******************************************************************************** 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/223/223.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 28833 1.0000 500 52248 1.0000 500 47595 1.0000 500 47765 1.0000 500 47856 1.0000 500 14712 1.0000 500 14735 1.0000 500 14924 1.0000 500 39914 1.0000 500 15952 1.0000 500 49586 1.0000 500 49952 1.0000 500 49994 1.0000 500 40844 1.0000 500 49998 1.0000 500 50000 1.0000 500 41031 1.0000 500 41231 1.0000 500 43813 1.0000 500 6231 1.0000 500 18735 1.0000 500 44196 1.0000 500 33571 1.0000 500 44221 1.0000 500 48335 1.0000 500 46975 1.0000 500 48852 1.0000 500 39996 1.0000 500 40842 1.0000 500 47579 1.0000 500 39838 1.0000 500 37827 1.0000 500 50388 1.0000 500 49816 1.0000 500 49148 1.0000 500 49996 1.0000 500 48068 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/223/223.seqs.fa -oc motifs/223 -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= 37 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= 18500 N= 37 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.259 C 0.250 G 0.235 T 0.256 Background letter frequencies (from dataset with add-one prior applied): A 0.259 C 0.250 G 0.235 T 0.256 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 8 llr = 169 E-value = 1.4e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A a:9:869889:95a:a::8:: pos.-specific C :a:a:3:11:a13:5:aa:3: probability G ::1:1111:1::1:::::3:a matrix T ::::1:::1:::1:5::::8: bits 2.1 * * * ** * 1.9 ** * * * *** * 1.7 ** * * * *** * 1.5 **** * *** * *** * Relative 1.3 **** * *** * ****** Entropy 1.0 **** * *** ******** (30.5 bits) 0.8 ***** ****** ******** 0.6 ************ ******** 0.4 ************ ******** 0.2 ********************* 0.0 --------------------- Multilevel ACACAAAAAACAAACACCATG consensus C C T GC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 49996 291 7.02e-13 GTGTAATAAA ACACAAAAAACAAATACCATG GAAACTCAAA 40842 287 7.02e-13 GTGTAATAAA ACACAAAAAACAAATACCATG GAAACTCAAA 50000 358 7.02e-13 GTGTAATAAA ACACAAAAAACAAATACCATG GAAACTCAAA 49998 279 7.02e-13 GTGTAATAAA ACACAAAAAACAAATACCATG GAAACTCAAA 47595 358 1.89e-10 TCACCTGTCA ACACACAGAACACACACCGTG TACACAAACA 39914 203 2.12e-09 ACACTCACTC ACACGCAACACCTACACCATG GTCCAATCGA 43813 195 2.56e-09 GGGAGAGTTC ACACTGGAAACACACACCGCG CGGGACGCGG 50388 15 5.18e-09 GATGGGCTCC ACGCAAACTGCAGACACCACG GAAGGGTCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49996 7e-13 290_[+1]_189 40842 7e-13 286_[+1]_193 50000 7e-13 357_[+1]_122 49998 7e-13 278_[+1]_201 47595 1.9e-10 357_[+1]_122 39914 2.1e-09 202_[+1]_277 43813 2.6e-09 194_[+1]_285 50388 5.2e-09 14_[+1]_465 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=8 49996 ( 291) ACACAAAAAACAAATACCATG 1 40842 ( 287) ACACAAAAAACAAATACCATG 1 50000 ( 358) ACACAAAAAACAAATACCATG 1 49998 ( 279) ACACAAAAAACAAATACCATG 1 47595 ( 358) ACACACAGAACACACACCGTG 1 39914 ( 203) ACACGCAACACCTACACCATG 1 43813 ( 195) ACACTGGAAACACACACCGCG 1 50388 ( 15) ACGCAAACTGCAGACACCACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 17760 bayes= 11.1157 E= 1.4e-010 195 -965 -965 -965 -965 200 -965 -965 175 -965 -91 -965 -965 200 -965 -965 153 -965 -91 -103 127 0 -91 -965 175 -965 -91 -965 153 -100 -91 -965 153 -100 -965 -103 175 -965 -91 -965 -965 200 -965 -965 175 -100 -965 -965 95 0 -91 -103 195 -965 -965 -965 -965 100 -965 97 195 -965 -965 -965 -965 200 -965 -965 -965 200 -965 -965 153 -965 9 -965 -965 0 -965 155 -965 -965 209 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 1.4e-010 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.125000 0.125000 0.625000 0.250000 0.125000 0.000000 0.875000 0.000000 0.125000 0.000000 0.750000 0.125000 0.125000 0.000000 0.750000 0.125000 0.000000 0.125000 0.875000 0.000000 0.125000 0.000000 0.000000 1.000000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.500000 0.250000 0.125000 0.125000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- ACACA[AC]AAAACA[AC]A[CT]ACC[AG][TC]G -------------------------------------------------------------------------------- Time 11.27 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 7 llr = 160 E-value = 1.5e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :3::1a::9:9:3::7::a:: pos.