******************************************************************************** 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/186/186.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1215 1.0000 500 1852 1.0000 500 1873 1.0000 500 20688 1.0000 500 21025 1.0000 500 22589 1.0000 500 2309 1.0000 500 25377 1.0000 500 262335 1.0000 500 264781 1.0000 500 2824 1.0000 500 33310 1.0000 500 33667 1.0000 500 36879 1.0000 500 38616 1.0000 500 416 1.0000 500 5336 1.0000 500 5631 1.0000 500 5641 1.0000 500 7089 1.0000 500 7567 1.0000 500 8448 1.0000 500 8768 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/186/186.seqs.fa -oc motifs/186 -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= 23 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= 11500 N= 23 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.260 C 0.237 G 0.231 T 0.272 Background letter frequencies (from dataset with add-one prior applied): A 0.260 C 0.237 G 0.231 T 0.272 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 23 llr = 260 E-value = 4.3e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 57::6833153397:961433 pos.-specific C 525932567246:37:38256 probability G :13:2:3222111:3:1::1: matrix T ::11:::::11:::::::4:2 bits 2.1 1.9 1.7 * 1.5 * * Relative 1.3 * * * * * Entropy 1.1 * * * * * * (16.3 bits) 0.8 * * * * **** * 0.6 ** ****** ***** * * 0.4 ********* ********** 0.2 ********************* 0.0 --------------------- Multilevel AACCAACCCACCAACAACACC consensus C G CCAA GAA CG C TAA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 25377 113 1.75e-11 CGTTGTTTGC AACCAACACACCAACAACTCC ATTCCATTCC 5336 386 7.98e-10 CATTAACCAA CACCAACCCGACAACAACTCT TCTTCTCCCC 1873 435 5.62e-08 CTCATAATCC CAGCAAACCACCACGAGCACA GAGCAAAAAA 20688 474 9.34e-08 CTTGTACCTC CACCAAAGCACCAAAAACTAC GCAACA 264781 160 1.34e-07 CATCATAGTA AACCGCGCCAAGAACAACAAC AATGGCAGCC 38616 479 1.91e-07 AGCCAAAAAC AACCAAGCCAACAACCCCCAC C 36879 224 1.91e-07 CATCTCCTCA AAGCACGCCTCCACCACCACA ACAGTTCAAA 22589 306 2.40e-07 CCACAGAGTA CCCCCCCCCCCAACCACCACC TCCTCTTTCA 21025 480 2.40e-07 CGAAGTTACC CACCACAACCCAAAGAACACA 1852 105 5.69e-07 TACAAGCATG AGCCCACACAGAAACAACACT TGCTTTCGTG 5641 1 1.68e-06 . AAGCAAAGCAACAACAGTAAC GATCAACGTA 7089 340 4.08e-06 GTGGAATGTC AACCGAACAGCAACGAACTGC TGGTCGATGT 2824 87 4.44e-06 GAGCGATGCA ACGTGCCCCATCAACAACAAC AAGGAGGCGG 1215 246 4.44e-06 CCCCAAAGCT CAACAACCGACAACCGACTAC ATAACCCATG 416 336 4.83e-06 TTAATACCGA AATCAACAGTGCAGCAACACC ATTTTTTATC 33667 479 8.49e-06 CATACCACCT CCTCCACACAACAACAAATTC A 7567 35 1.15e-05 GCACACAGTT AATCAACCACACAATACCCAC CCGACGAATC 