******************************************************************************** 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/321/321.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10096 1.0000 500 11101 1.0000 500 11487 1.0000 500 15605 1.0000 500 16372 1.0000 500 16501 1.0000 500 18530 1.0000 500 19837 1.0000 500 2010 1.0000 500 21309 1.0000 500 21727 1.0000 500 22308 1.0000 500 24303 1.0000 500 25878 1.0000 500 261161 1.0000 500 268616 1.0000 500 2837 1.0000 500 29771 1.0000 500 36563 1.0000 500 4320 1.0000 500 5119 1.0000 500 5557 1.0000 500 5689 1.0000 500 6517 1.0000 500 7180 1.0000 500 7796 1.0000 500 8004 1.0000 500 8439 1.0000 500 9270 1.0000 500 9471 1.0000 500 bd1757 1.0000 500 bd1758 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/321/321.seqs.fa -oc motifs/321 -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= 32 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= 16000 N= 32 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.255 C 0.231 G 0.239 T 0.275 Background letter frequencies (from dataset with add-one prior applied): A 0.255 C 0.231 G 0.239 T 0.275 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 19 llr = 223 E-value = 8.6e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1:11:1::6:2:5:63 pos.-specific C 993975793629:716 probability G ::2:::::1:::13:: matrix T :15:343114614:32 bits 2.1 1.9 * * 1.7 ** * * * 1.5 ** * * * Relative 1.3 ** * * * * Entropy 1.1 ** ** ** * * * (17.0 bits) 0.8 ** ***** * * * 0.6 ** ***** ******* 0.4 ** ************* 0.2 **************** 0.0 ---------------- Multilevel CCTCCCCCACTCACAC consensus C TTT CTA TGTA sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 2010 231 4.79e-09 TACTAATTAA CCCCCCTCACTCACAC GATGGCGCGT 21727 56 6.49e-09 CATGCAAGAA CCTCTCCCACTCTCAC CACCTCGACA 16501 439 7.06e-08 TTTGACACCC CCTCCCTCATTCTCTC CACTCAACAG 15605 439 7.06e-08 TTTGACACCC CCTCCCTCATTCTCTC CACTCAACAG 9471 457 9.38e-08 TCGCCTGTTT CCGCCTCCACACTCAC CCTCTTGGTT 5119 470 3.11e-07 CAAATACTGA CCTCTCTCCCTCTCTC GTCAACAGCA 11101 136 6.06e-07 GCCTCTCCCT CCTCCTCCTCCCACAA TCCATCCTAC 29771 158 7.43e-07 ACATCGTCAA CCTCTCCCACACACTT GCAAATCCAT bd1757 388 1.11e-06 GACGTCAGGT CTCCCCCCACTCTGAA CAAGCTGATC 16372 470 2.11e-06 CACACTTCTT CCCCCTCCCTCCACCA GTACAAAGTA 22308 355 2.29e-06 CGCTAATGCT ACCCTTTCATTCACAC CAATACGAAG 8439 290 2.71e-06 AGGTAGACCA CCGCCACCACACTGAC AGTCTCCCAC 2837 366 3.18e-06 AATACCATAC CCTCCTCTATTCAGTA ACACAGGTCG 10096 271 