-specific C :7aa7:9::71a17:::::a9 probability G ::::1:1a11:::1::a:::: matrix T a::::::::1::61a3:a::1 bits 2.1 ** * * * * 1.9 * ** * * * * **** 1.7 * ** * * * * **** 1.5 * ** **** ** * ***** Relative 1.3 * ** **** ** * ***** Entropy 1.0 **** **** ** ******* (32.9 bits) 0.8 ************ ******** 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel TCCCCACGACACTCTAGTACC consensus A A T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 49996 152 2.64e-13 CGCCATATCC TCCCCACGACACTCTAGTACC AAAGGTACAG 40842 148 2.64e-13 CGCCATATCC TCCCCACGACACTCTAGTACC AAAGGTACAG 50000 219 2.64e-13 CGCCATATCC TCCCCACGACACTCTAGTACC AAAGGTACAG 49998 140 2.64e-13 CGCCATATCC TCCCCACGACACTCTAGTACC AAAGGTACAG 47856 464 2.11e-10 CGCTTTTTTT TACCCACGATACATTTGTACC CTCCACGAAT 44196 62 6.97e-10 CGTTAACTGG TACCGAGGACCCACTAGTACT GCTACAGGGT 47595 258 7.53e-10 CCAATCACGA TCCCAACGGGACCGTTGTACC CTGCCCTATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49996 2.6e-13 151_[+2]_328 40842 2.6e-13 147_[+2]_332 50000 2.6e-13 218_[+2]_261 49998 2.6e-13 139_[+2]_340 47856 2.1e-10 463_[+2]_16 44196 7e-10 61_[+2]_418 47595 7.5e-10 257_[+2]_222 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=7 49996 ( 152) TCCCCACGACACTCTAGTACC 1 40842 ( 148) TCCCCACGACACTCTAGTACC 1 50000 ( 219) TCCCCACGACACTCTAGTACC 1 49998 ( 140) TCCCCACGACACTCTAGTACC 1 47856 ( 464) TACCCACGATACATTTGTACC 1 44196 ( 62) TACCGAGGACCCACTAGTACT 1 47595 ( 258) TCCCAACGGGACCGTTGTACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 17760 bayes= 11.1522 E= 1.5e-011 -945 -945 -945 197 14 151 -945 -945 -945 200 -945 -945 -945 200 -945 -945 -86 151 -71 -945 194 -945 -945 -945 -945 177 -71 -945 -945 -945 209 -945 172 -945 -71 -945 -945 151 -71 -84 172 -81 -945 -945 -945 200 -945 -945 14 -81 -945 116 -945 151 -71 -84 -945 -945 -945 197 146 -945 -945 16 -945 -945 209 -945 -945 -945 -945 197 194 -945 -945 -945 -945 200 -945 -945 -945 177 -945 -84 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 1.5e-011 0.000000 0.000000 0.000000 1.000000 0.285714 0.714286 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.142857 0.714286 0.142857 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 0.714286 0.142857 0.142857 0.857143 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.142857 0.000000 0.571429 0.000000 0.714286 0.142857 0.142857 0.000000 0.000000 0.000000 1.000000 0.714286 0.000000 0.000000 0.285714 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.857143 0.000000 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[CA]CCCACGACAC[TA]CT[AT]GTACC -------------------------------------------------------------------------------- Time 22.57 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 7 llr = 153 E-value = 5.3e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :a:1371::1a191::9::: pos.