******************************************************************************** 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/277/277.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 36572 1.0000 500 36728 1.0000 500 48553 1.0000 500 22568 1.0000 500 1758 1.0000 500 45428 1.0000 500 12909 1.0000 500 44648 1.0000 500 45896 1.0000 500 49917 1.0000 500 43887 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/277/277.seqs.fa -oc motifs/277 -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= 11 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= 5500 N= 11 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.260 C 0.234 G 0.231 T 0.275 Background letter frequencies (from dataset with add-one prior applied): A 0.260 C 0.234 G 0.231 T 0.275 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 11 llr = 113 E-value = 1.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::1:15::1:21 pos.-specific C :1172:a:98:: probability G 25::7::::15: matrix T 8583:5:a:139 bits 2.1 * 1.9 ** 1.7 *** 1.5 *** * Relative 1.3 * * **** * Entropy 1.1 * *** **** * (14.8 bits) 0.8 * ******** * 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TGTCGTCTCCGT consensus T T A T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 43887 465 1.82e-07 TAGGGTTGTT TTTCGTCTCCGT GTCTTTTGTC 36572 260 6.76e-07 GGCAGCAGTT TGTCGTCTCCAT CTTAAGGTCC 48553 75 1.15e-06 AGAACATTTC TTTTGACTCCGT CCTACTGAGG 45428 478 2.40e-06 AGTACAACCA TGACGTCTCCGT GTCGCGCTGT 22568 161 6.85e-06 CCGGCAGCTT TGCCGACTCCTT CGAAGCATGG 12909 81 1.05e-05 CAAGCGTATA TTTTCTCTCCTT TTAGATTGGC 45896 373 1.20e-05 AACACACAGG TGTTGTCTACGT TACCACCAAC 49917 34 1.48e-05 CGTCCAAAAA TTTCGACTCGAT TTCGTCTTTG 44648 22 1.83e-05 TCGGATTTAG GCTCGACTCCTT CAACATAGTA 1758 473 3.48e-05 AAGTTCCTCT TTTCAACTCCGA AACACGCGGG 36728 354 4.22e-05 ATGGGACCGC GGTCCTCTCTGT GCTCACAGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43887 1.8e-07 464_[+1]_24 36572 6.8e-07 259_[+1]_229 48553 1.1e-06 74_[+1]_414 45428 2.4e-06 477_[+1]_11 22568 6.8e-06 160_[+1]_328 12909 1.1e-05 80_[+1]_408 45896 1.2e-05 372_[+1]_116 49917 1.5e-05 33_[+1]_455 44648 1.8e-05 21_[+1]_467 1758 3.5e-05 472_[+1]_16 36728 4.2e-05 353_[+1]_135 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=11 43887 ( 465) TTTCGTCTCCGT 1 36572 ( 260) TGTCGTCTCCAT 1 48553 ( 75) TTTTGACTCCGT 1 45428 ( 478) TGACGTCTCCGT 1 22568 ( 161) TGCCGACTCCTT 1 12909 ( 81) TTTTCTCTCCTT 1 45896 ( 373) TGTTGTCTACGT 1 49917 ( 34) TTTCGACTCGAT 1 44648 ( 22) GCTCGACTCCTT 1 1758 ( 473) TTTCAACTCCGA 1 36728 ( 354) GGTCCTCTCTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5379 bayes= 9.28648 E= 1.4e+001 -1010 -1010 -35 157 -1010 -136 98 73 -152 -136 -1010 157 -1010 164 -1010 -1 -152 -36 165 -1010 80 -1010 -1010 99 -1010 210 -1010 -1010 -1010 -1010 -1010 186 -152 196 -1010 -1010 -1010 181 -134 -159 -52 -1010 124 -1 -152 -1010 -1010 173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 11 E= 1.4e+001 0.000000 0.000000 0.181818 0.818182 0.000000 0.090909 0.454545 0.454545 0.090909 0.090909 0.000000 0.818182 0.000000 0.727273 0.000000 0.272727 0.090909 0.181818 0.727273 0.000000 0.454545 0.000000 0.000000 0.545455 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.090909 0.909091 0.000000 0.000000 0.000000 0.818182 0.090909 0.090909 0.181818 0.000000 0.545455 0.272727 0.090909 0.000000 0.000000 0.909091 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[GT]T[CT]G[TA]CTCC[GT]T -------------------------------------------------------------------------------- Time 1.01 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 10 llr = 116 E-value = 2.