******************************************************************************** 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/57/57.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 4108 1.0000 500 4866 1.0000 500 bd1689 1.0000 500 bd1762 1.0000 500 bd1763 1.0000 500 bd393 1.0000 500 bd755 1.0000 500 bd803 1.0000 500 bd874 1.0000 500 bd922 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/57/57.seqs.fa -oc motifs/57 -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= 10 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= 5000 N= 10 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.255 C 0.226 G 0.232 T 0.287 Background letter frequencies (from dataset with add-one prior applied): A 0.255 C 0.226 G 0.232 T 0.287 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 5 llr = 96 E-value = 1.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 28::42:8448:628::a:: pos.-specific C 8:8a:8a:64:a:8:28:2a probability G :2::2::::::::::::::: matrix T ::2:4::2:22:4:282:8: bits 2.1 * * * * 1.9 * * * * * 1.7 * * * * * 1.5 * * * * * Relative 1.3 **** *** ** ** ** * Entropy 1.1 **** **** ** ******* (27.6 bits) 0.9 **** **** ********** 0.6 **** **** ********** 0.4 ******************** 0.2 ******************** 0.0 -------------------- Multilevel CACCACCACAACACATCATC consensus AGT TA TACT TATCT C sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- bd1689 197 1.30e-10 AACGAACCAT CACCAACAACACTCATCATC GACTATACAG bd874 336 5.61e-10 TATCTCTTCA CACCACCAACACAAATTATC TCAATCAGCA bd755 352 7.01e-10 ACGGCGGACA AACCGCCACAACACTTCATC CACTCTTCAA bd393 445 1.20e-09 TATATACAGA CATCTCCACTTCACATCATC CATCCTTCAC bd922 481 5.32e-09 CTCCCCGCTC CGCCTCCTCAACTCACCACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1689 1.3e-10 196_[+1]_284 bd874 5.6e-10 335_[+1]_145 bd755 7e-10 351_[+1]_129 bd393 1.2e-09 444_[+1]_36 bd922 5.3e-09 480_[+1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=5 bd1689 ( 197) CACCAACAACACTCATCATC 1 bd874 ( 336) CACCACCAACACAAATTATC 1 bd755 ( 352) AACCGCCACAACACTTCATC 1 bd393 ( 445) CATCTCCACTTCACATCATC 1 bd922 ( 481) CGCCTCCTCAACTCACCACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 4810 bayes= 10.1602 E= 1.5e+000 -35 182 -897 -897 165 -897 -21 -897 -897 182 -897 -52 -897 214 -897 -897 65 -897 -21 48 -35 182 -897 -897 -897 214 -897 -897 165 -897 -897 -52 65 141 -897 -897 65 82 -897 -52 165 -897 -897 -52 -897 214 -897 -897 123 -897 -897 48 -35 182 -897 -897 165 -897 -897 -52 -897 -18 -897 148 -897 182 -897 -52 197 -897 -897 -897 -897 -18 -897 148 -897 214 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 5 E= 1.5e+000 0.200000 0.800000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.400000 0.000000 0.200000 0.400000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.400000 0.600000 0.000000 0.000000 0.400000 0.400000 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.600000 0.000000 0.000000 0.400000 0.200000 0.800000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.000000 0.200000 0.000000 0.800000 0.000000 0.800000 0.000000 0.200000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA][AG][CT]C[ATG][CA]C[AT][CA][ACT][AT]C[AT][CA][AT][TC][CT]A[TC]C -------------------------------------------------------------------------------- Time 0.91 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 5 llr = 97 E-value = 1.7e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A a2:24a:842::a:822:a4: pos.