******************************************************************************** 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/410/410.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42443 1.0000 500 42556 1.0000 500 3362 1.0000 500 36322 1.0000 500 3251 1.0000 500 37291 1.0000 500 43490 1.0000 500 10073 1.0000 500 10005 1.0000 500 10882 1.0000 500 6454 1.0000 500 10718 1.0000 500 10781 1.0000 500 34965 1.0000 500 54411 1.0000 500 45596 1.0000 500 20342 1.0000 500 46029 1.0000 500 35958 1.0000 500 32688 1.0000 500 46282 1.0000 500 42670 1.0000 500 41507 1.0000 500 41577 1.0000 500 44279 1.0000 500 32588 1.0000 500 46796 1.0000 500 47047 1.0000 500 45542 1.0000 500 14251 1.0000 500 46164 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/410/410.seqs.fa -oc motifs/410 -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= 31 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= 15500 N= 31 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.254 C 0.254 G 0.236 T 0.256 Background letter frequencies (from dataset with add-one prior applied): A 0.254 C 0.254 G 0.236 T 0.256 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 6 llr = 117 E-value = 8.7e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 27:::a:5:::8::32:a3: pos.-specific C ::5:::a:::::a3::::2: probability G 82::a:::a27:::528:5: matrix T :25a:::5:832:7272::a bits 2.1 * * 1.9 **** * * * * 1.7 **** * * * * 1.5 * **** * * ** * Relative 1.3 * **** ** ** ** * Entropy 1.0 * ************ ** * (28.2 bits) 0.8 ************** *** * 0.6 ******************** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel GACTGACAGTGACTGTGAGT consensus T T T CA A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 47047 271 3.35e-11 TGTGACGGAT GACTGACAGTGACCATGAGT GAGCGCGCTA 20342 99 5.28e-11 AGGTTTCTCC GTCTGACAGTGACTGTGAGT CATGTGTAAA 54411 351 2.40e-10 TACACTGGGA GACTGACAGTTACCATGAAT TTACATTACT 43490 287 9.06e-10 AGATTGGGAA AATTGACTGTGACTGGGAAT AAGCGAACGA 37291 125 3.04e-09 GTTGCGATTG GGTTGACTGTTTCTGTGACT GTGCGTTTCC 32688 155 5.48e-09 GGTAGAATCT GATTGACTGGGACTTATAGT ATTGTCGGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47047 3.3e-11 270_[+1]_210 20342 5.3e-11 98_[+1]_382 54411 2.4e-10 350_[+1]_130 43490 9.1e-10 286_[+1]_194 37291 3e-09 124_[+1]_356 32688 5.5e-09 154_[+1]_326 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=6 47047 ( 271) GACTGACAGTGACCATGAGT 1 20342 ( 99) GTCTGACAGTGACTGTGAGT 1 54411 ( 351) GACTGACAGTTACCATGAAT 1 43490 ( 287) AATTGACTGTGACTGGGAAT 1 37291 ( 125) GGTTGACTGTTTCTGTGACT 1 32688 ( 155) GATTGACTGGGACTTATAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 14911 bayes= 10.9374 E= 8.7e-001 -61 -923 182 -923 139 -923 -50 -62 -923 98 -923 96 -923 -923 -923 196 -923 -923 208 -923 197 -923 -923 -923 -923 198 -923 -923 97 -923 -923 96 -923 -923 208 -923 -923 -923 -50 170 -923 -923 150 38 171 -923 -923 -62 -923 198 -923 -923 -923 39 -923 138 39 -923 108 -62 -61 -923 -50 138 -923 -923 182 -62 197 -923 -923 -923 39 -61 108 -923 -923 -923 -923 196 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 8.7e-001 0.166667 0.000000 0.833333 0.000000 0.666667 0.000000 0.166667 0.166667 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.666667 0.333333 0.833333 0.000000 0.000000 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 0.333333 0.000000 0.500000 0.166667 0.166667 0.000000 0.166667 0.666667 0.000000 0.000000 0.833333 0.166667 1.000000 0.000000 0.000000 0.000000 0.333333 0.166667 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GA[CT]TGAC[AT]GT[GT]AC[TC][GA]TGA[GA]T -------------------------------------------------------------------------------- Time 8.39 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 6 llr = 117 E-value = 2.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::::3832:25:::::2:2: pos.