******************************************************************************** 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/427/427.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10946 1.0000 500 11103 1.0000 500 11244 1.0000 500 19374 1.0000 500 20268 1.0000 500 2038 1.0000 500 20420 1.0000 500 2084 1.0000 500 2535 1.0000 500 262698 1.0000 500 263124 1.0000 500 264095 1.0000 500 31862 1.0000 500 32339 1.0000 500 35907 1.0000 500 38890 1.0000 500 5647 1.0000 500 5855 1.0000 500 6704 1.0000 500 7902 1.0000 500 9007 1.0000 500 9073 1.0000 500 9303 1.0000 500 9304 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/427/427.seqs.fa -oc motifs/427 -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= 24 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= 12000 N= 24 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.255 C 0.233 G 0.233 T 0.279 Background letter frequencies (from dataset with add-one prior applied): A 0.255 C 0.233 G 0.233 T 0.279 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 17 llr = 222 E-value = 2.2e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :78214543952972761713 pos.-specific C 812645544:581262:9267 probability G 11:12:13:1:::12:2::3: matrix T 11:121::3::::::12:1:: bits 2.1 1.9 1.7 * 1.5 * * * Relative 1.3 * * * ** * * Entropy 1.1 * * **** * * (18.9 bits) 0.8 * * * ***** * **** 0.6 *** ** ************ 0.4 **** **************** 0.2 ********************* 0.0 --------------------- Multilevel CAACCCAACAACAACAACACC consensus CAGACCA CA A T CGA sequence T GT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 5647 439 3.96e-10 GGAGGCAACA CAACACAGCAACAACAACAGC AAGCGGCTTT 10946 419 2.55e-09 CACGATCTGC CAACCAAGAAACAACCACCCC ACGTGCAGGA 38890 434 9.38e-09 TCAACAACAT CAACGCACTAACAACTACACA CACTCTATCT 2535 474 9.38e-09 GACACCGAAG CAAAGCAGTAACAACAGCAGC GAGAGC 32339 480 1.90e-07 CCTCCCTCTC CCCTTCCACAACAACAACACA 9007 458 2.10e-07 CCTCTTTCCC CCCCCCCCAACCAAACACACA AACTTCGACG 35907 473 2.10e-07 TAATCGATCC CAACCAAACGCCACAATCACC AACCACG 7902 480 3.07e-07 AAACCTTGAT CAACTTACCACACAGAACACC 5855 4 5.29e-07 GAA CAAACACACACCACAAGCCAC AGACCACCGA 6704 339 6.85e-07 GTCAGAAAGG CAACGAGATAAAAAGATCAGC AAAAAGAACA 9303 413 8.79e-07 TGTTCTCCCT CAACCACCTACAACAATCCGA CGAAGCAATC 262698 88 8.79e-07 GATCGAGCAT CTACTTCACAAAAGCAACAGC TAACTTGCAA 2038 358 1.12e-06 AGTCGACCAC CGACGACCAACCAACTACTCC TCGCCGATGT 11244 189 1.53e-06 TCGCTCTGAA GAATCAAGTACCAGCATCACA CCGAAGAGAA 264095 480 2.92e-06 AATTCAACTA CACATCCCAACCAACCAACAC 20420 409 4.08e-06 CTTCAACTTT GTCAACCAAAACCACAACACC GACGACCCGA 20268 381 4.36e-06 CTTTTTCGGA TAAGCCAGCAACAAGAGAACC GCACTATCAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5647 4e-10 438_[+1]_41 10946 2.5e-09 418_[+1]_61 38890 9.4e-09 433_[+1]_46 2535 9.4e-09 473_[+1]_6 32339 1.9e-07 479_[+1] 9007 2.1e-07 457_[+1]_22 35907 2.1e-07 472_[+1]_7 7902 3.1e-07 479_[+1] 5855 5.3e-07 3_[+1]_476 6704 6.8e-07 338_[+1]_141 9303 8.8e-07 412_[+1]_67 