******************************************************************************** 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/146/146.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10515 1.0000 500 11939 1.0000 500 1533 1.0000 500 1797 1.0000 500 18148 1.0000 500 21227 1.0000 500 22234 1.0000 500 2241 1.0000 500 24548 1.0000 500 24588 1.0000 500 25572 1.0000 500 3450 1.0000 500 35668 1.0000 500 4007 1.0000 500 41433 1.0000 500 4294 1.0000 500 4937 1.0000 500 5360 1.0000 500 6585 1.0000 500 6838 1.0000 500 7446 1.0000 500 7537 1.0000 500 8067 1.0000 500 8068 1.0000 500 8106 1.0000 500 899 1.0000 500 9551 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/146/146.seqs.fa -oc motifs/146 -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= 27 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= 13500 N= 27 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.265 C 0.235 G 0.229 T 0.271 Background letter frequencies (from dataset with add-one prior applied): A 0.265 C 0.235 G 0.229 T 0.271 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 16 llr = 223 E-value = 8.1e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 13:4::8::3::1:11:11:1 pos.-specific C :6231:11:1111::33:21: probability G 6:6::91:a1:7517:36319 matrix T 322391:9:49239365449: bits 2.1 * 1.9 * 1.7 * * 1.5 * * * * Relative 1.3 ** ** * * ** Entropy 1.1 ***** * * ** (20.2 bits) 0.9 * ***** ** ** * ** 0.6 *** ***** ** *** * ** 0.4 ********* ** ***** ** 0.2 ********************* 0.0 --------------------- Multilevel GCGATGATGTTGGTGTTGTTG consensus TA C A T TCCTG sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8068 22 4.26e-10 TGATGTGTCC GCCATGATGATGGTGTGGCTG GATGGAGGGC 8067 22 4.26e-10 TGATGTGTCC GCCATGATGATGGTGTGGCTG GATGGAGGGC 22234 364 4.26e-10 GCATCATTTA GTGATGATGATGGTTTTGTTG CTGCTGGCAG 41433 35 2.95e-09 TTAGTGCACG TCGCTGATGTTGATGCTGCTG ATTTCTGATG 4007 287 3.38e-09 CCTCGTCATG GCGCTGATGGTGGTGATGATG ATGGTGACGT 1533 27 2.33e-08 GGTGTTGGCG ACGATGATGCTTGTGTCTTTG CAACAGTGGT 24588 42 5.39e-08 TCAACATCAA TCGTTGATGTTGATGTTGGTA CACGTAGACA 9551 322 9.65e-08 TTCCAGTGAA TATTTGACGTTGGTGTGTTTG ATGTGAAGGT 6585 88 1.52e-07 GTGTGCTGCT GTGTTGCTGTTGGTGTTTGGG GTACGTTGCG 1797 222 1.52e-07 AGGACTAGTG TCGTTGCTGTTGCTTCCGTTG GACTCAGCGT 3450 242 6.57e-07 AGGCCACAGA GAGATTATGTTCCTTCTTTTG TAGACCAGGG 7446 338 1.16e-06 CTTTTGCGTC GACCCTGTGTTGTTGTTGTTG GAGTGAGTTG 7537 355 2.66e-06 TTGGCAAACC GCGATGACGACGTTGCCAATG GACGAGCCTC 21227 226 2.66e-06 GACTCTCCTC TTTCTGATGGTTTGTTCGTTG CAGTACTGAT 5360 189 2.82e-06 TATCGGAATT GATATGATGATCTGATTTGTG CAATGAAAAT 10515 350 6.78e-06 TTTGGCCAAA ACGCCGATGCTTGTGAGTGCG CAGAAATGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8068 4.3e-10 21_[+1]_458 8067 4.3e-10 21_[+1]_458 22234 4.3e-10 363_[+1]_116 41433 3e-09 34_[+1]_445 4007 3.4e-09 286_[+1]_193 1533 2.3e-08 26_[+1]_453 24588 5.4e-08 41_[+1]_438 9551 9.6e-08 321_[+1]_158 6585 1.5e-07 87_[+1]_392 1797 1.5e-07 221_[+1]_258 3450 6.6e-07 241_[+1]_238 7446 