4.70e-06 CTAACTAGTA CCCCCCCCCTCCGGTC CTCTGAAAAC 11487 474 5.44e-06 AATACGCACG CTTCTCCCCCTCAGAT GAAGATACAT 268616 442 6.27e-06 CTGTTGGCAG ACGCTTCCACACACAA CACACCACCA 5557 363 7.24e-06 CAGTTCATAT CCACCCCCGTTCACCC TCTGGTGTTG bd1758 433 2.18e-05 CCTCGTCTCG CCTCCTCTCCTTTCAT AATGCACAAT 6517 461 2.55e-05 TAGACTACTG CCCACTTCTTCCAGAC ATCACAACAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2010 4.8e-09 230_[+1]_254 21727 6.5e-09 55_[+1]_429 16501 7.1e-08 438_[+1]_46 15605 7.1e-08 438_[+1]_46 9471 9.4e-08 456_[+1]_28 5119 3.1e-07 469_[+1]_15 11101 6.1e-07 135_[+1]_349 29771 7.4e-07 157_[+1]_327 bd1757 1.1e-06 387_[+1]_97 16372 2.1e-06 469_[+1]_15 22308 2.3e-06 354_[+1]_130 8439 2.7e-06 289_[+1]_195 2837 3.2e-06 365_[+1]_119 10096 4.7e-06 270_[+1]_214 11487 5.4e-06 473_[+1]_11 268616 6.3e-06 441_[+1]_43 5557 7.2e-06 362_[+1]_122 bd1758 2.2e-05 432_[+1]_52 6517 2.6e-05 460_[+1]_24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=19 2010 ( 231) CCCCCCTCACTCACAC 1 21727 ( 56) CCTCTCCCACTCTCAC 1 16501 ( 439) CCTCCCTCATTCTCTC 1 15605 ( 439) CCTCCCTCATTCTCTC 1 9471 ( 457) CCGCCTCCACACTCAC 1 5119 ( 470) CCTCTCTCCCTCTCTC 1 11101 ( 136) CCTCCTCCTCCCACAA 1 29771 ( 158) CCTCTCCCACACACTT 1 bd1757 ( 388) CTCCCCCCACTCTGAA 1 16372 ( 470) CCCCCTCCCTCCACCA 1 22308 ( 355) ACCCTTTCATTCACAC 1 8439 ( 290) CCGCCACCACACTGAC 1 2837 ( 366) CCTCCTCTATTCAGTA 1 10096 ( 271) CCCCCCCCCTCCGGTC 1 11487 ( 474) CTTCTCCCCCTCAGAT 1 268616 ( 442) ACGCTTCCACACACAA 1 5557 ( 363) CCACCCCCGTTCACCC 1 bd1758 ( 433) CCTCCTCTCCTTTCAT 1 6517 ( 461) CCCACTTCTTCCAGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 15520 bayes= 10.5704 E= 8.6e-008 -128 195 -1089 -1089 -1089 195 -1089 -138 -227 45 -60 78 -227 203 -1089 -1089 -1089 157 -1089 20 -227 119 -1089 61 -1089 157 -1089 20 -1089 195 -1089 -138 118 19 -218 -138 -1089 132 -1089 61 -28 -13 -1089 107 -1089 203 -1089 -238 104 -1089 -218 61 -1089 157 40 -1089 118 -113 -1089 20 5 132 -1089 -80 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 19 E= 8.6e-008 0.105263 0.894737 0.000000 0.000000 0.000000 0.894737 0.000000 0.105263 0.052632 0.315789 0.157895 0.473684 0.052632 0.947368 0.000000 0.000000 0.000000 0.684211 0.000000 0.315789 0.052632 0.526316 0.000000 0.421053 0.000000 0.684211 0.000000 0.315789 0.000000 0.894737 0.000000 0.105263 0.578947 0.263158 0.052632 0.105263 0.000000 0.578947 0.000000 0.421053 0.210526 0.210526 0.000000 0.578947 0.000000 0.947368 0.000000 0.052632 0.526316 