******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= motifs/405/405.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10400 1.0000 500 14727 1.0000 500 1765 1.0000 500 20854 1.0000 500 20888 1.0000 500 20915 1.0000 500 21747 1.0000 500 22128 1.0000 500 22823 1.0000 500 22867 1.0000 500 23261 1.0000 500 23343 1.0000 500 24587 1.0000 500 24830 1.0000 500 2502 1.0000 500 25820 1.0000 500 262720 1.0000 500 263343 1.0000 500 263344 1.0000 500 26635 1.0000 500 269328 1.0000 500 2799 1.0000 500 2906 1.0000 500 2987 1.0000 500 31732 1.0000 500 31777 1.0000 500 34851 1.0000 500 35356 1.0000 500 3611 1.0000 500 36201 1.0000 500 3947 1.0000 500 4322 1.0000 500 5725 1.0000 500 5747 1.0000 500 6047 1.0000 500 6192 1.0000 500 6332 1.0000 500 6568 1.0000 500 7633 1.0000 500 9693 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/405/405.seqs.fa -oc motifs/405 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 40 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 20000 N= 40 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.271 C 0.224 G 0.244 T 0.262 Background letter frequencies (from dataset with add-one prior applied): A 0.270 C 0.224 G 0.244 T 0.262 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 35 llr = 312 E-value = 3.6e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 3:365:3:15:: pos.-specific C 13::::111::: probability G 6:73:a2182:9 matrix T :7115:49:3a: bits 2.2 1.9 * * 1.7 * ** 1.5 * ** Relative 1.3 * ** ** Entropy 1.1 * * ** ** (12.9 bits) 0.9 ** ** ** ** 0.6 ****** ** ** 0.4 ****** ***** 0.2 ************ 0.0 ------------ Multilevel GTGATGTTGATG consensus ACAGA A T sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 24830 40 4.57e-07 CCTTTGGTTC GTGATGTTGTTG ATGGCTTGTT 3611 277 8.31e-07 GGGAAGGTGT GTGAAGGTGATG AAAAAGCATT 31732 210 1.38e-06 AGTAAATAAC ATGAAGTTGATG TGACGTGCCC 14727 68 1.38e-06 TGGTATGCGT GTGGTGATGATG ATTGTGATGG 5747 232 2.84e-06 ACGTGACGAC ATGATGGTGATG ATGTATATTA 36201 145 3.34e-06 GATACTGGGC GTGATGGTGGTG GTCTGGTGGT 2502 170 4.12e-06 GAGAGGGATC GTAATGTTGTTG GAGAGGGTGA 2987 457 4.47e-06 GACGGTGTGG GTGGTGGTGTTG CAGGTTTGCT 21747 346 5.22e-06 GTGATACCTC GTAAAGTTGTTG GTGCTCTCCC 4322 34 6.51e-06 TTAGTGCTGA GCAAAGTTGATG CTGTTCCAGA 20888 46 7.40e-06 TGCCTGACAT GTAATGATGTTG CCCAGATGTG 6332 47 8.55e-06 TGATTTCCTT GTGGAGATGGTG AAGGATTTCC 23343 278 1.18e-05 GTTGTTGACT GTGGTGCTGATG CTGCTGTTGT 10400 327 1.92e-05 GCAGCTCATC GTGTAGATGATG TAGTAAGGGA 262720 245 2.09e-05 CTTTAGTAGT ATGATGTTCATG ACGAGGAAGG 6568 124 2.31e-05 TTGATGAGGT GTGATGGCGATG