******************************************************************************** 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/136/136.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10064 1.0000 500 10948 1.0000 500 11195 1.0000 500 21722 1.0000 500 22056 1.0000 500 22733 1.0000 500 23418 1.0000 500 261894 1.0000 500 262632 1.0000 500 268248 1.0000 500 2792 1.0000 500 2862 1.0000 500 2919 1.0000 500 33075 1.0000 500 3452 1.0000 500 4260 1.0000 500 4650 1.0000 500 5051 1.0000 500 5066 1.0000 500 6231 1.0000 500 6481 1.0000 500 7469 1.0000 500 7692 1.0000 500 7980 1.0000 500 8584 1.0000 500 8718 1.0000 500 9339 1.0000 500 9497 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/136/136.seqs.fa -oc motifs/136 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 28 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 14000 N= 28 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.256 C 0.230 G 0.235 T 0.280 Background letter frequencies (from dataset with add-one prior applied): A 0.255 C 0.230 G 0.235 T 0.280 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 26 llr = 249 E-value = 3.4e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1131843238558539 pos.-specific C 6238:6726:35:371 probability G :31::::6::2:22:: matrix T 35312:::12:::::: bits 2.1 1.9 1.7 1.5 * Relative 1.3 * * ** Entropy 1.1 **** * * ** (13.8 bits) 0.8 **** ** ** ** 0.6 * ******* ** ** 0.4 * ************* 0.2 **************** 0.0 ---------------- Multilevel CTCCACCGCAAAAACA consensus TGT AAAA CC CA sequence A G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 7692 454 1.08e-08 GTCGTCTCGC CTCCAACGCAACAGCA ATGGTTGGAA 2862 480 2.81e-08 CACCTCCCTT CTTCACAGCAACAACA ACATC 2919 454 5.80e-07 CCTGCACCTG CGCCACACCAAAAACA TACGGAGAGA 5051 104 6.68e-07 CGATGTTTTC CTCCACCGCACAATCA GTGGATCGAT 23418 480 6.68e-07 ACTCAACACA ATCCACCGAACAAACA GCATC 6231 447 1.00e-06 TTGTAACAAC TCACAACGCACAAGCA ACAAGCTCCA 22056 211 3.79e-06 ATGCATGCGC CATCACCGTAACACCA ACATGCACGC 21722 413 4.22e-06 GAAAACGAAA TTATACCGAACCAACA CAAAACACCG 2792 257 5.23e-06 GAACTGCCGC CGCCACCACAGCGAAA TACCGGAAAG 10948 219 6.44e-06 ATCTTCAACT TTTCACCCAAACGACA ACGGACGGAA 4650 47 7.13e-06 CTGTAGCACC ACTCAACACAAAACCA AACAACACCA 22733 443 9.59e-06 CTTCCAGCAC CTGCACAGCTCAACCA TCATCAGTCA 3452 481 1.40e-05 GCCGCTGCCT CCTCTACCCACAACCA AACC 4260 7 1.83e-05 GCAAAG TTCAACAACACAAACA AAGCTTTGGA 8718 117 2.00e-05 TTGCATTAAC TTTCTAAGCAACACAA CTACTCGAAA 11195 411 3.57e-05 CTCGATAAAA CTTCACCAAAATACAA TTTAGACATA 33075 264 3.86e-05 TTTTACAGCT TTTCAATGCAACGGCA GACGAAGCTT 5066 