******************************************************************************** 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/461/461.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10018 1.0000 500 11720 1.0000 500 24954 1.0000 500 6615 1.0000 500 8895 1.0000 500 8898 1.0000 500 8900 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/461/461.seqs.fa -oc motifs/461 -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= 7 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= 3500 N= 7 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.281 C 0.223 G 0.218 T 0.277 Background letter frequencies (from dataset with add-one prior applied): A 0.281 C 0.223 G 0.218 T 0.277 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 7 llr = 137 E-value = 8.2e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 7:::a97:37:::1:6a343: pos.-specific C 3:a9:11a71737:a4:734a probability G ::::::1::1::3:::::11: matrix T :a:1::::::37:9::::11: bits 2.2 * * * * 2.0 * * * * 1.8 ** * * * * * 1.5 **** * * * * Relative 1.3 ***** * * *** * * Entropy 1.1 ****** ** ***** ** * (28.2 bits) 0.9 ****************** * 0.7 ****************** * 0.4 ****************** * 0.2 ********************* 0.0 --------------------- Multilevel ATCCAAACCACTCTCAACACC consensus C A TCG C ACA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8898 458 2.51e-13 CACAATCAGA ATCCAAACCACTCTCAACACC ACCACCACAA 11720 458 2.51e-13 AACACAATTC ATCCAAACCACTCTCAACACC ACCACAGAAA 8895 460 2.35e-12 AGCACAATTC ATCCAAACCACTCTCAACCAC CACAGCAACA 8900 465 1.02e-11 AGCACAATTC ATCCAACCCACTCTCAACACC ACCACAGCAA 24954 467 5.94e-09 TCACAACGAA ATCCAAACAACCGACCACTGC AAATCCTTGC 10018 335 1.45e-08 ATGCATCTGT CTCCAAGCCGTCCTCCAAGTC CAAGAGCTCT 6615 335 2.97e-08 AGTGACATTG CTCTACACACTTGTCCAACAC TGAGGTTCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8898 2.5e-13 457_[+1]_22 11720 2.5e-13 457_[+1]_22 8895 2.3e-12 459_[+1]_20 8900 1e-11 464_[+1]_15 24954 5.9e-09 466_[+1]_13 10018 1.4e-08 334_[+1]_145 6615 3e-08 334_[+1]_145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=7 8898 ( 458) ATCCAAACCACTCTCAACACC 1 11720 ( 458) ATCCAAACCACTCTCAACACC 1 8895 ( 460) ATCCAAACCACTCTCAACCAC 1 8900 ( 465) ATCCAACCCACTCTCAACACC 1 24954 ( 467) ATCCAAACAACCGACCACTGC 1 10018 ( 335) CTCCAAGCCGTCCTCCAAGTC 1 6615 ( 335) CTCTACACACTTGTCCAACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3360 bayes= 9.51064 E= 8.2e-010 134 35 -945 -945 -945 -945 -945 185 -945 216 -945 -945 -945 194 -945 -95 183 -945 -945 -945 161 -64 -945 -945 134 -64 -61 -945 -945 216 -945 -945 2 168 -945 -945 134 -64 -61 -945 -945 168 -945 4 -945 35 -945 136 -945 168 39 -945 -98 -945 -945 163 -945 216 -945 -945 102 94 -945 -945 183 -945 -945 -945 2 168 -945 -945 61 35 -61 -95 2 94 -61 -95 -945 216 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 8.2e-010 0.714286 0.285714 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.857143 0.000000 0.142857 1.000000 0.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.714286 0.142857 0.142857 0.000000 0.000000 1.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 0.714286 0.142857 0.142857 0.000000 0.000000 0.714286 0.000000 0.285714 0.000000 0.285714 0.000000 0.714286 0.000000 0.714286 0.285714 0.000000 0.142857 0.000000 0.000000 0.857143 0.000000 1.000000 0.000000 0.000000 0.571429 0.428571 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 0.428571 0.285714 0.142857 0.142857 0.285714 0.428571 0.142857 0.142857 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AC]TCCAAAC[CA]A[CT][TC][CG]TC[AC]A[CA][AC][CA]C -------------------------------------------------------------------------------- Time 0.41 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 4 llr = 93 E-value = 1.0e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::a:3::8a8::538:::: pos.