CAGAAGCCGC 2906 283 2.31e-05 TTAAGCTGGA GTGGAGTTAATG GATTACGAGT 31777 229 3.04e-05 GCCATGTTGG GCGATGTTGCTG CTGCCGATGG 263344 416 3.04e-05 TTTGGCAGCT ACAAAGTTGTTG AGACGATTCC 263343 416 3.04e-05 TTTGGCAGCT ACAAAGTTGTTG AGACGATTCC 1765 286 3.31e-05 TCGTTGGTAG ATGATGTGGATG AAGAGCAGAA 22867 142 3.93e-05 GGAGGTGGCC ATGTTGTTGTTG GCGTGGTGAC 6047 53 4.70e-05 TGTTTACTCA CTAAAGATGTTG TCTCTAGTGC 3947 339 5.12e-05 GCATAGGCGA CCGAAGATGGTG ATGGCCATCC 22128 172 5.55e-05 TCGGAGGATC ATTGAGTTGATG TTCAACCCAT 6192 454 7.08e-05 AAAGCGAGTT GTGGTGATAGTG GTACATTTTA 269328 137 7.08e-05 AGGGCGGGGG ACGAAGTCGATG TGGGAGAAAC 5725 10 8.22e-05 TTGCTGTTG GCGATGGGGTTG AGCCAATGGC 22823 192 8.88e-05 ATCTCTCACT GCGATGGTAGTG AAAGGTTCAT 23261 177 1.03e-04 TATGGGAGTT GTGGATATGATG GATGCTGTCT 35356 309 1.45e-04 TTAAATACAT ATAGAGATCATG TAGAGGCTAA 34851 127 1.65e-04 AATACAGTCT CCAAAGCTGATG CGATCTGAGA 26635 372 1.87e-04 CTCGGTTCAT CTGATGATGATT TGCACGATGA 25820 18 1.87e-04 TTTGTGATGG GTGGTGGTGGTA TCTTCATGAT 9693 355 2.25e-04 AACATTCGGC GCTGTGTTCATG TGATGATTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24830 4.6e-07 39_[+1]_449 3611 8.3e-07 276_[+1]_212 31732 1.4e-06 209_[+1]_279 14727 1.4e-06 67_[+1]_421 5747 2.8e-06 231_[+1]_257 36201 3.3e-06 144_[+1]_344 2502 4.1e-06 169_[+1]_319 2987 4.5e-06 456_[+1]_32 21747 5.2e-06 345_[+1]_143 4322 6.5e-06 33_[+1]_455 20888 7.4e-06 45_[+1]_443 6332 8.6e-06 46_[+1]_442 23343 1.2e-05 277_[+1]_211 10400 1.9e-05 326_[+1]_162 262720 2.1e-05 244_[+1]_244 6568 2.3e-05 123_[+1]_365 2906 2.3e-05 282_[+1]_206 31777 3e-05 228_[+1]_260 263344 3e-05 415_[+1]_73 263343 3e-05 415_[+1]_73 1765 3.3e-05 285_[+1]_203 22867 3.9e-05 141_[+1]_347 6047 4.7e-05 52_[+1]_436 3947 5.1e-05 338_[+1]_150 22128 5.5e-05 171_[+1]_317 6192 7.1e-05 453_[+1]_35 269328 7.1e-05 136_[+1]_352 5725 8.2e-05 9_[+1]_479 22823 8.9e-05 191_[+1]_297 23261 0.0001 176_[+1]_312 35356 0.00015 308_[+1]_180 34851 0.00017 126_[+1]_362 26635 0.00019 371_[+1]_117 25820 0.00019 17_[+1]_471 9693 0.00023 354_[+1]_134 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=35 24830 ( 40) GTGATGTTGTTG 1 3611 ( 277) GTGAAGGTGATG 1 31732 ( 210) ATGAAGTTGATG 1 14727 ( 68) GTGGTGATGATG 1 5747 ( 232) ATGATGGTGATG 1 36201 ( 145) GTGATGGTGGTG 1 2502 ( 170) GTAATGTTGTTG 1 2987 ( 457) GTGGTGGTGTTG 1 21747 ( 346) GTAAAGTTGTTG 1 4322 ( 34) GCAAAGTTGATG 1 20888 ( 46) GTAATGATGTTG 1 6332 ( 47) GTGGAGATGGTG 1 23343 ( 278) GTGGTGCTGATG 1 10400 ( 327) GTGTAGATGATG 1 262720 ( 245) ATGATGTTCATG 1 6568 ( 124) GTGATGGCGATG 1 2906 ( 283) GTGGAGTTAATG 