261 4.18e-05 CCTGGTAGTT TACCAAAGAAGAAGAA GTTGAGCGAC 7980 291 4.51e-05 TACCTATGTA CGAGTACGAAACAACA GGAGAGGGGA 261894 4 4.51e-05 GGG AAACACCGAAAAGAAA GCAACAGGGC 9339 142 4.86e-05 CTAGAGAGTC CTACACCACTGAAGCC ATCGACCTCC 7469 45 5.24e-05 CTGCAGAACA CGATACCCCTGCACCA GAGACGACGA 10064 40 6.99e-05 TGATGTCGTC CGCCACCAAAAAGAAC GCCTGAAGCC 8584 82 8.60e-05 AATCATATTA TCATAAAGCTCCAACA GCTCCAACTT 268248 371 8.60e-05 GTAACACCTT CGGCAACGCGGAAGAA AATCATCGAG 9497 477 1.05e-04 ACGTCACTCT CGCATACGTAGCAACA GCCGAAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7692 1.1e-08 453_[+1]_31 2862 2.8e-08 479_[+1]_5 2919 5.8e-07 453_[+1]_31 5051 6.7e-07 103_[+1]_381 23418 6.7e-07 479_[+1]_5 6231 1e-06 446_[+1]_38 22056 3.8e-06 210_[+1]_274 21722 4.2e-06 412_[+1]_72 2792 5.2e-06 256_[+1]_228 10948 6.4e-06 218_[+1]_266 4650 7.1e-06 46_[+1]_438 22733 9.6e-06 442_[+1]_42 3452 1.4e-05 480_[+1]_4 4260 1.8e-05 6_[+1]_478 8718 2e-05 116_[+1]_368 11195 3.6e-05 410_[+1]_74 33075 3.9e-05 263_[+1]_221 5066 4.2e-05 260_[+1]_224 7980 4.5e-05 290_[+1]_194 261894 4.5e-05 3_[+1]_481 9339 4.9e-05 141_[+1]_343 7469 5.2e-05 44_[+1]_440 10064 7e-05 39_[+1]_445 8584 8.6e-05 81_[+1]_403 268248 8.6e-05 370_[+1]_114 9497 0.0001 476_[+1]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=26 7692 ( 454) CTCCAACGCAACAGCA 1 2862 ( 480) CTTCACAGCAACAACA 1 2919 ( 454) CGCCACACCAAAAACA 1 5051 ( 104) CTCCACCGCACAATCA 1 23418 ( 480) ATCCACCGAACAAACA 1 6231 ( 447) TCACAACGCACAAGCA 1 22056 ( 211) CATCACCGTAACACCA 1 21722 ( 413) TTATACCGAACCAACA 1 2792 ( 257) CGCCACCACAGCGAAA 1 10948 ( 219) TTTCACCCAAACGACA 1 4650 ( 47) ACTCAACACAAAACCA 1 22733 ( 443) CTGCACAGCTCAACCA 1 3452 ( 481) CCTCTACCCACAACCA 1 4260 ( 7) TTCAACAACACAAACA 1 8718 ( 117) TTTCTAAGCAACACAA 1 11195 ( 411) CTTCACCAAAATACAA 1 33075 ( 264) TTTCAATGCAACGGCA 1 5066 ( 261) TACCAAAGAAGAAGAA 1 7980 ( 291) CGAGTACGAAACAACA 1 261894 ( 4) AAACACCGAAAAGAAA 1 9339 ( 142) CTACACCACTGAAGCC 1 7469 ( 45) CGATACCCCTGCACCA 1 10064 ( 40) CGCCACCAAAAAGAAC 1 8584 ( 82) TCATAAAGCTCCAACA 1 268248 ( 371) CGGCAACGCGGAAGAA 1 9497 ( 477) CGCATACGTAGCAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 13580 bayes= 9.55736 E= 3.4e-003 -115 133 -1134 14 -115 -58 20 72 8 59 -161 14 -173 174 -261 -128 173 -1134 -1134 -86 73 133 -1134 -1134 8 159 -1134 -286 -15 -58 139 -1134 27 142 -1134 -186 166 -1134 -261 -86 85 42 -3 -1134 97 101 -1134 -286 166 -1134 -29 -1134 85 23 -3 -286 8 167 -1134 -1134 185 -158 -1134 -1134 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 26 E= 3.4e-003 0.115385 0.576923 0.000000 0.307692 