262698 8.8e-07 87_[+1]_392 2038 1.1e-06 357_[+1]_122 11244 1.5e-06 188_[+1]_291 264095 2.9e-06 479_[+1] 20420 4.1e-06 408_[+1]_71 20268 4.4e-06 380_[+1]_99 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=17 5647 ( 439) CAACACAGCAACAACAACAGC 1 10946 ( 419) CAACCAAGAAACAACCACCCC 1 38890 ( 434) CAACGCACTAACAACTACACA 1 2535 ( 474) CAAAGCAGTAACAACAGCAGC 1 32339 ( 480) CCCTTCCACAACAACAACACA 1 9007 ( 458) CCCCCCCCAACCAAACACACA 1 35907 ( 473) CAACCAAACGCCACAATCACC 1 7902 ( 480) CAACTTACCACACAGAACACC 1 5855 ( 4) CAAACACACACCACAAGCCAC 1 6704 ( 339) CAACGAGATAAAAAGATCAGC 1 9303 ( 413) CAACCACCTACAACAATCCGA 1 262698 ( 88) CTACTTCACAAAAGCAACAGC 1 2038 ( 358) CGACGACCAACCAACTACTCC 1 11244 ( 189) GAATCAAGTACCAGCATCACA 1 264095 ( 480) CACATCCCAACCAACCAACAC 1 20420 ( 409) GTCAACCAAAACCACAACACC 1 20268 ( 381) TAAGCCAGCAACAAGAGAACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 11520 bayes= 10.1978 E= 2.2e-006 -1073 182 -98 -224 147 -98 -198 -125 158 1 -1073 -1073 -12 134 -198 -125 -112 82 2 -25 69 101 -1073 -125 88 101 -198 -1073 47 60 34 -1073 21 82 -1073 7 188 -1073 -198 -1073 105 101 -1073 -1073 -12 171 -1073 -1073 179 -98 -1073 -1073 147 -40 -98 -1073 -12 134 -40 -1073 147 -40 -1073 -125 120 -1073 -40 -25 -112 192 -1073 -1073 147 1 -1073 -224 -112 134 34 -1073 21 160 -1073 -1073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 17 E= 2.2e-006 0.000000 0.823529 0.117647 0.058824 0.705882 0.117647 0.058824 0.117647 0.764706 0.235294 0.000000 0.000000 0.235294 0.588235 0.058824 0.117647 0.117647 0.411765 0.235294 0.235294 0.411765 0.470588 0.000000 0.117647 0.470588 0.470588 0.058824 0.000000 0.352941 0.352941 0.294118 0.000000 0.294118 0.411765 0.000000 0.294118 0.941176 0.000000 0.058824 0.000000 0.529412 0.470588 0.000000 0.000000 0.235294 0.764706 0.000000 0.000000 0.882353 0.117647 0.000000 0.000000 0.705882 0.176471 0.117647 0.000000 0.235294 0.588235 0.176471 0.000000 0.705882 0.176471 0.000000 0.117647 0.588235 0.000000 0.176471 0.235294 0.117647 0.882353 0.000000 0.000000 0.705882 0.235294 0.000000 0.058824 0.117647 0.588235 0.294118 0.000000 0.294118 0.705882 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CA[AC][CA][CGT][CA][AC][ACG][CAT]A[AC][CA]AA[CA]A[AT]C[AC][CG][CA] -------------------------------------------------------------------------------- Time 5.10 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 13 llr = 151 E-value = 8.8e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :71:4:12:11121: pos.-specific C a15a3a858:8514a probability G ::3:2::31:12::: matrix T :22:2:2:29:375: bits 2.1 * * * * 1.9 * * * * 1.7 * * * * 1.5 * * * * * Relative 1.3 * * * ** * Entropy 1.1 * * ** *** * (16.8 bits) 0.8 ** * ** *** * * 0.6 ** * ****** *** 0.4 ** * ****** *** 0.2 *************** 0.0 --------------- Multilevel CACCACCCCTCCTTC consensus TG C G TAC sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 9007 441 6.80e-09 TTTCCTCGGA CACCACCCCTCTTTC CCCCCCCCCC 