33310 11 1.34e-05 CAATTAATAG CACCCAGGCGCAGACACATCT TGGTAATGAT 8448 89 2.91e-05 TCAGCCCTCC CGGTAAGGCCTCAACAACCCA CGGATAGAAT 8768 373 3.11e-05 TTTGTGGAAT CTGCCAACCTCCACGAGCCCT TGTTTTTGCT 262335 202 3.11e-05 CTTGACCAGT CACCAACCTGAACCGACCTAA GCTTCCAAAC 2309 171 3.32e-05 GAACAGCTGA AAGCGAGCGAGAGAGAACTGA CACAAGGCAC 5631 343 4.59e-05 CTCTTTTTGT ACCCCACAGGAGAACATAACC GCAGCCCCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25377 1.7e-11 112_[+1]_367 5336 8e-10 385_[+1]_94 1873 5.6e-08 434_[+1]_45 20688 9.3e-08 473_[+1]_6 264781 1.3e-07 159_[+1]_320 38616 1.9e-07 478_[+1]_1 36879 1.9e-07 223_[+1]_256 22589 2.4e-07 305_[+1]_174 21025 2.4e-07 479_[+1] 1852 5.7e-07 104_[+1]_375 5641 1.7e-06 [+1]_479 7089 4.1e-06 339_[+1]_140 2824 4.4e-06 86_[+1]_393 1215 4.4e-06 245_[+1]_234 416 4.8e-06 335_[+1]_144 33667 8.5e-06 478_[+1]_1 7567 1.2e-05 34_[+1]_445 33310 1.3e-05 10_[+1]_469 8448 2.9e-05 88_[+1]_391 8768 3.1e-05 372_[+1]_107 262335 3.1e-05 201_[+1]_278 2309 3.3e-05 170_[+1]_309 5631 4.6e-05 342_[+1]_137 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=23 25377 ( 113) AACCAACACACCAACAACTCC 1 5336 ( 386) CACCAACCCGACAACAACTCT 1 1873 ( 435) CAGCAAACCACCACGAGCACA 1 20688 ( 474) CACCAAAGCACCAAAAACTAC 1 264781 ( 160) AACCGCGCCAAGAACAACAAC 1 38616 ( 479) AACCAAGCCAACAACCCCCAC 1 36879 ( 224) AAGCACGCCTCCACCACCACA 1 22589 ( 306) CCCCCCCCCCCAACCACCACC 1 21025 ( 480) CACCACAACCCAAAGAACACA 1 1852 ( 105) AGCCCACACAGAAACAACACT 1 5641 ( 1) AAGCAAAGCAACAACAGTAAC 1 7089 ( 340) AACCGAACAGCAACGAACTGC 1 2824 ( 87) ACGTGCCCCATCAACAACAAC 1 1215 ( 246) CAACAACCGACAACCGACTAC 1 416 ( 336) AATCAACAGTGCAGCAACACC 1 33667 ( 479) CCTCCACACAACAACAAATTC 1 7567 ( 35) AATCAACCACACAATACCCAC 1 33310 ( 11) CACCCAGGCGCAGACACATCT 1 8448 ( 89) CGGTAAGGCCTCAACAACCCA 1 8768 ( 373) CTGCCAACCTCCACGAGCCCT 1 262335 ( 202) CACCAACCTGAACCGACCTAA 1 2309 ( 171) AAGCGAGCGAGAGAGAACTGA 1 5631 ( 343) ACCCCACAGGAGAACATAACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 11040 bayes= 9.30716 E= 4.3e-009 100 101 -1117 -1117 142 -45 -141 -264 -258 114 40 -106 -1117 194 -1117 -164 112 14 -41 -1117 159 -13 -1117 -1117 0 101 18 -1117 0 125 -41 -1117 -158 155 -41 -264 88 -45 -9 -106 42 87 -82 -164 42 125 -141 -1117 174 -245 -141 -1117 133 36 -240 -1117 -258 146 18 -264 181 -245 -240 -1117 112 14 -82 -264 -100 180 -1117 -264 74 -45 -1117 53 42 114 -141 -264 0 125 -1117 -64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 23 E= 4.3e-009 0.521739 0.478261 0.000000 0.000000 0.695652 0.173913 0.086957 0.043478 0.043478 0.521739 0.304348 0.130435 0.000000 0.913043 0.000000 0.086957 