1 31777 ( 229) GCGATGTTGCTG 1 263344 ( 416) ACAAAGTTGTTG 1 263343 ( 416) ACAAAGTTGTTG 1 1765 ( 286) ATGATGTGGATG 1 22867 ( 142) ATGTTGTTGTTG 1 6047 ( 53) CTAAAGATGTTG 1 3947 ( 339) CCGAAGATGGTG 1 22128 ( 172) ATTGAGTTGATG 1 6192 ( 454) GTGGTGATAGTG 1 269328 ( 137) ACGAAGTCGATG 1 5725 ( 10) GCGATGGGGTTG 1 22823 ( 192) GCGATGGTAGTG 1 23261 ( 177) GTGGATATGATG 1 35356 ( 309) ATAGAGATCATG 1 34851 ( 127) CCAAAGCTGATG 1 26635 ( 372) CTGATGATGATT 1 25820 ( 18) GTGGTGGTGGTA 1 9693 ( 355) GCTGTGTTCATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 19560 bayes= 9.94673 E= 3.6e-010 8 -97 130 -1177 -1177 35 -1177 145 -7 -1177 149 -219 122 -1177 37 -219 76 -1177 -1177 105 -1177 -1177 200 -319 8 -197 -9 71 -1177 -197 -209 176 -166 -139 177 -1177 93 -297 -51 13 -1177 -1177 -1177 193 -324 -1177 195 -319 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 35 E= 3.6e-010 0.285714 0.114286 0.600000 0.000000 0.000000 0.285714 0.000000 0.714286 0.257143 0.000000 0.685714 0.057143 0.628571 0.000000 0.314286 0.057143 0.457143 0.000000 0.000000 0.542857 0.000000 0.000000 0.971429 0.028571 0.285714 0.057143 0.228571 0.428571 0.000000 0.057143 0.057143 0.885714 0.085714 0.085714 0.828571 0.000000 0.514286 0.028571 0.171429 0.285714 0.000000 0.000000 0.000000 1.000000 0.028571 0.000000 0.942857 0.028571 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GA][TC][GA][AG][TA]G[TAG]TG[AT]TG -------------------------------------------------------------------------------- Time 14.56 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 21 llr = 270 E-value = 6.3e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 72722a9:a493387565961 pos.-specific C 12273::a:3:16::512:16 probability G 14::5::::2:4:13:3:123 matrix T :21:::::::1111:::2::: bits 2.2 1.9 * * 1.7 * ** 1.5 * ** Relative 1.3 **** * * Entropy 1.1 **** * * * (18.5 bits) 0.9 ** **** * **** * 0.6 * ******* * ***** *** 0.4 * ********* ***** *** 0.2 * ******************* 0.0 --------------------- Multilevel AGACGAACAAAGCAACAAAAC consensus T C C AA GAGC GG sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 263344 56 6.46e-11 TATACCGCAA AGACGAACAAAGCAAAGTAAC ACTCTTGTGT 263343 56 6.46e-11 TATACCGCAA AGACGAACAAAGCAAAGTAAC ACTCTTGTGT 22867 479 1.35e-10 AACCCCCAAC AGACGAACACACCAACACAAC T 269328 2 1.08e-08 G ATCCAAACAAAGCAAAAAAGC AGCACACAGC 25820 385 3.08e-08 TGCAAATTGC AGTCAAACAAAGCAACCAAAC AAAGCAAAAG 22823 419 7.85e-08 ATCATCGGTG ACACCAACCGAACAGCAAAAC CAAAGCACCC 35356 456 3.01e-07 ATACGACGAC GAACAAACAAAGCAGAAGAAC TGAACAAAGC 23261 289 