******************************************************************************** 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/132/132.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10425 1.0000 500 10532 1.0000 500 10940 1.0000 500 1166 1.0000 500 16082 1.0000 500 16612 1.0000 500 21304 1.0000 500 24806 1.0000 500 25041 1.0000 500 268467 1.0000 500 32191 1.0000 500 35281 1.0000 500 37637 1.0000 500 38123 1.0000 500 4404 1.0000 500 4867 1.0000 500 5297 1.0000 500 5370 1.0000 500 7103 1.0000 500 7143 1.0000 500 8415 1.0000 500 9124 1.0000 500 940 1.0000 500 9964 1.0000 500 bd1869 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/132/132.seqs.fa -oc motifs/132 -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= 25 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= 12500 N= 25 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.257 C 0.228 G 0.236 T 0.278 Background letter frequencies (from dataset with add-one prior applied): A 0.257 C 0.228 G 0.236 T 0.278 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 12 llr = 176 E-value = 1.7e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :32::::1631:223::3:: pos.-specific C a3883386:468547771a8 probability G :::1:::313::3::::::2 matrix T :4:1883:313214:337:: bits 2.1 * * 1.9 * * 1.7 * * 1.5 * * * ** Relative 1.3 * ** * * ** Entropy 1.1 * ***** * *** ** (21.2 bits) 0.9 * ****** * *** ** 0.6 * ******* ** ****** 0.4 ********* ********** 0.2 ******************** 0.0 -------------------- Multilevel CTCCTTCCACCCCCCCCTCC consensus C CCTGTAT GTATTA sequence A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 38123 358 1.67e-09 CTCACCGGCT CCCCCTCCACCCACCCCACC GACATTCACT 4867 362 3.02e-09 TGAACGGCCC CTCCCTCCACCTCCACCTCC ACTTCCACCT 32191 309 1.22e-08 GACAGTAGGC CACCTTCCGCACCCCCCTCC GGACGGACAC 21304 257 1.53e-08 AGTGCTAATC CCCCTTCAAGCCGTCTCTCC TTGCCTCCTC 5297 245 2.13e-08 TAAAACTCCG CTACTCCGAATCCTCCCTCC TACTTTCACG 9964 478 4.84e-08 CACCAAGCCT CTCCTTCCTACCGTACTTCG ACA 16082 8 8.46e-08 ATTTCCA CTCCTTCCAACCTCCTTTCG AAAGGGACTC 7143 474 1.01e-07 TTAGCCAGCC CTCGTCCGACTCGCCTCTCC CTCAACC 9124 464 1.54e-07 CACCAAACGA CACCCTTGTTTCCTCCCTCC TCTCCCTACC 268467 413 6.00e-07 TTTCATGTCT CCCCTTTCTCTTCAACCCCC TCTTCAGACG 24806 163 6.79e-07 CACTACTTGC CCCTTTTGTGCCCTACTACC ATAAGCCTAC 8415 400 7.66e-07 CCCAAAACAA CAACTCCCAGCCAACTTACC TACACCCTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38123 1.7e-09 357_[+1]_123 4867 3e-09 361_[+1]_119 32191 1.2e-08 308_[+1]_172 21304 1.5e-08 256_[+1]_224 5297 2.1e-08 244_[+1]_236 9964 4.8e-08 477_[+1]_3 16082 8.5e-08 