******************************************************************************** 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/183/183.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 2380 1.0000 500 26405 1.0000 500 35136 1.0000 500 37118 1.0000 500 5947 1.0000 500 bd804 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/183/183.seqs.fa -oc motifs/183 -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= 6 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= 3000 N= 6 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.288 C 0.265 G 0.198 T 0.248 Background letter frequencies (from dataset with add-one prior applied): A 0.288 C 0.265 G 0.198 T 0.248 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 4 llr = 101 E-value = 2.6e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A a:5::aaa::aa:a:a::::: pos.-specific C ::::::::a5::a:a:5:::: probability G :a::a::::5:::::::55:a matrix T ::5a::::::::::::555a: bits 2.3 * * * 2.1 * ** ** 1.9 ** ****** ****** ** 1.6 ** ****** ****** ** Relative 1.4 ** ****** ****** ** Entropy 1.2 ** ************* **** (36.5 bits) 0.9 ********************* 0.7 ********************* 0.5 ********************* 0.2 ********************* 0.0 --------------------- Multilevel AGATGAAACCAACACACGGTG consensus T G TTT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 37118 85 1.40e-12 TGACTCTGGC AGTTGAAACGAACACATGTTG TTGACCTTGC 26405 304 1.40e-12 TGACTCTGGC AGTTGAAACGAACACATGTTG TTGACCTTGC 5947 115 9.19e-12 CTACTGATGG AGATGAAACCAACACACTGTG GGAGAGGAAG 35136 116 9.19e-12 CTACTGATGG AGATGAAACCAACACACTGTG GGAGAGGAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37118 1.4e-12 84_[+1]_395 26405 1.4e-12 303_[+1]_176 5947 9.2e-12 114_[+1]_365 35136 9.2e-12 115_[+1]_364 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=4 37118 ( 85) AGTTGAAACGAACACATGTTG 1 26405 ( 304) AGTTGAAACGAACACATGTTG 1 5947 ( 115) AGATGAAACCAACACACTGTG 1 35136 ( 116) AGATGAAACCAACACACTGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2880 bayes= 9.48985 E= 2.6e-005 179 -865 -865 -865 -865 -865 233 -865 79 -865 -865 101 -865 -865 -865 201 -865 -865 233 -865 179 -865 -865 -865 179 -865 -865 -865 179 -865 -865 -865 -865 191 -865 -865 -865 91 133 -865 179 -865 -865 -865 179 -865 -865 -865 -865 191 -865 -865 179 -865 -865 -865 -865 191 -865 -865 179 -865 -865 -865 -865 91 -865 101 -865 -865 133 101 -865 -865 133 101 -865 -865 -865 201 -865 -865 233 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 2.6e-005 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- AG[AT]TGAAAC[CG]AACACA[CT][GT][GT]TG -------------------------------------------------------------------------------- Time 0.34 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 6 llr = 117 E-value = 1.7e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 58:2::35:8:3a2253:::8 pos.-specific C :2:::::::::5::::2::8: probability G 5:::a375:::2::2:::3:2 matrix T ::a8:7::a2a::8755a72: bits 2.3 * 2.1 * * * * * 1.9 * * * * * * 1.6 * * * * * * Relative 1.4 *** * * ** * Entropy 1.2 *********** ** **** (28.1 bits) 0.9 *********** ** * **** 0.7 *********** **** **** 0.5 ********************* 0.2 ********************* 0.0 --------------------- Multilevel AATTGTGATATCATTATTTCA consensus G GAG A TA G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 37118 10 1.06e-11 AAGTTGTGA GATTGGGGTATCATTATTGCA CAAAAAACAA 26405 229 1.06e-11 TAAGTTGTGA GATTGGGGTATCATTATTGCA CAAAAAACAA 5947 302 1.96e-10 AGGACGATTT AATTGTAATATAATTTATTCA CATGTCTCTC 35136 303 1.96e-10 AGGACGATTT AATTGTAATATAATTTATTCA CATGTCTCTC 2380 109 6.03e-09 TACCCCCTGA AATTGTGGTTTCAAGATTTTA TGTTTGTTGC bd804 86 1.45e-08 CCGTAGATCG GCTAGTGATATGATATCTTCG TTAGAACTGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37118 1.1e-11 9_[+2]_470 26405 1.1e-11 228_[+2]_251 5947 2e-10 301_[+2]_178 35136 2e-10 302_[+2]_177 2380 6e-09 108_[+2]_371 bd804 1.4e-08 85_[+2]_394 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=6 37118 ( 10) GATTGGGGTATCATTATTGCA 1 26405 ( 229) GATTGGGGTATCATTATTGCA 1 5947 ( 302) AATTGTAATATAATTTATTCA 1 35136 ( 303) AATTGTAATATAATTTATTCA 1 2380 ( 109) AATTGTGGTTTCAAGATTTTA 1 bd804 ( 86) GCTAGTGATATGATATCTTCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2880 bayes= 8.90388 E= 1.7e-005 80 -923 133 -923 153 -67 -923 -923 -923 -923 -923 201 -79 -923 -923 174 -923 -923 233 -923 -923 -923 