3.63e-07 GATACAAGTA AGACGAACACTGATAAGAAGG ATGAGTCTGC 9693 162 4.37e-07 AATATCAAAC AAACGACCACAACAACACAGA GAGCAAAATG 31777 383 4.37e-07 TGTCGCCCTC ATCCGAACAGAACAACAACAA TGGCGCTGTT 6332 459 5.25e-07 CTAAATACCT TTCACAACACAACAACGAAAC AACGCAGATC 14727 476 6.84e-07 TCCAACCTAG CCATCAACACATCAACACAAC AGCG 20854 301 7.46e-07 GGTCGCCAAA AGACCAACAAAAAGAAAAGGG GCAGTGGAGG 2799 137 1.23e-06 GTCTGTCTAC GAAGGAACACAAAAGCAAAAG CTAGAATTTT 24587 11 1.33e-06 CAACCAAGGC ATACGAACACAATATAGCACC ATCATTTTGA 4322 85 1.69e-06 GACTCAATGA AGAACATCAGAGCTGCAAAAG CATTGGGGAT 20915 390 3.07e-06 CGTTCGGAGA CTTCCAACAATGCAACGTACG CTCATTTTCC 10400 298 4.06e-06 AAAGCAGTAA CCACCAACAGACAGGAGTAGC AGCTCATCGT 34851 394 6.06e-06 TGGTGGGGTG GAACGAACAAATTAACCCGAC GACGAACACT 6192 331 6.47e-06 AGGGGGTCAA AGCAAAAAAGAGAAGAAAAAG AGAGGGGATA 36201 336 1.50e-05 CAATACTCAT ACAAGAACAATCATAAATACA CAATACAATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263344 6.5e-11 55_[+2]_424 263343 6.5e-11 55_[+2]_424 22867 1.4e-10 478_[+2]_1 269328 1.1e-08 1_[+2]_478 25820 3.1e-08 384_[+2]_95 22823 7.9e-08 418_[+2]_61 35356 3e-07 455_[+2]_24 23261 3.6e-07 288_[+2]_191 9693 4.4e-07 161_[+2]_318 31777 4.4e-07 382_[+2]_97 6332 5.2e-07 458_[+2]_21 14727 6.8e-07 475_[+2]_4 20854 7.5e-07 300_[+2]_179 2799 1.2e-06 136_[+2]_343 24587 1.3e-06 10_[+2]_469 4322 1.7e-06 84_[+2]_395 20915 3.1e-06 389_[+2]_90 10400 4.1e-06 297_[+2]_182 34851 6.1e-06 393_[+2]_86 6192 6.5e-06 330_[+2]_149 36201 1.5e-05 335_[+2]_144 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=21 263344 ( 56) AGACGAACAAAGCAAAGTAAC 1 263343 ( 56) AGACGAACAAAGCAAAGTAAC 1 22867 ( 479) AGACGAACACACCAACACAAC 1 269328 ( 2) ATCCAAACAAAGCAAAAAAGC 1 25820 ( 385) AGTCAAACAAAGCAACCAAAC 1 22823 ( 419) ACACCAACCGAACAGCAAAAC 1 35356 ( 456) GAACAAACAAAGCAGAAGAAC 1 23261 ( 289) AGACGAACACTGATAAGAAGG 1 9693 ( 162) AAACGACCACAACAACACAGA 1 31777 ( 383) ATCCGAACAGAACAACAACAA 1 6332 ( 459) TTCACAACACAACAACGAAAC 1 14727 ( 476) CCATCAACACATCAACACAAC 1 20854 ( 301) AGACCAACAAAAAGAAAAGGG 1 2799 ( 137) GAAGGAACACAAAAGCAAAAG 1 24587 ( 11) ATACGAACACAATATAGCACC 1 4322 ( 85) AGAACATCAGAGCTGCAAAAG 1 20915 ( 390) CTTCCAACAATGCAACGTACG 1 10400 ( 298) CCACCAACAGACAGGAGTAGC 1 34851 ( 394) GAACGAACAAATTAACCCGAC 1 6192 ( 331) AGCAAAAAAGAGAAGAAAAAG 1 36201 ( 336) ACAAGAACAATCATAAATACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 19200 bayes= 11.3407 E= 6.3e-009 130 -65 -77 -246 -51 -24 65 -14 140 -24 -1104 -146 -51 167 -235 -246 -51 57 97 -1104 189 -1104 -1104 -1104 174 -223 -1104 -246 -250 209 -1104 -1104 182 -223 -1104 -1104 66 57 -3 -1104 166 -1104 -1104 -87 30 -65 82 -146 8 146 -1104 -146 149 -1104 -135 -87 130 -1104 23 -246 82 122 -1104 -1104 108 -123 45 -1104 82 9 -235 -14 166 -223 -135 -1104 119 -65 -3 -1104 -92 135 23 -1104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 21 E= 6.3e-009 0.666667 0.142857 0.142857 0.047619 0.190476 0.190476 0.380952 0.238095 0.714286 0.190476 0.000000 0.095238 0.190476 0.714286 0.047619 0.047619 0.190476 0.333333 0.476190 0.000000 1.000000 0.000000 0.000000 0.000000 0.904762 0.047619 0.000000 0.047619 0.047619 0.952381 0.000000 0.000000 0.952381 0.047619 0.000000 0.000000 0.428571 0.333333 0.238095 0.000000 0.857143 0.000000 0.000000 0.142857 0.333333 0.142857 0.428571 0.095238 0.285714 0.619048 0.000000 0.095238 0.761905 0.000000 0.095238 0.142857 0.666667 0.000000 0.285714 0.047619 0.476190 0.523810 0.000000 0.000000 0.571429 0.095238 0.333333 0.000000 0.476190 0.238095 0.047619 0.238095 0.857143 0.047619 0.095238 0.000000 0.619048 0.142857 0.238095 0.000000 0.142857 0.571429 0.285714 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- A[GT]AC[GC]AACA[ACG]A[GA][CA]A[AG][CA][AG][ACT]A[AG][CG] -------------------------------------------------------------------------------- Time 27.21 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 39 llr = 337 E-value = 5.0e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 133:31:2:222:55: pos.-specific C 661462737364923a probability G 11:2:1:11:2::3:: matrix T 2:64263525151:2: bits 2.2 1.9 * 1.7 * * 1.5 * * Relative 1.3 * * Entropy 1.1 * * * * (12.5 bits) 0.9 * * * * 0.6 ***** * * ** ** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CCTTCTCTCTCTCAAC consensus TAACACTC CGC GC sequence A C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 10400 482 1.69e-07 CGCGCACGCA CCTTCCTTCTCCCACC GCG 2799 283 8.97e-07 TGGTCTATTT CGTCCTCTCTCACAAC AGACGGGTGA 6332 189 1.04e-06 GTGAGGTTTG CCTTCTTTGTCCCACC CCTTCTATTG 3611 369 1.21e-06 ACTAGCACCC CCCCCTCCCCCCCCCC ACACACACAC 31732 230 2.82e-06 TGTGACGTGC CCTCTTTTGTCTCAAC ATATCTTCTT 6047 237 4.75e-06 TTTGGTTCCA CCTTCTCATCGTCAAC AGCATCTCCT 2502 352 5.38e-06 GGTGAGGGCT TCATCTCTCACTCATC TTCTCCTCTT 5725 326 9.83e-06 GTCAACTGAG CCTCCTCTTACCTAAC CCTATCTGTT 22128 276 9.83e-06 TCGACAACTG CCTCACCTCCGACGAC AATCGTAACC 26635 324 1.10e-05 CTTGTACCAG CCTCCCCCCTTACACC TCGACAACAT 9693 389 1.24e-05 GTCCTCATCA CCTCAACACTCTCCCC AACGTCCCAT 263344 349 1.24e-05 ATTTGAGTCC CCTGTTTCCTGCCGCC GATGTCAGAA 263343 349 1.24e-05 ATTTGAGTCC CCTGTTTCCTGCCGCC GATGTCAGAA 25820 266 