******************************************************************************** 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/68/68.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11996 1.0000 500 1499 1.0000 500 20656 1.0000 500 20997 1.0000 500 21124 1.0000 500 22167 1.0000 500 22713 1.0000 500 263663 1.0000 500 3659 1.0000 500 5414 1.0000 500 5942 1.0000 500 9972 1.0000 500 bd1620 1.0000 500 bd446 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/68/68.seqs.fa -oc motifs/68 -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= 14 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= 7000 N= 14 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.277 C 0.240 G 0.207 T 0.276 Background letter frequencies (from dataset with add-one prior applied): A 0.277 C 0.240 G 0.207 T 0.276 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 6 llr = 97 E-value = 3.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::::3::::::::: pos.-specific C 33:::3::5::73::5 probability G 72:aa57a58833a:: matrix T :5a::2:::22:3:a5 bits 2.3 ** * * 2.0 ** * * 1.8 *** * ** 1.6 *** * ** ** Relative 1.4 * *** * ** ** Entropy 1.1 * *** ****** ** (23.4 bits) 0.9 * *** ****** *** 0.7 * ********** *** 0.5 **************** 0.2 **************** 0.0 ---------------- Multilevel GTTGGGGGCGGCCGTC consensus CC CA G GG T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 263663 382 1.74e-09 GAGGGACGGT GTTGGCGGCGGCGGTT TCGTTGGACG 1499 21 2.09e-09 GTGCGAAAAG GTTGGGGGGGGGTGTT GCAGTCTACG 22713 249 1.23e-08 TTGGTAGATT CTTGGGAGGGGCGGTC ATGGTTGGGG 22167 318 1.66e-08 CACTCGGCAG CCTGGCGGCGGCCGTC GTTGTGGTTT 21124 142 9.03e-08 GCCGCGGGAG GCTGGGAGGGTGCGTT GGAGGCAGAG 9972 91 1.19e-07 TTGCCTCCGC GGTGGTGGCTGCTGTC ACTATTTCCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263663 1.7e-09 381_[+1]_103 1499 2.1e-09 20_[+1]_464 22713 1.2e-08 248_[+1]_236 22167 1.7e-08 317_[+1]_167 21124 9e-08 141_[+1]_343 9972 1.2e-07 90_[+1]_394 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=6 263663 ( 382) GTTGGCGGCGGCGGTT 1 1499 ( 21) GTTGGGGGGGGGTGTT 1 22713 ( 249) CTTGGGAGGGGCGGTC 1 22167 ( 318) CCTGGCGGCGGCCGTC 1 21124 ( 142) GCTGGGAGGGTGCGTT 1 9972 ( 91) GGTGGTGGCTGCTGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6790 bayes= 10.5908 E= 3.4e-001 -923 47 169 -923 -923 47 -31 86 -923 -923 -923 185 -923 -923 227 -923 -923 -923 227 -923 -923 47 127 -73 27 -923 169 -923 -923 -923 227 -923 -923 106 127 -923 -923 -923 201 -73 -923 -923 201 -73 -923 147 69 -923 -923 47 69 27 -923 -923 227 -923 -923 -923 -923 185 -923 106 -923 86 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 6 E= 3.4e-001 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.166667 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.500000 0.166667 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.833333 0.166667 0.000000 0.666667 0.333333 0.000000 0.000000 0.333333 0.333333 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GC][TC]TGG[GC][GA]G[CG]GG[CG][CGT]GT[CT] -------------------------------------------------------------------------------- Time 1.50 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 12 llr = 137 E-value = 3.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 77111:88:882443a pos.