7_[+1]_473 7143 1e-07 473_[+1]_7 9124 1.5e-07 463_[+1]_17 268467 6e-07 412_[+1]_68 24806 6.8e-07 162_[+1]_318 8415 7.7e-07 399_[+1]_81 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=12 38123 ( 358) CCCCCTCCACCCACCCCACC 1 4867 ( 362) CTCCCTCCACCTCCACCTCC 1 32191 ( 309) CACCTTCCGCACCCCCCTCC 1 21304 ( 257) CCCCTTCAAGCCGTCTCTCC 1 5297 ( 245) CTACTCCGAATCCTCCCTCC 1 9964 ( 478) CTCCTTCCTACCGTACTTCG 1 16082 ( 8) CTCCTTCCAACCTCCTTTCG 1 7143 ( 474) CTCGTCCGACTCGCCTCTCC 1 9124 ( 464) CACCCTTGTTTCCTCCCTCC 1 268467 ( 413) CCCCTTTCTCTTCAACCCCC 1 24806 ( 163) CCCTTTTGTGCCCTACTACC 1 8415 ( 400) CAACTCCCAGCCAACTTACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 12025 bayes= 11.5533 E= 1.7e-004 -1023 213 -1023 -1023 -4 54 -1023 59 -63 187 -1023 -1023 -1023 187 -150 -173 -1023 13 -1023 143 -1023 13 -1023 143 -1023 171 -1023 -15 -162 135 49 -1023 118 -1023 -150 26 -4 87 8 -173 -162 135 -1023 26 -1023 187 -1023 -74 -63 113 8 -173 -63 87 -1023 59 37 154 -1023 -1023 -1023 154 -1023 26 -1023 154 -1023 26 -4 -145 -1023 126 -1023 213 -1023 -1023 -1023 187 -50 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 12 E= 1.7e-004 0.000000 1.000000 0.000000 0.000000 0.250000 0.333333 0.000000 0.416667 0.166667 0.833333 0.000000 0.000000 0.000000 0.833333 0.083333 0.083333 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.750000 0.000000 0.750000 0.000000 0.250000 0.083333 0.583333 0.333333 0.000000 0.583333 0.000000 0.083333 0.333333 0.250000 0.416667 0.250000 0.083333 0.083333 0.583333 0.000000 0.333333 0.000000 0.833333 0.000000 0.166667 0.166667 0.500000 0.250000 0.083333 0.166667 0.416667 0.000000 0.416667 0.333333 0.666667 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.666667 0.000000 0.333333 0.250000 0.083333 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[TCA]CC[TC][TC][CT][CG][AT][CAG][CT]C[CG][CT][CA][CT][CT][TA]CC -------------------------------------------------------------------------------- Time 5.66 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 19 llr = 224 E-value = 9.6e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 21:3:32112212::22:2: pos.-specific C 3::12:222:::11:22112 probability G 5:83:74:83192392496: matrix T :9238128:57:56143:28 bits 2.1 1.9 1.7 * * 1.5 * * * Relative 1.3 ** * * * Entropy 1.1 ** * ** * * * * (17.0 bits) 0.9 ** ** ** ** * * * 0.6 *** ** ** ** ** * * 0.4 *** ** ***** ** *** 0.2 *************** **** 0.0 -------------------- Multilevel GTGATGGTGTTGTTGTGGGT consensus C TGCAA GA AG AT C sequence T C A G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 5297 