0.565217 0.260870 0.173913 0.000000 0.782609 0.217391 0.000000 0.000000 0.260870 0.478261 0.260870 0.000000 0.260870 0.565217 0.173913 0.000000 0.086957 0.695652 0.173913 0.043478 0.478261 0.173913 0.217391 0.130435 0.347826 0.434783 0.130435 0.086957 0.347826 0.565217 0.086957 0.000000 0.869565 0.043478 0.086957 0.000000 0.652174 0.304348 0.043478 0.000000 0.043478 0.652174 0.260870 0.043478 0.913043 0.043478 0.043478 0.000000 0.565217 0.260870 0.130435 0.043478 0.130435 0.826087 0.000000 0.043478 0.434783 0.173913 0.000000 0.391304 0.347826 0.521739 0.086957 0.043478 0.260870 0.565217 0.000000 0.173913 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AC]A[CG]C[AC][AC][CAG][CA]C[AG][CA][CA]A[AC][CG]A[AC]C[AT][CA][CA] -------------------------------------------------------------------------------- Time 5.02 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 18 llr = 215 E-value = 6.0e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1::2:2:2:311:1:::22: pos.-specific C :13:13233::2::1:22:: probability G 58:8218:3522a2291373 matrix T 417184153276:8717317 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 GGTGTTGTCGTTGTTGTGGT consensus T C C CGAG G T G sequence TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 1215 88 6.11e-10 ATGGTGGAAG GGTGTTGTTGTTGTTGTGAT GTCATTGTTG 264781 298 1.76e-08 AGGTTCGTTC TTTGTTGTTATTGTTGTTGT ATTTACGAAA 8768 136 1.93e-07 GTCGATGTTT TGCGTAGCCATTGTTGTGAG AGGATATTAT 1852 304 1.93e-07 CTTGTTTGCT TGTGTTCTTTGGGTTGTGGT GGGTAACTTC 21025 116 2.98e-07 GATTGTGGAG GGTGTTCCCTGTGTTGTTAT TATTGGAAGA 36879 85 3.32e-07 ACCGTCGGTG GGTGTCGCCGTCGTCGTCGG CTTGAGGTTG 7089 368 6.11e-07 TGCTGGTCGA TGTGCTGCTGTTGTTGCCGG CGGGCGGGCT 2824 321 6.74e-07 GTTCTTGCGG TGCGGAGATGTTGTTGTGTT GGCTGAAGCG 2309 285 8.99e-07 GGAGGCGTTG GCTGTGGAGGTTGGGGTGGT TGTTGATGAC 22589 361 1.42e-06 AAGTGCCCTC TGCGTCTCGATTGTTGCAGT CCCCGCCTCG 1873 232 1.85e-06 GGTGGCGGAA GGTGTCGTGGGCGATTTTGT ATATTTAACG 5336 212 2.20e-06 CGGCCATCTT GGTGTCGCGGAAGGTGCTGT GGAGTGTGTC 5631 185 2.60e-06 TATTAGGTAT GGTGTCGTGAAGGTGGTATT GAAACTGTAT 20688 33 3.06e-06 GTGGCCCACT AGTTTCGTCTGTGTGGTTGT TGCGAGTACG 416 394 4.54e-06 GGCGTCTTTT GGCAGGCACATTGTTGTTGT GCCCAACGTA 33667 265 5.28e-06 TGAAGGTGAG TGTAGAGTTGTGGGTGTAGG ATTGTTGCGG 262335 63 1.08e-05 AGGAACACTT ACCATTGTGTTTGTTGGCGT AATGAAAATG 33310 97 1.59e-05 ACGAGAGTCG GTCGTTGTCGTCGTGTGGGG GGATGAGAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1215 6.1e-10 87_[+2]_393 264781 1.8e-08 297_[+2]_183 8768 1.9e-07 135_[+2]_345 1852 1.9e-07 303_[+2]_177 21025 3e-07 115_[+2]_365 36879 3.3e-07 84_[+2]_396 7089 6.1e-07 