-specific C :373:a::9::7336: probability G :1:71:2113:1131: matrix T 3:3:8::1::213:1: bits 2.3 2.0 * 1.8 * * 1.6 * * * Relative 1.4 ** * * Entropy 1.1 ******* * (16.5 bits) 0.9 * ********* * 0.7 ************ * 0.5 ************ *** 0.2 **************** 0.0 ---------------- Multilevel AACGTCAACAACAACA consensus TCTC G CCA sequence TG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 9972 311 4.37e-10 CATACTTACC AACGTCAACAACAACA AGATCGTCCA 22713 25 2.09e-07 CTCACTGTAA TACGTCAACATCTCCA CACACCTCCT 1499 479 5.84e-07 TCACACATCA AACCACAACAACCACA TACGCC bd1620 59 7.87e-07 AAATGTTTTT TATGTCAACAACAATA AAATATGAAA 21124 234 2.05e-06 AACACTGATC ACCGTCAACGAACGAA GACGTCCGGT 5942 343 2.43e-06 TCAATGCATC AATGTCAACGACGAGA CTCCTCATAA 263663 190 2.65e-06 TCGAGTGCAA ACACTCAACGACACCA ACACTGAGAT 5414 244 2.88e-06 TTGCCATCCT AACATCAACAATCGCA ATCGGTCTGC 20656 3 5.90e-06 GA TACGGCAAGAACAAAA TCCAACACAT 11996 480 6.36e-06 TGCATGAAAT AACGTCGTCAAGTCCA ACACA 20997 375 1.19e-05 ACACACACAC TCTCTCGACATCACCA CATCGACAGC bd446 20 1.44e-05 GGAACGAAGA AGCGTCAGCAAATGAA TGCGAGGCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9972 4.4e-10 310_[+2]_174 22713 2.1e-07 24_[+2]_460 1499 5.8e-07 478_[+2]_6 bd1620 7.9e-07 58_[+2]_426 21124 2e-06 233_[+2]_251 5942 2.4e-06 342_[+2]_142 263663 2.6e-06 189_[+2]_295 5414 2.9e-06 243_[+2]_241 20656 5.9e-06 2_[+2]_482 11996 6.4e-06 479_[+2]_5 20997 1.2e-05 374_[+2]_110 bd446 1.4e-05 19_[+2]_465 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=12 9972 ( 311) AACGTCAACAACAACA 1 22713 ( 25) TACGTCAACATCTCCA 1 1499 ( 479) AACCACAACAACCACA 1 bd1620 ( 59) TATGTCAACAACAATA 1 21124 ( 234) ACCGTCAACGAACGAA 1 5942 ( 343) AATGTCAACGACGAGA 1 263663 ( 190) ACACTCAACGACACCA 1 5414 ( 244) AACATCAACAATCGCA 1 20656 ( 3) TACGGCAAGAACAAAA 1 11996 ( 480) AACGTCGTCAAGTCCA 1 20997 ( 375) TCTCTCGACATCACCA 1 bd446 ( 20) AGCGTCAGCAAATGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6790 bayes= 9.58982 E= 3.6e+001 127 -1023 -1023 27 127 6 -131 -1023 -173 147 -1023 -14 -173 6 169 -1023 -173 -1023 -131 159 -1023 206 -1023 -1023 159 -1023 -31 -1023 159 -1023 -131 -173 -1023 193 -131 -1023 144 -1023 27 -1023 159 -1023 -1023 -73 -73 147 -131 -173 59 6 -131 -14 59 47 27 -1023 -15 128 -131 -173 185 -1023 -1023 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 12 E= 3.6e+001 0.666667 0.000000 0.000000 0.333333 0.666667 0.250000 0.083333 0.000000 0.083333 0.666667 0.000000 0.250000 0.083333 0.250000 0.666667 0.000000 0.083333 0.000000 0.083333 0.833333 0.000000 1.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.833333 0.000000 0.083333 0.083333 0.000000 0.916667 0.083333 0.000000 0.750000 0.000000 0.250000 0.000000 0.833333 0.000000 0.000000 0.166667 0.166667 0.666667 0.083333 0.083333 0.416667 0.250000 0.083333 0.250000 0.416667 0.333333 0.250000 0.000000 0.250000 0.583333 0.083333 0.083333 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AT][AC][CT][GC]TCAAC[AG]AC[ACT][ACG][CA]A -------------------------------------------------------------------------------- Time 3.01 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 5 llr = 94 E-value = 1.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :6:2:42:6::::::28:6:: pos.