******************************************************************************** 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/386/386.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10109 1.0000 500 10984 1.0000 500 11529 1.0000 500 11641 1.0000 500 12207 1.0000 500 1716 1.0000 500 17860 1.0000 500 20728 1.0000 500 21820 1.0000 500 21880 1.0000 500 22338 1.0000 500 22391 1.0000 500 22702 1.0000 500 23039 1.0000 500 23253 1.0000 500 23565 1.0000 500 23603 1.0000 500 2530 1.0000 500 2600 1.0000 500 262217 1.0000 500 264018 1.0000 500 2641 1.0000 500 264486 1.0000 500 264854 1.0000 500 3861 1.0000 500 4184 1.0000 500 4293 1.0000 500 5361 1.0000 500 8769 1.0000 500 9180 1.0000 500 9289 1.0000 500 9502 1.0000 500 9555 1.0000 500 9557 1.0000 500 9558 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/386/386.seqs.fa -oc motifs/386 -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= 35 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= 17500 N= 35 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.270 C 0.227 G 0.239 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.270 C 0.227 G 0.239 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 28 llr = 280 E-value = 6.4e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 531724:96:3:4434 pos.-specific C 359166a1:a195253 probability G 21:1::::::5:::2: matrix T 12:13:::3:11:4:3 bits 2.1 * 1.9 * * 1.7 * * * 1.5 * ** * * Relative 1.3 * ** * * Entropy 1.1 * ** * * (14.4 bits) 0.9 * ***** * 0.6 ******** ** * 0.4 ******** ***** 0.2 **************** 0.0 ---------------- Multilevel ACCACCCAACGCCTCA consensus CA TA T A AAAC sequence G GT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 2600 403 1.67e-09 GCTCCTCACG CCCACCCAACGCCTCC GCCCTCCGCT 23039 463 1.89e-08 CGCTATTGAT ACCACCCAACGCCTAT CGTCATCAAA 264854 477 6.34e-07 TCACGTCATA CCCATCCATCACATCA CCAACTGG 1716 422 1.25e-06 TCTCCATTCC ATCACACATCGCCAGC ACTCCCCTCC 2641 422 2.32e-06 CCGCGAAAAG CCCGCCCAACCCCCCC CCGTCGAAAG 9180 280 2.62e-06 TATTTATGTC GCCACCCAACTCATGA GTAGTAAGTC 2530 311 2.62e-06 ACCTCCTACC AACGCCCAACGCATAC GCTTACACTG 20728 351 2.93e-06 ATCACTCTTG GGCACCCAACGCACCT CCCCATGCCT 4293 447 4.09e-06 AAACGCATAA AACAACCAACCCCAAC CCCAAGCTCA 9289 473 6.22e-06 TTCACGCCTC ATCACACAACTCCAAA ACACAATCAA 22702 446 7.60e-06 GAGGCAATCC ACCATCCACCACCTAC TTCATCTTCA 10984 367 7.60e-06 GCTTATCATA ACCCCCCCACACACCA TGCCCGCTTC 21880 238 8.36e-06 AAAATGGCGG CCAATCCAACCCAACA CGAGCGTTGC 21820 352 8.36e-06 TCACGCGTGT TTCACCCAACACAAGA CGAGCCTCCT 23603 146 1.01e-05 