-specific C ::a2:::2::2:738::::77 probability G a::88:258:223::a:7a23 matrix T :a::27:::a53:72:a2::: bits 2.1 * * * 1.9 *** * ** * 1.7 *** * ** * 1.5 ***** ** ** * Relative 1.3 ***** * ** *** * Entropy 1.0 ******* ** ***** * * (28.2 bits) 0.8 ******* ** ********* 0.6 ********** ********** 0.4 ********** ********** 0.2 ********************* 0.0 --------------------- Multilevel GTCGGTAGGTTACTCGTGGCC consensus A A TGC G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 41577 107 5.70e-13 TCAGGGTCTT GTCGGTAAGTTACTCGTGGCC TCCCTACTTC 41507 107 5.70e-13 TCAGGGTCTT GTCGGTAAGTTACTCGTGGCC TCCCTACTTC 46029 172 4.56e-10 ATAAAAGTTG GTCGGTAGGTTTCCTGTGGAC CGATAGTGAT 3362 416 2.28e-09 TCCGAATCGA GTCGGAAGATGTGCCGTGGCG ACACGATTCT 37291 244 7.36e-09 CCACCAATCC GTCCGTGGGTCGCTCGTAGCG CAGCCGATCA 45542 80 1.01e-08 TTTAAACGTT GTCGTAACGTAAGTCGTTGGC AAAGCTCGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 41577 5.7e-13 106_[+2]_373 41507 5.7e-13 106_[+2]_373 46029 4.6e-10 171_[+2]_308 3362 2.3e-09 415_[+2]_64 37291 7.4e-09 243_[+2]_236 45542 1e-08 79_[+2]_400 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=6 41577 ( 107) GTCGGTAAGTTACTCGTGGCC 1 41507 ( 107) GTCGGTAAGTTACTCGTGGCC 1 46029 ( 172) GTCGGTAGGTTTCCTGTGGAC 1 3362 ( 416) GTCGGAAGATGTGCCGTGGCG 1 37291 ( 244) GTCCGTGGGTCGCTCGTAGCG 1 45542 ( 80) GTCGTAACGTAAGTCGTTGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14880 bayes= 11.7232 E= 2.0e+000 -923 -923 208 -923 -923 -923 -923 196 -923 198 -923 -923 -923 -61 182 -923 -923 -923 182 -62 39 -923 -923 138 171 -923 -50 -923 39 -61 108 -923 -61 -923 182 -923 -923 -923 -923 196 -61 -61 -50 96 97 -923 -50 38 -923 139 50 -923 -923 39 -923 138 -923 171 -923 -62 -923 -923 208 -923 -923 -923 -923 196 -61 -923 150 -62 -923 -923 208 -923 -61 139 -50 -923 -923 139 50 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 2.0e+000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 0.833333 0.166667 0.333333 0.000000 0.000000 0.666667 0.833333 0.000000 0.166667 0.000000 0.333333 0.166667 0.500000 0.000000 0.166667 0.000000 0.833333 0.000000 0.000000 0.000000 0.000000 1.000000 0.166667 0.166667 0.166667 0.500000 0.500000 0.000000 0.166667 0.333333 0.000000 0.666667 0.333333 0.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.833333 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.166667 0.000000 0.666667 0.166667 0.000000 0.000000 1.000000 0.000000 0.166667 0.666667 0.166667 0.000000 0.000000 0.666667 0.333333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GTCGG[TA]A[GA]GTT[AT][CG][TC]CGTGGC[CG] -------------------------------------------------------------------------------- Time 16.93 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 11 llr = 168 E-value = 4.9e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 76:55:864a9176479:952 pos.-specific C ::a337:45::8::33:5:27 probability G 1::3:3::::1:32:::412: matrix T 24::2:2:1::1:24:11:11 bits 2.1 1.9 * * 1.7 * * 1.5 * ** * * Relative 1.3 * ** ** * * * Entropy 1.0 ** *** **** ** * (22.0 bits) 0.8 *** *** **** ** * * 0.6 *** ********** **** * 0.4 ******************* * 0.2 ********************* 0.0 --------------------- Multilevel AACAACAACAACAAAAACAAC consensus T CCG CA G TC G sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 44279 130 6.41e-11 CAACGGGTCC AACGCCAACAACAACAACAAC GCGGCACCCT 10882 177 2.70e-10 TACAAACAGC AACAACAACAATAATAACAAC AAGTTACATC 32688 471 9.01e-10 ACCGGAAGGC AACCACAACAACGACAACACC CTGCTGACC 10781 156 2.01e-09 CAACATTCCG AACAACAACAGCAGTAACAAC CATCAATCTT 34965 299 8.17e-08 GATCAAAGCA ATCGCGACTAACAATAAGAGC GCGACTGGAC 36322 327 1.11e-07 AGTCGGACCA GTCAACTAAAACAAACACAAA GTGTTCTTTC 46029 62 2.08e-07 CTCCAGAGCG TACCACACAAACATACACACA TATACAAACG 20342 300 2.08e-07 GTGACGGATG TACCTCTACAACGAAAAGATC TTCCCCGGCA 45542 