1.54e-05 CAGCAGTTTA TCATCTTCCCGTCGAC AAACGGACAC 269328 375 1.72e-05 CACAGCCATC TGATCCCTCTCTCAAC GTTTGGCGAG 2906 466 1.91e-05 TTGATGTTTC CCTTTTCTCTCCCGAA GAACTAGCTA 34851 343 2.62e-05 AAGCTGGGAT GTTCCTCCCTCTCGAC TTGTAGCTTG 22823 313 2.62e-05 GAGCCACTGG CCTTCACTTCATCAAC GTGACTTGCA 20915 157 2.62e-05 GGATTGTGGC CCACCTCCTAATCCAC AGAGCGAGTG 5747 20 2.90e-05 AAAGCTACTT CGACATCTCTCTCCTC CTTTGATTTC 22867 434 2.90e-05 TGCAACTTCA TCTTCTCACAGACACC TCATAACTTT 31777 13 3.54e-05 TCCCTCTCCA AATTCTTCCCCTCCAC AGCACTCTTC 24587 121 3.54e-05 CATGTCAGAT GCTTCTTCTCCTCGCC TGTCGTTTTG 262720 359 3.90e-05 CCGAGCAGGA TCTTATCTCACTTCAC TTCGCGAAAA 20854 414 3.90e-05 AGACTTTCTC GCTCACTCCTGTCGAC GACCTGTGCA 1765 308 5.18e-05 AAGAGCAGAA CAATACCGCTCTCACC ATGTTCTCGA 24830 272 5.68e-05 TGTTGGGTGA CATCATTTCCATCGTC ACGTCGGCGG 21747 229 5.68e-05 ACGGGGGAGC CATCACCACTTTCAAC GAAGATGAAG 23343 437 6.81e-05 AATTGGCCAT TACTATTCCCCCCAAC ATTACTTGTA 2987 5 7.45e-05 CTTC CAACCGCACACCCCAC ACCGAACATC 14727 335 7.45e-05 TCCAGGCGCG CCATTTTGCCCCCCCC CTTGCTTGAC 20888 376 1.05e-04 GCATGCTAAG CACGCGCTCTACCAAC TGAGCTAATC 36201 176 1.24e-04 TAGGGATAGT CACTCTCTCGGTCGCC GAAGATCGGC 23261 51 1.45e-04 CTGTCACGAT GCTGTACTCTATCAAC GTATTAAGGA 3947 466 1.57e-04 GGATGTGAAT CCTGTGCCGTCCCATC GACGTAGCCT 35356 416 1.70e-04 GACACAGAGC TCTGCTCTGAAACAAC TGTTCCTACA 4322 442 1.98e-04 CTGCTTCTCA ACACCTCACTGCTAAC TACAAATCGA 7633 450 2.13e-04 AGGTGCTCAC TATTCTTCTTCACGTC GTATTCGTTT 6192 173 2.84e-04 GGATGGCGGA CAACACCTCACCTATC AGTCAATAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10400 1.7e-07 481_[+3]_3 2799 9e-07 282_[+3]_202 6332 1e-06 188_[+3]_296 3611 1.2e-06 368_[+3]_116 31732 2.8e-06 229_[+3]_255 6047 4.8e-06 236_[+3]_248 2502 5.4e-06 351_[+3]_133 5725 9.8e-06 325_[+3]_159 22128 9.8e-06 275_[+3]_209 26635 1.1e-05 323_[+3]_161 9693 1.2e-05 388_[+3]_96 263344 1.2e-05 348_[+3]_136 263343 1.2e-05 348_[+3]_136 25820 1.5e-05 265_[+3]_219 269328 1.7e-05 374_[+3]_110 2906 1.9e-05 465_[+3]_19 34851 2.6e-05 342_[+3]_142 22823 2.6e-05 312_[+3]_172 20915 2.6e-05 156_[+3]_328 5747 2.9e-05 19_[+3]_465 22867 2.9e-05 433_[+3]_51 31777 3.5e-05 12_[+3]_472 24587 3.5e-05 120_[+3]_364 262720 3.9e-05 358_[+3]_126 20854 3.9e-05 413_[+3]_71 1765 5.2e-05 307_[+3]_177 24830 5.7e-05 271_[+3]_213 21747 5.7e-05 228_[+3]_256 23343 6.8e-05 436_[+3]_48 2987 7.4e-05 4_[+3]_480 14727 7.4e-05 334_[+3]_150 20888 0.0001 375_[+3]_109 36201 0.00012 175_[+3]_309 23261 0.00015 50_[+3]_434 3947 0.00016 465_[+3]_19 35356 0.00017 415_[+3]_69 4322 0.0002 441_[+3]_43 7633 0.00021 449_[+3]_35 