129 7.17e-10 GGAATCCAGC GTGTTGGTGTTGTTGAGGGC TGCAAGTAAT 9964 196 4.18e-09 AGTTGTACTA CTGTTGTTGTTGATGTGGGT GTTAATTTTT 38123 463 4.18e-09 CTGGCTCCTA CTGGTGGTGTTGGTGGTGGT CAACATCATG 10532 251 9.42e-08 ACGTACGATG ATGATGGCGGTGTGGGGGGT GATGGATCAT 5370 368 7.73e-07 ACCTGTACCT GTGTCTCTGTTGTTGTTGGC AACACTCGAA 21304 53 7.73e-07 ATAACATGTT GTTGTATTGTTGCGGTGGGT GAATCTGGAA 7103 256 9.39e-07 TGTTGAGTTG ATGATAATGTTGTTGTTGCC CTACTTTCTC 9124 237 1.36e-06 GTTTAGCTAG CTGTTGGTGATGTTGTCCTT AGGAGGGAGG 940 193 1.63e-06 TTCAGTGCTT CTGATAATCGTGTGGCGGCT AAGGGTATGT 8415 102 2.12e-06 CTGCTGACGT CTGTCGCTCTAGATGATGGT ACTGTTCTTG 268467 226 2.12e-06 TAGCTGATTA GATGTGATGTTGGTGAGGAT TGCGGGCATT 10425 265 2.12e-06 AGAACAAATC GTTGTGGTGGTGTGTCTGTT GGGGGTTCTG 32191 451 2.51e-06 GTGCGGTCGT GTTGTATCGTTGATGCCGGT TCATGGTTCT 16612 339 2.73e-06 TTCTCCTCGG ATGACAGCGATGTTGGCGGT CCGTTAACTG 24806 434 4.09e-06 CAGTAAAGAG GTGATGCACTTGGTTTGGGT TGTGTTGTAT 10940 225 4.09e-06 GGTCCAGCGG GTGATGCTAGAGGGGCAGGT ATTGGAACTC 25041 44 1.05e-05 AAAACCGTCT GTGGTGGTGAGATGGTAGAT GAAATGTAAG 4867 40 1.20e-05 GTGCATCCTT CTGCCGGTGAAGTCGTGGAC TTGTGCGGGT 35281 88 2.53e-05 GAAGCGTGGG GAGTTGATGGAGACGAAGTT AATGTATGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5297 7.2e-10 128_[+2]_352 9964 4.2e-09 195_[+2]_285 38123 4.2e-09 462_[+2]_18 10532 9.4e-08 250_[+2]_230 5370 7.7e-07 367_[+2]_113 21304 7.7e-07 52_[+2]_428 7103 9.4e-07 255_[+2]_225 9124 1.4e-06 236_[+2]_244 940 1.6e-06 192_[+2]_288 8415 2.1e-06 101_[+2]_379 268467 2.1e-06 225_[+2]_255 10425 2.1e-06 264_[+2]_216 32191 2.5e-06 450_[+2]_30 16612 2.7e-06 338_[+2]_142 24806 4.1e-06 433_[+2]_47 10940 4.1e-06 224_[+2]_256 25041 1.1e-05 43_[+2]_437 4867 1.2e-05 39_[+2]_441 35281 2.5e-05 87_[+2]_393 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=19 5297 ( 129) GTGTTGGTGTTGTTGAGGGC 1 9964 ( 196) CTGTTGTTGTTGATGTGGGT 1 38123 ( 463) CTGGTGGTGTTGGTGGTGGT 1 10532 ( 251) ATGATGGCGGTGTGGGGGGT 1 5370 ( 368) GTGTCTCTGTTGTTGTTGGC 1 21304 ( 53) GTTGTATTGTTGCGGTGGGT 1 7103 ( 256) ATGATAATGTTGTTGTTGCC 1 9124 ( 237) CTGTTGGTGATGTTGTCCTT 1 940 ( 193) CTGATAATCGTGTGGCGGCT 1 8415 ( 102) CTGTCGCTCTAGATGATGGT 1 268467 ( 226) GATGTGATGTTGGTGAGGAT 1 10425 ( 265) GTTGTGGTGGTGTGTCTGTT 1 32191 ( 451) GTTGTATCGTTGATGCCGGT 1 16612 ( 339) ATGACAGCGATGTTGGCGGT 1 24806 ( 434) GTGATGCACTTGGTTTGGGT 1 10940 ( 225) GTGATGCTAGAGGGGCAGGT 1 25041 ( 44) GTGGTGGTGAGATGGTAGAT 1 4867 ( 40) CTGCCGGTGAAGTCGTGGAC 1 35281 ( 88) GAGTTGATGGAGACGAAGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 12025 bayes= 9.49864 E= 9.6e-005 -70 47 115 -1089 -129 -1089 -1089 