TGATCATCGC CACCACCATCACCTCC ATCACCATCC 10109 185 1.01e-05 CGGGAATATA CTCACACAACATCTCT GGTACTGGTT 9558 454 1.11e-05 TCACTTTGCC CGCATACATCGCCCCA TCGATACACA 4184 449 1.11e-05 ACAACATTGA ATCCTCCAACGCAAGT GAAACAAGTC 23253 394 1.11e-05 GTGGCTTGCC AACACACAAAGCCACT TTGTTCATCT 262217 383 1.22e-05 ATATTTGCCA GCCACACCTCGCCCAC TCACATTCAC 9502 25 1.58e-05 CCGACACGAC GCAATACATCGCCTGC ATGGGGCGCT 23565 270 2.22e-05 CCAGAATGGA TACACCCAACACGACA CTGACAGCGA 17860 483 2.22e-05 ACAGTAAGCA AACAAACAACACTTCA GC 9555 483 2.81e-05 GATCTCATCA ACCTCACCACCCATCA GG 12207 274 3.53e-05 TACTACGAGA GCAAAACATCGCAAGA GAGCAACGCA 9557 410 4.09e-05 TCCACATCGC AACTCGCAACGCAACT ACGAACTCAC 264018 55 6.61e-05 TTCCGGGGAA ACACTCCATCGTCTCT TTCTGTTTGA 264486 45 1.59e-04 CGGTGGAAGT GCCGAACATCATCAAT GAAATGACCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2600 1.7e-09 402_[+1]_82 23039 1.9e-08 462_[+1]_22 264854 6.3e-07 476_[+1]_8 1716 1.3e-06 421_[+1]_63 2641 2.3e-06 421_[+1]_63 9180 2.6e-06 279_[+1]_205 2530 2.6e-06 310_[+1]_174 20728 2.9e-06 350_[+1]_134 4293 4.1e-06 446_[+1]_38 9289 6.2e-06 472_[+1]_12 22702 7.6e-06 445_[+1]_39 10984 7.6e-06 366_[+1]_118 21880 8.4e-06 237_[+1]_247 21820 8.4e-06 351_[+1]_133 23603 1e-05 145_[+1]_339 10109 1e-05 184_[+1]_300 9558 1.1e-05 453_[+1]_31 4184 1.1e-05 448_[+1]_36 23253 1.1e-05 393_[+1]_91 262217 1.2e-05 382_[+1]_102 9502 1.6e-05 24_[+1]_460 23565 2.2e-05 269_[+1]_215 17860 2.2e-05 482_[+1]_2 9555 2.8e-05 482_[+1]_2 12207 3.5e-05 273_[+1]_211 9557 4.1e-05 409_[+1]_75 264018 6.6e-05 54_[+1]_430 264486 0.00016 44_[+1]_440 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=28 2600 ( 403) CCCACCCAACGCCTCC 1 23039 ( 463) ACCACCCAACGCCTAT 1 264854 ( 477) CCCATCCATCACATCA 1 1716 ( 422) ATCACACATCGCCAGC 1 2641 ( 422) CCCGCCCAACCCCCCC 1 9180 ( 280) GCCACCCAACTCATGA 1 2530 ( 311) AACGCCCAACGCATAC 1 20728 ( 351) GGCACCCAACGCACCT 1 4293 ( 447) AACAACCAACCCCAAC 1 9289 ( 473) ATCACACAACTCCAAA 1 22702 ( 446) ACCATCCACCACCTAC 1 10984 ( 367) ACCCCCCCACACACCA 1 21880 ( 238) CCAATCCAACCCAACA 1 21820 ( 352) TTCACCCAACACAAGA 1 23603 ( 146) CACCACCATCACCTCC 1 10109 ( 185) CTCACACAACATCTCT 1 9558 ( 454) CGCATACATCGCCCCA 1 4184 ( 449) ATCCTCCAACGCAAGT 1 23253 ( 394) AACACACAAAGCCACT 1 262217 ( 383) GCCACACCTCGCCCAC 1 9502 ( 25) GCAATACATCGCCTGC 1 23565 ( 270) TACACCCAACACGACA 1 17860 ( 483) AACAAACAACACTTCA 1 9555 ( 483) ACCTCACCACCCATCA 1 12207 ( 274) GCAAAACATCGCAAGA 1 9557 ( 410) AACTCGCAACGCAACT 1 264018 ( 55) ACACTCCATCGTCTCT 1 264486 ( 45) GCCGAACATCATCAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 