1.2e-06 337_[+1]_142 7537 2.7e-06 354_[+1]_125 21227 2.7e-06 225_[+1]_254 5360 2.8e-06 188_[+1]_291 10515 6.8e-06 349_[+1]_130 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=16 8068 ( 22) GCCATGATGATGGTGTGGCTG 1 8067 ( 22) GCCATGATGATGGTGTGGCTG 1 22234 ( 364) GTGATGATGATGGTTTTGTTG 1 41433 ( 35) TCGCTGATGTTGATGCTGCTG 1 4007 ( 287) GCGCTGATGGTGGTGATGATG 1 1533 ( 27) ACGATGATGCTTGTGTCTTTG 1 24588 ( 42) TCGTTGATGTTGATGTTGGTA 1 9551 ( 322) TATTTGACGTTGGTGTGTTTG 1 6585 ( 88) GTGTTGCTGTTGGTGTTTGGG 1 1797 ( 222) TCGTTGCTGTTGCTTCCGTTG 1 3450 ( 242) GAGATTATGTTCCTTCTTTTG 1 7446 ( 338) GACCCTGTGTTGTTGTTGTTG 1 7537 ( 355) GCGATGACGACGTTGCCAATG 1 21227 ( 226) TTTCTGATGGTTTGTTCGTTG 1 5360 ( 189) GATATGATGATCTGATTTGTG 1 10515 ( 350) ACGCCGATGCTTGTGAGTGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12960 bayes= 10.3977 E= 8.1e-010 -108 -1064 130 21 -8 126 -1064 -53 -1064 -33 145 -53 72 41 -1064 -11 -1064 -91 -1064 169 -1064 -1064 193 -111 161 -91 -187 -1064 -1064 -91 -1064 169 -1064 -1064 213 -1064 24 -91 -87 69 -1064 -191 -1064 179 -1064 -91 158 -53 -108 -91 113 -11 -1064 -1064 -87 169 -208 -1064 158 -11 -108 9 -1064 121 -1064 9 13 89 -208 -1064 130 47 -108 -33 13 69 -1064 -191 -187 169 -208 -1064 203 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 16 E= 8.1e-010 0.125000 0.000000 0.562500 0.312500 0.250000 0.562500 0.000000 0.187500 0.000000 0.187500 0.625000 0.187500 0.437500 0.312500 0.000000 0.250000 0.000000 0.125000 0.000000 0.875000 0.000000 0.000000 0.875000 0.125000 0.812500 0.125000 0.062500 0.000000 0.000000 0.125000 0.000000 0.875000 0.000000 0.000000 1.000000 0.000000 0.312500 0.125000 0.125000 0.437500 0.000000 0.062500 0.000000 0.937500 0.000000 0.125000 0.687500 0.187500 0.125000 0.125000 0.500000 0.250000 0.000000 0.000000 0.125000 0.875000 0.062500 0.000000 0.687500 0.250000 0.125000 0.250000 0.000000 0.625000 0.000000 0.250000 0.250000 0.500000 0.062500 0.000000 0.562500 0.375000 0.125000 0.187500 0.250000 0.437500 0.000000 0.062500 0.062500 0.875000 0.062500 0.000000 0.937500 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GT][CA]G[ACT]TGATG[TA]TG[GT]T[GT][TC][TCG][GT][TG]TG -------------------------------------------------------------------------------- Time 7.51 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 12 llr = 184 E-value = 1.6e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 38::1::4:63:::::42::1 pos.-specific C 317::61:8:2::::3:1:3: probability G 522832963352:a4166186 matrix T ::2263:::118a:66:29:3 bits 2.1 * 1.9 ** 1.7 * ** 1.5 * * ** * Relative 1.3 * * * *** ** Entropy 1.1 * *** **** * ** (22.2 bits) 0.9 *** *** **** * *** 0.6 ********** ****** *** 0.4 ********** ********** 0.2 ********************* 0.0 --------------------- Multilevel GACGTCGGCAGTTGTTGGTGG consensus A GT AGGA GCA CT sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8068 198 3.46e-11 CTGATAGATA GAGGTCGGCGGTTGTTGGTGG TTCGAGGTAA 8067 198 3.46e-11 CTGATAGATA GAGGTCGGCGGTTGTTGGTGG