******************************************************************************** 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/323/323.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42466 1.0000 500 42481 1.0000 500 47826 1.0000 500 48445 1.0000 500 4741 1.0000 500 49711 1.0000 500 44041 1.0000 500 4003 1.0000 500 12243 1.0000 500 45794 1.0000 500 48047 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/323/323.seqs.fa -oc motifs/323 -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 0.267 C 0.250 G 0.221 T 0.262 Background letter frequencies (from dataset with add-one prior applied): A 0.267 C 0.250 G 0.221 T 0.262 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 7 llr = 112 E-value = 4.8e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 33:414::9374:7aa3:96: pos.-specific C 73a33:aa13111:::73::6 probability G :4:161:::3:393:::7141 matrix T :::1:4:::111::::::::3 bits 2.2 2.0 * ** ** 1.7 * ** ** 1.5 * ** * ** Relative 1.3 * *** * ** ** Entropy 1.1 * * *** ******** (23.2 bits) 0.9 * * *** * ******** 0.7 * * * *** * ********* 0.4 *** ***** * ********* 0.2 ********* *********** 0.0 --------------------- Multilevel CGCAGACCAAAAGAAACGAAC consensus AA CCT C G G AC GT sequence C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 12243 457 2.20e-10 CCTTTGTCAC CGCAGACCAAAGGAAACGAAG TTGCCATTGT 42481 224 2.58e-09 AAGGGAAGAT CGCCGTCCATAAGAAACCAGT CGTCGAATGG 45794 364 7.39e-09 TTGTGCAATC CGCAGGCCCGAAGAAAAGAGC GACGTGACGA 4741 289 3.24e-08 TCTTGAAACA CACACTCCAAAACGAACGAAT ACCGGACCAT 44041 39 5.99e-08 ACACTTATAT CCCCATCCAGCCGGAACGAGC GAATTCCCCC 48445 155 8.34e-08 CATTGGAGGC AACTGACCACATGAAAACAAC CCTTGTGATC 42466 295 1.50e-07 AGCGAATAGG ACCGCACCACTGGAAACGGAC TTTGGAAATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 12243 2.2e-10 456_[+1]_23 42481 2.6e-09 223_[+1]_256 45794 7.4e-09 363_[+1]_116 4741 3.2e-08 288_[+1]_191 44041 6e-08 38_[+1]_441 48445 8.3e-08 154_[+1]_325 42466 1.5e-07 294_[+1]_185 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=7 12243 ( 457) CGCAGACCAAAGGAAACGAAG 1 42481 ( 224) CGCCGTCCATAAGAAACCAGT 1 45794 ( 364) CGCAGGCCCGAAGAAAAGAGC 1 4741 ( 289) CACACTCCAAAACGAACGAAT 1 44041 ( 39) CCCCATCCAGCCGGAACGAGC 1 48445 ( 155) AACTGACCACATGAAAACAAC 1 42466 ( 295) ACCGCACCACTGGAAACGGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5280 bayes= 9.40072 E= 4.8e+001 10 152 -945 -945 10 19 96 -945 -945 200 -945 -945 68 19 -63 -87 -90 19 137 -945 68 -945 -63 71 -945 200 -945 -945 -945 200 -945 -945 168 -80 -945 -945 10 19 37 -87 142 -80 -945 -87 68 -80 37 -87 -945 -80 196 -945 142 -945 37 -945 190 -945 -945 -945 190 -945 -945 -945 10 152 -945 -945 -945 19 169 -945 168 -945 -63 -945 109 -945 96 -945 -945 119 -63 12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 4.8e+001 0.285714 0.714286 0.000000 0.000000 0.285714 0.285714 0.428571 0.000000 0.000000 1.000000 0.000000 0.000000 0.428571 0.285714 0.142857 0.142857 0.142857 0.285714 0.571429 0.000000 0.428571 0.000000 0.142857 0.428571 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.857143 0.142857 0.000000 0.000000 0.285714 0.285714 0.285714 0.142857 0.714286 0.142857 0.000000 0.142857 