******************************************************************************** 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/410/410.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11713 1.0000 500 19421 1.0000 500 2028 1.0000 500 20778 1.0000 500 21334 1.0000 500 22869 1.0000 500 23207 1.0000 500 23572 1.0000 500 24307 1.0000 500 24580 1.0000 500 25593 1.0000 500 261181 1.0000 500 262554 1.0000 500 263930 1.0000 500 264655 1.0000 500 269263 1.0000 500 31136 1.0000 500 31515 1.0000 500 34647 1.0000 500 35459 1.0000 500 41068 1.0000 500 6240 1.0000 500 6630 1.0000 500 7582 1.0000 500 8143 1.0000 500 8979 1.0000 500 9353 1.0000 500 9454 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/410/410.seqs.fa -oc motifs/410 -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= 28 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= 14000 N= 28 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.262 C 0.242 G 0.225 T 0.270 Background letter frequencies (from dataset with add-one prior applied): A 0.262 C 0.242 G 0.225 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 28 llr = 273 E-value = 6.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 25137221:3::34:2:331: pos.-specific C 833438:66:646:9234258 probability G ::41::1:2:12:2:131:21 matrix T :312::721834:5:553531 bits 2.2 1.9 1.7 1.5 * Relative 1.3 * * * Entropy 1.1 * ** * * * (14.1 bits) 0.9 * ** ** * * * 0.6 * ******* * * * 0.4 ** *********** * * 0.2 ********************* 0.0 --------------------- Multilevel CAGCACTCCTCCCTCTTCTCC consensus TCAC ATGATTAA CGAAT sequence C T CTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 41068 122 3.76e-11 CTTTTGTCCC CTGAACTCCTCTCTCTTCTCC TCCGTAACTC 263930 455 1.72e-08 CCAACAACCT CCCTACTCCTCTCTCTCACCC GAACCCACCG 8979 231 4.26e-08 AAGATAGTGG CAGTACTCTTCTATCTTCACC TCGGCGATGA 9353 409 5.06e-08 AAAACGCTTT CCGCACTCCTCTCACTTTGCC ATCTGCACAC 7582 418 2.44e-07 ATGTTGACCA CTTCACTCCTCACTCTTATCC CGACCATTAT 24580 31 2.82e-07 GTGCAACGGG CACAACACCTCCAACCTATGC ATCCAAAGTC 31136 129 5.63e-07 CAACAATACA CAGCACTTGTTTCTCACCACC AGCTAGCTTG 24307 410 1.37e-06 TTTCACTCTT CTCACCTCCTTGCACTTGTTC CAGACGGAGA 9454 383 1.54e-06 AACACCCACA CACCCAACCTCTCGCCTCCCC AACCCACGTT 34647 86 3.06e-06 CACTTTTCGT CCACCCTCCTCCCTCCCTTCG TCCGTGATGA 20778 15 6.40e-06 CGATACTTCT CACAACTCCAGCCAGTGCTCC TAGTTCACAC 6240 353 7.07e-06 TTTCGGTCTC CTTACCTCTTCCCTCCGTCTC CTTCCTCGCA 6630 240 7.80e-06 AACGGACATA AAGAACTTGTTGCTCTTCTAC GATCTTCAGA 8143 170 1.51e-05 ATCAAGTTTG ACGCACGCTTCTCACAGAACC GCTTGAGACT 23572 35 1.51e-05 GTAGCTCGAA CTCTACTACTATCACTGTTGC TGCTTCTTTC 262554 407 1.65e-05 TATGCCATAA CAACAATTGTTTCGCTCAACC ACTGCACTTG 261181 71 1.97e-05 ATCCAACATA CAGAACAACTTGAACTTCTTT