169 -1089 -1089 174 -40 30 -212 42 19 -1089 -12 -1089 151 3 -1089 153 -240 -29 -12 83 -81 -229 -53 -1089 151 -229 -53 174 -1089 -29 -1089 15 92 -29 -1089 -217 141 -229 -1089 200 -1089 -29 -212 -17 92 -1089 -112 42 106 -1089 -1089 192 -140 -29 -12 -58 60 -70 -53 83 -8 -1089 -212 200 -1089 -70 -112 129 -81 -1089 -12 -1089 151 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 19 E= 9.6e-005 0.157895 0.315789 0.526316 0.000000 0.105263 0.000000 0.000000 0.894737 0.000000 0.000000 0.789474 0.210526 0.315789 0.052632 0.315789 0.315789 0.000000 0.210526 0.000000 0.789474 0.263158 0.000000 0.684211 0.052632 0.210526 0.210526 0.421053 0.157895 0.052632 0.157895 0.000000 0.789474 0.052632 0.157895 0.789474 0.000000 0.210526 0.000000 0.263158 0.526316 0.210526 0.000000 0.052632 0.736842 0.052632 0.000000 0.947368 0.000000 0.210526 0.052632 0.210526 0.526316 0.000000 0.105263 0.315789 0.578947 0.000000 0.000000 0.894737 0.105263 0.210526 0.210526 0.157895 0.421053 0.157895 0.157895 0.421053 0.263158 0.000000 0.052632 0.947368 0.000000 0.157895 0.105263 0.578947 0.157895 0.000000 0.210526 0.000000 0.789474 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GC]T[GT][AGT][TC][GA][GAC]TG[TGA][TA]G[TAG][TG]G[TAC][GT]GG[TC] -------------------------------------------------------------------------------- Time 11.21 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 21 llr = 227 E-value = 2.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 75:16:5544:52569:152: pos.-specific C 21:3::121:2:311:3:11: probability G :194:a225473532:5912a matrix T :2124:11:212:::11:24: bits 2.1 * 1.9 * 1.7 * * * 1.5 * * * Relative 1.3 * * * * * Entropy 1.1 * * * * * (15.6 bits) 0.9 * ** * * * * 0.6 * * ** * * * **** * 0.4 * * ** ********** * 0.2 ******************* * 0.0 --------------------- Multilevel AAGGAGAAGAGAGAAAGGATG consensus CT CT G AGCGCGG C A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 1166 8 2.59e-09 AAAACTT ATGCTGAAATGGGAAAGGATG AAAAGAATGC 5370 131 1.62e-08 CTTCTTGCAA AAGGAGAAGAGAGGAAGAACG TTATGATGAT 4867 418 1.00e-07 AACAGCGTGC ACGGAGAGAGCAGAAAGGCTG GTTGGAGAGT bd1869 114 5.79e-07 TTTATGAATA CAGTTGAAGGCAAAAAGGCAG CCGGTTACTG 21304 74 6.49e-07 GCGGTGGGTG AATCTGGAAGGAAGAAGGAGG AGCGAGTAGG 16082 318 8.10e-07 AGCTCAAAGA AATCAGGAGAGAGGAATGTTG AACAAGATCT 268467 110 1.53e-06 TTAGCCGAGC ATGCAGCAGACGCAGACGACG ACGCCGCACC 25041 142 1.87e-06 TTGTGAGTGA CAGGAGAAAGGTGAAACTGTG GCTGTGCATT 32191 156 2.28e-06 TGAGCCGACA ATGGTGGCGAGGGAGAGAAGG AGAACGTTCA 940 434 4.00e-06 CTTTTCTCTG GCGGTGAACGGACGAACGTTG AACGTAAGAA 4404 204 5.23e-06 