16975 bayes= 11.2025 E= 6.4e-007 78 14 -16 -188 -11 114 -174 -56 -92 191 -1145 -1145 133 -67 -115 -188 -60 133 -1145 -8 54 133 -274 -1145 -1145 214 -1145 -1145 172 -108 -1145 -1145 125 -267 -1145 28 -292 208 -1145 -1145 25 -67 96 -188 -1145 197 -1145 -130 54 124 -274 -288 54 -35 -1145 70 -11 124 -16 -1145 54 50 -1145 11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 28 E= 6.4e-007 0.464286 0.250000 0.214286 0.071429 0.250000 0.500000 0.071429 0.178571 0.142857 0.857143 0.000000 0.000000 0.678571 0.142857 0.107143 0.071429 0.178571 0.571429 0.000000 0.250000 0.392857 0.571429 0.035714 0.000000 0.000000 1.000000 0.000000 0.000000 0.892857 0.107143 0.000000 0.000000 0.642857 0.035714 0.000000 0.321429 0.035714 0.964286 0.000000 0.000000 0.321429 0.142857 0.464286 0.071429 0.000000 0.892857 0.000000 0.107143 0.392857 0.535714 0.035714 0.035714 0.392857 0.178571 0.000000 0.428571 0.250000 0.535714 0.214286 0.000000 0.392857 0.321429 0.000000 0.285714 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [ACG][CA]CA[CT][CA]CA[AT]C[GA]C[CA][TA][CAG][ACT] -------------------------------------------------------------------------------- Time 10.91 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 34 llr = 312 E-value = 5.0e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::213::21:1412: pos.-specific C ::13:12:1::21::1 probability G 167:621a3:853124 matrix T 9425347:59112866 bits 2.1 1.9 * 1.7 * 1.5 * * Relative 1.3 * * ** Entropy 1.1 ** * ** * (13.3 bits) 0.9 *** * ** ** * * 0.6 *** * ** ** *** 0.4 ***** ** ** *** 0.2 **************** 0.0 ---------------- Multilevel TGGTGTTGTTGGATTT consensus TTCTA G CG G sequence A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 20728 185 3.69e-07 TGTTGTGTTG TTGTGTTGTTGTTTTT TGTGTCTATG 2641 173 4.32e-07 ATTGTAAGCG TGGAGGTGATGGATTG AGATGATGTG 9502 215 6.94e-07 ATTCAAGTTG TTGAGATGTTGCTTTT ACGTTGAAGT 21820 175 8.04e-07 GGGCGCGCCA TGGTTTTGGTGGGTGT GAGCGGAAAG 9289 3 3.15e-06 CC TGGAGTTGTTTCGTTG TTGGTATTGC 2600 130 3.57e-06 AGCTTGTACA TGGTGTTGGTGTGTAG AAAGAGGAGT 22338 380 4.04e-06 ATCAACAAAC TTGTGATGTTTGGTGT TGTTACTTGC 21880 76 4.04e-06 TGTACGGCGG TGGCGCTGGTGTGTTG TTTCTGTGAG 17860 200 6.46e-06 TGCGCGCATC TGCCGATGATGGATGT TCGACGATCG 8769 42 7.23e-06 GCTGCTGTTT TGGAGATGGAGGATAT GAGGTCTGCT 264018 426 7.23e-06 GTGTTACTAC TTGCGATGGTGAGTGT GTGGATTGCA 9555 6 8.07e-06 CGTTC TGCTGTTGTAGGATAT TGGGTGATTT 22391 232 8.07e-06 TGATTTACAG TTGTTTTGTAGGAGTT CCGCCGTGAA 23565 15 9.00e-06 AGTGGAACTG TGTTGACGGTGGATGG