CCTGGGTGGA 21334 428 1.97e-05 TGTACGCAAC ACCAACACCTCCAGCCTTCGC CCTACCAACA 22869 434 2.77e-05 GAGCTCTCCG CCACCCGCCACCCACTCGCTC ACCGCCTCTC 269263 312 4.83e-05 ACAACAACAG CAACAATCCTGGCTCGGCTAC TTTTTTGGCA 25593 341 6.51e-05 ACCGCAAGGC CAGCACTACATTGGCAGCATC CTCCCTTCGC 23207 55 7.00e-05 ACAATGGCGT CCTGCCTCGACCCACGGCCTC CCTATTAGCG 31515 255 7.52e-05 CAGCAGACGT CAGTAAAACACCATCCGAAGC CAAAGCAAGT 2028 389 8.66e-05 TCATTCTTTG CTTGCCTCTTTTCTCTTTTGT ATATTCAGGA 264655 371 1.14e-04 TCATTCGCCG ATGTCCTTCATGAACTTCAAC AGATTGAAGC 35459 183 1.47e-04 TCATAAAAGC CAGTACTCGTCCAGTACTTCT TTCGTATTGA 19421 461 1.67e-04 TACCCCAACT AACACCATGTCCATCTTAACA GTGGGTGCAA 11713 107 3.34e-04 AAGCCTTTCT CTCCAAGTCACCATCACATTG ATTGTCAACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41068 3.8e-11 121_[+1]_358 263930 1.7e-08 454_[+1]_25 8979 4.3e-08 230_[+1]_249 9353 5.1e-08 408_[+1]_71 7582 2.4e-07 417_[+1]_62 24580 2.8e-07 30_[+1]_449 31136 5.6e-07 128_[+1]_351 24307 1.4e-06 409_[+1]_70 9454 1.5e-06 382_[+1]_97 34647 3.1e-06 85_[+1]_394 20778 6.4e-06 14_[+1]_465 6240 7.1e-06 352_[+1]_127 6630 7.8e-06 239_[+1]_240 8143 1.5e-05 169_[+1]_310 23572 1.5e-05 34_[+1]_445 262554 1.7e-05 406_[+1]_73 261181 2e-05 70_[+1]_409 21334 2e-05 427_[+1]_52 22869 2.8e-05 433_[+1]_46 269263 4.8e-05 311_[+1]_168 25593 6.5e-05 340_[+1]_139 23207 7e-05 54_[+1]_425 31515 7.5e-05 254_[+1]_225 2028 8.7e-05 388_[+1]_91 264655 0.00011 370_[+1]_109 35459 0.00015 182_[+1]_297 19421 0.00017 460_[+1]_19 11713 0.00033 106_[+1]_373 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=28 41068 ( 122) CTGAACTCCTCTCTCTTCTCC 1 263930 ( 455) CCCTACTCCTCTCTCTCACCC 1 8979 ( 231) CAGTACTCTTCTATCTTCACC 1 9353 ( 409) CCGCACTCCTCTCACTTTGCC 1 7582 ( 418) CTTCACTCCTCACTCTTATCC 1 24580 ( 31) CACAACACCTCCAACCTATGC 1 31136 ( 129) CAGCACTTGTTTCTCACCACC 1 24307 ( 410) CTCACCTCCTTGCACTTGTTC 1 9454 ( 383) CACCCAACCTCTCGCCTCCCC 1 34647 ( 86) CCACCCTCCTCCCTCCCTTCG 1 20778 ( 15) CACAACTCCAGCCAGTGCTCC 1 6240 ( 353) CTTACCTCTTCCCTCCGTCTC 1 6630 ( 240) AAGAACTTGTTGCTCTTCTAC 1 8143 ( 170) ACGCACGCTTCTCACAGAACC 1 23572 ( 35) CTCTACTACTATCACTGTTGC 1 262554 ( 407) CAACAATTGTTTCGCTCAACC 1 261181 ( 71) CAGAACAACTTGAACTTCTTT 1 21334 ( 428) ACCAACACCTCCAGCCTTCGC 1 22869 ( 434) CCACCCGCCACCCACTCGCTC 1 269263 ( 312) CAACAATCCTGGCTCGGCTAC 1 25593 ( 341) CAGCACTACATTGGCAGCATC 1 23207 ( 55) CCTGCCTCGACCCACGGCCTC 1 31515 ( 255) CAGTAAAACACCATCCGAAGC 1 2028 ( 389) CTTGCCTCTTTTCTCTTTTGT 1 264655 ( 371) ATGTCCTTCATGAACTTCAAC 1 35459 ( 183) CAGTACTCGTCCAGTACTTCT 1 19421 ( 461) AACACCATGTCCATCTTAACA 1 11713 ( 107) CTCCAAGTCACCATCACATTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13440 bayes= 9.51064 E= 6.5e-002 -56 176 -1145 -1145 82 5 -1145 8 -88 