******************************************************************************** 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/203/203.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42428 1.0000 500 41659 1.0000 500 17628 1.0000 500 9143 1.0000 500 46371 1.0000 500 46453 1.0000 500 36970 1.0000 500 46999 1.0000 500 47017 1.0000 500 37341 1.0000 500 47357 1.0000 500 47613 1.0000 500 2607 1.0000 500 22703 1.0000 500 7634 1.0000 500 15863 1.0000 500 49502 1.0000 500 49514 1.0000 500 49908 1.0000 500 3262 1.0000 500 33731 1.0000 500 44645 1.0000 500 11145 1.0000 500 12312 1.0000 500 50053 1.0000 500 46452 1.0000 500 46888 1.0000 500 37363 1.0000 500 40235 1.0000 500 38548 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/203/203.seqs.fa -oc motifs/203 -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= 30 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= 15000 N= 30 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.270 G 0.230 T 0.241 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.270 G 0.230 T 0.241 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 8 llr = 104 E-value = 3.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1::::a:1:1:9 pos.-specific C ::::::a3:::: probability G :8::9::1a:6: matrix T 93aa1::5:941 bits 2.1 ** * 1.9 ** ** * 1.7 ** ** * 1.5 * ***** ** * Relative 1.3 ******* ** * Entropy 1.1 ******* **** (18.7 bits) 0.8 ******* **** 0.6 ******* **** 0.4 ******* **** 0.2 ************ 0.0 ------------ Multilevel TGTTGACTGTGA consensus T C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 49502 370 4.09e-08 AGATTCTCGT TGTTGACTGTGA AGGTTGGATG 3262 19 1.30e-07 CTCTGTCTGG TGTTGACCGTGA GTGCTTCCAT 40235 169 1.72e-07 TGGACCCAAT TTTTGACTGTGA GGAAAAAGGT 46452 180 2.11e-07 TCAAATTTTG TGTTGACGGTGA CGGAACTGCC 47613 12 6.51e-07 ATTTCACAGC AGTTGACTGTGA ACACTTTACC 49908 459 1.54e-06 TCACGACCAG TGTTGACCGTTT TTATTTTCTC 46999 237 2.05e-06 CAGCTGTTAT TTTTTACTGTTA GTCTTTTTTT 36970 331 2.96e-06 GCAATCAGTG TGTTGACAGATA TGCGGCAAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49502 4.1e-08 369_[+1]_119 3262 1.3e-07 18_[+1]_470 40235 1.7e-07 168_[+1]_320 46452 2.1e-07 179_[+1]_309 47613 6.5e-07 11_[+1]_477 49908 1.5e-06 458_[+1]_30 46999 2e-06 236_[+1]_252 36970 3e-06 330_[+1]_158 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=8 49502 ( 370) TGTTGACTGTGA 1 3262 ( 19) TGTTGACCGTGA 1 40235 ( 169) TTTTGACTGTGA 1 46452 ( 180) TGTTGACGGTGA 1 47613 ( 12) AGTTGACTGTGA 1 49908 ( 459) TGTTGACCGTTT 1 46999 ( 237) TTTTTACTGTTA 1 36970 ( 331) TGTTGACAGATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 14670 bayes= 11.5771 E= 3.5e+000 -104 -965 -965 186 -965 -965 170 5 -965 -965 -965 205 -965 -965 -965 205 -965 -965 193 -95 195 -965 -965 -965 -965 189 -965 -965 -104 -11 -88 105 -965 -965 212 -965 -104 -965 -965 186 -965 -965 144 64 176 -965 -965 -95 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 8 E= 3.5e+000 0.125000 0.000000 0.000000 0.875000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.875000 0.125000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.125000 0.250000 0.125000 0.500000 0.000000 0.000000 1.000000 0.000000 0.125000 0.000000 0.000000 0.875000 0.000000 0.000000 0.625000 0.375000 0.875000 0.000000 0.000000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[GT]TTGAC[TC]GT[GT]A -------------------------------------------------------------------------------- Time 6.98 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 5 llr = 85 E-value = 1.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A a:::8::::::26:88 pos.-specific C :2a::a6::::::::: probability G :8:a::22::882a:2 matrix T ::::2:28aa2:2:2: bits 2.1 * ** * 1.9 * ** * ** * 1.7 * ** * ** * 1.5 * ** * *** * Relative 1.3 ****** ***** *** Entropy 1.1 ****** ***** *** (24.5 bits) 0.8 ****** ***** *** 0.6 **************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel AGCGACCTTTGGAGAA consensus C T GG TAG TG sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 38548 388 2.12e-09 CACTGTTACG AGCGACCTTTTGAGAA AGAAAGGATG 17628 200 2.12e-09 AATGACAGCG AGCGACCTTTGAAGAA GGCTCGCTTG 47613 217 4.31e-09 CTGCGGACAA AGCGTCGTTTGGAGAA CATCTTCCAT 46371 69 1.80e-08 AGGTGCAAAA ACCGACTTTTGGTGAA AAGAGTAGAT 2607 189 5.44e-08 GATCAATCGC AGCGACCGTTGGGGTG GGAGTCCCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38548 2.1e-09 387_[+2]_97 17628 2.1e-09 199_[+2]_285 47613 4.3e-09 216_[+2]_268 46371 1.8e-08 68_[+2]_416 2607 5.4e-08 188_[+2]_296 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=5 