-specific C :6:8::a:42a2:6222a::a probability G ::a:2::::2:::4:2::::: matrix T :2::4::224:8:::46::6: bits 2.1 * * * * * 1.9 * * ** * * ** * 1.7 * * ** * * ** * 1.5 * * ** * * ** * Relative 1.3 * ** *** * * * ** * Entropy 1.1 * ** *** ***** ** * (27.9 bits) 0.9 * ** *** ***** **** 0.6 **** *** ***** **** 0.4 ********* ***** ***** 0.2 ********* ***** ***** 0.0 --------------------- Multilevel ACGCAACAATCTACATTCATC consensus A AT TCA C GCAA A sequence T G TC CC G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- bd874 265 4.62e-10 CCCTGCGCCG ACGCTACACCCTAGACACAAC CACCGAACCA bd755 464 6.31e-10 GTCTCTGCTG ACGCGACATGCTACATCCATC ATCACTGATA bd1689 114 7.64e-10 CACCATGATT ATGATACAATCTACATTCATC CAATTCCAAT 4108 315 1.11e-09 GATACTTCAG ACGCAACAATCCACCATCAAC TGACTAATGA bd393 333 2.42e-09 ATATCATAGG AAGCAACTCACTAGAGTCATC GGGTCTGATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd874 4.6e-10 264_[+2]_215 bd755 6.3e-10 463_[+2]_16 bd1689 7.6e-10 113_[+2]_366 4108 1.1e-09 314_[+2]_165 bd393 2.4e-09 332_[+2]_147 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=5 bd874 ( 265) ACGCTACACCCTAGACACAAC 1 bd755 ( 464) ACGCGACATGCTACATCCATC 1 bd1689 ( 114) ATGATACAATCTACATTCATC 1 4108 ( 315) ACGCAACAATCCACCATCAAC 1 bd393 ( 333) AAGCAACTCACTAGAGTCATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4800 bayes= 10.1572 E= 1.7e+000 197 -897 -897 -897 -35 141 -897 -52 -897 -897 211 -897 -35 182 -897 -897 65 -897 -21 48 197 -897 -897 -897 -897 214 -897 -897 165 -897 -897 -52 65 82 -897 -52 -35 -18 -21 48 -897 214 -897 -897 -897 -18 -897 148 197 -897 -897 -897 -897 141 78 -897 165 -18 -897 -897 -35 -18 -21 48 -35 -18 -897 106 -897 214 -897 -897 197 -897 -897 -897 65 -897 -897 106 -897 214 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 1.7e+000 1.000000 0.000000 0.000000 0.000000 0.200000 0.600000 0.000000 0.200000 0.000000 0.000000 1.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.400000 0.000000 0.200000 0.400000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.400000 0.400000 0.000000 0.200000 0.200000 0.200000 0.200000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 1.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.800000 0.200000 0.000000 0.000000 0.200000 0.200000 0.200000 0.400000 0.200000 0.200000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.000000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- A[CAT]G[CA][ATG]AC[AT][ACT][TACG]C[TC]A[CG][AC][TACG][TAC]CA[TA]C -------------------------------------------------------------------------------- Time 1.77 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 10 llr = 117 E-value = 1.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :17:141:31:616: pos.