******************************************************************************** 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/214/214.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10050 1.0000 500 10158 1.0000 500 10810 1.0000 500 10886 1.0000 500 1554 1.0000 500 15977 1.0000 500 1672 1.0000 500 18091 1.0000 500 20664 1.0000 500 20881 1.0000 500 22521 1.0000 500 22763 1.0000 500 23013 1.0000 500 23651 1.0000 500 2409 1.0000 500 25733 1.0000 500 2575 1.0000 500 2578 1.0000 500 262994 1.0000 500 263375 1.0000 500 263558 1.0000 500 264143 1.0000 500 264628 1.0000 500 267929 1.0000 500 268446 1.0000 500 2702 1.0000 500 28148 1.0000 500 30380 1.0000 500 32760 1.0000 500 3280 1.0000 500 33798 1.0000 500 36076 1.0000 500 3803 1.0000 500 3837 1.0000 500 38559 1.0000 500 38647 1.0000 500 3963 1.0000 500 4333 1.0000 500 4502 1.0000 500 5246 1.0000 500 5599 1.0000 500 6200 1.0000 500 6693 1.0000 500 6934 1.0000 500 7188 1.0000 500 7216 1.0000 500 7602 1.0000 500 789 1.0000 500 7937 1.0000 500 8038 1.0000 500 8986 1.0000 500 9543 1.0000 500 9803 1.0000 500 9848 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/214/214.seqs.fa -oc motifs/214 -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= 54 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= 27000 N= 54 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.254 C 0.233 G 0.249 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.254 C 0.233 G 0.249 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 24 llr = 288 E-value = 6.0e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :33:2:6561297:43:93:7 pos.-specific C 93:67613258::8139:1a: probability G :2211:1213:1:1231:1:3 matrix T 1353:41:211:3231:15:: bits 2.1 * 1.9 * 1.7 * * 1.5 * * ** * Relative 1.3 * * ** * Entropy 1.1 * * ** * ** ** (17.3 bits) 0.8 * ** **** ** ** 0.6 * ** * **** ** ** 0.4 * *********** ** ** 0.2 * ******************* 0.0 --------------------- Multilevel CATCCCAAACCAACAACATCA consensus CAT T C G T TC A G sequence TG GG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8038 459 3.05e-09 AGCCAAAGCA CTCCCCAAACCAACGACATCA CTACCAAATT 38647 165 9.28e-09 GCATCAGCAT CTGCCCAAAGCAACAGCAGCA ACAACGGTGA 9543 342 1.18e-07 TTTGCACCTA CATCACAACTCAACGGCAACA CCCGAAACCT 3837 480 1.18e-07 TTCACAACGG CTGCCCACGACAACACCAACA 7937 359 1.33e-07 TCGTATCTCT CCTCACACACCACCTACAACA GCAAAGAACC 25733 164 1.50e-07 TTTGACAGTA CCAACCAATGCAACTCCATCA TTTGCCCAAG 3803 121 2.11e-07 CTTGTTGTTG CATCCTACACCAACCAGTTCA ATGACTATGC 23013 130 4.05e-07 CCTTCACCTT CATTCTTCTCCAACGCCAACG CACAGAGATT 2575 301 4.50e-07 CCCCTTCGCA CAGCGCCGAGCAACAGCAACA AATTTTGAAA 22763 464 4.99e-07 AAGATCTCTT CCATCTAGCCCATCTCCACCA CTAATCAAGA 3280 438 9.07e-07 TCGTCGTGAG CGAGCTACGCAAACAACAACA ACCGAATCTC 789 355 9.99e-07 