0.000000 0.052632 0.421053 0.000000 0.684211 0.315789 0.000000 0.578947 0.105263 0.000000 0.315789 0.263158 0.578947 0.000000 0.157895 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CC[TC]C[CT][CT][CT]C[AC][CT][TAC]C[AT][CG][AT][CA] -------------------------------------------------------------------------------- Time 9.23 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 17 llr = 235 E-value = 4.2e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :2:24132:3:18:1885176 pos.-specific C 6564162:93:9::9:228:4 probability G 112:::2:142::1::1212: matrix T 42245228::8:29:2:111: bits 2.1 1.9 1.7 * * * 1.5 * * * Relative 1.3 * ****** Entropy 1.1 ** ******* * (19.9 bits) 0.8 * * ** ******* *** 0.6 * * ** ** ******* *** 0.4 ****** ********** *** 0.2 ****** ************** 0.0 --------------------- Multilevel CCCTTCATCGTCATCAAACAA consensus TTTCATCA A C GC sequence A G C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 16501 268 2.83e-10 CCATGCCACG CCCTTCTTCGTCATCTAACAA CGATGCAATT 15605 268 2.83e-10 CCATGCCACG CCCTTCTTCGTCATCTAACAA CGATGCAATT 24303 4 1.14e-08 ATT CTCATCGTCGTCATCAATCGA AGACGTGATG 21727 108 3.22e-08 TACCCAACGG TCCAACTTCGGCTTCAAACAC ATATCCCTCG 16372 433 3.99e-08 GTCTGTCACC CTCCTCCACATCAGCAACCAA CCGACTCACA 6517 157 8.99e-08 GTCGTCAGGA TTGCAAATCCTCATCAACCAA TACAAACCTC 21309 274 1.09e-07 AATCTCTTGG CCCTATGTGGTCTTCAAACAA CACCAAGATG 4320 85 1.31e-07 TGCCCGTCTT CGCATCCTCCTCATCAAAGGA AGAGCGAATG bd1757 475 2.45e-07 AAAATCCTCT CCTCTCATCATAATCACGCAC CAACA 29771 414 2.45e-07 GGACTATTGA TCCTTCCTCCTCTTCAAATGC TTCTGCTTCG 36563 417 2.67e-07 TGTCACCGCA TTTTTCTTCATCATCAGGCAA GCCGGTCCAA 11487 234 3.16e-07 CCTACATGCA CATCATCACATCATCAATCAC CAACTGATGC 19837 347 8.08e-07 TGCGGTGAAA GAGTACATCGGCAGCAAACAA ATAAGAGTTG 11101 76 1.16e-06 CAGTCCATCT CATCATGACATCATCAACCTA CCATTGCCGT 25878 451 1.24e-06 ATTTCCATTC TCGTCAGACCTCATCAAACGC CAACACATCT 8439 395 1.52e-06 AATAATCCTC TCCATCATCGTCATAACCAAC CTCGCCTCCT bd1758 390 1.62e-06 CAACACGCTC CCCCATATCCGCATCTCGGAC TCATCGTCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 16501 2.8e-10 267_[+2]_212 15605 2.8e-10 267_[+2]_212 24303 1.1e-08 3_[+2]_476 21727 3.2e-08 107_[+2]_372 16372 4e-08 432_[+2]_47 6517 9e-08 156_[+2]_323 21309 1.1e-07 273_[+2]_206 4320 1.3e-07 84_[+2]_395 bd1757 2.5e-07 474_[+2]_5 29771 2.5e-07 413_[+2]_66 36563 2.7e-07 416_[+2]_63 11487 3.2e-07 233_[+2]_246 19837 8.1e-07 346_[+2]_133 11101 1.2e-06 75_[+2]_404 25878 1.2e-06 450_[+2]_29 8439 