TGGTATGATG 23039 189 9.00e-06 CGCTGACGGT TGGCGGCGTTGGTTTC TGGGAAATAT 11529 42 1.12e-05 CCCTGAAACA GGGATGTGTTGGTTTT GCTCCACGGA 23253 16 1.37e-05 AGAGTGACTC TTTCGTTGGTGCCTTT ACGACTGTGG 23603 196 1.68e-05 AAGTTTCATT TTGCGACGTAGGATAT GACGCATTGT 11641 119 2.04e-05 GGTGTGGTTA TGGTTTTGTAGGAGAT GAGACGAACA 9558 32 2.24e-05 AGTTGCGATG TGGATCGGTTGCGTTT GCTTCAATTG 22702 154 2.46e-05 TGGCTTTGGT GTCAGTTGTTGGTTTG TATTGGCAGC 10109 14 2.46e-05 ATTTTGCACA TGGTGTTGTTTCAGGG AGGCAGCAGT 5361 213 2.97e-05 TCAGAGTCGC TGTTTTGGGTGGAGTT GTCCTTCAGT 264486 81 3.24e-05 AAATTTTGGA TGTTTCTGCTGGTTTG ACGTTCAGTT 9180 164 3.54e-05 AATGCTACTA TTGTTGTGTTTCATAT AATAAAATAT 10984 304 3.87e-05 TCCATTTGAA TTTTGATGATGACTTT CTCAACGCAC 262217 338 5.43e-05 CTTGACAGGT TGCTTGCGTTGAGTTG TCGCCCATTT 9557 163 6.91e-05 GATCAAAATT TTGAGTGAGTGGATTT GAATTTCGAA 12207 14 6.91e-05 AATGACCTCA TGTTTCTGTTAGATTG AAATGTTCTA 4293 129 9.39e-05 GAGGTGAACA TTGCGTGGATGCAATG GTGAGAGAGT 1716 158 1.09e-04 TTTGGCTCAG TGTCGGCGATGGGATT GCATTGCATT 264854 269 1.17e-04 GTACCCGGCA TGGTAATGATGTATTC CGGCCAACGT 4184 2 1.76e-04 G GTGCGTCGTTTATTTG GAGGAGACAT 3861 8 4.08e-04 CGACGGG TTGCAATGCTGATGTG TGTCTTTGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20728 3.7e-07 184_[+2]_300 2641 4.3e-07 172_[+2]_312 9502 6.9e-07 214_[+2]_270 21820 8e-07 174_[+2]_310 9289 3.2e-06 2_[+2]_482 2600 3.6e-06 129_[+2]_355 22338 4e-06 379_[+2]_105 21880 4e-06 75_[+2]_409 17860 6.5e-06 199_[+2]_285 8769 7.2e-06 41_[+2]_443 264018 7.2e-06 425_[+2]_59 9555 8.1e-06 5_[+2]_479 22391 8.1e-06 231_[+2]_253 23565 9e-06 14_[+2]_470 23039 9e-06 188_[+2]_296 11529 1.1e-05 41_[+2]_443 23253 1.4e-05 15_[+2]_469 23603 1.7e-05 195_[+2]_289 11641 2e-05 118_[+2]_366 9558 2.2e-05 31_[+2]_453 22702 2.5e-05 153_[+2]_331 10109 2.5e-05 13_[+2]_471 5361 3e-05 212_[+2]_272 264486 3.2e-05 80_[+2]_404 9180 3.5e-05 163_[+2]_321 10984 3.9e-05 303_[+2]_181 262217 5.4e-05 337_[+2]_147 9557 6.9e-05 162_[+2]_322 12207 6.9e-05 13_[+2]_471 4293 9.4e-05 128_[+2]_356 1716 0.00011 157_[+2]_327 264854 0.00012 268_[+2]_216 4184 0.00018 1_[+2]_483 3861 0.00041 7_[+2]_477 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=34 20728 ( 185) TTGTGTTGTTGTTTTT 1 2641 ( 173) TGGAGGTGATGGATTG 1 9502 ( 215) TTGAGATGTTGCTTTT 1 21820 ( 175) TGGTTTTGGTGGGTGT 1 9289 ( 3) TGGAGTTGTTTCGTTG 1 2600 ( 130) TGGTGTTGGTGTGTAG 1 22338 ( 380) TTGTGATGTTTGGTGT 1 21880 ( 76) TGGCGCTGGTGTGTTG 1 17860 ( 200) TGCCGATGATGGATGT 1 8769 ( 42) TGGAGATGGAGGATAT 1 264018 ( 426) TTGCGATGGTGAGTGT 1 9555 ( 6) TGCTGTTGTAGGATAT 1 22391 ( 232) TTGTTTTGTAGGAGTT 1 23565 ( 15) TGTTGACGGTGGATGG 1 23039 ( 189) TGGCGGCGTTGGTTTC 1 11529 ( 42) GGGATGTGTTGGTTTT 1 23253 ( 16) TTTCGTTGGTGCCTTT 1 23603 ( 196) TTGCGACGTAGGATAT 1 11641 ( 119) TGGTTTTGTAGGAGAT 1 9558 ( 32) TGGATCGGTTGCGTTT 1 22702 ( 154) GTCAGTTGTTGGTTTG 1 10109 ( 14) TGGTGTTGTTTCAGGG 1 5361 ( 213) TGTTTTGGGTGGAGTT 1 264486 ( 81) TGTTTCTGCTGGTTTG 1 9180 ( 164) TTGTTGTGTTTCATAT 1 10984 ( 304) TTTTGATGATGACTTT 1 262217 ( 338) TGCTTGCGTTGAGTTG 1 9557 ( 163) TTGAGTGAGTGGATTT 1 12207 ( 14) TGTTTCTGTTAGATTG 1 4293 ( 129) TTGCGTGGATGCAATG 1 1716 ( 158) TGTCGGCGATGGGATT 1 264854 ( 269) TGGTAATGATGTATTC 1 4184 ( 2) GTGCGTCGTTTATTTG 1 3861 ( 8) TTGCAATGCTGATGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 16975 bayes= 9.03045 E= 5.0e-008 -1173 -1173 -143 179 -1173 -1173 130 64 -1173 -95 150 -36 -20 37 -1173 83 -220 -1173 144 16 12 -95 -44 64 -1173 -36 -102 142 -320 -1173 202 -1173 -61 -195 15 92 -88 -1173 -1173 169 -320 -1173 179 -84 -88 -14 115 -116 71 -195 15 -17 -220 -1173 -70 159 -61 -1173 -44 129 -1173 -195 68 108 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 34 E= 5.0e-008 0.000000 0.000000 0.088235 0.911765 0.000000 0.000000 0.588235 0.411765 0.000000 0.117647 0.676471 0.205882 0.235294 0.294118 0.000000 0.470588 0.058824 0.000000 0.647059 0.294118 0.294118 0.117647 0.176471 0.411765 0.000000 0.176471 0.117647 0.705882 0.029412 0.000000 0.970588 0.000000 0.176471 0.058824 0.264706 0.500000 0.147059 0.000000 0.000000 0.852941 0.029412 0.000000 0.823529 0.147059 0.147059 0.205882 0.529412 0.117647 0.441176 0.058824 0.264706 0.235294 0.058824 0.000000 0.147059 0.794118 0.176471 0.000000 0.176471 0.647059 0.000000 0.058824 0.382353 0.558824 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[GT][GT][TCA][GT][TA]TG[TG]TG[GC][AGT]TT[TG] -------------------------------------------------------------------------------- Time 21.10 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 14 sites = 16 llr = 188 E-value = 5.4e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2831:8:629a821 pos.-specific C 8:8:929:51:::: probability G :1::11113::::7 matrix T 11:9:::31::383 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 CACTCACACAAATG consensus A TG T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 9502 278 7.69e-09 ACTCCTCAGT CACTCACTCAAATG CCACCGCCAA 10109 289 2.45e-08 CATCAACGCA CACTCACAAAAATG GCAGTCAAAT 3861 242 6.90e-08 GTCCTTGCCT CAATCACTCAAATG CAGAACGGGC 9555 319 2.34e-07 TTCTGATGCA CTCTCACAGAAATG CTGCCTCTGC 12207 100 3.73e-07 