41 80 -92 29 70 -165 -33 137 41 -1145 -1145 -56 176 -1145 -1145 -29 -1145 -107 133 -88 141 -1145 -33 -1145 141 -7 -92 -7 -1145 -1145 147 -287 133 -165 8 -287 70 -33 54 29 141 -265 -1145 44 -1145 -33 78 -1145 194 -265 -292 -56 -18 -165 99 -1145 5 34 78 12 70 -165 -11 12 -18 -265 78 -129 94 -33 -11 -287 170 -165 -133 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 28 E= 6.5e-002 0.178571 0.821429 0.000000 0.000000 0.464286 0.250000 0.000000 0.285714 0.142857 0.321429 0.392857 0.142857 0.321429 0.392857 0.071429 0.214286 0.678571 0.321429 0.000000 0.000000 0.178571 0.821429 0.000000 0.000000 0.214286 0.000000 0.107143 0.678571 0.142857 0.642857 0.000000 0.214286 0.000000 0.642857 0.214286 0.142857 0.250000 0.000000 0.000000 0.750000 0.035714 0.607143 0.071429 0.285714 0.035714 0.392857 0.178571 0.392857 0.321429 0.642857 0.035714 0.000000 0.357143 0.000000 0.178571 0.464286 0.000000 0.928571 0.035714 0.035714 0.178571 0.214286 0.071429 0.535714 0.000000 0.250000 0.285714 0.464286 0.285714 0.392857 0.071429 0.250000 0.285714 0.214286 0.035714 0.464286 0.107143 0.464286 0.178571 0.250000 0.035714 0.785714 0.071429 0.107143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[ATC][GC][CAT][AC]C[TA][CT][CG][TA][CT][CT][CA][TA]C[TC][TGC][CAT][TAC][CT]C -------------------------------------------------------------------------------- Time 6.33 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 8 llr = 119 E-value = 5.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 9::1::13343:a53: pos.-specific C :1::::::::1::1:6 probability G 15a98a98864a:::4 matrix T :4::3:::::3::48: bits 2.2 * * * 1.9 * * ** 1.7 * * ** 1.5 * ** ** ** Relative 1.3 * ******* ** Entropy 1.1 * ******** ** ** (21.4 bits) 0.9 * ******** ** ** 0.6 ********** ** ** 0.4 ********** ***** 0.2 **************** 0.0 ---------------- Multilevel AGGGGGGGGGGGAATC consensus T T AAAA TAG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 8143 386 1.48e-09 AACGTGACAG AGGGGGGGGGTGAATG CTACCCCGTC 6630 157 1.91e-09 TCAGTGTGAT ATGGGGGGGGTGAATC AAGATTTATC 41068 68 1.12e-08 CCTTGACACG AGGGGGGGAGGGATTG TGAGTTTGGC 263930 360 5.36e-08 ACGTGACACC ACGGGGGGGAGGAAAC CATTTTCCCC 269263 449 5.84e-08 TCGTCAGTGG AGGGTGGAGAGGAATC TGCCAAACGG 262554 331 2.75e-07 CTTCTATCAT GTGGTGGGGGAGATTG GTGAGAGTGA 264655 146 5.63e-07 GAACCAAACA ATGGGGGAGACGACAC CGACTTGGAT 6240 220 6.79e-07 GGCCGAGTAA AGGAGGAGAGAGATTC ACGGTGTCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8143 1.5e-09 385_[+2]_99 6630 1.9e-09 156_[+2]_328 41068 1.1e-08 67_[+2]_417 263930 5.4e-08 359_[+2]_125 269263 5.8e-08 448_[+2]_36 262554 2.7e-07 330_[+2]_154 264655 5.6e-07 145_[+2]_339 6240 6.8e-07 219_[+2]_265 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=8 