38548 ( 388) AGCGACCTTTTGAGAA 1 17628 ( 200) AGCGACCTTTGAAGAA 1 47613 ( 217) AGCGTCGTTTGGAGAA 1 46371 ( 69) ACCGACTTTTGGTGAA 1 2607 ( 189) AGCGACCGTTGGGGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 14550 bayes= 11.7579 E= 1.8e+002 195 -897 -897 -897 -897 -43 180 -897 -897 188 -897 -897 -897 -897 212 -897 163 -897 -897 -27 -897 188 -897 -897 -897 115 -20 -27 -897 -897 -20 173 -897 -897 -897 205 -897 -897 -897 205 -897 -897 180 -27 -37 -897 180 -897 122 -897 -20 -27 -897 -897 212 -897 163 -897 -897 -27 163 -897 -20 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 5 E= 1.8e+002 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.200000 0.200000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.200000 0.000000 0.800000 0.000000 0.600000 0.000000 0.200000 0.200000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.800000 0.000000 0.200000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- A[GC]CG[AT]C[CGT][TG]TT[GT][GA][AGT]G[AT][AG] -------------------------------------------------------------------------------- Time 14.64 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 4 llr = 85 E-value = 2.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::335::3:3::::::3:::: pos.-specific C ::::::::::535::a:::a: probability G :8885::5a8:33a8::a8:: matrix T a3:::aa3::553:3:8:3:a bits 2.1 * ** * * * * 1.9 * ** * * * * ** 1.7 * ** * * * * ** 1.5 * ** * * * * ** Relative 1.3 **** ** ** ******** Entropy 1.1 ******* *** ******** (30.8 bits) 0.8 ******* *** ******** 0.6 *********** ******** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel TGGGATTGGGCTCGGCTGGCT consensus TAAG A ATCG T A T sequence T GT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 33731 96 9.84e-13 GTGTTCATGA TGGGGTTGGGCTGGGCTGGCT TCTTCACAAT 46453 225 1.21e-10 GCTCACCTTT TGGGATTGGGTCCGTCTGTCT CCCTGTCGTT 40235 205 1.98e-10 TTCGAATAAG TTAGGTTAGGTTTGGCTGGCT CAACCATAAC 44645 25 7.04e-10 CCTCGAGCGT TGGAATTTGACGCGGCAGGCT CATAGATACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 33731 9.8e-13 95_[+3]_384 46453 1.2e-10 224_[+3]_255 40235 2e-10 204_[+3]_275 44645 7e-10 24_[+3]_455 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=4 33731 ( 96) TGGGGTTGGGCTGGGCTGGCT 1 46453 ( 225) TGGGATTGGGTCCGTCTGTCT 1 40235 ( 205) TTAGGTTAGGTTTGGCTGGCT 1 44645 ( 25) TGGAATTTGACGCGGCAGGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 14400 bayes= 12.5505 E= 2.0e+002 -865 -865 -865 205 -865 -865 170 5 -5 -865 170 -865 -5 -865 170 -865 95 -865 112 -865 -865 -865 -865 205 -865 -865 -865 205 -5 -865 112 5 -865 -865 212 -865 -5 -865 170 -865 -865 88 -865 105 -865 -11 12 105 -865 88 12 5 -865 -865 212 -865 -865 -865 170 5 -865 188 -865 -865 -5 -865 -865 163 -865 -865 212 -865 -865 -865 170 5 -865 188 -865 -865 -865 -865 -865 205 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 2.0e+002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.250000 0.000000 0.750000 0.000000 0.250000 0.000000 0.750000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.500000 0.250000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.250000 0.250000 0.500000 0.000000 0.500000 0.250000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[GT][GA][GA][AG]TT[GAT]G[GA][CT][TCG][CGT]G[GT]C[TA]G[GT]CT -------------------------------------------------------------------------------- Time 21.86 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42428 3.80e-01 500 41659 8.66e-01 500 17628 5.76e-05 199_[+2(2.12e-09)]_285 9143 4.17e-01 500 46371 1.52e-04 68_[+2(1.80e-08)]_416 46453 1.04e-07 224_[+3(1.21e-10)]_255 36970 7.37e-03 330_[+1(2.96e-06)]_158 46999 1.25e-02 236_[+1(2.05e-06)]_168_\ [+1(7.86e-05)]_72 47017 1.22e-01 463_[+1(7.39e-05)]_25 37341 3.58e-01 500 47357 6.67e-01 500 47613 1.15e-07 11_[+1(6.51e-07)]_135_\ [+2(2.07e-05)]_42_[+2(4.31e-09)]_268 2607 4.28e-04 188_[+2(5.44e-08)]_296 22703 3.15e-01 500 7634 1.46e-01 500 15863 1.77e-01 500 49502 5.69e-04 369_[+1(4.09e-08)]_119 49514 8.51e-01 500 49908 6.50e-04 47_[+3(4.32e-05)]_390_\ [+1(1.54e-06)]_30 3262 2.63e-04 18_[+1(1.30e-07)]_470 33731 8.58e-09 95_[+3(9.84e-13)]_384 44645 5.23e-06 24_[+3(7.04e-10)]_455 11145 4.23e-01 500 12312 9.49e-01 500 50053 6.34e-01 500 46452 1.74e-06 114_[+2(5.29e-06)]_49_\ [+1(2.11e-07)]_193_[+3(7.32e-05)]_95 46888 2.23e-01 500 37363 9.91e-01 500 40235 7.66e-10 168_[+1(1.72e-07)]_24_\ [+3(1.98e-10)]_275 38548 1.19e-06 348_[+1(8.89e-05)]_27_\ [+2(2.12e-09)]_97 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************