262698 269 9.94e-09 CTCGAAGACC CACCACCCCTCTTCC TTTGGTATCA 20420 442 1.18e-07 CGACCCGACA CACCGCCCCTCGTCC TCAAACTCCT 6704 465 6.90e-07 ACTCCCTCTC CTTCCCCACTCCTTC CTTCAACCAC 11103 6 1.47e-06 TGAAG CAGCACTACTCGTTC AAACTCTATC 2084 9 2.10e-06 CAGAGATT CACCTCCGTTCCACC CGCTGTGGCC 38890 239 2.90e-06 TCGTCATCAT CACCACCGCTACTAC TACCACCCAA 263124 10 2.90e-06 TCACCATCA CCGCCCCCCTCATCC TCGTCATCAC 5647 123 4.29e-06 AACGATGCCA CTGCCCAGCTCTTTC GTTTCCTACA 10946 6 4.96e-06 ATCTT CAACCCCACACCTCC AAACCTACCT 264095 209 6.60e-06 CTCATCTTGC CACCACTCGTCTATC TCCTCTGTCA 32339 459 8.06e-06 CGTCCGCACT CATCGCCCTTCCCTC CCTCTCCCCT 5855 283 1.18e-05 TCAGTGTCAA CTGCTCCGCTGCATC CTTGAAAATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9007 6.8e-09 440_[+2]_45 262698 9.9e-09 268_[+2]_217 20420 1.2e-07 441_[+2]_44 6704 6.9e-07 464_[+2]_21 11103 1.5e-06 5_[+2]_480 2084 2.1e-06 8_[+2]_477 38890 2.9e-06 238_[+2]_247 263124 2.9e-06 9_[+2]_476 5647 4.3e-06 122_[+2]_363 10946 5e-06 5_[+2]_480 264095 6.6e-06 208_[+2]_277 32339 8.1e-06 458_[+2]_27 5855 1.2e-05 282_[+2]_203 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=13 9007 ( 441) CACCACCCCTCTTTC 1 262698 ( 269) CACCACCCCTCTTCC 1 20420 ( 442) CACCGCCCCTCGTCC 1 6704 ( 465) CTTCCCCACTCCTTC 1 11103 ( 6) CAGCACTACTCGTTC 1 2084 ( 9) CACCTCCGTTCCACC 1 38890 ( 239) CACCACCGCTACTAC 1 263124 ( 10) CCGCCCCCCTCATCC 1 5647 ( 123) CTGCCCAGCTCTTTC 1 10946 ( 6) CAACCCCACACCTCC 1 264095 ( 209) CACCACTCGTCTATC 1 32339 ( 459) CATCGCCCTTCCCTC 1 5855 ( 283) CTGCTCCGCTGCATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 11664 bayes= 10.973 E= 8.8e+000 -1035 210 -1035 -1035 144 -160 -1035 -28 -173 99 40 -86 -1035 210 -1035 -1035 59 40 -60 -86 -1035 210 -1035 -1035 -173 172 -1035 -86 -14 99 40 -1035 -1035 172 -159 -86 -173 -1035 -1035 172 -173 186 -159 -1035 -173 99 -60 14 -14 -160 -1035 131 -173 72 -1035 95 -1035 210 -1035 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 13 E= 8.8e+000 0.000000 1.000000 0.000000 0.000000 0.692308 0.076923 0.000000 0.230769 0.076923 0.461538 0.307692 0.153846 0.000000 1.000000 0.000000 0.000000 0.384615 0.307692 0.153846 0.153846 0.000000 1.000000 0.000000 0.000000 0.076923 0.769231 0.000000 0.153846 0.230769 0.461538 0.307692 0.000000 0.000000 0.769231 0.076923 0.153846 0.076923 0.000000 0.000000 0.923077 0.076923 0.846154 0.076923 0.000000 0.076923 0.461538 0.153846 0.307692 0.230769 0.076923 0.000000 0.692308 0.076923 0.384615 0.000000 0.538462 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[AT][CG]C[AC]CC[CGA]CTC[CT][TA][TC]C -------------------------------------------------------------------------------- Time 10.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 24 llr = 220 E-value = 4.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 3:1121:1:13:53:: pos.