TAAATCACAG CAGCCCAATCTGACCACATCA CCCACACTCC 20664 57 1.10e-06 TTTCGAAAAC CGTCGCAAACCAAGAAGATCG CACCATGGTT 4333 354 1.45e-06 ACAAACATGC CTACCTAGAGCGTCGCCACCA TAGCCTAATC 6934 60 1.59e-06 TCTGGAAACT CTTTCTTAATCATTTCCATCA CCACCTTCTC 3963 179 1.59e-06 ACTATCTCTA CTTCGTGCAGCAATGGCATCA TCTATCTGGC 2409 434 2.08e-06 ATTTTGTACC CCTGCTCATCCATCATCATCG TCTCCTTCCC 38559 361 2.47e-06 AGTGGCCTCC CGTTCCGAATCAATACCACCG ATCGCCCACC 7602 262 4.40e-06 GGCGGATATT TATCACGAACAAACTTCATCA TGCTATTCGT 10810 299 5.14e-06 GTCTGCGTCC CCTCCCAACCAATCTGCTGCG ACGAAGAACC 263558 323 6.00e-06 CAACTGCTCT CCAGCTCCCCAATCAACAACG TCGTCCCCCG 263375 459 8.08e-06 GTCTACACTC TAATCTACACCAAGAAGATCG GCACTCCACT 1672 273 8.68e-06 GCTGTGCAAG CGATCCAAAGTGTTAGCATCA AATAAAACAA 15977 463 1.00e-05 ACAACAACCC CAGCACTGAACAACCCCTTCA CTAACGCATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8038 3e-09 458_[+1]_21 38647 9.3e-09 164_[+1]_315 9543 1.2e-07 341_[+1]_138 3837 1.2e-07 479_[+1] 7937 1.3e-07 358_[+1]_121 25733 1.5e-07 163_[+1]_316 3803 2.1e-07 120_[+1]_359 23013 4.1e-07 129_[+1]_350 2575 4.5e-07 300_[+1]_179 22763 5e-07 463_[+1]_16 3280 9.1e-07 437_[+1]_42 789 1e-06 354_[+1]_125 20664 1.1e-06 56_[+1]_423 4333 1.5e-06 353_[+1]_126 6934 1.6e-06 59_[+1]_420 3963 1.6e-06 178_[+1]_301 2409 2.1e-06 433_[+1]_46 38559 2.5e-06 360_[+1]_119 7602 4.4e-06 261_[+1]_218 10810 5.1e-06 298_[+1]_181 263558 6e-06 322_[+1]_157 263375 8.1e-06 458_[+1]_21 1672 8.7e-06 272_[+1]_207 15977 1e-05 462_[+1]_17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=24 8038 ( 459) CTCCCCAAACCAACGACATCA 1 38647 ( 165) CTGCCCAAAGCAACAGCAGCA 1 9543 ( 342) CATCACAACTCAACGGCAACA 1 3837 ( 480) CTGCCCACGACAACACCAACA 1 7937 ( 359) CCTCACACACCACCTACAACA 1 25733 ( 164) CCAACCAATGCAACTCCATCA 1 3803 ( 121) CATCCTACACCAACCAGTTCA 1 23013 ( 130) CATTCTTCTCCAACGCCAACG 1 2575 ( 301) CAGCGCCGAGCAACAGCAACA 1 22763 ( 464) CCATCTAGCCCATCTCCACCA 1 3280 ( 438) CGAGCTACGCAAACAACAACA 1 789 ( 355) CAGCCCAATCTGACCACATCA 1 20664 ( 57) CGTCGCAAACCAAGAAGATCG 1 4333 ( 354) CTACCTAGAGCGTCGCCACCA 1 6934 ( 60) CTTTCTTAATCATTTCCATCA 1 3963 ( 179) CTTCGTGCAGCAATGGCATCA 1 2409 ( 434) CCTGCTCATCCATCATCATCG 1 38559 ( 361) CGTTCCGAATCAATACCACCG 1 7602 ( 262) TATCACGAACAAACTTCATCA 1 10810 ( 299) CCTCCCAACCAATCTGCTGCG 1 263558 ( 323) CCAGCTCCCCAATCAACAACG 1 263375 ( 459) TAATCTACACCAAGAAGATCG 1 1672 ( 273) CGATCCAAAGTGTTAGCATCA 1 15977 ( 463) CAGCACTGAACAACCCCTTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 25920 bayes= 11.1757 E= 6.0e-005 -1123 198 -1123 -166 39 10 -58 -8 20 -248 -26 80 -261 132 -99 -8 -61 160 -99 -1123 -1123 132 -1123 66 130 -90 -99 -108 98 52 -58 -1123 120 -48 -158 -66 -161 122 1 -108 -61 169 -1123 -166 178 -1123 -99 -1123 139 -248 -1123 14 -1123 169 -158 -66 71 -90 -26 -8 39 52 1 -166 -1123 191 -99 -1123 178 -1123 -1123 -108 20 -90 -158 92 -1123 210 -1123 -1123 148 -1123 23 -1123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 24 E= 6.0e-005 0.000000 0.916667 0.000000 0.083333 0.333333 0.250000 0.166667 0.250000 0.291667 0.041667 0.208333 0.458333 0.041667 0.583333 0.125000 0.250000 0.166667 0.708333 0.125000 0.000000 0.000000 0.583333 0.000000 0.416667 0.625000 0.125000 0.125000 0.125000 0.500000 0.333333 0.166667 0.000000 0.583333 0.166667 0.083333 0.166667 0.083333 0.541667 0.250000 0.125000 0.166667 0.750000 0.000000 0.083333 0.875000 0.000000 0.125000 0.000000 0.666667 0.041667 0.000000 0.291667 0.000000 0.750000 0.083333 0.166667 0.416667 0.125000 0.208333 0.250000 0.333333 0.333333 0.250000 0.083333 0.000000 0.875000 0.125000 0.000000 0.875000 0.000000 0.000000 0.125000 0.291667 0.125000 0.083333 0.500000 0.000000 1.000000 0.000000 0.000000 0.708333 0.000000 0.291667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[ACT][TAG][CT]C[CT]A[AC]A[CG]CA[AT]C[ATG][ACG]CA[TA]C[AG] -------------------------------------------------------------------------------- Time 23.12 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 34 llr = 366 E-value = 3.1e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::::1:111:122612321 pos.-specific C ::2:1::2:131111111:1 probability G 91:871a1472826457367 matrix T 198228:5515:51:4:211 bits 2.1 * 1.9 * 1.7 * 1.5 * * Relative 1.3 ** * Entropy 1.1 ***** * * (15.5 bits) 0.8 ******* * 0.6 ******* ** * ** * ** 0.4 ******* **** **** ** 0.2 ***************** ** 0.0 -------------------- Multilevel GTTGGTGTTGTGTGAGGAGG consensus C T CG C AAGT GA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 264628 360 2.37e-08 CAAAGAAGGC GTTGGTGATTTGTGATGAAG GGAGAGATTT 2702 243 3.65e-08 CTGGGGGGAT GTTGGTGTGGCGAGAGAGGT GTATCTGATG 4333 153 4.20e-08 CCATGCCGCA GTGGGTGTGGTGTGAGGAAG AGGAACAAAT 3963 369 6.35e-08 GAGTGGCTTG GTCGGTGATGTGTGAGGCGT GAATTGGAGA 5599 234 7.25e-08 GTGTAAACAT GTTGTTGCGGTGTGGGCTGG GAGAGTGGAT 2409 139 2.58e-07 GTGCCATCGC GTTGGTGTTGTGGGATAGCG CCAAGGCAAC 32760 24 3.28e-07 TGAGGGTGTT GTTGGTGTGTTGTTGTGGAG TTGGTTTATT 2578 218 3.68e-07 ATACCATGGT GTTGGTGTGATGTGGTAGGT TCGTTGAGCT 15977 224 4.64e-07 CGGCAGGCCG GTCGTTGTGGGGGGGGGAAG CAGAAATGAC 7602 138 7.27e-07 AGATTGGAGG GTTGTTGTTGTATGAGATGT TTTGGCGGGC 8986 172 8.11e-07 TGAATGGCTT GTTGTTGCTATGTCATGAGG GAGGGTGCCG 23013 57 9.04e-07 GGGCACGCAC GGTGGTGGGCCGTGGGGGGG TGGGCGGGCT 20664 374 1.01e-06 TACCAATGGT GTTTGTGCTGCATGATCTGG GGGTAGACGC 6693 187 1.70e-06 GTGGTTTGAG GTTGGTGATCGGTGATGGAC GCTTCTCTTT 6200 85 3.39e-06 CTCGCACATC GTTGGGGTGACGCAAGGTGG AGGCTGATGG 7188 293 4.94e-06 CTGTGTATCA GTTTGAGTTGAGTGACGAGG ATATGAAGAT 6934 154 4.94e-06 TGGCAGAGTT GTTGGAGCGGCCTACGGAGG TGGAGTGGTA 4502 271 4.94e-06 