0.115385 0.153846 0.269231 0.461538 0.269231 0.346154 0.076923 0.307692 0.076923 0.769231 0.038462 0.115385 0.846154 0.000000 0.000000 0.153846 0.423077 0.576923 0.000000 0.000000 0.269231 0.692308 0.000000 0.038462 0.230769 0.153846 0.615385 0.000000 0.307692 0.615385 0.000000 0.076923 0.807692 0.000000 0.038462 0.153846 0.461538 0.307692 0.230769 0.000000 0.500000 0.461538 0.000000 0.038462 0.807692 0.000000 0.192308 0.000000 0.461538 0.269231 0.230769 0.038462 0.269231 0.730769 0.000000 0.000000 0.923077 0.076923 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][TG][CTA]CA[CA][CA][GA][CA]A[ACG][AC]A[ACG][CA]A -------------------------------------------------------------------------------- Time 8.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 22 llr = 247 E-value = 3.4e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 311::1531:11:32::21:: pos.-specific C :21:21:2::2::::3:1333 probability G 6375:7::8a:4715413147 matrix T :4:57:551:7535349454: bits 2.1 * 1.9 * 1.7 * 1.5 * * Relative 1.3 * * * * Entropy 1.1 * * ** * * * (16.2 bits) 0.8 ***** *** * * * 0.6 * ***** ***** * * 0.4 * *********** *** ** 0.2 * ******************* 0.0 --------------------- Multilevel GTGTTGATGGTTGTGGTTTGG consensus AG GC TA GTATT GCTC sequence AC C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 6231 323 9.73e-11 GATGATTGTT GGGTTGATGGTTGTGTTTCTG GTGGAATGGA 2862 75 2.57e-10 ATCCATCGTG GCGGTGATGGTTGTGTTGTGG CATGTTTCTT 22733 251 1.63e-08 AAGGTCCACG ATGTTGATGGTTGTTGTTTGC ATCAAGAAGC 21722 219 6.71e-08 TGAGGACCTA GTGTCGATGGTTGTACTTCGC GTTCACTCAG 5051 282 4.17e-07 GCAGGTGGGT GGAGTGAAGGTTGGTGTTTTG CTTGTTTGGT 6481 423 4.68e-07 GTAGGATGGG TTGGTGTTGGTGGAGCTATCG ACGCCAGAGA 7980 371 1.67e-06 ACACTCGAAG AGGGTGAAAGTGGTTGTCTTG CTCGACGTGA 2792 178 1.67e-06 TTATTTTGCC AAGTTGAAGGCGTAGCTGCCG ATCTAACACG 10064 326 2.45e-06 TCTGTCGGTG GAGGTCATGGTTGGATTTGTG GTGAGAGGAG 5066 146 3.23e-06 AACGACAGAG GGGGTATCGGATGTTGTACGG GCAGCTGCTG 262632 136 3.53e-06 TACGACGATC GTGTGATTGGTGTTGTTGTCG ACGCTCTCCG 3452 136 4.57e-06 TGCTTCCTTG AGAGCGTAGGTTGAGGTTGTC TTAAGTTTGC 7469 179 4.98e-06 AGCCTTCGCG ACGGCGTCGGCGTTGGTTTCC AAAGAGTACA 4260 439 5.41e-06 TGACCAGCGT CTGGTGATGGTAGATGTGAGG TGTAATACAG 268248 207 5.41e-06 AAGCTTTTTG GGTTTGTCGGTGGAATTGCCC TCCTAACTCT 9339 205 5.87e-06 GCATCCTCCG ATGTCAATGGTGTTACTACCG CCGAAGACGA 7692 387 6.37e-06 CCCGCCTCCT GTGTTCTCTGTTGATCTTCGC AATCCAGATT 10948 390 1.09e-05 TTGACACCGA ACGTCGTTGGCGTTGTGATGG AAGTCGAAGC 11195 345 1.18e-05 GTGTTCGATG GTATTGTTAGTTTGACTTTTG TTAGATATTC 4650 234 1.36e-05 TGTTGGACGC