TTCGAGGTAA 4294 437 2.08e-10 GGTACCTGTT GACGTCGGCACTTGTCGGTCG CGTCATACTA 7537 227 6.98e-09 GTAGACCGAA GACGGCGGCGATTGTCAATGT TATGGTGAAG 1533 4 9.68e-09 TCG CGCGTTGACAGTTGGTGTTGG CGACGATGAT 899 185 2.40e-08 ATGTGACCTA ACCGTCGACAGTTGGGAGTGG GATGTATTGC 7446 458 6.38e-08 TTTCTGTGTT CACGTTGGCAGTTGGCAGGCT TCCGTCCACT 35668 385 1.03e-07 ATCTGAGCAA CATGGTGGCAATTGTCACTGG TGCAAGGTGA 21227 254 2.93e-07 TTGCAGTACT GATTGCGACAGGTGGTAATGT TGCTTCAGTG 24548 100 3.53e-07 CACGGAACAC GACGAGGGGGTTTGGTGGTGA GGTTTGAGGA 2241 335 6.92e-07 GTTGCCCTCG AGCGTCGAGTAGTGTTGGTCT TCCAGAACCA 1797 50 1.12e-06 GGGGGATAAT AACTGGCAGACTTGTTGTTGG GCAGGTTCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8068 3.5e-11 197_[+2]_282 8067 3.5e-11 197_[+2]_282 4294 2.1e-10 436_[+2]_43 7537 7e-09 226_[+2]_253 1533 9.7e-09 3_[+2]_476 899 2.4e-08 184_[+2]_295 7446 6.4e-08 457_[+2]_22 35668 1e-07 384_[+2]_95 21227 2.9e-07 253_[+2]_226 24548 3.5e-07 99_[+2]_380 2241 6.9e-07 334_[+2]_145 1797 1.1e-06 49_[+2]_430 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=12 8068 ( 198) GAGGTCGGCGGTTGTTGGTGG 1 8067 ( 198) GAGGTCGGCGGTTGTTGGTGG 1 4294 ( 437) GACGTCGGCACTTGTCGGTCG 1 7537 ( 227) GACGGCGGCGATTGTCAATGT 1 1533 ( 4) CGCGTTGACAGTTGGTGTTGG 1 899 ( 185) ACCGTCGACAGTTGGGAGTGG 1 7446 ( 458) CACGTTGGCAGTTGGCAGGCT 1 35668 ( 385) CATGGTGGCAATTGTCACTGG 1 21227 ( 254) GATTGCGACAGGTGGTAATGT 1 24548 ( 100) GACGAGGGGGTTTGGTGGTGA 1 2241 ( 335) AGCGTCGAGTAGTGTTGGTCT 1 1797 ( 50) AACTGGCAGACTTGTTGTTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12960 bayes= 11.1757 E= 1.6e-005 -8 9 113 -1023 150 -149 -46 -1023 -1023 150 -46 -70 -1023 -1023 186 -70 -167 -1023 54 111 -1023 131 -46 -11 -1023 -149 200 -1023 65 -1023 135 -1023 -1023 167 13 -1023 114 -1023 54 -170 -8 -50 113 -170 -1023 -1023 -46 162 -1023 -1023 -1023 188 -1023 -1023 212 -1023 -1023 -1023 86 111 -1023 50 -146 111 65 -1023 135 -1023 -67 -149 135 -70 -1023 -1023 -146 176 -1023 9 171 -1023 -167 -1023 135 30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 12 E= 1.6e-005 0.250000 0.250000 0.500000 0.000000 0.750000 0.083333 0.166667 0.000000 0.000000 0.666667 0.166667 0.166667 0.000000 0.000000 0.833333 0.166667 0.083333 0.000000 0.333333 0.583333 0.000000 0.583333 0.166667 0.250000 0.000000 0.083333 0.916667 0.000000 0.416667 0.000000 0.583333 0.000000 0.000000 0.750000 0.250000 0.000000 0.583333 0.000000 0.333333 0.083333 0.250000 0.166667 0.500000 0.083333 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.416667 0.583333 0.000000 0.333333 0.083333 0.583333 0.416667 0.000000 0.583333 0.000000 0.166667 0.083333 0.583333 0.166667 0.000000 0.000000 0.083333 0.916667 0.000000 0.250000 0.750000 0.000000 0.083333 0.000000 0.583333 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GAC]ACG[TG][CT]G[GA][CG][AG][GA]TTG[TG][TC][GA]GT[GC][GT] -------------------------------------------------------------------------------- Time 14.89 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 22 llr = 228 E-value = 2.5e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 17735:187353397: pos.