8143 ( 386) AGGGGGGGGGTGAATG 1 6630 ( 157) ATGGGGGGGGTGAATC 1 41068 ( 68) AGGGGGGGAGGGATTG 1 263930 ( 360) ACGGGGGGGAGGAAAC 1 269263 ( 449) AGGGTGGAGAGGAATC 1 262554 ( 331) GTGGTGGGGGAGATTG 1 264655 ( 146) ATGGGGGAGACGACAC 1 6240 ( 220) AGGAGGAGAGAGATTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 13580 bayes= 10.7283 E= 5.6e-001 174 -965 -85 -965 -965 -95 115 47 -965 -965 215 -965 -107 -965 196 -965 -965 -965 174 -11 -965 -965 215 -965 -107 -965 196 -965 -7 -965 174 -965 -7 -965 174 -965 51 -965 147 -965 -7 -95 74 -11 -965 -965 215 -965 193 -965 -965 -965 93 -95 -965 47 -7 -965 -965 147 -965 137 74 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 8 E= 5.6e-001 0.875000 0.000000 0.125000 0.000000 0.000000 0.125000 0.500000 0.375000 0.000000 0.000000 1.000000 0.000000 0.125000 0.000000 0.875000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.125000 0.000000 0.875000 0.000000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.750000 0.000000 0.375000 0.000000 0.625000 0.000000 0.250000 0.125000 0.375000 0.250000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.125000 0.000000 0.375000 0.250000 0.000000 0.000000 0.750000 0.000000 0.625000 0.375000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- A[GT]GG[GT]GG[GA][GA][GA][GAT]GA[AT][TA][CG] -------------------------------------------------------------------------------- Time 13.10 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 27 llr = 249 E-value = 3.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 31:1:::1:61:121: pos.-specific C :1:121:14:::11:1 probability G 6173:8246:472:82 matrix T 17348184:4536717 bits 2.2 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 GTGTTGTGGATGTTGT consensus A TGC TCTGTGA G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 31515 458 3.57e-09 TGAGTGATTT GTGTTGTTGTTGTTGT TGTTGGGGAA 11713 379 2.15e-08 ATTCCCCTCC GTGCTGTGGTGGTTGT TTGTTGATAG 24307 237 3.74e-07 AGCCACGGGC GTGTTGTAGAGGTTGC AAAGGAATTA 24580 210 1.04e-06 GATGATGATC ATGATGGTGAGGTTGT CAGAGTCCAC 9353 1 1.19e-06 . TTGGCGTGGAGGTTGT CATGGTGTTG 6240 189 2.01e-06 TTTGCTCATC GTTTTGTTGAGGAAGT CTACGGGCCG 262554 227 2.01e-06 AGTGACATTC ATGGCGTGGAAGGTGT ATCTTCCGAT 7582 396 2.28e-06 CCAACATTTC GTTTTGTAGTTGATGT TGACCACTTC 8143 103 2.92e-06 TTCCCTCTCC GTGTTGGCGTTGGTGT CAGTGCAGAT 263930 232 9.11e-06 GCTCCTTGCT GTGGTGTTCTGTTTTT GTCCTGGTGA 261181 321 1.38e-05 TTGATTGGAG GCTTTCTTGATGTTGT CTCGGCTATT 2028 284 1.38e-05 TTACTCGTTC GTGTTGTGCAGGGAAG GAGTAACCAC 8979 288 1.68e-05 ATTGCGGCTC AGGTTGTTCAGGGAGT GTTAGGCTTT 25593 165 1.85e-05 TATAACTTAA GAGATGTTGATTTAGG TACATGGATG 269263 422 2.24e-05 GAAATGAAGG AGGGTGGGGATGTCGT ATCGTCAGTG 264655 73 4.21e-05 TGAGCTGGGA