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::a:33:1211:266a pos.-specific C 91:9:1:::731:22: probability G :9:172126:17422: matrix T 1::::49722524::: bits 2.1 1.9 * * 1.7 **** * 1.5 **** * * Relative 1.3 ***** * * Entropy 1.1 ***** * * (16.7 bits) 0.8 ***** ** * * * 0.6 ***** **** * *** 0.4 ***** **** ***** 0.2 **************** 0.0 ---------------- Multilevel CGACGTTTGCTGGAAA consensus AA GATCTTCC sequence G T AGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 1758 361 4.19e-09 TCGTTAAGGC CGACGATTGCTGAAAA TGGAAATGTC 45428 281 3.24e-08 TGCGTACCAT CGACGGTTGCCGTACA AAGGGGATTG 48553 28 2.61e-07 GATGCAAGGA CGACGTTAGTTGGAAA TCGAAATGGG 44648 290 1.36e-06 CAGCGAGTTA CCACGATTGCTGTGGA ACCCCCTTTC 43887 67 1.49e-06 ACTGAAGCTT CGACGTGGTCCGGAAA CACCGTTGGT 49917 286 2.50e-06 AAACACGCTG CGACGCTTTCAGTCAA GTTTCGTCTA 22568 108 4.25e-06 AAATTGCGCT CGACATTTGACTGCAA TTGCCTTAGA 36728 450 6.15e-06 ATTCGGAAAT CGACATTTGTTCAAGA GTTCGTCGCA 45896 329 1.47e-05 GATCAATGCT TGACAGTGACTGTGAA TTATTCTACG 36572 32 1.72e-05 CCGAGCGGAA CGAGGATTACGTGACA CACAAATCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1758 4.2e-09 360_[+2]_124 45428 3.2e-08 280_[+2]_204 48553 2.6e-07 27_[+2]_457 44648 1.4e-06 289_[+2]_195 43887 1.5e-06 66_[+2]_418 49917 2.5e-06 285_[+2]_199 22568 4.2e-06 107_[+2]_377 36728 6.2e-06 449_[+2]_35 45896 1.5e-05 328_[+2]_156 36572 1.7e-05 31_[+2]_453 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=10 1758 ( 361) CGACGATTGCTGAAAA 1 45428 ( 281) CGACGGTTGCCGTACA 1 48553 ( 28) CGACGTTAGTTGGAAA 1 44648 ( 290) CCACGATTGCTGTGGA 1 43887 ( 67) CGACGTGGTCCGGAAA 1 49917 ( 286) CGACGCTTTCAGTCAA 1 22568 ( 108) CGACATTTGACTGCAA 1 36728 ( 450) CGACATTTGTTCAAGA 1 45896 ( 329) TGACAGTGACTGTGAA 1 36572 ( 32) CGAGGATTACGTGACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 5335 bayes= 9.30861 E= 2.3e+002 -997 194 -997 -146 -997 -122 196 -997 194 -997 -997 -997 -997 194 -121 -997 20 -997 160 -997 20 -122 -21 54 -997 -997 -121 171 -138 -997 -21 135 -38 -997 138 -46 -138 158 -997 -46 -138 36 -121 86 -997 -122 160 -46 -38 -997 79 54 120 -23 -21 -997 120 -23 -21 -997 194 -997 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 10 E= 2.3e+002 0.000000 0.900000 0.000000 0.100000 0.000000 0.100000 0.900000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.900000 0.100000 0.000000 0.300000 0.000000 0.700000 0.000000 0.300000 0.100000 0.200000 0.400000 0.000000 0.000000 0.100000 0.900000 0.100000 0.000000 0.200000 0.700000 0.200000 0.000000 0.600000 0.200000 0.100000 0.700000 0.000000 0.200000 0.100000 0.300000 0.100000 0.500000 0.000000 0.100000 0.700000 0.200000 0.200000 0.000000 0.400000 0.400000 0.600000 0.200000 0.200000 0.000000 0.600000 0.200000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CGAC[GA][TAG]T[TG][GAT][CT][TC][GT][GTA][ACG][ACG]A -------------------------------------------------------------------------------- Time 2.12 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 7 llr = 82 E-value = 1.