [GA][CG][ACG]GA[AG][CT][AG]T[GT]TCG[GT]T[GA][GA][CT]A[AC]
 768 --------------------------------------------------------------------------------
 769
 770
 771
 772
 773 Time 32.47 secs.
 774
 775 ********************************************************************************
 776
 777
 778 ********************************************************************************
 779 SUMMARY OF MOTIFS
 780 ********************************************************************************
 781
 782 --------------------------------------------------------------------------------
 783         Combined block diagrams: non-overlapping sites with p-value < 0.0001
 784 --------------------------------------------------------------------------------
 785 SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
 786 -------------            ----------------  -------------
 787 SGD_Scer_YDL205C                 6.46e-34  110_[+1(1.67e-11)]_358_[+2(3.06e-13)]_52_[+5(1.62e-11)]_92_[+3(3.00e-13)]_22_[+4(6.31e-10)]_54_[+5(2.69e-05)]_57
 788 MIT_Spar_c429_3020               3.43e-29  110_[+1(1.67e-11)]_173_[-4(1.29e-05)]_174_[+2(9.57e-12)]_49_[+5(9.46e-05)]_92_[+3(3.00e-13)]_22_[+4(6.31e-10)]_55_[+5(4.67e-08)]_55
 789 MIT_Smik_c193_2483               1.01e-24  112_[+1(1.63e-10)]_21_[-3(6.96e-05)]_319_[+2(1.25e-09)]_50_[+5(3.96e-09)]_91_[+3(1.45e-10)]_22_[+4(6.31e-10)]_130
 790 MIT_Sbay_c841_3215               6.11e-27  39_[+4(6.88e-05)]_57_[+1(5.77e-11)]_371_[+2(2.31e-11)]_49_[+5(1.26e-08)]_108_[+3(3.16e-11)]_22_[+4(6.31e-10)]_104
 791 WashU_Skud_Contig1850.5          2.40e-28  110_[+1(5.77e-11)]_272_[-3(9.23e-05)]_71_[+2(5.55e-10)]_52_[+5(1.81e-09)]_53_[-1(8.53e-05)]_22_[+3(3.00e-13)]_22_[+4(6.31e-10)]_123
 792 SGD_Scer_YDR047W                 4.48e-22  173_[+5(1.01e-10)]_44_[+1(7.68e-10)]_31_[-2(1.18e-09)]_158_[-4(1.01e-06)]_134_[+2(4.56e-05)]_77_[+3(2.43e-10)]_268
 793 MIT_Spar_c130_3923               3.62e-24  22_[+4(6.45e-05)]_133_[+5(4.79e-11)]_44_[+1(4.70e-10)]_32_[-2(2.77e-10)]_25_[-4(8.79e-08)]_124_[-1(9.89e-05)]_222_[+3(2.43e-10)]_36_[+4(1.03e-05)]_143_[+2(2.11e-05)]_54
 794 MIT_Sbay_c896_21277              4.53e-19  143_[+5(3.29e-08)]_14_[+4(6.08e-07)]_13_[+1(2.60e-10)]_13_[-2(1.64e-10)]_493_[+2(7.81e-05)]_197_[-3(4.38e-08)]_12
 795 WashU_Skud_Contig1362.1          3.15e-19  137_[+5(5.96e-09)]_28_[+4(1.07e-06)]_[+1(9.83e-10)]_25_[-2(6.00e-10)]_252_[-2(2.11e-05)]_165_[+3(2.69e-08)]_39
 796 --------------------------------------------------------------------------------
 797
 798 ********************************************************************************
 799
 800
 801 ********************************************************************************
 802 Stopped because nmotifs = 5 reached.
 803 ********************************************************************************
 804
 805 CPU: dhn02990.mrc-dunn.cam.ac.uk
 806
 807 ********************************************************************************