-specific C ::41:3:31:33:::: probability G 71371:76:54:513a matrix T :921763:9416:67: bits 2.1 * 1.9 * 1.7 * 1.5 * * Relative 1.3 * * * Entropy 1.1 ** * ** (13.2 bits) 0.8 ** * * ** ** 0.6 ** * ***** ** ** 0.4 ** ******* ***** 0.2 **************** 0.0 ---------------- Multilevel GTCGTTGGTGGTATTG consensus A G CTC TACGAG sequence T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 7902 242 1.38e-07 TGGTGTCGTT GTGGTTGCTTGCGTTG TCAGGGGGGA 2535 63 4.53e-07 TCATCGTGTG GTGGACGGTGCTGTTG GCGCACAATG 9304 253 1.23e-06 GCTTGGCACC GTCGTTGGCGCCGTTG GCGTTGAGTT 9007 48 2.68e-06 TATGGAGACA ATCGTTGCTTACATGG TGTCCTTGAG 2038 480 2.68e-06 TGTAAACTCC ATCGTTGCTAATATTG CAAGC 9303 227 3.84e-06 GTTGGTGTAC ATCGTTGGTTGGGTTG ATGAGTAGTT 38890 304 4.87e-06 AGCGTCCGAA GTGGTCTCTGCCATGG TACGTCTCCA 32339 285 6.09e-06 ATGATGGAAT GTTGGTGGTTGCGAGG GGATGGTGCC 6704 100 6.80e-06 AAAGAAGGGT GTTGTCGTTGATGTTG TTAATCAGAA 5855 459 1.04e-05 CCTTGGTGAT ATAATTGGTGATATTG TTGTGATATC 2084 270 1.04e-05 TTGGGTGCTG ATCGGTGGTTGTGGTG GAGGAGACGG 263124 218 1.71e-05 TCAATGGATT GGAGGTGGTTGTATTG TTTGTCTAGA 11244 157 2.27e-05 CCGTAAGGAA GTCGTCGATTGTACGG CGAGGTTCGC 31862 1 2.98e-05 . GTTGACAGTGATATTG GTAGATGTGT 35907 330 3.26e-05 CCGTTTGCTT GTGGTCTGTATCAATG AAAGGGAATA 262698 58 3.56e-05 GAGACGTTTG GGCTTTGCTGCTATGG CATCGATCGA 5647 294 3.87e-05 TTTTACGGAA ATGGTAGATTCTAATG ACTATTTTAC 20268 109 3.87e-05 CTACACGGGG TTGATTGGTGGTGTGG GGGGAGCTTC 264095 87 4.22e-05 CATGCACCAT GTTCTTTGTGTTGATG CTTGCCGAGG 9073 65 5.87e-05 TTCCGAAGGT GTCCATTGTAGTGTGG GGTTAGCGCG 10946 323 1.25e-04 GTAGCTGTTT GTCGACGAAGGCAATG AACGGCCATA 20420 16 1.64e-04 ACATCTGCGG GTGTTTTGTTATCGTG TGAAGAAGAG 19374 141 1.75e-04 TATTGAACAT GTTGCTTGCGACGATG CTGATATCTG 11103 42 1.87e-04 ATATTGAGGA GTATTATCTTCTAATG CAACTTCATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7902 1.4e-07 241_[+3]_243 2535 4.5e-07 62_[+3]_422 9304 1.2e-06 252_[+3]_232 9007 2.7e-06 47_[+3]_437 2038 2.7e-06 479_[+3]_5 9303 3.8e-06 226_[+3]_258 38890 4.9e-06 303_[+3]_181 32339 6.1e-06 284_[+3]_200 6704 6.8e-06 99_[+3]_385 5855 1e-05 458_[+3]_26 2084 1e-05 269_[+3]_215 263124 1.7e-05 217_[+3]_267 11244 2.3e-05 156_[+3]_328 31862 3e-05 [+3]_484 35907 3.3e-05 329_[+3]_155 262698 3.6e-05 57_[+3]_427 5647 3.9e-05 293_[+3]_191 20268 3.9e-05 108_[+3]_376 264095 4.2e-05 86_[+3]_398 9073 5.9e-05 64_[+3]_420 10946 0.00012 322_[+3]_162 20420 0.00016 15_[+3]_469 19374 0.00018 140_[+3]_344 11103 0.00019 41_[+3]_443 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=24 7902 ( 242) GTGGTTGCTTGCGTTG 1 2535 ( 63) GTGGACGGTGCTGTTG 1 9304 ( 253) GTCGTTGGCGCCGTTG 1 9007 ( 48) ATCGTTGCTTACATGG 1 2038 ( 480) ATCGTTGCTAATATTG 1 9303 ( 227) ATCGTTGGTTGGGTTG 1 38890 ( 304) GTGGTCTCTGCCATGG 1 32339 ( 285) GTTGGTGGTTGCGAGG 1 6704 ( 100) GTTGTCGTTGATGTTG 1 5855 ( 459) ATAATTGGTGATATTG 1 2084 ( 270) ATCGGTGGTTGTGGTG 1 263124 ( 218) GGAGGTGGTTGTATTG 1 11244 ( 157) GTCGTCGATTGTACGG 1 31862 ( 1) GTTGACAGTGATATTG 1 35907 ( 330) GTGGTCTGTATCAATG 1 262698 ( 58) GGCTTTGCTGCTATGG 1 5647 ( 294) ATGGTAGATTCTAATG 1 20268 ( 109) TTGATTGGTGGTGTGG 1 264095 ( 87) GTTCTTTGTGTTGATG 1 9073 ( 