-specific C :3:::::::::::a:3:5:38 probability G a::a:::aa3::a:55:5a8: matrix T :8a::a8::::3::::3:::3 bits 2.2 * * ** ** * 2.0 * * ** ** * 1.8 * **** ** * ** * 1.5 * **** ** * ** * Relative 1.3 * **** ** * ** *** Entropy 1.1 *************** ***** (33.5 bits) 0.9 *************** ***** 0.7 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GTTGATTGGAAAGCAGACGGC consensus C A G T GATG CT sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8898 100 1.24e-13 CGGAGATATT GTTGATTGGAAAGCGGAGGGC ATGGTGGTTG 8895 167 1.24e-13 AACCCCTATT GTTGATTGGAAAGCGGAGGGC ACGGTGGTTG 24954 116 3.59e-11 AGCGGACTTG GCTGATTGGGAAGCAAACGGC ATGATGATAT 6615 76 2.12e-10 ATTGCTGAGT GTTGATAGGAATGCACTCGCT TGCAGGCTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8898 1.2e-13 99_[+2]_380 8895 1.2e-13 166_[+2]_313 24954 3.6e-11 115_[+2]_364 6615 2.1e-10 75_[+2]_404 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=4 8898 ( 100) GTTGATTGGAAAGCGGAGGGC 1 8895 ( 167) GTTGATTGGAAAGCGGAGGGC 1 24954 ( 116) GCTGATTGGGAAGCAAACGGC 1 6615 ( 76) GTTGATAGGAATGCACTCGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3360 bayes= 9.71253 E= 1.0e-002 -865 -865 219 -865 -865 16 -865 143 -865 -865 -865 185 -865 -865 219 -865 183 -865 -865 -865 -865 -865 -865 185 -17 -865 -865 143 -865 -865 219 -865 -865 -865 219 -865 141 -865 20 -865 183 -865 -865 -865 141 -865 -865 -15 -865 -865 219 -865 -865 216 -865 -865 83 -865 120 -865 -17 16 120 -865 141 -865 -865 -15 -865 116 120 -865 -865 -865 219 -865 -865 16 178 -865 -865 174 -865 -15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 1.0e-002 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.250000 0.250000 0.500000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.750000 0.000000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[TC]TGAT[TA]GG[AG]A[AT]GC[AG][GAC][AT][CG]G[GC][CT] -------------------------------------------------------------------------------- Time 0.81 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 4 llr = 93 E-value = 7.9e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::a:::3::::83:a:88::: pos.-specific C a::a::3a::a3:a:8:::3a probability G :a::a3::5:::5::::3::: matrix T :::::85:5a::3::33:a8: bits 2.2 ** ** * * * * 2.0 ** ** * * * * 1.8 ***** * ** ** * * 1.5 ***** * ** ** * * Relative 1.3 ***** * ** *** * * Entropy 1.1 ****** ***** ******** (33.4 bits) 0.9 ****** ***** ******** 0.7 ****** ***** ******** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CGACGTTCGTCAGCACAATTC consensus GA T CA TTG C sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 8900 444 4.02e-13 GCTTCTATTG CGACGTTCTTCAGCACAATTC ATCCAACCCA 8895 439 9.05e-13 CGAACAACAA CGACGTCCTTCAGCACAATTC ATCCAAACCA 11720 437 2.15e-12 TCTCCGAATG CGACGTTCGTCAACACAATTC ATCCAAACCA 10018 392 2.03e-10 AGAAAGAAGA CGACGGACGTCCTCATTGTCC TCGTTCCTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8900 4e-13 443_[+3]_36 8895 9e-13 438_[+3]_41 11720 2.1e-12 436_[+3]_43 10018 2e-10 391_[+3]_88 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=4 8900 ( 444) CGACGTTCTTCAGCACAATTC 1 8895 ( 439) CGACGTCCTTCAGCACAATTC 1 11720 ( 437) CGACGTTCGTCAACACAATTC 1 10018 ( 392) CGACGGACGTCCTCATTGTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3360 bayes= 9.71253 E= 7.9e-002 -865 216 -865 -865 -865 -865 219 -865 183 -865 -865 -865 -865 216 -865 -865 -865 -865 219 -865 -865 -865 20 143 -17 16 -865 85 -865 216 -865 -865 -865 -865 120 85 -865 -865 -865 185 -865 216 -865 -865 141 16 -865 -865 -17 -865 120 -15 -865 216 -865 -865 183 -865 -865 -865 -865 174 -865 -15 141 -865 -865 -15 141 -865 20 -865 -865 -865 -865 185 -865 16 -865 143 -865 216 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 7.9e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.250000 0.250000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.250000 0.000000 0.500000 0.250000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.750000 0.000000 0.000000 0.250000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CGACG[TG][TAC]C[GT]TC[AC][GAT]CA[CT][AT][AG]T[TC]C -------------------------------------------------------------------------------- Time 1.19 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10018 5.71e-11 334_[+1(1.45e-08)]_36_\ [+3(2.03e-10)]_88 11720 2.62e-17 436_[+3(2.15e-12)]_[+1(2.51e-13)]_\ 22 24954 2.38e-11 115_[+2(3.59e-11)]_330_\ [+1(5.94e-09)]_13 6615 2.50e-10 75_[+2(2.12e-10)]_238_\ [+1(2.97e-08)]_145 8895 6.50e-26 166_[+2(1.24e-13)]_251_\ [+3(9.05e-13)]_[+1(2.35e-12)]_20 8898 3.62e-18 99_[+2(1.24e-13)]_337_\ [+1(2.51e-13)]_22 8900 3.37e-16 443_[+3(4.02e-13)]_[+1(1.02e-11)]_\ 15 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************