6192 0.00028 172_[+3]_312 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=39 10400 ( 482) CCTTCCTTCTCCCACC 1 2799 ( 283) CGTCCTCTCTCACAAC 1 6332 ( 189) CCTTCTTTGTCCCACC 1 3611 ( 369) CCCCCTCCCCCCCCCC 1 31732 ( 230) CCTCTTTTGTCTCAAC 1 6047 ( 237) CCTTCTCATCGTCAAC 1 2502 ( 352) TCATCTCTCACTCATC 1 5725 ( 326) CCTCCTCTTACCTAAC 1 22128 ( 276) CCTCACCTCCGACGAC 1 26635 ( 324) CCTCCCCCCTTACACC 1 9693 ( 389) CCTCAACACTCTCCCC 1 263344 ( 349) CCTGTTTCCTGCCGCC 1 263343 ( 349) CCTGTTTCCTGCCGCC 1 25820 ( 266) TCATCTTCCCGTCGAC 1 269328 ( 375) TGATCCCTCTCTCAAC 1 2906 ( 466) CCTTTTCTCTCCCGAA 1 34851 ( 343) GTTCCTCCCTCTCGAC 1 22823 ( 313) CCTTCACTTCATCAAC 1 20915 ( 157) CCACCTCCTAATCCAC 1 5747 ( 20) CGACATCTCTCTCCTC 1 22867 ( 434) TCTTCTCACAGACACC 1 31777 ( 13) AATTCTTCCCCTCCAC 1 24587 ( 121) GCTTCTTCTCCTCGCC 1 262720 ( 359) TCTTATCTCACTTCAC 1 20854 ( 414) GCTCACTCCTGTCGAC 1 1765 ( 308) CAATACCGCTCTCACC 1 24830 ( 272) CATCATTTCCATCGTC 1 21747 ( 229) CATCACCACTTTCAAC 1 23343 ( 437) TACTATTCCCCCCAAC 1 2987 ( 5) CAACCGCACACCCCAC 1 14727 ( 335) CCATTTTGCCCCCCCC 1 20888 ( 376) CACGCGCTCTACCAAC 1 36201 ( 176) CACTCTCTCGGTCGCC 1 23261 ( 51) GCTGTACTCTATCAAC 1 3947 ( 466) CCTGTGCCGTCCCATC 1 35356 ( 416) TCTGCTCTGAAACAAC 1 4322 ( 442) ACACCTCACTGCTAAC 1 7633 ( 450) TATTCTTCTTCACGTC 1 6192 ( 173) CAACACCTCACCTATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 19400 bayes= 9.17951 E= 5.0e-003 -240 152 -125 -35 -8 152 -166 -335 -8 -113 -1193 129 -1193 87 -66 74 -8 133 -1193 -54 -181 -13 -166 129 -1193 157 -1193 35 -81 57 -225 82 -1193 173 -125 -77 -40 19 -324 97 -81 133 -8 -235 -81 68 -1193 90 -1193 200 -1193 -135 92 -13 21 -1193 99 46 -1193 -77 -340 212 -1193 -1193 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 39 E= 5.0e-003 0.051282 0.641026 0.102564 0.205128 0.256410 0.641026 0.076923 0.025641 0.256410 0.102564 0.000000 0.641026 0.000000 0.410256 0.153846 0.435897 0.256410 0.564103 0.000000 0.179487 0.076923 0.205128 0.076923 0.641026 0.000000 0.666667 0.000000 0.333333 0.153846 0.333333 0.051282 0.461538 0.000000 0.743590 0.102564 0.153846 0.205128 0.256410 0.025641 0.512821 0.153846 0.564103 0.230769 0.051282 0.153846 0.358974 0.000000 0.487179 0.000000 0.897436 0.000000 0.102564 0.512821 0.205128 0.282051 0.000000 0.538462 0.307692 0.000000 0.153846 0.025641 0.974359 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT][CA][TA][TC][CA][TC][CT][TC]C[TCA][CG][TC]C[AGC][AC]C -------------------------------------------------------------------------------- Time 39.58 