AGTATACGGA AAGTTAACATCAGGAAGGAAG CCACGAGAGC 10940 96 5.23e-06 CACCTAACAG CAGCAGTCGTGTCCAACGACG TTGACTTCCA 35281 167 6.78e-06 AAGTGAGTAG AGGTAGAGAAGGGATATGATG TATAAAGTTG 5297 100 7.38e-06 GCCGTCGTCA AAGGAGCTGTTGGGGAGGAGG AATCCAGCGT 37637 129 8.02e-06 AGTGCTACAC TAGATGGGGAGACAAACGTTG CTGGATATCG 9124 192 9.45e-06 CCCGCAGAGG CAGGAGGACGTGACAAGGTTG TGCGATGATG 7143 205 1.30e-05 CCGGAACGCG ATGATGAACTGAAGGATGAGG TTGTTCTCTT 10532 307 2.04e-05 AACAGAAACA CAGCAGTTGAGACAGCCGAAG AGTCACATGC 9964 33 2.20e-05 GTTGATGGGA ACGTTGTCGACGGTAAGGCTG CGTGAGCTGG 8415 276 2.20e-05 CACTCGTCGG ATGCAGAGAGGTCACTGGGAG GGGAACTTAT 16612 226 3.82e-05 ATGTCAACCA AGGGAGAAAGGTGCCTCGGAG AAAGTACGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1166 2.6e-09 7_[+3]_472 5370 1.6e-08 130_[+3]_349 4867 1e-07 417_[+3]_62 bd1869 5.8e-07 113_[+3]_366 21304 6.5e-07 73_[+3]_406 16082 8.1e-07 317_[+3]_162 268467 1.5e-06 109_[+3]_370 25041 1.9e-06 141_[+3]_338 32191 2.3e-06 155_[+3]_324 940 4e-06 433_[+3]_46 4404 5.2e-06 203_[+3]_276 10940 5.2e-06 95_[+3]_384 35281 6.8e-06 166_[+3]_313 5297 7.4e-06 99_[+3]_380 37637 8e-06 128_[+3]_351 9124 9.5e-06 191_[+3]_288 7143 1.3e-05 204_[+3]_275 10532 2e-05 306_[+3]_173 9964 2.2e-05 32_[+3]_447 8415 2.2e-05 275_[+3]_204 16612 3.8e-05 225_[+3]_254 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=21 1166 ( 8) ATGCTGAAATGGGAAAGGATG 1 5370 ( 131) AAGGAGAAGAGAGGAAGAACG 1 4867 ( 418) ACGGAGAGAGCAGAAAGGCTG 1 bd1869 ( 114) CAGTTGAAGGCAAAAAGGCAG 1 21304 ( 74) AATCTGGAAGGAAGAAGGAGG 1 16082 ( 318) AATCAGGAGAGAGGAATGTTG 1 268467 ( 110) ATGCAGCAGACGCAGACGACG 1 25041 ( 142) CAGGAGAAAGGTGAAACTGTG 1 32191 ( 156) ATGGTGGCGAGGGAGAGAAGG 1 940 ( 434) GCGGTGAACGGACGAACGTTG 1 4404 ( 204) AAGTTAACATCAGGAAGGAAG 1 10940 ( 96) CAGCAGTCGTGTCCAACGACG 1 35281 ( 167) AGGTAGAGAAGGGATATGATG 1 5297 ( 100) AAGGAGCTGTTGGGGAGGAGG 1 37637 ( 129) TAGATGGGGAGACAAACGTTG 1 9124 ( 192) CAGGAGGACGTGACAAGGTTG 1 7143 ( 205) ATGATGAACTGAAGGATGAGG 1 10532 ( 307) CAGCAGTTGAGACAGCCGAAG 1 9964 ( 33) ACGTTGTCGACGGTAAGGCTG 1 8415 ( 276) ATGCAGAGAGGTCACTGGGAG 1 16612 ( 226) AGGGAGAAAGGTGCCTCGGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12000 bayes= 9.46124 E= 2.6e+001 137 6 -231 -254 102 -68 -131 -22 -1104 -1104 194 -154 -143 54 69 -54 115 -1104 -1104 63 -243 -1104 201 -1104 102 -126 1 -96 102 -26 -31 -154 57 -68 101 -1104 57 -1104 69 -22 -1104 6 149 -154 89 -1104 50 -54 -43 32 115 -1104 89 -68 50 -254 127 -126 1 -254 174 -226 -1104 -154 -1104 54 115 -96 -143 -1104 186 -254 102 -68 -73 -54 -11 -68 -31 63 -1104 -1104 208 -1104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 