GCAGTCAACT GTTGGAGAGGGGAAGGGGGA ATGCAATAGA 10886 297 4.94e-06 TTGGAGAGTG GTTTCGGTGGTGGAATGGGG ATTTAGACGA 36076 335 5.93e-06 TGGCATCAAT GTCGGTGTTGGAGGCAGAGG CAGCGGAGGG 268446 211 6.50e-06 GCAACGGCAA TTCGGTGCAGTGAGGGGAGT AACCAAAGGA 2575 43 8.48e-06 CGGTCTTGAA GTTGGGGGTGGGCAACGAGG ATCGTATGAT 262994 97 9.25e-06 GGACTGGCTT TTTGGTGATTGGAGAGGCGA GGTATTCCTC 8038 131 1.01e-05 GATCTGCCTT GATTTTGCTGTGTAATGAAG GAAGCAGTCG 10158 104 1.01e-05 GGGTGAGAGT GCCGGTGGGGTGAGGGGTTG GAAGTGGAGC 33798 393 1.10e-05 AAAGGGCCAG TTTGGTGTTGCGAAATACAC CGTGCATGCA 7216 362 1.30e-05 GAGCAGTGAC GTCGTTGTTTCGTCGTCGGG ATCCATCCAG 9848 212 1.67e-05 TGGTGTCACT GTTCGTGTGGTGGAGGCGGA CATGGTGTGA 28148 278 1.67e-05 GGTGGAACAG TTTGCTGTGCTGTGAGTGGG GAGGCAGTTC 3280 45 2.13e-05 CGTTGGTACA TTTTGTGTTGTAGGCTGCAG ATCCAGAAGT 38559 253 2.30e-05 CAGAGCCACC GTCTGGGGTGCGTGAAGTTG AAATAATTCT 3803 369 2.49e-05 CAAGTGCCAT GTTGGAGGGGTGATGAGATG ATGGACGGAT 22521 74 3.65e-05 GCGACGGGGA GTTGGTGCATCATGGGACTG CTTCTATCAT 9803 56 5.27e-05 CAGTCTCGGC GGTGTTGCTGCCAGATGTGC CGAGGCGAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 264628 2.4e-08 359_[+2]_121 2702 3.7e-08 242_[+2]_238 4333 4.2e-08 152_[+2]_328 3963 6.4e-08 368_[+2]_112 5599 7.3e-08 233_[+2]_247 2409 2.6e-07 138_[+2]_342 32760 3.3e-07 23_[+2]_457 2578 3.7e-07 217_[+2]_263 15977 4.6e-07 223_[+2]_257 7602 7.3e-07 137_[+2]_343 8986 8.1e-07 171_[+2]_309 23013 9e-07 56_[+2]_424 20664 1e-06 373_[+2]_107 6693 1.7e-06 186_[+2]_294 6200 3.4e-06 84_[+2]_396 7188 4.9e-06 292_[+2]_188 6934 4.9e-06 153_[+2]_327 4502 4.9e-06 270_[+2]_210 10886 4.9e-06 296_[+2]_184 36076 5.9e-06 334_[+2]_146 268446 6.5e-06 210_[+2]_270 2575 8.5e-06 42_[+2]_438 262994 9.3e-06 96_[+2]_384 8038 1e-05 130_[+2]_350 10158 1e-05 103_[+2]_377 33798 1.1e-05 392_[+2]_88 7216 1.3e-05 361_[+2]_119 9848 1.7e-05 211_[+2]_269 28148 1.7e-05 277_[+2]_203 3280 2.1e-05 44_[+2]_436 38559 2.3e-05 252_[+2]_228 3803 2.5e-05 368_[+2]_112 22521 3.7e-05 73_[+2]_407 9803 5.3e-05 55_[+2]_425 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=34 264628 ( 360) GTTGGTGATTTGTGATGAAG 1 2702 ( 243) GTTGGTGTGGCGAGAGAGGT 1 4333 ( 153) GTGGGTGTGGTGTGAGGAAG 1 3963 ( 369) GTCGGTGATGTGTGAGGCGT 1 5599 ( 234) GTTGTTGCGGTGTGGGCTGG 1 2409 ( 139) GTTGGTGTTGTGGGATAGCG 1 32760 ( 24) GTTGGTGTGTTGTTGTGGAG 1 2578 ( 218) GTTGGTGTGATGTGGTAGGT 1 15977 ( 224) GTCGTTGTGGGGGGGGGAAG 1 7602 ( 138) GTTGTTGTTGTATGAGATGT 1 8986 ( 172) GTTGTTGCTATGTCATGAGG 1 23013 ( 57) GGTGGTGGGCCGTGGGGGGG 1 20664 ( 374) GTTTGTGCTGCATGATCTGG 1 6693 ( 187) GTTGGTGATCGGTGATGGAC 1 6200 ( 85) GTTGGGGTGACGCAAGGTGG 1 7188 ( 293) GTTTGAGTTGAGTGACGAGG 1 6934 ( 154) GTTGGAGCGGCCTACGGAGG 1 4502 ( 271) GTTGGAGAGGGGAAGGGGGA 1 10886 ( 297) GTTTCGGTGGTGGAATGGGG 1 36076 ( 335) GTCGGTGTTGGAGGCAGAGG 1 268446 ( 211) TTCGGTGCAGTGAGGGGAGT 