65) GTCCATTGTAGTGTGG 1 10946 ( 323) GTCGACGAAGGCAATG 1 20420 ( 16) GTGTTTTGTTATCGTG 1 19374 ( 141) GTTGCTTGCGACGATG 1 11103 ( 42) GTATTATCTTCTAATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 11640 bayes= 8.91886 E= 4.0e+001 -3 -1123 161 -274 -1123 -1123 -148 171 -103 69 33 -42 -161 -148 161 -116 -61 -248 -90 125 -161 32 -1123 116 -261 -1123 152 6 -103 10 133 -274 -261 -148 -1123 165 -103 -1123 98 58 19 10 69 -174 -1123 52 -248 116 97 -248 98 -1123 19 -248 -148 106 -1123 -1123 33 134 -1123 -1123 210 -1123 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 24 E= 4.0e+001 0.250000 0.000000 0.708333 0.041667 0.000000 0.000000 0.083333 0.916667 0.125000 0.375000 0.291667 0.208333 0.083333 0.083333 0.708333 0.125000 0.166667 0.041667 0.125000 0.666667 0.083333 0.291667 0.000000 0.625000 0.041667 0.000000 0.666667 0.291667 0.125000 0.250000 0.583333 0.041667 0.041667 0.083333 0.000000 0.875000 0.125000 0.000000 0.458333 0.416667 0.291667 0.250000 0.375000 0.083333 0.000000 0.333333 0.041667 0.625000 0.500000 0.041667 0.458333 0.000000 0.291667 0.041667 0.083333 0.583333 0.000000 0.000000 0.291667 0.708333 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA]T[CGT]GT[TC][GT][GC]T[GT][GAC][TC][AG][TA][TG]G -------------------------------------------------------------------------------- Time 14.79 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10946 4.76e-08 5_[+2(4.96e-06)]_398_[+1(2.55e-09)]_\ 61 11103 1.09e-03 5_[+2(1.47e-06)]_480 11244 3.02e-04 156_[+3(2.27e-05)]_16_\ [+1(1.53e-06)]_291 19374 4.40e-01 500 20268 1.80e-03 108_[+3(3.87e-05)]_256_\ [+1(4.36e-06)]_99 2038 4.66e-05 357_[+1(1.12e-06)]_101_\ [+3(2.68e-06)]_5 20420 1.65e-06 408_[+1(4.08e-06)]_12_\ [+2(1.18e-07)]_44 2084 2.06e-04 8_[+2(2.10e-06)]_246_[+3(1.04e-05)]_\ 215 2535 1.02e-07 62_[+3(4.53e-07)]_148_\ [+3(7.43e-05)]_231_[+1(9.38e-09)]_6 262698 1.10e-08 57_[+3(3.56e-05)]_14_[+1(8.79e-07)]_\ 160_[+2(9.94e-09)]_168_[+1(6.81e-05)]_28 263124 6.67e-04 9_[+2(2.90e-06)]_193_[+3(1.71e-05)]_\ 267 264095 1.35e-05 86_[+3(4.22e-05)]_106_\ [+2(6.60e-06)]_256_[+1(2.92e-06)] 31862 8.87e-02 [+3(2.98e-05)]_484 32339 2.48e-07 284_[+3(6.09e-06)]_116_\ [+1(9.18e-05)]_21_[+2(8.06e-06)]_6_[+1(1.90e-07)] 35907 1.23e-04 329_[+3(3.26e-05)]_127_\ [+1(2.10e-07)]_7 38890 5.03e-09 8_[+1(9.79e-05)]_209_[+2(2.90e-06)]_\ 50_[+3(4.87e-06)]_114_[+1(9.38e-09)]_46 5647 2.62e-09 122_[+2(4.29e-06)]_156_\ [+3(3.87e-05)]_129_[+1(3.96e-10)]_41 5855 1.42e-06 3_[+1(5.29e-07)]_258_[+2(1.18e-05)]_\ 161_[+3(1.04e-05)]_26 6704 9.40e-08 99_[+3(6.80e-06)]_223_\ [+1(6.85e-07)]_105_[+2(6.90e-07)]_21 7902 3.54e-07 241_[+3(1.38e-07)]_222_\ [+1(3.07e-07)] 9007 1.88e-10 47_[+3(2.68e-06)]_216_\ [+3(2.98e-05)]_145_[+2(6.80e-09)]_2_[+1(2.10e-07)]_22 9073 9.76e-02 64_[+3(5.87e-05)]_420 9303 2.59e-05 9_[+1(9.18e-05)]_196_[+3(3.84e-06)]_\ 170_[+1(8.79e-07)]_67 9304 1.27e-02 252_[+3(1.23e-06)]_232 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************