21 E= 2.6e+001 0.666667 0.238095 0.047619 0.047619 0.523810 0.142857 0.095238 0.238095 0.000000 0.000000 0.904762 0.095238 0.095238 0.333333 0.380952 0.190476 0.571429 0.000000 0.000000 0.428571 0.047619 0.000000 0.952381 0.000000 0.523810 0.095238 0.238095 0.142857 0.523810 0.190476 0.190476 0.095238 0.380952 0.142857 0.476190 0.000000 0.380952 0.000000 0.380952 0.238095 0.000000 0.238095 0.666667 0.095238 0.476190 0.000000 0.333333 0.190476 0.190476 0.285714 0.523810 0.000000 0.476190 0.142857 0.333333 0.047619 0.619048 0.095238 0.238095 0.047619 0.857143 0.047619 0.000000 0.095238 0.000000 0.333333 0.523810 0.142857 0.095238 0.000000 0.857143 0.047619 0.523810 0.142857 0.142857 0.190476 0.238095 0.142857 0.190476 0.428571 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AC][AT]G[GC][AT]G[AG]A[GA][AGT][GC][AG][GC][AG][AG]A[GC]GA[TA]G -------------------------------------------------------------------------------- Time 16.78 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10425 6.60e-03 264_[+2(2.12e-06)]_216 10532 2.45e-05 250_[+2(9.42e-08)]_36_\ [+3(2.04e-05)]_173 10940 2.63e-04 95_[+3(5.23e-06)]_108_\ [+2(4.09e-06)]_256 1166 2.00e-05 7_[+3(2.59e-09)]_472 16082 1.35e-06 7_[+1(8.46e-08)]_290_[+3(8.10e-07)]_\ 162 16612 1.34e-03 225_[+3(3.82e-05)]_92_\ [+2(2.73e-06)]_142 21304 3.53e-10 52_[+2(7.73e-07)]_1_[+3(6.49e-07)]_\ 162_[+1(1.53e-08)]_224 24806 4.36e-05 162_[+1(6.79e-07)]_251_\ [+2(4.09e-06)]_47 25041 3.54e-04 43_[+2(1.05e-05)]_78_[+3(1.87e-06)]_\ 338 268467 5.85e-08 109_[+3(1.53e-06)]_95_\ [+2(2.12e-06)]_167_[+1(6.00e-07)]_68 32191 2.73e-09 155_[+3(2.28e-06)]_132_\ [+1(1.22e-08)]_122_[+2(2.51e-06)]_30 35281 5.02e-04 87_[+2(2.53e-05)]_59_[+3(6.78e-06)]_\ 313 37637 2.03e-02 128_[+3(8.02e-06)]_351 38123 2.19e-10 357_[+1(1.67e-09)]_85_\ [+2(4.18e-09)]_18 4404 2.46e-02 203_[+3(5.23e-06)]_276 4867 1.76e-10 39_[+2(1.20e-05)]_302_\ [+1(3.02e-09)]_36_[+3(1.00e-07)]_62 5297 6.81e-12 99_[+3(7.38e-06)]_8_[+2(7.17e-10)]_\ 96_[+1(2.13e-08)]_236 5370 5.56e-07 130_[+3(1.62e-08)]_216_\ [+2(7.73e-07)]_113 7103 1.97e-03 255_[+2(9.39e-07)]_225 7143 3.53e-05 204_[+3(1.30e-05)]_167_\ [+3(9.02e-05)]_60_[+1(1.01e-07)]_7 8415 8.17e-07 101_[+2(2.12e-06)]_154_\ [+3(2.20e-05)]_103_[+1(7.66e-07)]_81 9124 5.93e-08 191_[+3(9.45e-06)]_24_\ [+2(1.36e-06)]_207_[+1(1.54e-07)]_17 940 6.33e-05 192_[+2(1.63e-06)]_221_\ [+3(4.00e-06)]_46 9964 2.11e-10 32_[+3(2.20e-05)]_142_\ [+2(4.18e-09)]_262_[+1(4.84e-08)]_3 bd1869 3.38e-03 113_[+3(5.79e-07)]_366 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************