-specific C 9316:a9:15227:19 probability G ::1:2:::2:11:111 matrix T ::113::1:214:::: bits 2.1 1.9 * 1.7 * * * 1.5 * * * Relative 1.3 * ** ** * Entropy 1.1 ** *** ** * (14.9 bits) 0.9 ** *** ** * 0.6 **** **** **** 0.4 ********** **** 0.2 **************** 0.0 ---------------- Multilevel CAACACCAACATCAAC consensus C AT ACAA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 41433 473 5.16e-10 ACAAAGCACA CAACACCAACAACAAC CCAACCAACA 3450 397 3.77e-08 TGAATACTGC CACCGCCAACATCAAC TCCTATATGC 1533 462 9.29e-08 GCAACGGGAC CATCACCAACACCAAC GGAACCAACC 24588 438 5.81e-07 GCAAACCAAA CAACTCTAACAACAAC TAACACAGCG 25572 401 6.60e-07 ATAAAACAAA CAACACCAAAGCAAAC ACACCAAATA 5360 418 1.46e-06 AACTGAAGGA CAACTCCACCCAAAAC AGCGACTCTG 18148 54 1.46e-06 TACGCGCTAA CCAAACCAAACCAAAC CAAGCCAACA 9551 126 2.20e-06 TGCCCTCCTT CAACTTCAGCATCAAC TTCAACTCTC 8068 476 2.70e-06 TGCCCCCTCC CCACACCAATATAAAG CACAACACC 8067 476 2.70e-06 TGCCCCCTCC CCACACCAATATAAAG CACAACACC 2241 484 2.99e-06 GGATCAAGTT CCACGCCAGCAGCACC G 11939 275 9.04e-06 TCAGTGATGA CAATACCATCAACAGC AGCAAACTCA 899 420 1.17e-05 CACAAAACAA AAAAGCCAACAAAAGC GAAGAATTAA 4937 133 1.17e-05 ATCTACTAGT CAAGGCCAGAATCGAC CCTCCGAATG 35668 226 2.05e-05 GCTTCACTCT CACTTCCTGCAACAAC TCACACCGAC 21227 10 2.22e-05 CGTCCTCGT CAAATCCAAACTCGTC GGCGATTCTG 6838 95 2.39e-05 CGCTGTGTTG CCGAACAAACTACAAC AAGCAGTCAA 10515 479 2.58e-05 CGCTTACTAG CCAAACCTAACGCAGC TCAGCA 4294 274 3.98e-05 CTTTCCCACA AATCACCAAATTCGAC CATGTACTCC 1797 362 4.58e-05 AGGTAGCAAG CCAAGCAAAAGTCACC GAGCAAAATG 8106 394 5.25e-05 CTTGTCGTCT CACCTCCTCTTTCAAC CTACTACTCT 4007 1 6.40e-05 . CAGCACCCATCCCACC GTTGGCAGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41433 5.2e-10 472_[+3]_12 3450 3.8e-08 396_[+3]_88 1533 9.3e-08 461_[+3]_23 24588 5.8e-07 437_[+3]_47 25572 6.6e-07 400_[+3]_84 5360 1.5e-06 417_[+3]_67 18148 1.5e-06 53_[+3]_431 9551 2.2e-06 125_[+3]_359 8068 2.7e-06 475_[+3]_9 8067 2.7e-06 475_[+3]_9 2241 3e-06 483_[+3]_1 11939 9e-06 274_[+3]_210 899 1.2e-05 419_[+3]_65 4937 1.2e-05 132_[+3]_352 35668 2.1e-05 225_[+3]_259 21227 2.2e-05 9_[+3]_475 6838 2.4e-05 94_[+3]_390 10515 2.6e-05 478_[+3]_6 4294 4e-05 273_[+3]_211 1797 4.6e-05 361_[+3]_123 8106 5.3e-05 393_[+3]_91 4007 6.4e-05 [+3]_484 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=22 41433 ( 473) CAACACCAACAACAAC 1 3450 ( 397) CACCGCCAACATCAAC 1 1533 ( 462) CATCACCAACACCAAC 1 24588 ( 438) CAACTCTAACAACAAC 1 25572 ( 401) CAACACCAAAGCAAAC 1 5360 ( 418) CAACTCCACCCAAAAC 1 18148 ( 54) CCAAACCAAACCAAAC 1 9551 ( 126) CAACTTCAGCATCAAC 1 8068 ( 476) CCACACCAATATAAAG 1 8067 ( 476) CCACACCAATATAAAG 1 2241 ( 484) CCACGCCAGCAGCACC 1 11939 ( 275) CAATACCATCAACAGC 1 899 ( 420) AAAAGCCAACAAAAGC 1 4937 ( 133) CAAGGCCAGAATCGAC 1 35668 ( 226) CACTTCCTGCAACAAC 1 21227 ( 10) CAAATCCAAACTCGTC 1 6838 ( 95) CCGAACAAACTACAAC 1 10515 ( 479) CCAAACCTAACGCAGC 1 4294 ( 274) AATCACCAAATTCGAC 