GGCTTGTTTGTGGCGTTGGTG GTTAGTTAGC 22056 96 2.49e-05 ACCTGATACC GCGGTGTATGATGTGTGCTTG CTGTACTTTC 8718 196 5.56e-05 AGTGAACAGC GACTTCAAGGCAGAGGTGAGG GAGGAAGAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6231 9.7e-11 322_[+2]_157 2862 2.6e-10 74_[+2]_405 22733 1.6e-08 250_[+2]_229 21722 6.7e-08 218_[+2]_261 5051 4.2e-07 281_[+2]_198 6481 4.7e-07 422_[+2]_57 7980 1.7e-06 370_[+2]_109 2792 1.7e-06 177_[+2]_302 10064 2.5e-06 325_[+2]_154 5066 3.2e-06 145_[+2]_334 262632 3.5e-06 135_[+2]_344 3452 4.6e-06 135_[+2]_344 7469 5e-06 178_[+2]_301 4260 5.4e-06 438_[+2]_41 268248 5.4e-06 206_[+2]_273 9339 5.9e-06 204_[+2]_275 7692 6.4e-06 386_[+2]_93 10948 1.1e-05 389_[+2]_90 11195 1.2e-05 344_[+2]_135 4650 1.4e-05 233_[+2]_246 22056 2.5e-05 95_[+2]_384 8718 5.6e-05 195_[+2]_284 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=22 6231 ( 323) GGGTTGATGGTTGTGTTTCTG 1 2862 ( 75) GCGGTGATGGTTGTGTTGTGG 1 22733 ( 251) ATGTTGATGGTTGTTGTTTGC 1 21722 ( 219) GTGTCGATGGTTGTACTTCGC 1 5051 ( 282) GGAGTGAAGGTTGGTGTTTTG 1 6481 ( 423) TTGGTGTTGGTGGAGCTATCG 1 7980 ( 371) AGGGTGAAAGTGGTTGTCTTG 1 2792 ( 178) AAGTTGAAGGCGTAGCTGCCG 1 10064 ( 326) GAGGTCATGGTTGGATTTGTG 1 5066 ( 146) GGGGTATCGGATGTTGTACGG 1 262632 ( 136) GTGTGATTGGTGTTGTTGTCG 1 3452 ( 136) AGAGCGTAGGTTGAGGTTGTC 1 7469 ( 179) ACGGCGTCGGCGTTGGTTTCC 1 4260 ( 439) CTGGTGATGGTAGATGTGAGG 1 268248 ( 207) GGTTTGTCGGTGGAATTGCCC 1 9339 ( 205) ATGTCAATGGTGTTACTACCG 1 7692 ( 387) GTGTTCTCTGTTGATCTTCGC 1 10948 ( 390) ACGTCGTTGGCGTTGTGATGG 1 11195 ( 345) GTATTGTTAGTTTGACTTTTG 1 4650 ( 234) GGCTTGTTTGTGGCGTTGGTG 1 22056 ( 96) GCGGTGTATGATGTGTGCTTG 1 8718 ( 196) GACTTCAAGGCAGAGGTGAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13440 bayes= 9.60806 E= 3.4e-002 32 -233 133 -262 -91 -34 44 38 -91 -134 163 -262 -1110 -1110 95 96 -1110 -2 -237 138 -91 -75 163 -1110 97 -1110 -1110 84 9 -34 -1110 96 -149 -1110 172 -104 -1110 -1110 209 -1110 -149 -34 -1110 138 -149 -1110 80 84 -1110 -1110 163 -4 32 -233 -78 84 -17 -1110 109 -4 -1110 25 63 38 -1110 -1110 -137 170 -49 -134 44 55 -149 47 -78 70 -1110 25 63 38 -1110 25 163 -1110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 22 E= 3.4e-002 0.318182 0.045455 0.590909 0.045455 0.136364 0.181818 0.318182 0.363636 0.136364 0.090909 0.727273 0.045455 0.000000 0.000000 0.454545 0.545455 0.000000 0.227273 0.045455 0.727273 0.136364 0.136364 0.727273 0.000000 0.500000 0.000000 0.000000 0.500000 0.272727 0.181818 0.000000 0.545455 0.090909 0.000000 0.772727 0.136364 0.000000 0.000000 1.000000 0.000000 0.090909 0.181818 0.000000 0.727273 