1.5e-06 394_[+2]_85 bd1758 1.6e-06 389_[+2]_90 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=17 16501 ( 268) CCCTTCTTCGTCATCTAACAA 1 15605 ( 268) CCCTTCTTCGTCATCTAACAA 1 24303 ( 4) CTCATCGTCGTCATCAATCGA 1 21727 ( 108) TCCAACTTCGGCTTCAAACAC 1 16372 ( 433) CTCCTCCACATCAGCAACCAA 1 6517 ( 157) TTGCAAATCCTCATCAACCAA 1 21309 ( 274) CCCTATGTGGTCTTCAAACAA 1 4320 ( 85) CGCATCCTCCTCATCAAAGGA 1 bd1757 ( 475) CCTCTCATCATAATCACGCAC 1 29771 ( 414) TCCTTCCTCCTCTTCAAATGC 1 36563 ( 417) TTTTTCTTCATCATCAGGCAA 1 11487 ( 234) CATCATCACATCATCAATCAC 1 19837 ( 347) GAGTACATCGGCAGCAAACAA 1 11101 ( 76) CATCATGACATCATCAACCTA 1 25878 ( 451) TCGTCAGACCTCATCAAACGC 1 8439 ( 395) TCCATCATCGTCATAACCAAC 1 bd1758 ( 390) CCCCATATCCGCATCTCGGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 15360 bayes= 10.6132 E= 4.2e-009 -1073 135 -202 36 -53 120 -202 -23 -1073 135 -44 -23 -12 61 -1073 58 69 -197 -1073 94 -112 148 -1073 -23 21 3 -2 -23 -12 -1073 -1073 147 -1073 203 -202 -1073 21 35 79 -1073 -1073 -1073 -44 158 -211 203 -1073 -1073 169 -1073 -1073 -64 -1073 -1073 -102 168 -211 203 -1073 -1073 169 -1073 -1073 -64 158 -39 -202 -1073 88 3 -44 -122 -211 173 -102 -222 147 -1073 -2 -222 121 83 -1073 -1073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 17 E= 4.2e-009 0.000000 0.588235 0.058824 0.352941 0.176471 0.529412 0.058824 0.235294 0.000000 0.588235 0.176471 0.235294 0.235294 0.352941 0.000000 0.411765 0.411765 0.058824 0.000000 0.529412 0.117647 0.647059 0.000000 0.235294 0.294118 0.235294 0.235294 0.235294 0.235294 0.000000 0.000000 0.764706 0.000000 0.941176 0.058824 0.000000 0.294118 0.294118 0.411765 0.000000 0.000000 0.000000 0.176471 0.823529 0.058824 0.941176 0.000000 0.000000 0.823529 0.000000 0.000000 0.176471 0.000000 0.000000 0.117647 0.882353 0.058824 0.941176 0.000000 0.000000 0.823529 0.000000 0.000000 0.176471 0.764706 0.176471 0.058824 0.000000 0.470588 0.235294 0.176471 0.117647 0.058824 0.764706 0.117647 0.058824 0.705882 0.000000 0.235294 0.058824 0.588235 0.411765 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT][CT][CT][TCA][TA][CT][ACGT][TA]C[GAC]TCATCAA[AC]C[AG][AC] -------------------------------------------------------------------------------- Time 17.61 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 32 llr = 291 E-value = 2.8e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 253:31621131:71: pos.