394 2.87e-07 CCGTCAAGAA AACACGAAAAACAGAATGAAT GGGATTCTGT 10005 375 2.87e-07 GAGTTCCAAT ATCATGACCAAAAATAAGGAC GATGAAAAGG 45596 459 3.89e-07 ACCCTCACGC ATCGACACAAACGTCCATAGC GCCTTTTTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44279 6.4e-11 129_[+3]_350 10882 2.7e-10 176_[+3]_303 32688 9e-10 470_[+3]_9 10781 2e-09 155_[+3]_324 34965 8.2e-08 298_[+3]_181 36322 1.1e-07 326_[+3]_153 46029 2.1e-07 61_[+3]_418 20342 2.1e-07 299_[+3]_180 45542 2.9e-07 393_[+3]_86 10005 2.9e-07 374_[+3]_105 45596 3.9e-07 458_[+3]_21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=11 44279 ( 130) AACGCCAACAACAACAACAAC 1 10882 ( 177) AACAACAACAATAATAACAAC 1 32688 ( 471) AACCACAACAACGACAACACC 1 10781 ( 156) AACAACAACAGCAGTAACAAC 1 34965 ( 299) ATCGCGACTAACAATAAGAGC 1 36322 ( 327) GTCAACTAAAACAAACACAAA 1 46029 ( 62) TACCACACAAACATACACACA 1 20342 ( 300) TACCTCTACAACGAAAAGATC 1 45542 ( 394) AACACGAAAAACAGAATGAAT 1 10005 ( 375) ATCATGACCAAAAATAAGGAC 1 45596 ( 459) ATCGACACAAACGTCCATAGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14880 bayes= 11.4276 E= 4.9e+000 151 -1010 -137 -49 132 -1010 -1010 50 -1010 198 -1010 -1010 84 10 21 -1010 110 10 -1010 -49 -1010 152 21 -1010 168 -1010 -1010 -49 132 52 -1010 -1010 51 110 -1010 -149 197 -1010 -1010 -1010 184 -1010 -137 -1010 -148 169 -1010 -149 151 -1010 21 -1010 132 -1010 -37 -49 51 10 -1010 50 151 10 -1010 -1010 184 -1010 -1010 -149 -1010 110 63 -149 184 -1010 -137 -1010 110 -48 -37 -149 -48 152 -1010 -149 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 11 E= 4.9e+000 0.727273 0.000000 0.090909 0.181818 0.636364 0.000000 0.000000 0.363636 0.000000 1.000000 0.000000 0.000000 0.454545 0.272727 0.272727 0.000000 0.545455 0.272727 0.000000 0.181818 0.000000 0.727273 0.272727 0.000000 0.818182 0.000000 0.000000 0.181818 0.636364 0.363636 0.000000 0.000000 0.363636 0.545455 0.000000 0.090909 1.000000 0.000000 0.000000 0.000000 0.909091 0.000000 0.090909 0.000000 0.090909 0.818182 0.000000 0.090909 0.727273 0.000000 0.272727 0.000000 0.636364 0.000000 0.181818 0.181818 0.363636 0.272727 0.000000 0.363636 0.727273 0.272727 0.000000 0.000000 0.909091 0.000000 0.000000 0.090909 0.000000 0.545455 0.363636 0.090909 0.909091 0.000000 0.090909 0.000000 0.545455 0.181818 0.181818 0.090909 0.181818 0.727273 0.000000 0.090909 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- A[AT]C[ACG][AC][CG]A[AC][CA]AAC[AG]A[ATC][AC]A[CG]AAC -------------------------------------------------------------------------------- Time 25.19 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42443 9.32e-01 500 42556 3.61e-01 500 3362 6.81e-05 415_[+2(2.28e-09)]_64 36322 5.87e-04 326_[+3(1.11e-07)]_153 3251 2.25e-01 161_[+1(5.53e-05)]_319 37291 1.75e-09 124_[+1(3.04e-09)]_99_\ [+2(7.36e-09)]_236 43490 9.70e-06 286_[+1(9.06e-10)]_194 10073 1.90e-01 500 10005 1.10e-03 374_[+3(2.87e-07)]_105 10882 5.51e-07 13_[+1(7.56e-05)]_143_\ [+3(2.70e-10)]_279_[+3(8.22e-05)]_3 6454 8.44e-01 500 10718 1.98e-01 500 10781 1.57e-05 98_[+3(9.75e-06)]_36_[+3(2.01e-09)]_\ 324 34965 9.93e-04 298_[+3(8.17e-08)]_181 54411 1.19e-05 350_[+1(2.40e-10)]_130 45596 3.98e-03 458_[+3(3.89e-07)]_21 20342 8.58e-10 98_[+1(5.28e-11)]_181_\ [+3(2.08e-07)]_62_[+1(5.53e-06)]_98 46029 6.57e-10 61_[+3(2.08e-07)]_89_[+2(4.56e-10)]_\ 308 35958 8.46e-01 500 32688 2.56e-11 121_[+2(9.58e-05)]_12_\ [+1(5.48e-09)]_296_[+3(9.01e-10)]_9 46282 6.59e-01 500 42670 7.46e-01 500 41507 9.54e-09 106_[+2(5.70e-13)]_373 41577 9.01e-09 106_[+2(5.70e-13)]_373 44279 6.57e-07 129_[+3(6.41e-11)]_350 32588 1.40e-01 65_[+2(4.59e-05)]_414 46796 5.24e-01 500 47047 1.76e-06 270_[+1(3.35e-11)]_210 45542 1.28e-07 79_[+2(1.01e-08)]_293_\ [+3(2.87e-07)]_8_[+3(7.21e-05)]_57 14251 2.77e-01 500 46164 3.70e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************