-specific C ::1::3:::::9:::::::3 probability G ::6::::a:::::9::1a:: matrix T a:397:9:a9::1:aa::a7 bits 2.1 * * 1.9 ** ** * ** ** 1.7 ** ** * ** ** 1.5 ** * ****** ****** Relative 1.3 ** * ************* Entropy 1.0 ** ***************** (31.6 bits) 0.8 ** ***************** 0.6 ******************** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TAGTTATGTTACAGTTAGTT consensus T AC C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 49996 325 1.07e-12 ACTCAAAAGC TAGTTATGTTACAGTTAGTT AGCTATTGCC 40842 321 1.07e-12 ACTCAAAAGC TAGTTATGTTACAGTTAGTT AGCTATTGCC 50000 392 1.07e-12 ACTCAAAAGC TAGTTATGTTACAGTTAGTT AGCTATTGCC 49998 313 1.07e-12 ACTCAAAAGC TAGTTATGTTACAGTTAGTT AGCTATTGCC 49994 56 4.25e-10 TTACATTAGG TATTACAGTTACAGTTAGTC TTATGTTTTT 37827 240 5.55e-10 ATTGGTACAG TACTACTGTTACTGTTAGTC GCACGATAAT 47595 116 3.45e-09 TACCACAATA TATATATGTAAAAATTGGTT GTTTGGGAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49996 1.1e-12 324_[+3]_156 40842 1.1e-12 320_[+3]_160 50000 1.1e-12 391_[+3]_89 49998 1.1e-12 312_[+3]_168 49994 4.3e-10 55_[+3]_425 37827 5.5e-10 239_[+3]_241 47595 3.4e-09 115_[+3]_365 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=7 49996 ( 325) TAGTTATGTTACAGTTAGTT 1 40842 ( 321) TAGTTATGTTACAGTTAGTT 1 50000 ( 392) TAGTTATGTTACAGTTAGTT 1 49998 ( 313) TAGTTATGTTACAGTTAGTT 1 49994 ( 56) TATTACAGTTACAGTTAGTC 1 37827 ( 240) TACTACTGTTACTGTTAGTC 1 47595 ( 116) TATATATGTAAAAATTGGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 17797 bayes= 11.1552 E= 5.3e-010 -945 -945 -945 197 194 -945 -945 -945 -945 -81 128 16 -86 -945 -945 174 14 -945 -945 148 146 19 -945 -945 -86 -945 -945 174 -945 -945 209 -945 -945 -945 -945 197 -86 -945 -945 174 194 -945 -945 -945 -86 177 -945 -945 172 -945 -945 -84 -86 -945 187 -945 -945 -945 -945 197 -945 -945 -945 197 172 -945 -71 -945 -945 -945 209 -945 -945 -945 -945 197 -945 19 -945 148 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 7 E= 5.3e-010 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.142857 0.571429 0.285714 0.142857 0.000000 0.000000 0.857143 0.285714 0.000000 0.000000 0.714286 0.714286 0.285714 0.000000 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.142857 0.000000 0.000000 0.857143 1.000000 0.000000 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.857143 0.000000 0.000000 0.142857 0.142857 0.000000 0.857143 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.857143 0.000000 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.285714 0.000000 0.714286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TA[GT]T[TA][AC]TGTTACAGTTAGT[TC] -------------------------------------------------------------------------------- Time 34.48 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 28833 3.79e-01 500 52248 1.56e-01 238_[+2(6.47e-05)]_241 47595 5.60e-17 115_[+3(3.45e-09)]_122_\ [+2(7.53e-10)]_79_[+1(1.89e-10)]_122 47765 3.22e-01 500 47856 8.61e-07 138_[+3(8.74e-05)]_305_\ [+2(2.11e-10)]_16 14712 5.97e-01 500 14735 2.83e-02 326_[+1(7.31e-05)]_153 14924 6.05e-01 500 39914 5.08e-05 202_[+1(2.12e-09)]_277 15952 4.28e-01 500 49586 6.70e-01 500 49952 9.09e-01 500 49994 2.98e-06 55_[+3(4.25e-10)]_425 40844 5.80e-02 14_[+3(1.61e-05)]_466 49998 4.94e-26 139_[+2(2.64e-13)]_118_\ [+1(7.02e-13)]_13_[+3(1.07e-12)]_168 50000 4.94e-26 120_[+3(8.53e-05)]_78_\ [+2(2.64e-13)]_118_[+1(7.02e-13)]_13_[+3(1.07e-12)]_89 41031 4.26e-01 500 41231 2.29e-01 500 43813 2.36e-05 194_[+1(2.56e-09)]_285 6231 8.24e-02 277_[+3(3.05e-05)]_203 18735 6.30e-02 387_[+3(6.86e-05)]_93 44196 3.36e-06 61_[+2(6.97e-10)]_418 33571 3.27e-01 500 44221 8.33e-01 500 48335 9.90e-02 225_[+3(1.96e-05)]_255 46975 2.52e-01 500 48852 9.44e-01 500 39996 9.60e-01 500 40842 4.94e-26 147_[+2(2.64e-13)]_118_\ [+1(7.02e-13)]_13_[+3(1.07e-12)]_160 47579 3.01e-01 500 39838 8.03e-01 500 37827 7.44e-06 239_[+3(5.55e-10)]_9_[+3(6.70e-05)]_\ 212 50388 1.56e-04 14_[+1(5.18e-09)]_465 49816 6.59e-01 500 49148 7.51e-01 500 49996 4.94e-26 151_[+2(2.64e-13)]_118_\ [+1(7.02e-13)]_13_[+3(1.07e-12)]_156 48068 8.46e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************