CGGCAACAAA CAATCCCTCAAATG TTGTTCTTAC 9558 262 4.65e-07 AATTCAAATC CACTCACTCAAAAT TTTGATCCAA 2530 285 6.51e-07 CAACAGGAGT AACTCCCAGAAATG AAACCTCCTA 2600 425 1.48e-06 CTCCGCCCTC CGCTCAGACAAATG CATTAAACCC 23253 266 1.82e-06 GCTGAGACAC ATCTCACAAAAATG ATGGGTGCCA 4184 378 2.73e-06 ATAAGCTGCA CAATCACACAATTA AGGGTATCGT 22391 377 4.07e-06 TGAGTATATT AACTCAGAGAATTG TGGCGGGAAC 21880 220 5.04e-06 AATTTTGCTC CACTCGCGAAAATG GCGGCCAATC 9557 19 6.31e-06 TTTGTGCTTT CACTCACATCATTG ATAGAAGAAA 23039 233 8.27e-06 TTACCACAAT CACACCCACAATTT TCATTGCCGA 9180 245 1.08e-05 ACGCGTCTCA TACTCACTGAAAAT GTCGATCTGA 10984 225 1.08e-05 TACTTGGACA CAATGACACAAAAT ATTTGGACAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9502 7.7e-09 277_[+3]_209 10109 2.5e-08 288_[+3]_198 3861 6.9e-08 241_[+3]_245 9555 2.3e-07 318_[+3]_168 12207 3.7e-07 99_[+3]_387 9558 4.6e-07 261_[+3]_225 2530 6.5e-07 284_[+3]_202 2600 1.5e-06 424_[+3]_62 23253 1.8e-06 265_[+3]_221 4184 2.7e-06 377_[+3]_109 22391 4.1e-06 376_[+3]_110 21880 5e-06 219_[+3]_267 9557 6.3e-06 18_[+3]_468 23039 8.3e-06 232_[+3]_254 9180 1.1e-05 244_[+3]_242 10984 1.1e-05 224_[+3]_262 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=14 seqs=16 9502 ( 278) CACTCACTCAAATG 1 10109 ( 289) CACTCACAAAAATG 1 3861 ( 242) CAATCACTCAAATG 1 9555 ( 319) CTCTCACAGAAATG 1 12207 ( 100) CAATCCCTCAAATG 1 9558 ( 262) CACTCACTCAAAAT 1 2530 ( 285) AACTCCCAGAAATG 1 2600 ( 425) CGCTCAGACAAATG 1 23253 ( 266) ATCTCACAAAAATG 1 4184 ( 378) CAATCACACAATTA 1 22391 ( 377) AACTCAGAGAATTG 1 21880 ( 220) CACTCGCGAAAATG 1 9557 ( 19) CACTCACATCATTG 1 23039 ( 233) CACACCCACAATTT 1 9180 ( 245) TACTCACTGAAAAT 1 10984 ( 225) CAATGACACAAAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 17045 bayes= 10.7932 E= 5.4e-004 -53 172 -1064 -208 159 -1064 -193 -108 -11 172 -1064 -1064 -211 -1064 -1064 183 -1064 204 -193 -1064 147 -28 -193 -1064 -1064 194 -93 -1064 121 -1064 -193 24 -53 114 7 -208 179 -186 -1064 -1064 189 -1064 -1064 -1064 147 -1064 -1064 -8 -53 -1064 -1064 162 -211 -1064 153 -8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 16 E= 5.4e-004 0.187500 0.750000 0.000000 0.062500 0.812500 0.000000 0.062500 0.125000 0.250000 0.750000 0.000000 0.000000 0.062500 0.000000 0.000000 0.937500 0.000000 0.937500 0.062500 0.000000 0.750000 0.187500 0.062500 0.000000 0.000000 0.875000 0.125000 0.000000 0.625000 0.000000 0.062500 0.312500 0.187500 0.500000 0.250000 0.062500 0.937500 0.062500 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.187500 0.000000 0.000000 0.812500 