-specific C ::64:2:::62:2:6:24::: probability G a24:a28a448:4a42:622a matrix T :2:4:2:::::a4::6::28: bits 2.3 * * * * * 2.0 * * * * * 1.8 * * * * * * 1.6 * * * ** * * Relative 1.4 * * ** ** * * Entropy 1.1 * * * ****** ** ** ** (27.1 bits) 0.9 * * * ****** ** ** ** 0.7 * * * ****** ** ** ** 0.5 ***** *************** 0.2 ***** *************** 0.0 --------------------- Multilevel GACCGAGGACGTGGCTAGATG consensus GGT CA GGC T GACCGG sequence T A G C G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 22167 146 4.09e-11 GCGAGCGAAC GAGCGAGGGCGTGGCTAGAGG TAGAATTGGC 21124 161 4.47e-10 GTGCGTTGGA GGCAGAGGAGGTGGCGAGATG ATTGCATGAT 20656 353 5.65e-10 TTTTTTTTGC GACCGGGGAGGTTGGTACTTG GAATCGATAC 20997 202 6.60e-09 ACCTCCAGGT GACTGCAGACGTCGGTCCATG GAGTTATATG 9972 423 1.07e-08 CTACTCTCCG GTGTGTGGGCCTTGCAAGGTG AGATGCCTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22167 4.1e-11 145_[+3]_334 21124 4.5e-10 160_[+3]_319 20656 5.6e-10 352_[+3]_127 20997 6.6e-09 201_[+3]_278 9972 1.1e-08 422_[+3]_57 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=5 22167 ( 146) GAGCGAGGGCGTGGCTAGAGG 1 21124 ( 161) GGCAGAGGAGGTGGCGAGATG 1 20656 ( 353) GACCGGGGAGGTTGGTACTTG 1 20997 ( 202) GACTGCAGACGTCGGTCCATG 1 9972 ( 423) GTGTGTGGGCCTTGCAAGGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 6720 bayes= 11.3352 E= 1.0e+002 -897 -897 227 -897 111 -897 -5 -46 -897 132 95 -897 -47 74 -897 53 -897 -897 227 -897 53 -26 -5 -46 -47 -897 195 -897 -897 -897 227 -897 111 -897 95 -897 -897 132 95 -897 -897 -26 195 -897 -897 -897 -897 185 -897 -26 95 53 -897 -897 227 -897 -897 132 95 -897 -47 -897 -5 112 153 -26 -897 -897 -897 74 153 -897 111 -897 -5 -46 -897 -897 -5 153 -897 -897 227 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 1.0e+002 0.000000 0.000000 1.000000 0.000000 0.600000 0.000000 0.200000 0.200000 0.000000 0.600000 0.400000 0.000000 0.200000 0.400000 0.000000 0.400000 0.000000 0.000000 1.000000 0.000000 0.400000 0.200000 0.200000 0.200000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.400000 0.400000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.200000 0.000000 0.200000 0.600000 0.800000 0.200000 0.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.600000 0.000000 0.200000 0.200000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[AGT][CG][CTA]G[ACGT][GA]G[AG][CG][GC]T[GTC]G[CG][TAG][AC][GC][AGT][TG]G -------------------------------------------------------------------------------- Time 4.44 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11996 1.67e-02 479_[+2(6.36e-06)]_5 1499 5.12e-10 20_[+1(2.09e-09)]_442_\ [+2(5.84e-07)]_6 20656 7.39e-08 2_[+2(5.90e-06)]_334_[+3(5.65e-10)]_\ 127 20997 1.71e-06 201_[+3(6.60e-09)]_152_\ [+2(1.19e-05)]_110 21124 5.18e-12 141_[+1(9.03e-08)]_3_[+3(4.47e-10)]_\ 52_[+2(2.05e-06)]_251 22167 4.52e-11 145_[+3(4.09e-11)]_151_\ [+1(1.66e-08)]_167 22713 1.02e-09 24_[+2(2.09e-07)]_208_\ [+1(1.23e-08)]_89_[+3(9.22e-06)]_126 263663 1.39e-07 189_[+2(2.65e-06)]_31_\ [+1(7.85e-05)]_129_[+1(1.74e-09)]_103 3659 9.41e-01 500 5414 2.74e-02 243_[+2(2.88e-06)]_241 5942 2.66e-02 342_[+2(2.43e-06)]_142 9972 4.62e-14 90_[+1(1.19e-07)]_146_\ [+1(4.11e-05)]_42_[+2(4.37e-10)]_96_[+3(1.07e-08)]_57 bd1620 1.43e-02 58_[+2(7.87e-07)]_426 bd446 4.29e-02 19_[+2(1.44e-05)]_465 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************