1 2575 ( 43) GTTGGGGGTGGGCAACGAGG 1 262994 ( 97) TTTGGTGATTGGAGAGGCGA 1 8038 ( 131) GATTTTGCTGTGTAATGAAG 1 10158 ( 104) GCCGGTGGGGTGAGGGGTTG 1 33798 ( 393) TTTGGTGTTGCGAAATACAC 1 7216 ( 362) GTCGTTGTTTCGTCGTCGGG 1 9848 ( 212) GTTCGTGTGGTGGAGGCGGA 1 28148 ( 278) TTTGCTGTGCTGTGAGTGGG 1 3280 ( 45) TTTTGTGTTGTAGGCTGCAG 1 38559 ( 253) GTCTGGGGTGCGTGAAGTTG 1 3803 ( 369) GTTGGAGGGGTGATGAGATG 1 22521 ( 74) GTTGGTGCATCATGGGACTG 1 9803 ( 56) GGTGTTGCTGCCAGATGTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 25974 bayes= 9.64506 E= 3.1e-009 -1173 -1173 178 -84 -311 -298 -208 174 -1173 -18 -308 153 -1173 -298 167 -58 -1173 -198 156 -36 -111 -1173 -108 153 -1173 -1173 201 -1173 -79 1 -76 83 -211 -1173 83 92 -153 -140 144 -84 -311 34 -50 92 -79 -198 167 -1173 -11 -198 -50 100 -11 -198 138 -216 114 -140 50 -1173 -153 -198 92 53 -53 -98 144 -316 35 -66 38 -36 -11 -298 131 -117 -153 -140 144 -84 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 34 E= 3.1e-009 0.000000 0.000000 0.852941 0.147059 0.029412 0.029412 0.058824 0.882353 0.000000 0.205882 0.029412 0.764706 0.000000 0.029412 0.794118 0.176471 0.000000 0.058824 0.735294 0.205882 0.117647 0.000000 0.117647 0.764706 0.000000 0.000000 1.000000 0.000000 0.147059 0.235294 0.147059 0.470588 0.058824 0.000000 0.441176 0.500000 0.088235 0.088235 0.676471 0.147059 0.029412 0.294118 0.176471 0.500000 0.147059 0.058824 0.794118 0.000000 0.235294 0.058824 0.176471 0.529412 0.235294 0.058824 0.647059 0.058824 0.558824 0.088235 0.352941 0.000000 0.088235 0.058824 0.470588 0.382353 0.176471 0.117647 0.676471 0.029412 0.323529 0.147059 0.323529 0.205882 0.235294 0.029412 0.617647 0.117647 0.088235 0.088235 0.676471 0.147059 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GT[TC]G[GT]TG[TC][TG]G[TC]G[TA][GA][AG][GT]G[AGT][GA]G -------------------------------------------------------------------------------- Time 45.49 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 38 llr = 351 E-value = 7.6e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 5::66346:a33523 pos.-specific C :::41:21:::121: probability G 34a13733a:66257 matrix T 26::::1:::1112: bits 2.1 * * 1.9 * ** 1.7 * ** 1.5 * ** Relative 1.3 * ** Entropy 1.1 ** ** * (13.3 bits) 0.8 *** * *** * 0.6 ***** **** * 0.4 ****** ***** * 0.2 *************** 0.0 --------------- Multilevel ATGAAGAAGAGGAGG consensus GG CGAGG AAGAA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 5599 86 7.02e-08 GAGTATGACG GTGAAGAAGAGGAGA TGGTTCGTTG 2575 15 1.15e-07 CACCACTTGC ATGAGGAGGAGGAGG CGGCGGTCTT 9543 241 1.55e-07 TCTCGTAGTC AGGCAAAAGAGGAGG CCTTTCTCGT 9848 238 3.92e-07 CGGACATGGT GTGAGGGAGAGGAAG CTGCACGATC 262994 294 4.94e-07 CGTTGTTTCG GGGCAAGAGAGGAGG GTCCGTGTTG 23013 340 1.10e-06 CTCTCGTTGA