0.090909 0.000000 0.409091 0.500000 0.000000 0.000000 0.727273 0.272727 0.318182 0.045455 0.136364 0.500000 0.227273 0.000000 0.500000 0.272727 0.000000 0.272727 0.363636 0.363636 0.000000 0.000000 0.090909 0.909091 0.181818 0.090909 0.318182 0.409091 0.090909 0.318182 0.136364 0.454545 0.000000 0.272727 0.363636 0.363636 0.000000 0.272727 0.727273 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA][TG]G[TG][TC]G[AT][TA]GGT[TG][GT][TA][GTA][GTC]T[TG][TC][GTC][GC] -------------------------------------------------------------------------------- Time 16.14 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 28 llr = 245 E-value = 3.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :93467:7257223:5 pos.-specific C ::4:11:13:1:1151 probability G a:2631a:45:76244 matrix T :121:1:21:21:51: bits 2.1 1.9 * * 1.7 * * 1.5 * * Relative 1.3 * * Entropy 1.1 ** * * (12.6 bits) 0.8 ** * * * * * 0.6 ** ***** **** ** 0.4 ** ***** **** ** 0.2 ** ************* 0.0 ---------------- Multilevel GACGAAGAGGAGGTCA consensus AAG CA AAGG sequence G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 261894 401 1.77e-08 TTGGAATCCG GAAGAAGACGAGGTGA GACGATTGTA 8584 480 7.10e-07 ATGTACGGTC GACGGAGACGTGGGCG AACTG 6231 352 1.23e-06 TGGTGGAATG GAGAAAGCCGAGGTGA TTGTAGCAAG 2792 457 2.34e-06 CGAAACCTTA GAAAGAGAGGATGACA GTCGCCGTCC 8718 217 2.98e-06 AGAGGTGAGG GAGGAAGAGGAGCTCC ATGGCTTACC 33075 315 3.77e-06 TTCGCATGTT GAAAAAGAGAAGTTCA GTTCGATAAA 2919 387 3.77e-06 ATTCATAGTG GACACAGAAAAGGAGA GATCGCTCTG 5066 226 5.97e-06 GGGGAACGTC GCCGAAGAGGAAGTCG GTTGATTGTC 4650 125 6.68e-06 GATATTTCAC GACGAGGTAGAGGCCA ACGATTGTGA 7980 97 7.45e-06 GATCGACTTG GACGGGGAGGAGACGG ATTCCATGCG 6481 102 8.31e-06 GATCGGATAT GATAGAGTGAAGATCG TACAACCATT 2862 293 1.03e-05 GCTGGTGTTG GAATGGGAGGAGGTGG GAGGCTTCCA 268248 158 1.55e-05 AGATGAAGTA GACGAAGAAACAATCG ATGCGTATAG 9497 437 2.08e-05 CAATCAACGA GACAAGGAGAAGCCGG AAATCATACG 10064 298 2.52e-05 TCTCTTTGTA GATGGCGAGGAAGGCG TCTCTGTCGG 262632 297 4.36e-05 ACTTCTTTTG GTGGAAGCCAAGGGGA GGTGTCACTC 9339 362 4.76e-05 GGAAGGGACT GAGGAAGTGATTGAGG GACTAATGAA 3452 52 4.76e-05 GTCATGTTTT GAAGAAGTCAAAGATA GCGCCATATG 4260 211 5.67e-05 CTTCCCCGGA GAGAGAGCGATAGACA TGGCTTTACT 11195 59 5.67e-05 AGTGATTGGA GGCAGAGACGAGGTTG TATCGTTGAC 7469 253 6.17e-05 ATTAGCCAGA GATGTAGAGGCGATGA AGGCAGAAGA 22733 194 6.17e-05 GATGAATGAC GACACAGTAAAGAAGA TCAACACAGT 10948 59 7.93e-05 GACGATTGTT GACGGCGAAAGGGGCA GGCCTACCTA 5051 231 1.28e-04 TGTTGGTACG GATGAAGACATGCTGT GGTTGTGGCT 7692 165 1.49e-04 TTTTTTTTTA GAAAAAAAAACGGGCG GGCGGGCGGG 22056 6 2.67e-04 