367_[+2]_113 2824 6.7e-07 320_[+2]_160 2309 9e-07 284_[+2]_196 22589 1.4e-06 360_[+2]_120 1873 1.9e-06 231_[+2]_249 5336 2.2e-06 211_[+2]_269 5631 2.6e-06 184_[+2]_296 20688 3.1e-06 32_[+2]_448 416 4.5e-06 393_[+2]_87 33667 5.3e-06 264_[+2]_216 262335 1.1e-05 62_[+2]_418 33310 1.6e-05 96_[+2]_384 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=18 1215 ( 88) GGTGTTGTTGTTGTTGTGAT 1 264781 ( 298) TTTGTTGTTATTGTTGTTGT 1 8768 ( 136) TGCGTAGCCATTGTTGTGAG 1 1852 ( 304) TGTGTTCTTTGGGTTGTGGT 1 21025 ( 116) GGTGTTCCCTGTGTTGTTAT 1 36879 ( 85) GGTGTCGCCGTCGTCGTCGG 1 7089 ( 368) TGTGCTGCTGTTGTTGCCGG 1 2824 ( 321) TGCGGAGATGTTGTTGTGTT 1 2309 ( 285) GCTGTGGAGGTTGGGGTGGT 1 22589 ( 361) TGCGTCTCGATTGTTGCAGT 1 1873 ( 232) GGTGTCGTGGGCGATTTTGT 1 5336 ( 212) GGTGTCGCGGAAGGTGCTGT 1 5631 ( 185) GGTGTCGTGAAGGTGGTATT 1 20688 ( 33) AGTTTCGTCTGTGTGGTTGT 1 416 ( 394) GGCAGGCACATTGTTGTTGT 1 33667 ( 265) TGTAGAGTTGTGGGTGTAGG 1 262335 ( 63) ACCATTGTGTTTGTTGGCGT 1 33310 ( 97) GTCGTTGTCGTCGTGTGGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 11063 bayes= 9.39569 E= 6.0e-003 -123 -1081 112 52 -1081 -109 175 -129 -1081 49 -1081 129 -64 -1081 175 -229 -1081 -209 -47 152 -64 49 -105 52 -1081 -51 175 -229 -64 49 -1081 88 -1081 49 53 29 9 -1081 112 -29 -123 -1081 -5 129 -222 -51 -47 117 -1081 -1081 212 -1081 -222 -1081 -47 152 -1081 -209 -5 141 -1081 -1081 195 -129 -1081 -51 -105 141 -64 -51 53 29 -64 -1081 165 -129 -1081 -1081 27 141 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 18 E= 6.0e-003 0.111111 0.000000 0.500000 0.388889 0.000000 0.111111 0.777778 0.111111 0.000000 0.333333 0.000000 0.666667 0.166667 0.000000 0.777778 0.055556 0.000000 0.055556 0.166667 0.777778 0.166667 0.333333 0.111111 0.388889 0.000000 0.166667 0.777778 0.055556 0.166667 0.333333 0.000000 0.500000 0.000000 0.333333 0.333333 0.333333 0.277778 0.000000 0.500000 0.222222 0.111111 0.000000 0.222222 0.666667 0.055556 0.166667 0.166667 0.611111 0.000000 0.000000 1.000000 0.000000 0.055556 0.000000 0.166667 0.777778 0.000000 0.055556 0.222222 0.722222 0.000000 0.000000 0.888889 0.111111 0.000000 0.166667 0.111111 0.722222 0.166667 0.166667 0.333333 0.333333 0.166667 0.000000 0.722222 0.111111 0.000000 0.000000 0.277778 0.722222 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT]G[TC]GT[TC]G[TC][CGT][GAT][TG]TGT[TG]GT[GT]G[TG] -------------------------------------------------------------------------------- Time 10.20 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 11 llr = 171 E-value = 8.4e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :54:55:8:5416:832544: pos.