0.062500 0.000000 0.687500 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CA[CA]TCAC[AT][CG]AA[AT]T[GT] -------------------------------------------------------------------------------- Time 31.20 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10109 1.70e-07 13_[+2(2.46e-05)]_155_\ [+1(1.01e-05)]_88_[+3(2.45e-08)]_198 10984 4.50e-05 224_[+3(1.08e-05)]_65_\ [+2(3.87e-05)]_47_[+1(7.60e-06)]_118 11529 3.43e-02 41_[+2(1.12e-05)]_443 11641 1.00e-01 118_[+2(2.04e-05)]_366 12207 1.49e-05 13_[+2(6.91e-05)]_70_[+3(3.73e-07)]_\ 160_[+1(3.53e-05)]_211 1716 1.18e-03 421_[+1(1.25e-06)]_63 17860 1.51e-03 120_[+2(9.39e-05)]_63_\ [+2(6.46e-06)]_267_[+1(2.22e-05)]_2 20728 1.71e-05 184_[+2(3.69e-07)]_150_\ [+1(2.93e-06)]_134 21820 1.07e-04 174_[+2(8.04e-07)]_161_\ [+1(8.36e-06)]_11_[+2(3.24e-05)]_106 21880 3.43e-06 75_[+2(4.04e-06)]_128_\ [+3(5.04e-06)]_4_[+1(8.36e-06)]_247 22338 3.82e-02 379_[+2(4.04e-06)]_105 22391 7.77e-05 181_[+2(3.24e-05)]_34_\ [+2(8.07e-06)]_129_[+3(4.07e-06)]_110 22702 2.32e-03 153_[+2(2.46e-05)]_276_\ [+1(7.60e-06)]_39 23039 4.46e-08 188_[+2(9.00e-06)]_28_\ [+3(8.27e-06)]_216_[+1(1.89e-08)]_22 23253 5.27e-06 15_[+2(1.37e-05)]_66_[+2(6.38e-05)]_\ 152_[+3(1.82e-06)]_114_[+1(1.11e-05)]_91 23565 1.89e-03 14_[+2(9.00e-06)]_239_\ [+1(2.22e-05)]_215 23603 2.27e-03 145_[+1(1.01e-05)]_34_\ [+2(1.68e-05)]_289 2530 4.05e-05 284_[+3(6.51e-07)]_12_\ [+1(2.62e-06)]_174 2600 4.13e-10 129_[+2(3.57e-06)]_257_\ [+1(1.67e-09)]_6_[+3(1.48e-06)]_62 262217 6.41e-03 337_[+2(5.43e-05)]_29_\ [+1(1.22e-05)]_102 264018 3.28e-03 54_[+1(6.61e-05)]_355_\ [+2(7.23e-06)]_59 2641 2.23e-06 172_[+2(4.32e-07)]_98_\ [+2(4.99e-05)]_119_[+1(2.32e-06)]_63 264486 7.69e-03 80_[+2(3.24e-05)]_404 264854 1.06e-03 476_[+1(6.34e-07)]_8 3861 4.14e-04 241_[+3(6.90e-08)]_245 4184 6.92e-05 377_[+3(2.73e-06)]_57_\ [+1(1.11e-05)]_36 4293 3.73e-03 128_[+2(9.39e-05)]_302_\ [+1(4.09e-06)]_38 5361 9.93e-02 212_[+2(2.97e-05)]_272 8769 5.59e-02 41_[+2(7.23e-06)]_443 9180 1.64e-05 163_[+2(3.54e-05)]_65_\ [+3(1.08e-05)]_21_[+1(2.62e-06)]_205 9289 1.63e-04 2_[+2(3.15e-06)]_454_[+1(6.22e-06)]_\ 12 9502 3.36e-09 24_[+1(1.58e-05)]_174_\ [+2(6.94e-07)]_47_[+3(7.69e-09)]_209 9555 1.20e-06 5_[+2(8.07e-06)]_215_[+2(6.38e-05)]_\ 66_[+3(2.34e-07)]_150_[+1(2.81e-05)]_2 9557 1.99e-04 18_[+3(6.31e-06)]_130_\ [+2(6.91e-05)]_57_[+3(5.38e-05)]_62_[+3(8.87e-05)]_84_[+1(4.09e-05)]_75 9558 2.42e-06 31_[+2(2.24e-05)]_214_\ [+3(4.65e-07)]_178_[+1(1.11e-05)]_31 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************