TCACC GATGATGATGTTGTCA CAAATTCACT 23418 316 4.56e-04 TGTCATTCAA GAATATGGCGAGATCA AAAGCCGGTT 21722 201 1.12e-03 CCCTAAAATA TTGGAAGATGAGGACC TAGTGTCGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 261894 1.8e-08 400_[+3]_84 8584 7.1e-07 479_[+3]_5 6231 1.2e-06 351_[+3]_133 2792 2.3e-06 456_[+3]_28 8718 3e-06 216_[+3]_268 33075 3.8e-06 314_[+3]_170 2919 3.8e-06 386_[+3]_98 5066 6e-06 225_[+3]_259 4650 6.7e-06 124_[+3]_360 7980 7.5e-06 96_[+3]_388 6481 8.3e-06 101_[+3]_383 2862 1e-05 292_[+3]_192 268248 1.5e-05 157_[+3]_327 9497 2.1e-05 436_[+3]_48 10064 2.5e-05 297_[+3]_187 262632 4.4e-05 296_[+3]_188 9339 4.8e-05 361_[+3]_123 3452 4.8e-05 51_[+3]_433 4260 5.7e-05 210_[+3]_274 11195 5.7e-05 58_[+3]_426 7469 6.2e-05 252_[+3]_232 22733 6.2e-05 193_[+3]_291 10948 7.9e-05 58_[+3]_426 5051 0.00013 230_[+3]_254 7692 0.00015 164_[+3]_320 22056 0.00027 5_[+3]_479 23418 0.00046 315_[+3]_169 21722 0.0011 200_[+3]_284 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=28 261894 ( 401) GAAGAAGACGAGGTGA 1 8584 ( 480) GACGGAGACGTGGGCG 1 6231 ( 352) GAGAAAGCCGAGGTGA 1 2792 ( 457) GAAAGAGAGGATGACA 1 8718 ( 217) GAGGAAGAGGAGCTCC 1 33075 ( 315) GAAAAAGAGAAGTTCA 1 2919 ( 387) GACACAGAAAAGGAGA 1 5066 ( 226) GCCGAAGAGGAAGTCG 1 4650 ( 125) GACGAGGTAGAGGCCA 1 7980 ( 97) GACGGGGAGGAGACGG 1 6481 ( 102) GATAGAGTGAAGATCG 1 2862 ( 293) GAATGGGAGGAGGTGG 1 268248 ( 158) GACGAAGAAACAATCG 1 9497 ( 437) GACAAGGAGAAGCCGG 1 10064 ( 298) GATGGCGAGGAAGGCG 1 262632 ( 297) GTGGAAGCCAAGGGGA 1 9339 ( 362) GAGGAAGTGATTGAGG 1 3452 ( 52) GAAGAAGTCAAAGATA 1 4260 ( 211) GAGAGAGCGATAGACA 1 11195 ( 59) GGCAGAGACGAGGTTG 1 7469 ( 253) GATGTAGAGGCGATGA 1 22733 ( 194) GACACAGTAAAGAAGA 1 10948 ( 59) GACGGCGAAAGGGGCA 1 5051 ( 231) GATGAAGACATGCTGT 1 7692 ( 165) GAAAAAAAAACGGGCG 1 22056 ( 6) GATGATGATGTTGTCA 1 23418 ( 316) GAATATGGCGAGATCA 1 21722 ( 201) TTGGAAGATGAGGACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 13580 bayes= 8.91886 E= 3.4e+002 -1145 -1145 204 -297 175 -268 -271 -197 -3 64 -13 -65 48 -1145 128 -197 116 -168 45 -297 148 -168 -72 -197 -284 -1145 204 -1145 141 -110 -271 -65 -25 31 87 -197 86 -1145 119 -1145 141 -110 -271 -65 -52 -1145 160 -138 -25 -110 145 -297 -3 -110 -40 73 -1145 122 74 -197 97 -168 74 -297 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 28 E= 3.4e+002 0.000000 0.000000 0.964286 0.035714 0.857143 0.035714 0.035714 0.071429 0.250000 0.357143 0.214286 0.178571 0.357143 0.000000 0.571429 0.071429 0.571429 0.071429 0.321429 0.035714 0.714286 0.071429 0.142857 0.071429 0.035714 0.000000 0.964286 