75 142 21 -923 175 -923 80 -923 133 -923 -923 -923 -923 201 153 -923 -923 -57 -923 -923 -923 201 21 91 -25 -923 179 -923 -923 -923 -79 -923 -923 174 -79 -923 -25 142 80 -923 -923 101 21 -67 -923 101 -923 -923 -923 201 -923 -923 75 142 -923 165 -923 -57 153 -923 -25 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 1.7e-005 0.500000 0.000000 0.500000 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.166667 0.000000 0.000000 0.833333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.333333 0.000000 0.666667 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.833333 0.000000 0.000000 0.166667 0.000000 0.000000 0.000000 1.000000 0.333333 0.500000 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.833333 0.166667 0.000000 0.166667 0.666667 0.500000 0.000000 0.000000 0.500000 0.333333 0.166667 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.833333 0.000000 0.166667 0.833333 0.000000 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AG]ATTG[TG][GA][AG]TAT[CA]ATT[AT][TA]T[TG]CA -------------------------------------------------------------------------------- Time 0.65 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 6 llr = 115 E-value = 4.0e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A a:2::::8a8:75a285:23: pos.-specific C :73:::7:::33::::5::2: probability G ::32:::2:2::5::::8::a matrix T :328aa3:::7:::82:285: bits 2.3 * 2.1 ** * 1.9 * ** * * * 1.6 * ** * * * * Relative 1.4 * *** * ** ** * Entropy 1.2 * *** **** **** ** * (27.6 bits) 0.9 ** **************** * 0.7 ** **************** * 0.5 ** ****************** 0.2 ********************* 0.0 --------------------- Multilevel ACCTTTCAAATAAATAAGTTG consensus TG T CCG C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 5947 249 5.78e-12 CCCCCTAACA ACGTTTCAAACAGATACGTTG CGTCGAGTCC 35136 250 5.78e-12 CCCCCTAACA ACGTTTCAAACAGATACGTTG CGTCGAGTCC 37118 170 2.03e-10 GTCCACCTTC ACCTTTTAAATCAATAAGTAG GGGTCAATAA 26405 389 2.03e-10 GTCCACCTTC ACCTTTTAAATCAATAAGTAG GGGTCAATAA 2380 147 1.53e-08 TGCGAGGAAA ATTGTTCGAGTAAATAATTTG TGACTAAGTA bd804 260 1.72e-08 CAGAGAAATC ATATTTCAAATAGAATCGACG GAGACATCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5947 5.8e-12 248_[+3]_231 35136 5.8e-12 249_[+3]_230 37118 2e-10 169_[+3]_310 26405 2e-10 388_[+3]_91 2380 1.5e-08 146_[+3]_333 bd804 1.7e-08 259_[+3]_220 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=6 5947 ( 249) ACGTTTCAAACAGATACGTTG 1 35136 ( 250) ACGTTTCAAACAGATACGTTG 1 37118 ( 170) ACCTTTTAAATCAATAAGTAG 1 26405 ( 389) ACCTTTTAAATCAATAAGTAG 1 2380 ( 147) ATTGTTCGAGTAAATAATTTG 1 bd804 ( 260) ATATTTCAAATAGAATCGACG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2880 bayes= 8.90388 E= 4.0e-005 179 -923 -923 -923 -923 133 -923 42 -79 33 75 -57 -923 -923 -25 174 -923 -923 -923 201 -923 -923 -923 201 -923 133 -923 42 153 -923 -25 -923 179 -923 -923 -923 153 -923 -25 -923 -923 33 -923 142 121 33 -923 -923 80 -923 133 -923 179 -923 -923 -923 -79 -923 -923 174 153 -923 -923 -57 80 91 -923 -923 -923 -923 207 -57 -79 -923 -923 174 21 -67 -923 101 -923 -923 233 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 4.0e-005 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.166667 0.333333 0.333333 0.166667 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 0.833333 0.000000 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.000000 0.333333 0.000000 0.666667 0.666667 0.333333 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.833333 0.833333 0.000000 0.000000 0.166667 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 0.833333 0.166667 0.166667 0.000000 0.000000 0.833333 0.333333 0.166667 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- A[CT][CG]TTT[CT]AAA[TC][AC][AG]ATA[AC]GT[TA]G -------------------------------------------------------------------------------- Time 0.95 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2380 6.33e-09 108_[+2(6.03e-09)]_17_\ [+3(1.53e-08)]_333 26405 5.48e-22 228_[+2(1.06e-11)]_54_\ [+1(1.40e-12)]_64_[+3(2.03e-10)]_91 35136 1.82e-21 115_[+1(9.19e-12)]_113_\ [+3(5.78e-12)]_32_[+2(1.96e-10)]_177 37118 5.48e-22 9_[+2(1.06e-11)]_54_[+1(1.40e-12)]_\ 64_[+3(2.03e-10)]_310 5947 1.82e-21 114_[+1(9.19e-12)]_113_\ [+3(5.78e-12)]_32_[+2(1.96e-10)]_178 bd804 4.93e-09 85_[+2(1.45e-08)]_153_\ [+3(1.72e-08)]_220 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************