ATGCCGAAGAAGAGG GTGGTGATGG 268446 300 1.60e-06 GGGTAGTTGG AGGCAGGAGAGGTGG CTATGACCCC 1554 434 1.60e-06 CCACCTGCCG AGGAAGAGGAGGAAA GATCTCAAAG 7188 267 3.63e-06 TCCAGAGCAT ATGAAGGAGAACATG GCTGTGTATC 32760 56 4.89e-06 GGTTTATTTT GTGAGGAGGAGGGAG GCTCGTTCGG 7602 96 5.64e-06 GTGTGAGGTT GTGAAGAGGAAGTGG GAGCTGTATG 28148 245 5.64e-06 CCAACAAATG GGGAGGGAGAGACGG AAGCAGGGGG 7216 312 6.49e-06 AGTCTCAGGA AGGCAGAGGAGCAAG TTCAAAGTAC 6693 286 7.44e-06 TCCAAAACAC AGGAAGGAGAAAATA TATTTACACT 4502 291 1.23e-05 GGAAGGGGGA ATGCAATAGAAAAGG CGTTTGTCAG 2702 113 1.23e-05 GCACATGCTC GTGAGGCGGAGAAGA GCATCATTGT 267929 3 1.23e-05 GC TTGAGGCAGAAGATG GACTCCTTCT 3280 190 1.93e-05 TGATTCCATT GTGAAGTAGATGATG AATGGCAGCG 3963 334 2.15e-05 GATGAAGTTT GTGCGGCGGAGGCAG CGTTTGCCGA 36076 291 2.63e-05 TGGTACGCCG AGGCCGAAGATGATG ATGGTGCATC 2409 206 2.90e-05 GCTTGTGTAG AGGCCAGAGAGGTGG ACATTGATGT 10886 149 3.50e-05 GACACGAACA GTGAAAGAGAGCACG AAGGACAAGA 20664 5 4.19e-05 ATAA AGGCCAAAGAAGGGA AAAGTTACGT 10050 361 4.19e-05 GCACGGGCGT TGGAGGAGGAAAGGG GTCTCCATGG 25733 43 4.57e-05 TATTGTAGGG AGGCAACAGAAAGGA AGGAGCAACA 33798 418 4.97e-05 TACACCGTGC ATGCAACCGAAGATG TGGAGGTTGG 2578 257 5.84e-05 TGTTGATGGA TGGCGGGCGAGGAGA CGACGCATTT 263558 15 6.32e-05 ATAAGAATAT TTGCAAAGGAGACAG TTAATGGCTT 23651 320 7.34e-05 CAGCATCTTT GGGAAGCAGATACGA CCCTGGACAT 15977 131 7.89e-05 AAGTAAATCT CGGCAGCAGAGGGTG CCATGAGCAC 264628 80 9.08e-05 CAACGCATGA ATGAGAGCGAGAATA AGTTGCAGTG 3803 414 9.72e-05 ATCAAAAGCC GTGGAGAGGAGACTG GAACCGGGGG 264143 122 1.18e-04 GATTTATGGC TTGAGAGAGAACTGG CCACAAAGCT 6934 352 1.33e-04 TGACATGTTC ATGACGTGGAGTAAG CTCCCGCCAA 10158 146 1.33e-04 TAGGTAGGTT GTGGAGAGGAGCCAG AGGGCGATGG 5246 29 1.49e-04 TCTGTAGAAT ATGAAGGAGATTGAA ACATGAGCAT 3837 302 1.49e-04 AGAAGTGAAT TTGAGTAAGAGGGGA TAAGCTATTT 22763 212 1.58e-04 CCTTGTCGAG AGGAAATAGAAGGCA GAAACATAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5599 7e-08 85_[+3]_400 2575 1.1e-07 14_[+3]_471 9543 1.6e-07 240_[+3]_245 9848 3.9e-07 237_[+3]_248 262994 4.9e-07 293_[+3]_192 23013 1.1e-06 339_[+3]_146 268446 1.6e-06 299_[+3]_186 1554 1.6e-06 433_[+3]_52 7188 3.6e-06 266_[+3]_219 32760 4.9e-06 55_[+3]_430 7602 5.6e-06 95_[+3]_390 28148 5.6e-06 244_[+3]_241 7216 6.5e-06 311_[+3]_174 6693 7.4e-06 285_[+3]_200 4502 1.2e-05 290_[+3]_195 2702 1.2e-05 112_[+3]_373 267929 1.2e-05 2_[+3]_483 3280 1.9e-05 189_[+3]_296 3963 2.1e-05 333_[+3]_152 36076 2.6e-05 290_[+3]_195 2409 2.9e-05 205_[+3]_280 10886 3.5e-05 148_[+3]_337 20664 4.2e-05 4_[+3]_481 10050 4.2e-05 360_[+3]_125 25733 4.6e-05 42_[+3]_443 33798 5e-05 417_[+3]_68 2578 5.8e-05 256_[+3]_229 263558 6.3e-05 14_[+3]_471 23651 7.3e-05 319_[+3]_166 15977 7.9e-05 130_[+3]_355 264628 9.1e-05 79_[+3]_406 3803 9.7e-05 413_[+3]_72 264143 0.00012 121_[+3]_364 6934 0.00013 