-specific C ::15:::::12:121 probability G a92484:85:8:8:9 matrix T :::1129228:4:2: bits 2.1 * 1.9 * 1.7 ** * 1.5 ** * Relative 1.3 ** ** * * Entropy 1.1 ** * ** * * * (16.8 bits) 0.9 *** * ** **** * 0.6 ***** ** ****** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel GGACGATGGTGAGAG consensus GG G TA CT C sequence T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- bd755 143 6.01e-10 AACTGCCGAT GGACGGTGGTGAGAG GAGGAGGTAG bd393 273 1.86e-07 AGTTACACGA GGACGAAGATGAGAG AGTGACTGGT bd1763 146 4.81e-07 AAAGCGAGAG GGGGGATGGAGAGAG GATACAACTA bd922 265 7.13e-07 GATGTTAGAT GGACGGTGGTCTCAG TCGAGGAGAG bd1689 346 1.25e-06 GTTTTGTGTG GGGGGATTGTGAGTG AGAATGCAAC 4108 252 3.61e-06 GACTGACAGT GGACGTTGATGTATG GTGTTCGCAT bd1762 217 4.85e-06 GCAAAGCAAA GGATGTTGTCGAGAG TGTAGAGGAG 4866 119 4.85e-06 TGGCTTGAGG GGAGTGTTTTGTGAG ATTGAGAGCT bd803 97 8.98e-06 CGGGCCGAGG GACGGGTGATGTGCG AGAGAGCCGC bd874 200 1.09e-05 GACATTTTGA GGACAATGGTCAGCC AGCCTGCATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd755 6e-10 142_[+3]_343 bd393 1.9e-07 272_[+3]_213 bd1763 4.8e-07 145_[+3]_340 bd922 7.1e-07 264_[+3]_221 bd1689 1.2e-06 345_[+3]_140 4108 3.6e-06 251_[+3]_234 bd1762 4.9e-06 216_[+3]_269 4866 4.9e-06 118_[+3]_367 bd803 9e-06 96_[+3]_389 bd874 1.1e-05 199_[+3]_286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=10 bd755 ( 143) GGACGGTGGTGAGAG 1 bd393 ( 273) GGACGAAGATGAGAG 1 bd1763 ( 146) GGGGGATGGAGAGAG 1 bd922 ( 265) GGACGGTGGTCTCAG 1 bd1689 ( 346) GGGGGATTGTGAGTG 1 4108 ( 252) GGACGTTGATGTATG 1 bd1762 ( 217) GGATGTTGTCGAGAG 1 4866 ( 119) GGAGTGTTTTGTGAG 1 bd803 ( 97) GACGGGTGATGTGCG 1 bd874 ( 200) GGACAATGGTCAGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 4860 bayes= 8.92184 E= 1.2e+001 -997 -997 211 -997 -135 -997 195 -997 146 -117 -21 -997 -997 114 79 -152 -135 -997 178 -152 65 -997 79 -52 -135 -997 -997 165 -997 -997 178 -52 24 -997 111 -52 -135 -117 -997 148 -997 -18 178 -997 123 -997 -997 48 -135 -117 178 -997 123 -18 -997 -52 -997 -117 195 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 1.2e+001 0.000000 0.000000 1.000000 0.000000 0.100000 0.000000 0.900000 0.000000 0.700000 0.100000 0.200000 0.000000 0.000000 0.500000 0.400000 0.100000 0.100000 0.000000 0.800000 0.100000 0.400000 0.000000 0.400000 0.200000 0.100000 0.000000 0.000000 0.900000 0.000000 0.000000 0.800000 0.200000 0.300000 0.000000 0.500000 0.200000 0.100000 0.100000 0.000000 0.800000 0.000000 0.200000 0.800000 0.000000 0.600000 0.000000 0.000000 0.400000 0.100000 0.100000 0.800000 0.000000 0.600000 0.200000 0.000000 0.200000 0.000000 0.100000 0.900000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GG[AG][CG]G[AGT]T[GT][GAT]T[GC][AT]G[ACT]G -------------------------------------------------------------------------------- Time 2.59 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4108 1.48e-09 251_[+3(3.61e-06)]_48_\ [+2(1.11e-09)]_14_[+1(8.88e-06)]_131 4866 7.41e-03 118_[+3(4.85e-06)]_367 bd1689 1.11e-14 113_[+2(7.64e-10)]_62_\ [+1(1.30e-10)]_114_[+3(8.99e-05)]_[+3(1.25e-06)]_140 bd1762 4.15e-02 216_[+3(4.85e-06)]_269 bd1763 2.13e-03 145_[+3(4.81e-07)]_340 bd393 4.44e-14 272_[+3(1.86e-07)]_45_\ [+2(2.42e-09)]_91_[+1(1.20e-09)]_36 bd755 3.15e-17 100_[+2(7.70e-05)]_21_\ [+3(6.01e-10)]_194_[+1(7.01e-10)]_92_[+2(6.31e-10)]_16 bd803 5.12e-02 96_[+3(8.98e-06)]_389 bd874 2.12e-13 199_[+3(1.09e-05)]_50_\ [+2(4.62e-10)]_50_[+1(5.61e-10)]_145 bd922 1.55e-07 264_[+3(7.13e-07)]_201_\ [+1(5.32e-09)] -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************