1 1797 ( 362) CCAAGCAAAAGTCACC 1 8106 ( 394) CACCTCCTCTTTCAAC 1 4007 ( 1) CAGCACCCATCCCACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 13095 bayes= 9.5705 E= 2.5e-003 -154 195 -1110 -1110 136 44 -1110 -1110 136 -79 -133 -157 4 133 -233 -157 91 -1110 -1 1 -1110 202 -1110 -257 -154 188 -1110 -257 163 -237 -1110 -99 136 -137 -33 -257 26 109 -1110 -57 104 -5 -133 -99 26 -37 -133 60 4 163 -1110 -1110 170 -1110 -75 -1110 136 -79 -75 -257 -1110 195 -133 -1110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 22 E= 2.5e-003 0.090909 0.909091 0.000000 0.000000 0.681818 0.318182 0.000000 0.000000 0.681818 0.136364 0.090909 0.090909 0.272727 0.590909 0.045455 0.090909 0.500000 0.000000 0.227273 0.272727 0.000000 0.954545 0.000000 0.045455 0.090909 0.863636 0.000000 0.045455 0.818182 0.045455 0.000000 0.136364 0.681818 0.090909 0.181818 0.045455 0.318182 0.500000 0.000000 0.181818 0.545455 0.227273 0.090909 0.136364 0.318182 0.181818 0.090909 0.409091 0.272727 0.727273 0.000000 0.000000 0.863636 0.000000 0.136364 0.000000 0.681818 0.136364 0.136364 0.045455 0.000000 0.909091 0.090909 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[AC]A[CA][ATG]CCAA[CA][AC][TA][CA]AAC -------------------------------------------------------------------------------- Time 21.98 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10515 9.35e-04 349_[+1(6.78e-06)]_108_\ [+3(2.58e-05)]_6 11939 4.92e-02 274_[+3(9.04e-06)]_210 1533 1.41e-12 3_[+2(9.68e-09)]_2_[+1(2.33e-08)]_\ 414_[+3(9.29e-08)]_23 1797 2.07e-07 49_[+2(1.12e-06)]_151_\ [+1(1.52e-07)]_119_[+3(4.58e-05)]_123 18148 1.86e-02 53_[+3(1.46e-06)]_431 21227 4.27e-07 9_[+3(2.22e-05)]_200_[+1(2.66e-06)]_\ 7_[+2(2.93e-07)]_145_[+1(1.84e-05)]_3_[+1(5.93e-05)]_36 22234 1.88e-05 363_[+1(4.26e-10)]_116 2241 5.68e-05 334_[+2(6.92e-07)]_128_\ [+3(2.99e-06)]_1 24548 3.77e-03 99_[+2(3.53e-07)]_380 24588 2.10e-07 41_[+1(5.39e-08)]_375_\ [+3(5.81e-07)]_47 25572 5.15e-03 400_[+3(6.60e-07)]_84 3450 7.78e-07 241_[+1(6.57e-07)]_134_\ [+3(3.77e-08)]_88 35668 2.78e-05 59_[+2(7.95e-05)]_145_\ [+3(2.05e-05)]_143_[+2(1.03e-07)]_95 4007 1.19e-06 [+3(6.40e-05)]_270_[+1(3.38e-09)]_\ 193 41433 1.29e-10 34_[+1(2.95e-09)]_417_\ [+3(5.16e-10)]_12 4294 3.13e-07 273_[+3(3.98e-05)]_147_\ [+2(2.08e-10)]_43 4937 1.97e-02 132_[+3(1.17e-05)]_352 5360 5.26e-05 188_[+1(2.82e-06)]_208_\ [+3(1.46e-06)]_67 6585 4.06e-04 87_[+1(1.52e-07)]_392 6838 6.93e-02 94_[+3(2.39e-05)]_390 7446 1.71e-06 337_[+1(1.16e-06)]_50_\ [+2(1.12e-06)]_28_[+2(6.38e-08)]_22 7537 7.39e-07 226_[+2(6.98e-09)]_107_\ [+1(2.66e-06)]_125 8067 3.73e-15 21_[+1(4.26e-10)]_69_[+2(3.66e-05)]_\ 65_[+2(3.46e-11)]_257_[+3(2.70e-06)]_9 8068 3.73e-15 21_[+1(4.26e-10)]_69_[+2(3.66e-05)]_\ 65_[+2(3.46e-11)]_257_[+3(2.70e-06)]_9 8106 1.72e-01 393_[+3(5.25e-05)]_91 899 9.14e-06 184_[+2(2.40e-08)]_214_\ [+3(1.17e-05)]_65 9551 6.50e-06 125_[+3(2.20e-06)]_180_\ [+1(9.65e-08)]_158 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************