351_[+3]_134 10158 0.00013 145_[+3]_340 5246 0.00015 28_[+3]_457 3837 0.00015 301_[+3]_184 22763 0.00016 211_[+3]_274 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=38 5599 ( 86) GTGAAGAAGAGGAGA 1 2575 ( 15) ATGAGGAGGAGGAGG 1 9543 ( 241) AGGCAAAAGAGGAGG 1 9848 ( 238) GTGAGGGAGAGGAAG 1 262994 ( 294) GGGCAAGAGAGGAGG 1 23013 ( 340) ATGCCGAAGAAGAGG 1 268446 ( 300) AGGCAGGAGAGGTGG 1 1554 ( 434) AGGAAGAGGAGGAAA 1 7188 ( 267) ATGAAGGAGAACATG 1 32760 ( 56) GTGAGGAGGAGGGAG 1 7602 ( 96) GTGAAGAGGAAGTGG 1 28148 ( 245) GGGAGGGAGAGACGG 1 7216 ( 312) AGGCAGAGGAGCAAG 1 6693 ( 286) AGGAAGGAGAAAATA 1 4502 ( 291) ATGCAATAGAAAAGG 1 2702 ( 113) GTGAGGCGGAGAAGA 1 267929 ( 3) TTGAGGCAGAAGATG 1 3280 ( 190) GTGAAGTAGATGATG 1 3963 ( 334) GTGCGGCGGAGGCAG 1 36076 ( 291) AGGCCGAAGATGATG 1 2409 ( 206) AGGCCAGAGAGGTGG 1 10886 ( 149) GTGAAAGAGAGCACG 1 20664 ( 5) AGGCCAAAGAAGGGA 1 10050 ( 361) TGGAGGAGGAAAGGG 1 25733 ( 43) AGGCAACAGAAAGGA 1 33798 ( 418) ATGCAACCGAAGATG 1 2578 ( 257) TGGCGGGCGAGGAGA 1 263558 ( 15) TTGCAAAGGAGACAG 1 23651 ( 320) GGGAAGCAGATACGA 1 15977 ( 131) CGGCAGCAGAGGGTG 1 264628 ( 80) ATGAGAGCGAGAATA 1 3803 ( 414) GTGGAGAGGAGACTG 1 264143 ( 122) TTGAGAGAGAACTGG 1 6934 ( 352) ATGACGTGGAGTAAG 1 10158 ( 146) GTGGAGAGGAGCCAG 1 5246 ( 29) ATGAAGGAGATTGAA 1 3837 ( 302) TTGAGTAAGAGGGGA 1 22763 ( 212) AGGAAATAGAAGGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 26244 bayes= 9.62476 E= 7.6e-004 90 -314 46 -74 -1189 -1189 76 113 -1189 -1189 201 -1189 112 76 -224 -1189 112 -82 34 -1189 31 -1189 140 -332 63 -34 34 -133 125 -156 34 -1189 -1189 -1189 201 -1189 198 -1189 -1189 -1189 31 -1189 122 -133 5 -82 115 -232 105 -56 -24 -133 -10 -214 93 -16 31 -1189 146 -1189 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 38 E= 7.6e-004 0.473684 0.026316 0.342105 0.157895 0.000000 0.000000 0.421053 0.578947 0.000000 0.000000 1.000000 0.000000 0.552632 0.394737 0.052632 0.000000 0.552632 0.131579 0.315789 0.000000 0.315789 0.000000 0.657895 0.026316 0.394737 0.184211 0.315789 0.105263 0.605263 0.078947 0.315789 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.315789 0.000000 0.578947 0.105263 0.263158 0.131579 0.552632 0.052632 0.526316 0.157895 0.210526 0.105263 0.236842 0.052632 0.473684 0.236842 0.315789 0.000000 0.684211 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AG][TG]G[AC][AG][GA][AG][AG]GA[GA][GA][AG][GAT][GA] -------------------------------------------------------------------------------- Time 67.54 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10050 3.74e-02 360_[+3(4.19e-05)]_125 10158 1.12e-02 103_[+2(1.01e-05)]_377 10810 1.08e-02 298_[+1(5.14e-06)]_181 10886 2.09e-03 148_[+3(3.50e-05)]_133_\ [+2(4.94e-06)]_184 1554 7.69e-03 433_[+3(1.60e-06)]_52 15977 4.06e-06 130_[+3(7.89e-05)]_78_\ [+2(4.64e-07)]_219_[+1(1.00e-05)]_17 1672 5.96e-03 272_[+1(8.68e-06)]_207 18091 7.97e-01 500 20664 1.04e-06 4_[+3(4.19e-05)]_37_[+1(1.10e-06)]_\ 296_[+2(1.01e-06)]_107 20881 3.56e-01 500 22521 2.44e-02 73_[+2(3.65e-05)]_407 22763 6.49e-04 463_[+1(4.99e-07)]_16 23013 1.39e-08 56_[+2(9.04e-07)]_53_[+1(4.05e-07)]_\ 189_[+3(1.10e-06)]_146 23651 1.27e-01 319_[+3(7.34e-05)]_166 2409 3.89e-07 138_[+2(2.58e-07)]_47_\ [+3(2.90e-05)]_213_[+1(2.08e-06)]_46 25733 6.02e-05 42_[+3(4.57e-05)]_106_\ [+1(1.50e-07)]_316 2575 1.50e-08 14_[+3(1.15e-07)]_13_[+2(8.48e-06)]_\ 35_[+3(4.97e-05)]_188_[+1(4.50e-07)]_70_[+1(6.47e-06)]_88 2578 1.81e-04 217_[+2(3.68e-07)]_19_\ [+3(5.84e-05)]_229 262994 4.97e-05 96_[+2(9.25e-06)]_95_[+3(6.49e-06)]_\ 67_[+3(4.94e-07)]_83_[+3(3.50e-05)]_94 263375 7.01e-02 458_[+1(8.08e-06)]_21 263558 1.28e-03 14_[+3(6.32e-05)]_293_\ [+1(6.00e-06)]_157 264143 1.79e-01 500 264628 4.05e-05 79_[+3(9.08e-05)]_265_\ [+2(2.37e-08)]_13_[+2(8.57e-05)]_88 267929 1.89e-02 2_[+3(1.23e-05)]_483 268446 2.59e-05 210_[+2(6.50e-06)]_14_\ [+3(2.63e-05)]_40_[+3(1.60e-06)]_186 2702 1.48e-05 112_[+3(1.23e-05)]_115_\ [+2(3.65e-08)]_238 28148 1.36e-03 244_[+3(5.64e-06)]_18_\ [+2(1.67e-05)]_203 30380 7.73e-01 500 32760 4.52e-05 23_[+2(3.28e-07)]_12_[+3(4.89e-06)]_\ 430 3280 6.73e-06 44_[+2(2.13e-05)]_125_\ [+3(1.93e-05)]_233_[+1(9.07e-07)]_42 33798 5.51e-03 392_[+2(1.10e-05)]_5_[+3(4.97e-05)]_\ 68 36076 1.87e-03 290_[+3(2.63e-05)]_29_\ [+2(5.93e-06)]_146 3803 8.73e-06 120_[+1(2.11e-07)]_227_\ [+2(2.49e-05)]_25_[+3(9.72e-05)]_72 3837 7.85e-05 479_[+1(1.18e-07)] 38559 6.77e-04 252_[+2(2.30e-05)]_88_\ [+1(2.47e-06)]_119 38647 1.88e-04 139_[+1(3.34e-05)]_4_[+1(9.28e-09)]_\ 315 3963 6.49e-08 178_[+1(1.59e-06)]_130_\ [+2(8.48e-06)]_19_[+2(6.35e-08)]_112 4333 4.49e-08 152_[+2(4.20e-08)]_181_\ [+1(1.45e-06)]_126 4502 4.35e-04 270_[+2(4.94e-06)]_[+3(1.23e-05)]_\ 195 5246 1.97e-01 500 5599 1.74e-07 23_[+2(1.81e-05)]_42_[+3(7.02e-08)]_\ 133_[+2(7.25e-08)]_247 6200 2.75e-02 84_[+2(3.39e-06)]_396 6693 6.33e-05 186_[+2(1.70e-06)]_79_\ [+3(7.44e-06)]_200 6934 1.64e-05 59_[+1(1.59e-06)]_73_[+2(4.94e-06)]_\ 244_[+2(6.51e-05)]_63 7188 2.11e-04 266_[+3(3.63e-06)]_11_\ [+2(4.94e-06)]_188 7216 1.05e-03 311_[+3(6.49e-06)]_35_\ [+2(1.30e-05)]_119 7602 4.47e-07 95_[+3(5.64e-06)]_27_[+2(7.27e-07)]_\ 104_[+1(4.40e-06)]_218 789 9.74e-03 354_[+1(9.99e-07)]_125 7937 1.61e-03 358_[+1(1.33e-07)]_121 8038 1.37e-06 130_[+2(1.01e-05)]_308_\ [+1(3.05e-09)]_21 8986 3.05e-03 171_[+2(8.11e-07)]_309 9543 6.83e-07 240_[+3(1.55e-07)]_86_\ [+1(1.18e-07)]_138 9803 2.02e-02 55_[+2(5.27e-05)]_391_\ [+1(8.00e-05)]_13 9848 1.54e-04 122_[+3(1.55e-05)]_74_\ [+2(1.67e-05)]_6_[+3(3.92e-07)]_248 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************