0.428571 0.142857 0.285714 0.142857 0.000000 0.142857 0.857143 0.000000 0.714286 0.000000 0.285714 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.857143 0.000000 0.142857 0.000000 0.571429 0.000000 0.428571 0.000000 0.000000 0.571429 0.142857 0.285714 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA][GAC]C[AC][GC][AT]CCA[ACG]A[AG]G[AG]AA[CA][GC]A[AG][CT] -------------------------------------------------------------------------------- Time 1.05 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 18 sites = 7 llr = 103 E-value = 2.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1:::::::43:17:::94 pos.-specific C :3a:::164:411::9:6 probability G :::a:134161313:1:: matrix T 97::a96::144:7a:1: bits 2.2 * 2.0 *** * 1.7 *** * 1.5 *** ** Relative 1.3 * **** *** Entropy 1.1 ****** * **** (21.2 bits) 0.9 ****** * ****** 0.7 ******** ** ****** 0.4 *********** ****** 0.2 ****************** 0.0 ------------------ Multilevel TTCGTTTCAGCTATTCAC consensus C GGCATG G A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------ 12243 314 1.89e-11 CCATGAAAAC TTCGTTTCCGCTATTCAC CACTCTATTT 45794 146 4.14e-09 CAGAAACTCT TTCGTTGCAGTTAGTCAC CGTTAGTTAG 47826 398 2.61e-08 CGACCAAACG TTCGTTGGGGCAATTCAC ATCATCATCA 49711 83 5.47e-08 AAAACGACAC TCCGTTTCCGGCATTCAA AGATCTTGAG 48047 480 4.36e-07 GCTCCGGTCT TTCGTGTGATTGATTCTC ACC 48445 107 4.88e-07 GAGGTTAGTA ATCGTTTGCATGGGTCAA TGCCAGCCCC 4741 268 9.84e-07 AACGGTCGAA TCCGTTCCAACTCTTGAA ACACACACTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 12243 1.9e-11 313_[+2]_169 45794 4.1e-09 145_[+2]_337 47826 2.6e-08 397_[+2]_85 49711 5.5e-08 82_[+2]_400 48047 4.4e-07 479_[+2]_3 48445 4.9e-07 106_[+2]_376 4741 9.8e-07 267_[+2]_215 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=18 seqs=7 12243 ( 314) TTCGTTTCCGCTATTCAC 1 45794 ( 146) TTCGTTGCAGTTAGTCAC 1 47826 ( 398) TTCGTTGGGGCAATTCAC 1 49711 ( 83) TCCGTTTCCGGCATTCAA 1 48047 ( 480) TTCGTGTGATTGATTCTC 1 48445 ( 107) ATCGTTTGCATGGGTCAA 1 4741 ( 268) TCCGTTCCAACTCTTGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 5313 bayes= 9.40972 E= 2.4e+002 -90 -945 -945 171 -945 19 -945 144 -945 200 -945 -945 -945 -945 218 -945 -945 -945 -945 193 -945 -945 -63 171 -945 -80 37 112 -945 119 96 -945 68 78 -63 -945 10 -945 137 -87 -945 78 -63 71 -90 -80 37 71 142 -80 -63 -945 -945 -945 37 144 -945 -945 -945 193 -945 178 -63 -945 168 -945 -945 -87 68 119 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 7 E= 2.4e+002 0.142857 0.000000 0.000000 0.857143 0.000000 0.285714 0.000000 0.714286 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 0.142857 0.857143 0.000000 0.142857 0.285714 0.571429 0.000000 0.571429 0.428571 0.000000 0.428571 0.428571 0.142857 0.000000 0.285714 0.000000 0.571429 0.142857 0.000000 0.428571 0.142857 0.428571 0.142857 0.142857 0.285714 0.428571 0.714286 0.142857 0.142857 0.000000 0.000000 0.000000 0.285714 0.714286 0.000000 0.000000 0.000000 1.000000 0.000000 0.857143 0.142857 0.000000 0.857143 0.000000 0.000000 0.142857 0.428571 0.571429 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[TC]CGTT[TG][CG][AC][GA][CT][TG]A[TG]TCA[CA] -------------------------------------------------------------------------------- Time 2.09 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 13 sites = 7 llr = 87 E-value = 2.6e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::::::::1:1:: pos.