-specific C ::2:41::1:::1::: probability G 7419334248439:2a matrix T 1:41:6164135:37: bits 2.1 1.9 * 1.7 * * 1.5 * * * Relative 1.3 * * * * Entropy 1.1 * * ** * (13.1 bits) 0.8 * * * * **** 0.6 ** * ** * **** 0.4 ** ************* 0.2 **************** 0.0 ---------------- Multilevel GATGCTATTGGTGATG consensus AGA AGGAG AG TG sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 5119 381 6.30e-07 GGCGTAAGAA GAAGATGATGATGATG AAGAAGAAGT 268616 51 6.30e-07 AATGGGTGAT GGAGCGATGGGAGATG GTACTGGTTC 5689 43 7.35e-07 TCTTCTTGTA GAGGGTATTGTGGATG GTTCAAGAGG 21727 229 1.76e-06 GTCTGTTTCG GATGCCATGGTTGTTG GTGTGAAGTG 261161 22 2.29e-06 GACGAGTATC GATGATTTTGATGATG ACAAGAAGTG 22308 189 2.97e-06 GGTACATCTC AGAGATATGGAAGATG CCGGATAACC 16372 134 3.78e-06 AGGGAGCACC GAAGATGAGGAGGAGG GGAAGTGGCG 8004 183 5.39e-06 ATGATGTGCG GGTGCTGTGTGTGTTG CGTCGGTGGG 5557 20 5.39e-06 TCTCATCGTC GACGCCATTGTTGTTG GAAAGAGCGA 24303 169 1.14e-05 CAAGAGCGAC GATGCAAAGGAGGAGG ACAAAAGTTG 7180 18 1.26e-05 ACGGATGGCA GAGGAGATGGGTGAAG TTGTGGTCTT 19837 61 1.26e-05 TGGGCGGTGG AGAGATAGGGAAGATG GAGGAGAGAG 11487 124 1.26e-05 GTGTAGTTGG GGTTCGATTGGTGTTG ATGCATTGCC 6517 276 1.70e-05 TGAAGAAGAT AGAGATGGTGTGGTTG CTCCAGATCT 21309 303 1.70e-05 AACACCAAGA TGTGATATCGGGGTTG AGTTTGTTTC bd1757 99 1.87e-05 GAGATCGGAT TACGACATGGTTGATG TATTGTGCAT 36563 37 1.87e-05 TCCCGCTAAT GATGGTAGTGTCGATG CTCGTTGTAC 16501 290 2.06e-05 ATCTAACAAC GATGCAATTGTTCATG GGTCGCTTCT 15605 290 2.06e-05 ATCTAACAAC GATGCAATTGTTCATG GGTCGCTTCT 18530 37 2.70e-05 GCTTGGCACT GGAGGGTTGGTGGAGG CACGAGGGAT 2837 90 2.95e-05 TACAACTCTC AGCTGTATTGGTGATG ATCACTCAGA 2010 405 3.83e-05 ATGGAGACGA TACGAGATAGGTGATG TTTCACTCGC 8439 120 4.17e-05 TTCCTTTGCT GGTGCTGTGAAGGTGG GTGGCAGAGG 29771 358 4.53e-05 CTTCAAGGGG AAAGGGGGCGGGGATG CCACGTCAAG 9471 233 6.79e-05 ATAATGCGGG GAGGGGGTTTGGGTTG TGGTCGCTCG 11101 347 6.79e-05 GTTCCATGTA GAGGGGAACGAGGAGG GAGATCCTGA 9270 440 7.33e-05 CAATCATGTT GGTGCTGAAGAGGAAG AGCGGCCCGA 25878 236 7.91e-05 GACGATGATG AGAACTGATGATGATG TTCGTCTTTT 10096 396 8.53e-05 ACTGCAGTAC AGAGGTAAGAGTGAGG CAGATTGTTT bd1758 63 1.06e-04 GTTCAAGATG GTTGATGTGTGTGTTG GTGCGTGATT 7796 375 1.14e-04 ATGAGGCTAT GCAGCTGGTGGAGAGG GGAGGCAACC 4320 206 2.11e-04 TGTAAACGTT TGCGCTGTTGTTGTTA ACGGTAGTGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5119 6.3e-07 380_[+3]_104 268616 6.3e-07 50_[+3]_434 5689 7.3e-07 42_[+3]_442 21727 1.8e-06 228_[+3]_256 261161 2.3e-06 21_[+3]_463 22308 3e-06 188_[+3]_296 16372 3.8e-06 133_[+3]_351 8004 5.4e-06 182_[+3]_302 5557 5.4e-06 19_[+3]_465 24303 1.1e-05 