-specific C :241::22:11121::::2:: probability G a::9558:a546292685159 matrix T :43:::::::22:::1::411 bits 2.1 * * 1.9 * * 1.7 * * * * * 1.5 * * * * * * * Relative 1.3 * * *** ** * * Entropy 1.1 * ****** ** ** * (22.4 bits) 0.8 * ****** ***** * 0.6 * ******* ******* ** 0.4 ********** ******* ** 0.2 ********************* 0.0 --------------------- Multilevel GAAGGAGAGAAGAGAGGGAGG consensus TC AG GG A ATA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 25377 189 1.89e-09 GCCCCGGCGG GAAGGAGAGGGGAGGGGACAG AAGTACACAC 33667 65 2.15e-09 TTGATTGAAT GACGAGGAGGAGAGAGGGTGT TGTTGCGTGT 2824 405 7.88e-09 GGAGGGTTGT GTCGGAGAGAGTCGAGGACGG TTCGTGGTGC 1873 199 8.77e-09 CTACAATATT GAAGGAGAGAACAGAGGAGGG GAGGTGGCGG 8768 239 2.16e-08 CGGAGCAGCT GCCGAGCAGATGAGAAGGTGG AGAACAAAGT 20688 265 3.11e-08 CCGTTGTGTA GTAGAGGCGACGGGAGGAAGG GTGAAATCAA 262335 133 3.70e-08 CTGCGGAGTG GAAGGAGAGAAAGGAGAGAGG CATCTTCAGA 36879 345 4.77e-08 TGATCGGGTA GTTGAAGAGGTGAGAGAGATG GTACAACGAC 21025 8 7.13e-08 GAGGGAG GTCGAGGAGGGGACGAGGTAG ACTCCACCGG 2309 25 2.32e-07 GTGAACTCGT GATCGGGAGGATAGATGATAG TTCGCTGGTG 22589 73 4.63e-07 AGGGTAATTT GCTGGACCGCGGCGAAGGAAG CTGCGGGGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25377 1.9e-09 188_[+3]_291 33667 2.2e-09 64_[+3]_415 2824 7.9e-09 404_[+3]_75 1873 8.8e-09 198_[+3]_281 8768 2.2e-08 238_[+3]_241 20688 3.1e-08 264_[+3]_215 262335 3.7e-08 132_[+3]_347 36879 4.8e-08 344_[+3]_135 21025 7.1e-08 7_[+3]_472 2309 2.3e-07 24_[+3]_455 22589 4.6e-07 72_[+3]_407 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=11 25377 ( 189) GAAGGAGAGGGGAGGGGACAG 1 33667 ( 65) GACGAGGAGGAGAGAGGGTGT 1 2824 ( 405) GTCGGAGAGAGTCGAGGACGG 1 1873 ( 199) GAAGGAGAGAACAGAGGAGGG 1 8768 ( 239) GCCGAGCAGATGAGAAGGTGG 1 20688 ( 265) GTAGAGGCGACGGGAGGAAGG 1 262335 ( 133) GAAGGAGAGAAAGGAGAGAGG 1 36879 ( 345) GTTGAAGAGGTGAGAGAGATG 1 21025 ( 8) GTCGAGGAGGGGACGAGGTAG 1 2309 ( 25) GATCGGGAGGATAGATGATAG 1 22589 ( 73) GCTGGACCGCGGCGAAGGAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 11040 bayes= 10.9968 E= 8.4e-006 -1010 -1010 212 -1010 80 -38 -1010 42 48 61 -1010 1 -1010 -138 198 -1010 80 -1010 124 -1010 107 -1010 98 -1010 -1010 -38 183 -1010 165 -38 -1010 -1010 -1010 -1010 212 -1010 80 -138 98 -1010 48 -138 66 -58 -151 -138 146 -58 129 -38 -34 -1010 -1010 -138 198 -1010 165 -1010 -34 -1010 7 -1010 146 -158 -52 -1010 183 -1010 80 -1010 124 -1010 48 -38 -134 42 48 -1010 124 -158 -1010 -1010 198 -158 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 11 E= 8.4e-006 0.000000 0.000000 1.000000 0.000000 0.454545 0.181818 0.000000 0.363636 