-specific C :::a:7:6::197 probability G :4:::31196::: matrix T a6a:a:93:4713 bits 2.2 2.0 * *** 1.7 * *** 1.5 * *** * Relative 1.3 * *** * * * Entropy 1.1 ******* ** ** (18.0 bits) 0.9 ******* ***** 0.7 ************* 0.4 ************* 0.2 ************* 0.0 ------------- Multilevel TTTCTCTCGGTCC consensus G G T T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------- 4741 56 6.22e-08 TTGGTCCCTG TGTCTCTCGTTCC AAAGTTGGTT 45794 424 2.56e-07 CAGTTGAACC TTTCTCTCGTTCT TTTTGCGAAG 12243 339 7.96e-07 CACCACTCTA TTTCTCTGGGTCT CATTTCCCTC 4003 152 1.05e-06 TAGGTGAGGA TGTCTCTCATTCC GGAGTCTCCT 44041 136 1.05e-06 AAAAAGACCG TGTCTGTCGGACC CGCAGCTGCC 47826 232 1.13e-06 CCTATGTCTT TTTCTCTTGGTTC ACTGGATGAT 49711 223 5.70e-06 CTATCTTCCG TTTCTGGTGGCCC TTCACAGTCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4741 6.2e-08 55_[+3]_432 45794 2.6e-07 423_[+3]_64 12243 8e-07 338_[+3]_149 4003 1e-06 151_[+3]_336 44041 1e-06 135_[+3]_352 47826 1.1e-06 231_[+3]_256 49711 5.7e-06 222_[+3]_265 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=13 seqs=7 4741 ( 56) TGTCTCTCGTTCC 1 45794 ( 424) TTTCTCTCGTTCT 1 12243 ( 339) TTTCTCTGGGTCT 1 4003 ( 152) TGTCTCTCATTCC 1 44041 ( 136) TGTCTGTCGGACC 1 47826 ( 232) TTTCTCTTGGTTC 1 49711 ( 223) TTTCTGGTGGCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 5368 bayes= 9.4246 E= 2.6e+002 -945 -945 -945 193 -945 -945 96 112 -945 -945 -945 193 -945 200 -945 -945 -945 -945 -945 193 -945 152 37 -945 -945 -945 -63 171 -945 119 -63 12 -90 -945 196 -945 -945 -945 137 71 -90 -80 -945 144 -945 178 -945 -87 -945 152 -945 12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 7 E= 2.6e+002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.428571 0.571429 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.714286 0.285714 0.000000 0.000000 0.000000 0.142857 0.857143 0.000000 0.571429 0.142857 0.285714 0.142857 0.000000 0.857143 0.000000 0.000000 0.000000 0.571429 0.428571 0.142857 0.142857 0.000000 0.714286 0.000000 0.857143 0.000000 0.142857 0.000000 0.714286 0.000000 0.285714 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[TG]TCT[CG]T[CT]G[GT]TC[CT] -------------------------------------------------------------------------------- Time 3.14 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42466 2.63e-03 294_[+1(1.50e-07)]_185 42481 8.23e-06 223_[+1(2.58e-09)]_256 47826 6.99e-07 231_[+3(1.13e-06)]_153_\ [+2(2.61e-08)]_85 48445 1.57e-07 106_[+2(4.88e-07)]_30_\ [+1(8.34e-08)]_325 4741 1.02e-10 55_[+3(6.22e-08)]_199_\ [+2(9.84e-07)]_3_[+1(3.24e-08)]_191 49711 9.97e-06 82_[+2(5.47e-08)]_122_\ [+3(5.70e-06)]_265 44041 1.97e-06 38_[+1(5.99e-08)]_76_[+3(1.05e-06)]_\ 352 4003 1.42e-02 151_[+3(1.05e-06)]_336 12243 3.53e-16 313_[+2(1.89e-11)]_7_[+3(7.96e-07)]_\ 105_[+1(2.20e-10)]_23 45794 5.64e-13 145_[+2(4.14e-09)]_200_\ [+1(7.39e-09)]_39_[+3(2.56e-07)]_64 48047 7.15e-03 479_[+2(4.36e-07)]_3 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************