168_[+3]_316 7180 1.3e-05 17_[+3]_467 19837 1.3e-05 60_[+3]_424 11487 1.3e-05 123_[+3]_361 6517 1.7e-05 275_[+3]_209 21309 1.7e-05 302_[+3]_182 bd1757 1.9e-05 98_[+3]_386 36563 1.9e-05 36_[+3]_448 16501 2.1e-05 289_[+3]_195 15605 2.1e-05 289_[+3]_195 18530 2.7e-05 36_[+3]_448 2837 3e-05 89_[+3]_395 2010 3.8e-05 404_[+3]_80 8439 4.2e-05 119_[+3]_365 29771 4.5e-05 357_[+3]_127 9471 6.8e-05 232_[+3]_252 11101 6.8e-05 346_[+3]_138 9270 7.3e-05 439_[+3]_45 25878 7.9e-05 235_[+3]_249 10096 8.5e-05 395_[+3]_89 bd1758 0.00011 62_[+3]_422 7796 0.00011 374_[+3]_110 4320 0.00021 205_[+3]_279 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=32 5119 ( 381) GAAGATGATGATGATG 1 268616 ( 51) GGAGCGATGGGAGATG 1 5689 ( 43) GAGGGTATTGTGGATG 1 21727 ( 229) GATGCCATGGTTGTTG 1 261161 ( 22) GATGATTTTGATGATG 1 22308 ( 189) AGAGATATGGAAGATG 1 16372 ( 134) GAAGATGAGGAGGAGG 1 8004 ( 183) GGTGCTGTGTGTGTTG 1 5557 ( 20) GACGCCATTGTTGTTG 1 24303 ( 169) GATGCAAAGGAGGAGG 1 7180 ( 18) GAGGAGATGGGTGAAG 1 19837 ( 61) AGAGATAGGGAAGATG 1 11487 ( 124) GGTTCGATTGGTGTTG 1 6517 ( 276) AGAGATGGTGTGGTTG 1 21309 ( 303) TGTGATATCGGGGTTG 1 bd1757 ( 99) TACGACATGGTTGATG 1 36563 ( 37) GATGGTAGTGTCGATG 1 16501 ( 290) GATGCAATTGTTCATG 1 15605 ( 290) GATGCAATTGTTCATG 1 18530 ( 37) GGAGGGTTGGTGGAGG 1 2837 ( 90) AGCTGTATTGGTGATG 1 2010 ( 405) TACGAGATAGGTGATG 1 8439 ( 120) GGTGCTGTGAAGGTGG 1 29771 ( 358) AAAGGGGGCGGGGATG 1 9471 ( 233) GAGGGGGTTTGGGTTG 1 11101 ( 347) GAGGGGAACGAGGAGG 1 9270 ( 440) GGTGCTGAAGAGGAAG 1 25878 ( 236) AGAACTGATGATGATG 1 10096 ( 396) AGAGGTAAGAGTGAGG 1 bd1758 ( 63) GTTGATGTGTGTGTTG 1 7796 ( 375) GCAGCTGGTGGAGAGG 1 4320 ( 206) TGCGCTGTTGTTGTTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 15520 bayes= 8.91886 E= 2.8e-006 -22 -1164 146 -114 97 -288 87 -313 43 -56 -93 45 -303 -1164 192 -214 43 81 7 -1164 -144 -130 7 103 114 -1164 65 -214 -22 -1164 -61 118 -203 -130 77 67 -203 -1164 182 -155 29 -1164 65 18 -103 -288 53 86 -1164 -189 197 -1164 143 -1164 -1164 18 -203 -1164 -13 139 -303 -1164 202 -1164 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 32 E= 2.8e-006 0.218750 0.000000 0.656250 0.125000 0.500000 0.031250 0.437500 0.031250 0.343750 0.156250 0.125000 0.375000 0.031250 0.000000 0.906250 0.062500 0.343750 0.406250 0.250000 0.000000 0.093750 0.093750 0.250000 0.562500 0.562500 0.000000 0.375000 0.062500 0.218750 0.000000 0.156250 0.625000 0.062500 0.093750 0.406250 0.437500 0.062500 0.000000 0.843750 