GTGGTGTTGTATCTGC TCTTTTCGCG 22869 40 4.58e-05 CATAGCAGTC ATTGCGTTGATTTAGG ATGATCGTGT 19421 329 4.98e-05 CAAGAGGGAA GTGCCGTACTTGGAGG CCTTTCGGGC 31136 358 6.37e-05 ATCTGGGTGT GTTCTTTGGATCTTGT GTGTCGCGAA 41068 195 6.90e-05 CTTCCACTAC AAGTTGTCGATGTTAG ATTCTGCATT 34647 48 8.07e-05 TTGGGTCCCG TCGTTCTGCTTGTTGT AGTAAAAAAC 23207 312 1.01e-04 TTGCATGGTA GTGCCGGTCATGCTGC CACTGTAGGG 23572 177 1.17e-04 GCAATCTTTC GTGGTTTGCTATGCGT TTTCGCTATC 9454 106 1.26e-04 AAAGCAAATG ATGATGGGCTGTTTTT GATCATCCGC 20778 362 1.35e-04 AATCGATTCT GTGATCTGGAATACGT TCCTACTCTT 21334 338 1.45e-04 GAGCCAGCTA AATTTTTGCTGGATGT CACTATGTCG 35459 88 2.02e-04 ACGAAATACT GATGCGTACATGTTAG ATTGCATTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31515 3.6e-09 457_[+3]_27 11713 2.1e-08 378_[+3]_106 24307 3.7e-07 236_[+3]_248 24580 1e-06 209_[+3]_275 9353 1.2e-06 [+3]_484 6240 2e-06 188_[+3]_296 262554 2e-06 226_[+3]_258 7582 2.3e-06 395_[+3]_89 8143 2.9e-06 102_[+3]_382 263930 9.1e-06 231_[+3]_253 261181 1.4e-05 320_[+3]_164 2028 1.4e-05 283_[+3]_201 8979 1.7e-05 287_[+3]_197 25593 1.9e-05 164_[+3]_320 269263 2.2e-05 421_[+3]_63 264655 4.2e-05 72_[+3]_412 22869 4.6e-05 39_[+3]_445 19421 5e-05 328_[+3]_156 31136 6.4e-05 357_[+3]_127 41068 6.9e-05 194_[+3]_290 34647 8.1e-05 47_[+3]_437 23207 0.0001 311_[+3]_173 23572 0.00012 176_[+3]_308 9454 0.00013 105_[+3]_379 20778 0.00014 361_[+3]_123 21334 0.00014 337_[+3]_147 35459 0.0002 87_[+3]_397 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=27 31515 ( 458) GTGTTGTTGTTGTTGT 1 11713 ( 379) GTGCTGTGGTGGTTGT 1 24307 ( 237) GTGTTGTAGAGGTTGC 1 24580 ( 210) ATGATGGTGAGGTTGT 1 9353 ( 1) TTGGCGTGGAGGTTGT 1 6240 ( 189) GTTTTGTTGAGGAAGT 1 262554 ( 227) ATGGCGTGGAAGGTGT 1 7582 ( 396) GTTTTGTAGTTGATGT 1 8143 ( 103) GTGTTGGCGTTGGTGT 1 263930 ( 232) GTGGTGTTCTGTTTTT 1 261181 ( 321) GCTTTCTTGATGTTGT 1 2028 ( 284) GTGTTGTGCAGGGAAG 1 8979 ( 288) AGGTTGTTCAGGGAGT 1 25593 ( 165) GAGATGTTGATTTAGG 1 269263 ( 422) AGGGTGGGGATGTCGT 1 264655 ( 73) GTGGTGTTGTATCTGC 1 22869 ( 40) ATTGCGTTGATTTAGG 1 19421 ( 329) GTGCCGTACTTGGAGG 1 31136 ( 358) GTTCTTTGGATCTTGT 1 41068 ( 195) AAGTTGTCGATGTTAG 1 34647 ( 48) TCGTTCTGCTTGTTGT 1 23207 ( 312) GTGCCGGTCATGCTGC 1 23572 ( 177) GTGGTTTGCTATGCGT 1 9454 ( 106) ATGATGGGCTGTTTTT 1 20778 ( 362) GTGATCTGGAATACGT 1 21334 ( 338) AATTTTTGCTGGATGT 1 35459 ( 88) GATGCGTACATGTTAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 13580 bayes= 9.54139 E= 3.6e-001 18 -1140 148 -187 -82 -171 -160 138 -1140 -1140 172 -6 -82 -71 40 59 -1140 -12 -1140 152 -1140 -112 179 -128 -1140 -1140 -28 159 -82 -171 86 45 -1140 61 148 -1140 117 -1140 -1140 59 -82 -1140 72 83 -1140 -271 164 -6 -82 -171 -2 104 -24 -112 -1140 130 -124 -1140 186 -187 -1140 -112 -2 130 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 27 E= 3.6e-001 0.296296 0.000000 0.629630 0.074074 0.148148 0.074074 0.074074 0.703704 0.000000 0.000000 0.740741 0.259259 0.148148 0.148148 0.296296 0.407407 0.000000 0.222222 0.000000 0.777778 0.000000 0.111111 0.777778 0.111111 0.000000 0.000000 0.185185 0.814815 0.148148 0.074074 0.407407 0.370370 0.000000 0.370370 0.629630 0.000000 0.592593 0.000000 0.000000 0.407407 0.148148 0.000000 0.370370 0.481481 0.000000 0.037037 0.703704 0.259259 0.148148 0.074074 0.222222 0.555556 0.222222 0.111111 0.000000 0.666667 0.111111 0.000000 0.814815 0.074074 0.000000 0.111111 0.222222 0.666667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA]T[GT][TG][TC]GT[GT][GC][AT][TG][GT][TG][TA]G[TG] -------------------------------------------------------------------------------- Time 19.43 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11713 4.47e-05 378_[+3(2.15e-08)]_106 19421 2.37e-02 328_[+3(4.98e-05)]_156 2028 3.55e-03 283_[+3(1.38e-05)]_89_\ [+1(8.66e-05)]_91 20778 6.99e-03 14_[+1(6.40e-06)]_435_\ [+1(8.08e-05)]_9 21334 1.78e-02 427_[+1(1.97e-05)]_52 22869 9.01e-03 39_[+3(4.58e-05)]_378_\ [+1(2.77e-05)]_46 23207 3.10e-03 54_[+1(7.00e-05)]_264_\ [+2(6.89e-05)]_145 23572 7.21e-04 34_[+1(1.51e-05)]_191_\ [+2(4.71e-05)]_238 24307 8.49e-06 236_[+3(3.74e-07)]_157_\ [+1(1.37e-06)]_70 24580 2.03e-06 30_[+1(2.82e-07)]_158_\ [+3(1.04e-06)]_275 25593 9.69e-03 164_[+3(1.85e-05)]_160_\ [+1(6.51e-05)]_139 261181 2.80e-03 70_[+1(1.97e-05)]_229_\ [+3(1.38e-05)]_164 262554 2.42e-07 226_[+3(2.01e-06)]_88_\ [+2(2.75e-07)]_60_[+1(1.65e-05)]_73 263930 3.90e-10 231_[+3(9.11e-06)]_112_\ [+2(5.36e-08)]_79_[+1(1.72e-08)]_25 264655 3.78e-05 72_[+3(4.21e-05)]_57_[+2(5.63e-07)]_\ 339 269263 1.38e-06 25_[+2(5.36e-05)]_199_\ [+2(3.02e-05)]_55_[+1(4.83e-05)]_89_[+3(2.24e-05)]_11_[+2(5.84e-08)]_36 31136 5.74e-04 128_[+1(5.63e-07)]_208_\ [+3(6.37e-05)]_127 31515 6.15e-07 181_[+2(9.87e-05)]_57_\ [+1(7.52e-05)]_182_[+3(3.57e-09)]_27 34647 1.18e-03 47_[+3(8.07e-05)]_22_[+1(3.06e-06)]_\ 394 35459 9.64e-02 500 41068 1.91e-12 67_[+2(1.12e-08)]_38_[+1(3.76e-11)]_\ 52_[+3(6.90e-05)]_290 6240 2.55e-07 112_[+2(4.17e-05)]_60_\ [+3(2.01e-06)]_15_[+2(6.79e-07)]_117_[+1(7.07e-06)]_127 6630 5.80e-07 156_[+2(1.91e-09)]_67_\ [+1(7.80e-06)]_240 7582 9.45e-06 395_[+3(2.28e-06)]_6_[+1(2.44e-07)]_\ 62 8143 2.60e-09 102_[+3(2.92e-06)]_51_\ [+1(1.51e-05)]_56_[+2(7.37e-05)]_123_[+2(1.48e-09)]_99 8979 6.02e-06 230_[+1(4.26e-08)]_36_\ [+3(1.68e-05)]_197 9353 1.92e-06 [+3(1.19e-06)]_11_[+3(8.71e-05)]_\ 365_[+1(5.06e-08)]_71 9454 2.67e-03 382_[+1(1.54e-06)]_97 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************