0.363636 0.363636 0.000000 0.272727 0.000000 0.090909 0.909091 0.000000 0.454545 0.000000 0.545455 0.000000 0.545455 0.000000 0.454545 0.000000 0.000000 0.181818 0.818182 0.000000 0.818182 0.181818 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.454545 0.090909 0.454545 0.000000 0.363636 0.090909 0.363636 0.181818 0.090909 0.090909 0.636364 0.181818 0.636364 0.181818 0.181818 0.000000 0.000000 0.090909 0.909091 0.000000 0.818182 0.000000 0.181818 0.000000 0.272727 0.000000 0.636364 0.090909 0.181818 0.000000 0.818182 0.000000 0.454545 0.000000 0.545455 0.000000 0.363636 0.181818 0.090909 0.363636 0.363636 0.000000 0.545455 0.090909 0.000000 0.000000 0.909091 0.090909 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[AT][ACT]G[GA][AG]GAG[AG][AG]GAGA[GA]G[GA][AT][GA]G -------------------------------------------------------------------------------- Time 14.45 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1215 6.66e-08 87_[+2(6.11e-10)]_138_\ [+1(4.44e-06)]_234 1852 3.68e-06 104_[+1(5.69e-07)]_178_\ [+2(1.93e-07)]_177 1873 4.84e-11 128_[+3(7.41e-05)]_49_\ [+3(8.77e-09)]_12_[+2(1.85e-06)]_183_[+1(5.62e-08)]_45 20688 4.04e-10 32_[+2(3.06e-06)]_212_\ [+3(3.11e-08)]_188_[+1(9.34e-08)]_6 21025 2.41e-10 7_[+3(7.13e-08)]_87_[+2(2.98e-07)]_\ 38_[+1(8.88e-05)]_132_[+2(2.58e-05)]_133_[+1(2.40e-07)] 22589 5.82e-09 72_[+3(4.63e-07)]_212_\ [+1(2.40e-07)]_34_[+2(1.42e-06)]_120 2309 1.85e-07 24_[+3(2.32e-07)]_125_\ [+1(3.32e-05)]_93_[+2(8.99e-07)]_196 25377 3.58e-12 112_[+1(1.75e-11)]_55_\ [+3(1.89e-09)]_291 262335 3.13e-07 62_[+2(1.08e-05)]_11_[+3(6.20e-05)]_\ 18_[+3(3.70e-08)]_48_[+1(3.11e-05)]_28_[+3(6.36e-05)]_229 264781 7.24e-08 159_[+1(1.34e-07)]_117_\ [+2(1.76e-08)]_183 2824 1.00e-09 86_[+1(4.44e-06)]_100_\ [+1(6.24e-05)]_92_[+2(6.74e-07)]_1_[+3(2.01e-05)]_42_[+3(7.88e-09)]_5_\ [+2(9.86e-05)]_50 33310 2.61e-03 10_[+1(1.34e-05)]_65_[+2(1.59e-05)]_\ 384 33667 3.68e-09 64_[+3(2.15e-09)]_179_\ [+2(5.28e-06)]_194_[+1(8.49e-06)]_1 36879 1.48e-10 84_[+2(3.32e-07)]_119_\ [+1(1.91e-07)]_100_[+3(4.77e-08)]_135 38616 8.06e-04 478_[+1(1.91e-07)]_1 416 3.19e-04 235_[+1(4.59e-05)]_79_\ [+1(4.83e-06)]_37_[+2(4.54e-06)]_87 5336 3.08e-08 211_[+2(2.20e-06)]_154_\ [+1(7.98e-10)]_94 5631 9.84e-04 184_[+2(2.60e-06)]_138_\ [+1(4.59e-05)]_137 5641 5.75e-03 [+1(1.68e-06)]_479 7089 4.78e-05 339_[+1(4.08e-06)]_7_[+2(6.11e-07)]_\ 113 7567 6.71e-02 34_[+1(1.15e-05)]_445 8448 1.07e-01 88_[+1(2.91e-05)]_391 8768 4.80e-09 135_[+2(1.93e-07)]_83_\ [+3(2.16e-08)]_113_[+1(3.11e-05)]_107 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************