0.000000 0.678571 0.107143 0.035714 0.178571 0.214286 0.285714 0.428571 0.071429 0.464286 0.000000 0.535714 0.000000 0.678571 0.107143 0.035714 0.178571 0.178571 0.000000 0.714286 0.107143 0.214286 0.107143 0.642857 0.035714 0.250000 0.107143 0.178571 0.464286 0.000000 0.535714 0.392857 0.071429 0.500000 0.071429 0.392857 0.035714 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GA[CAG][GA][AG]AGA[GCA][GA]AG[GA][TA][CG][AG] -------------------------------------------------------------------------------- Time 23.93 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10064 5.79e-05 39_[+1(6.99e-05)]_209_\ [+3(9.33e-05)]_17_[+3(2.52e-05)]_12_[+2(2.45e-06)]_154 10948 7.24e-05 58_[+3(7.93e-05)]_144_\ [+1(6.44e-06)]_155_[+2(1.09e-05)]_90 11195 2.53e-04 58_[+3(5.67e-05)]_270_\ [+2(1.18e-05)]_45_[+1(3.57e-05)]_74 21722 4.68e-06 218_[+2(6.71e-08)]_173_\ [+1(4.22e-06)]_72 22056 2.54e-04 95_[+2(2.49e-05)]_94_[+1(3.79e-06)]_\ 274 22733 2.52e-07 193_[+3(6.17e-05)]_41_\ [+2(1.63e-08)]_171_[+1(9.59e-06)]_42 23418 2.83e-03 479_[+1(6.68e-07)]_5 261894 2.21e-05 3_[+1(4.51e-05)]_381_[+3(1.77e-08)]_\ 84 262632 8.01e-04 135_[+2(3.53e-06)]_140_\ [+3(4.36e-05)]_188 268248 9.01e-05 157_[+3(1.55e-05)]_33_\ [+2(5.41e-06)]_143_[+1(8.60e-05)]_114 2792 5.04e-07 177_[+2(1.67e-06)]_58_\ [+1(5.23e-06)]_184_[+3(2.34e-06)]_28 2862 4.67e-12 74_[+2(2.57e-10)]_197_\ [+3(1.03e-05)]_171_[+1(2.81e-08)]_5 2919 3.11e-05 386_[+3(3.77e-06)]_51_\ [+1(5.80e-07)]_31 33075 1.24e-03 263_[+1(3.86e-05)]_35_\ [+3(3.77e-06)]_170 3452 4.29e-05 51_[+3(4.76e-05)]_68_[+2(4.57e-06)]_\ 68_[+2(4.24e-05)]_235_[+1(1.40e-05)]_4 4260 7.29e-05 6_[+1(1.83e-05)]_188_[+3(5.67e-05)]_\ 212_[+2(5.41e-06)]_41 4650 1.11e-05 46_[+1(7.13e-06)]_62_[+3(6.68e-06)]_\ 93_[+2(1.36e-05)]_246 5051 8.10e-07 103_[+1(6.68e-07)]_162_\ [+2(4.17e-07)]_198 5066 1.34e-05 145_[+2(3.23e-06)]_59_\ [+3(5.97e-06)]_19_[+1(4.18e-05)]_224 6231 7.38e-12 322_[+2(9.73e-11)]_8_[+3(1.23e-06)]_\ 79_[+1(1.00e-06)]_38 6481 9.78e-05 101_[+3(8.31e-06)]_305_\ [+2(4.68e-07)]_57 7469 1.80e-04 44_[+1(5.24e-05)]_118_\ [+2(4.98e-06)]_53_[+3(6.17e-05)]_232 7692 2.61e-07 113_[+1(2.58e-05)]_257_\ [+2(6.37e-06)]_46_[+1(1.08e-08)]_31 7980 9.72e-06 96_[+3(7.45e-06)]_178_\ [+1(4.51e-05)]_64_[+2(1.67e-06)]_109 8584 5.92e-04 81_[+1(8.60e-05)]_382_\ [+3(7.10e-07)]_5 8718 4.60e-05 116_[+1(2.00e-05)]_63_\ [+2(5.56e-05)]_[+3(2.98e-06)]_268 9339 1.56e-04 141_[+1(4.86e-05)]_47_\ [+2(5.87e-06)]_136_[+3(4.76e-05)]_123 9497 1.63e-02 436_[+3(2.08e-05)]_48 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************