0.093750 0.312500 0.000000 0.375000 0.312500 0.125000 0.031250 0.343750 0.500000 0.000000 0.062500 0.937500 0.000000 0.687500 0.000000 0.000000 0.312500 0.062500 0.000000 0.218750 0.718750 0.031250 0.000000 0.968750 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA][AG][TA]G[CAG][TG][AG][TA][TG]G[GAT][TG]G[AT][TG]G -------------------------------------------------------------------------------- Time 25.55 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10096 1.17e-03 270_[+1(4.70e-06)]_109_\ [+3(8.53e-05)]_89 11101 1.06e-06 75_[+2(1.16e-06)]_39_[+1(6.06e-07)]_\ 195_[+3(6.79e-05)]_101_[+2(9.58e-05)]_16 11487 5.30e-07 123_[+3(1.26e-05)]_94_\ [+2(3.16e-07)]_219_[+1(5.44e-06)]_11 15605 2.32e-11 267_[+2(2.83e-10)]_1_[+3(2.06e-05)]_\ 133_[+1(7.06e-08)]_46 16372 1.13e-08 133_[+3(3.78e-06)]_122_\ [+1(9.77e-05)]_145_[+2(3.99e-08)]_16_[+1(2.11e-06)]_15 16501 2.32e-11 267_[+2(2.83e-10)]_1_[+3(2.06e-05)]_\ 133_[+1(7.06e-08)]_46 18530 1.50e-01 36_[+3(2.70e-05)]_448 19837 2.27e-04 60_[+3(1.26e-05)]_270_\ [+2(8.08e-07)]_133 2010 2.46e-06 230_[+1(4.79e-09)]_158_\ [+3(3.83e-05)]_80 21309 1.29e-05 273_[+2(1.09e-07)]_8_[+3(1.70e-05)]_\ 182 21727 2.11e-11 55_[+1(6.49e-09)]_36_[+2(3.22e-08)]_\ 100_[+3(1.76e-06)]_117_[+1(3.98e-05)]_123 22308 8.04e-05 188_[+3(2.97e-06)]_150_\ [+1(2.29e-06)]_130 24303 4.11e-07 3_[+2(1.14e-08)]_144_[+3(1.14e-05)]_\ 316 25878 1.12e-03 235_[+3(7.91e-05)]_199_\ [+2(1.24e-06)]_29 261161 1.79e-02 21_[+3(2.29e-06)]_463 268616 8.30e-05 50_[+3(6.30e-07)]_375_\ [+1(6.27e-06)]_43 2837 8.01e-04 89_[+3(2.95e-05)]_260_\ [+1(3.18e-06)]_119 29771 2.20e-07 157_[+1(7.43e-07)]_184_\ [+3(4.53e-05)]_40_[+2(2.45e-07)]_66 36563 6.62e-05 36_[+3(1.87e-05)]_292_\ [+2(9.28e-05)]_51_[+2(2.67e-07)]_63 4320 2.16e-04 84_[+2(1.31e-07)]_395 5119 5.59e-07 380_[+3(6.30e-07)]_73_\ [+1(3.11e-07)]_15 5557 4.60e-04 19_[+3(5.39e-06)]_327_\ [+1(7.24e-06)]_122 5689 3.28e-03 42_[+3(7.35e-07)]_442 6517 8.96e-07 156_[+2(8.99e-08)]_98_\ [+3(1.70e-05)]_169_[+1(2.55e-05)]_24 7180 7.53e-02 17_[+3(1.26e-05)]_467 7796 2.18e-01 500 8004 5.04e-03 182_[+3(5.39e-06)]_302 8439 3.38e-06 119_[+3(4.17e-05)]_154_\ [+1(2.71e-06)]_89_[+2(1.52e-06)]_85 9270 1.10e-01 439_[+3(7.33e-05)]_45 9471 1.45e-04 232_[+3(6.79e-05)]_208_\ [+1(9.38e-08)]_28 bd1757 1.42e-07 98_[+3(1.87e-05)]_273_\ [+1(1.11e-06)]_71_[+2(2.45e-07)]_5 bd1758 5.11e-05 389_[+2(1.62e-06)]_22_\ [+1(2.18e-05)]_52 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************