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :63a::1::::: pos.-specific C :1::4a6::4:1 probability G a:6:6::::::: matrix T :31:::3aa6a9 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 GAGAGCCTTTTT consensus TA C T C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 45896 443 1.33e-07 TTTGTATCCC GAGAGCCTTCTT TTCAAATCGC 36728 137 4.24e-07 AGCTGACAAG GAAAGCCTTTTT TCATTGTTGA 48553 2 1.66e-06 A GAGAGCCTTTTC TGTTGATGCA 45428 367 2.97e-06 GAGAGATGGA GTGACCTTTTTT GCGTGCGTGC 36572 471 3.17e-06 AGCATTTCGA GTAACCCTTCTT AATCTGTAAC 12909 403 3.79e-06 ACAATTCCAC GCGAGCTTTCTT TGCTAGAGCT 44648 328 8.50e-06 GTCGTATTGT GATACCATTTTT GTGCGTAGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 45896 1.3e-07 442_[+3]_46 36728 4.2e-07 136_[+3]_352 48553 1.7e-06 1_[+3]_487 45428 3e-06 366_[+3]_122 36572 3.2e-06 470_[+3]_18 12909 3.8e-06 402_[+3]_86 44648 8.5e-06 327_[+3]_161 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=7 45896 ( 443) GAGAGCCTTCTT 1 36728 ( 137) GAAAGCCTTTTT 1 48553 ( 2) GAGAGCCTTTTC 1 45428 ( 367) GTGACCTTTTTT 1 36572 ( 471) GTAACCCTTCTT 1 12909 ( 403) GCGAGCTTTCTT 1 44648 ( 328) GATACCATTTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5379 bayes= 9.42755 E= 1.6e+003 -945 -945 211 -945 113 -71 -945 6 13 -945 130 -94 194 -945 -945 -945 -945 87 130 -945 -945 209 -945 -945 -86 129 -945 6 -945 -945 -945 186 -945 -945 -945 186 -945 87 -945 106 -945 -945 -945 186 -945 -71 -945 164 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 1.6e+003 0.000000 0.000000 1.000000 0.000000 0.571429 0.142857 0.000000 0.285714 0.285714 0.000000 0.571429 0.142857 1.000000 0.000000 0.000000 0.000000 0.000000 0.428571 0.571429 0.000000 0.000000 1.000000 0.000000 0.000000 0.142857 0.571429 0.000000 0.285714 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.428571 0.000000 0.571429 0.000000 0.000000 0.000000 1.000000 0.000000 0.142857 0.000000 0.857143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[AT][GA]A[GC]C[CT]TT[TC]TT -------------------------------------------------------------------------------- Time 3.13 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36572 8.78e-07 31_[+2(1.72e-05)]_212_\ [+1(6.76e-07)]_199_[+3(3.17e-06)]_18 36728 2.33e-06 136_[+3(4.24e-07)]_205_\ [+1(4.22e-05)]_84_[+2(6.15e-06)]_35 48553 1.74e-08 1_[+3(1.66e-06)]_14_[+2(2.61e-07)]_\ 31_[+1(1.15e-06)]_414 22568 5.43e-04 107_[+2(4.25e-06)]_37_\ [+1(6.85e-06)]_328 1758 4.54e-06 360_[+2(4.19e-09)]_96_\ [+1(3.48e-05)]_16 45428 8.60e-09 280_[+2(3.24e-08)]_70_\ [+3(2.97e-06)]_99_[+1(2.40e-06)]_11 12909 2.68e-04 80_[+1(1.05e-05)]_310_\ [+3(3.79e-06)]_86 44648 4.20e-06 21_[+1(1.83e-05)]_256_\ [+2(1.36e-06)]_22_[+3(8.50e-06)]_161 45896 5.82e-07 328_[+2(1.47e-05)]_28_\ [+1(1.20e-05)]_58_[+3(1.33e-07)]_46 49917 3.47e-04 33_[+1(1.48e-05)]_240_\ [+2(2.50e-06)]_199 43887 7.49e-06 66_[+2(1.49e-06)]_382_\ [+1(1.82e-07)]_24 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************