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10400 3.40e-07 297_[+2(4.06e-06)]_8_[+1(1.92e-05)]_\ 72_[+3(1.10e-05)]_21_[+3(8.13e-05)]_18_[+3(1.69e-07)]_3 14727 1.52e-06 67_[+1(1.38e-06)]_255_\ [+3(7.45e-05)]_125_[+2(6.84e-07)]_4 1765 1.28e-02 285_[+1(3.31e-05)]_10_\ [+3(5.18e-05)]_177 20854 5.61e-04 300_[+2(7.46e-07)]_92_\ [+3(3.90e-05)]_71 20888 2.89e-03 45_[+1(7.40e-06)]_443 20915 9.29e-04 156_[+3(2.62e-05)]_217_\ [+2(3.07e-06)]_90 21747 1.80e-03 228_[+3(5.68e-05)]_101_\ [+1(5.22e-06)]_143 22128 5.67e-03 171_[+1(5.55e-05)]_92_\ [+3(9.83e-06)]_209 22823 3.55e-06 191_[+1(8.88e-05)]_109_\ [+3(2.62e-05)]_90_[+2(7.85e-08)]_1_[+2(9.99e-05)]_39 22867 5.74e-09 141_[+1(3.93e-05)]_280_\ [+3(2.90e-05)]_29_[+2(1.35e-10)]_1 23261 6.91e-05 288_[+2(3.63e-07)]_191 23343 8.56e-03 277_[+1(1.18e-05)]_3_[+1(7.61e-05)]_\ 132_[+3(6.81e-05)]_48 24587 5.66e-04 10_[+2(1.33e-06)]_89_[+3(3.54e-05)]_\ 364 24830 4.77e-04 39_[+1(4.57e-07)]_220_\ [+3(5.68e-05)]_213 2502 4.47e-04 169_[+1(4.12e-06)]_170_\ [+3(5.38e-06)]_133 25820 1.83e-06 265_[+3(1.54e-05)]_103_\ [+2(3.08e-08)]_95 262720 6.10e-04 244_[+1(2.09e-05)]_102_\ [+3(3.90e-05)]_17_[+2(8.22e-05)]_88 263343 1.05e-09 55_[+2(6.46e-11)]_272_\ [+3(1.24e-05)]_51_[+1(3.04e-05)]_73 263344 1.05e-09 55_[+2(6.46e-11)]_272_\ [+3(1.24e-05)]_51_[+1(3.04e-05)]_73 26635 1.17e-02 323_[+3(1.10e-05)]_161 269328 3.36e-07 1_[+2(1.08e-08)]_114_[+1(7.08e-05)]_\ 226_[+3(1.72e-05)]_110 2799 1.21e-05 136_[+2(1.23e-06)]_125_\ [+3(8.97e-07)]_202 2906 4.93e-03 282_[+1(2.31e-05)]_171_\ [+3(1.91e-05)]_19 2987 4.20e-03 4_[+3(7.45e-05)]_436_[+1(4.47e-06)]_\ 32 31732 9.64e-05 209_[+1(1.38e-06)]_8_[+3(2.82e-06)]_\ 255 31777 8.35e-06 12_[+3(3.54e-05)]_200_\ [+1(3.04e-05)]_142_[+2(4.37e-07)]_97 34851 2.72e-04 342_[+3(2.62e-05)]_35_\ [+2(6.06e-06)]_86 35356 8.91e-05 455_[+2(3.01e-07)]_24 3611 1.22e-05 276_[+1(8.31e-07)]_80_\ [+3(1.21e-06)]_116 36201 7.90e-05 144_[+1(3.34e-06)]_179_\ [+2(1.50e-05)]_144 3947 2.08e-02 338_[+1(5.12e-05)]_150 4322 3.13e-05 33_[+1(6.51e-06)]_39_[+2(1.69e-06)]_\ 395 5725 1.62e-03 9_[+1(8.22e-05)]_304_[+3(9.83e-06)]_\ 159 5747 1.28e-03 19_[+3(2.90e-05)]_196_\ [+1(2.84e-06)]_257 6047 1.56e-03 52_[+1(4.70e-05)]_172_\ [+3(4.75e-06)]_248 6192 1.02e-03 330_[+2(6.47e-06)]_102_\ [+1(7.08e-05)]_35 6332 1.33e-07 46_[+1(8.55e-06)]_130_\ [+3(1.04e-06)]_211_[+3(3.90e-05)]_27_[+2(5.25e-07)]_21 6568 1.33e-01 123_[+1(2.31e-05)]_365 7633 1.02e-01 500 9693 1.86e-05 161_[+2(4.37e-07)]_206_\ [+3(1.24e-05)]_96 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************