******************************************************************************** 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/270/270.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 17226 1.0000 500 32379 1.0000 500 8890 1.0000 500 47232 1.0000 500 38878 1.0000 500 50485 1.0000 500 45065 1.0000 500 45283 1.0000 500 45285 1.0000 500 27082 1.0000 500 46215 1.0000 500 39430 1.0000 500 47336 1.0000 500 46750 1.0000 500 47084 1.0000 500 49613 1.0000 500 50108 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/270/270.seqs.fa -oc motifs/270 -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= 17 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= 8500 N= 17 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.264 C 0.242 G 0.229 T 0.265 Background letter frequencies (from dataset with add-one prior applied): A 0.264 C 0.242 G 0.229 T 0.265 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 10 llr = 131 E-value = 9.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::129:::9:9:2:9 pos.-specific C :6354:3131a:1:71 probability G 3:::21::5:::9:3: matrix T 74742:792::1:8:: bits 2.1 * 1.9 * 1.7 * * 1.5 * * **** * Relative 1.3 * * ******* Entropy 1.1 *** *** ******* (18.9 bits) 0.9 *** *** ******* 0.6 **** *********** 0.4 **** *********** 0.2 **** *********** 0.0 ---------------- Multilevel TCTCCATTGACAGTCA consensus GTCTA C C AG sequence G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 27082 485 4.62e-09 ACTCTATCTC TTTCCATTCACAGTCA 45285 476 1.56e-08 TAGGCAGCTG TCTCGATTGACAGTGA AGGCTAAAT 17226 288 2.00e-08 TTATTGTTAG GCTTCATTCACAGTCA GTTTCACCAT 49613 390 4.61e-07 TGCGATTGAT TCTTTACTGACAGAGA CAGTTTCCGC 39430 108 5.49e-07 AATGTCCTCC TTCCAATCGACAGTCA GGATGATTTA 38878 337 5.94e-07 TGTGCTCGTT TTTTCGTTGACAGACA CTAGTGTTAA 47084 51 6.89e-07 AACGGGTCTT TTTCCACTTCCAGTCA GGTCGAGCTG 50108 188 1.39e-06 TTTCACATAC GCCCGACTGACACTCA ACGGACGTCT 45065 46 2.12e-06 AGAGTACGGT GCCAAATTTACAGTGA TCTACACAAT 46750 287 2.38e-06 TCTACGTACT TCTTTATTCACTGTCC GTGTCAGCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 27082 4.6e-09 484_[+1] 45285 1.6e-08 475_[+1]_9 17226 2e-08 287_[+1]_197 49613 4.6e-07 389_[+1]_95 39430 5.5e-07 107_[+1]_377 38878 5.9e-07 336_[+1]_148 47084 6.9e-07 50_[+1]_434 50108 1.4e-06 187_[+1]_297 45065 2.1e-06 45_[+1]_439 46750 2.4e-06 286_[+1]_198 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=10 27082 ( 485) TTTCCATTCACAGTCA 1 45285 ( 476) TCTCGATTGACAGTGA 1 17226 ( 288) GCTTCATTCACAGTCA 1 49613 ( 390) TCTTTACTGACAGAGA 1 39430 ( 108) TTCCAATCGACAGTCA 1 38878 ( 337) TTTTCGTTGACAGACA 1 47084 ( 51) TTTCCACTTCCAGTCA 1 50108 ( 188) GCCCGACTGACACTCA 1 45065 ( 46) GCCAAATTTACAGTGA 1 46750 ( 287) TCTTTATTCACTGTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8245 bayes= 9.93744 E= 9.8e-001 -997 -997 39 140 -997 131 -997 59 -997 31 -997 140 -140 104 -997 59 -40 72 -19 -41 177 -997 -119 -997 -997 31 -997 140 -997 -128 -997 176 -997 31 113 -41 177 -128 -997 -997 -997 204 -997 -997 177 -997 -997 -141 -997 -128 198 -997 -40 -997 -997 159 -997 153 39 -997 177 -128 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 10 E= 9.8e-001 0.000000 0.000000 0.300000 0.700000 0.000000 0.600000 0.000000 0.400000 0.000000 0.300000 0.000000 0.700000 0.100000 0.500000 0.000000 0.400000 0.200000 0.400000 0.200000 0.200000 0.900000 0.000000 0.100000 0.000000 0.000000 0.300000 0.000000 0.700000 0.000000 0.100000 0.000000 0.900000 0.000000 0.300000 0.500000 0.200000 0.900000 0.100000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.900000 0.000000 0.000000 0.100000 0.000000 0.100000 0.900000 0.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.700000 0.300000 0.000000 0.900000 0.100000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TG][CT][TC][CT][CAGT]A[TC]T[GCT]ACAG[TA][CG]A -------------------------------------------------------------------------------- Time 3.34 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 8 llr = 108 E-value = 1.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1:::4935:1:61::: pos.-specific C 9:4:6:4:::::3:1a probability G ::44::3:a19:5::: matrix T :a36:115:8141a9: bits 2.1 * * 1.9 * * * * 1.7 * * * * 1.5 ** * * *** Relative 1.3 ** * * * *** Entropy 1.1 ** *** * ** *** (19.6 bits) 0.9 ** *** ***** *** 0.6 ** *** ***** *** 0.4 ****** ***** *** 0.2 **************** 0.0 ---------------- Multilevel CTCTCACAGTGAGTTC consensus GGA AT TC sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 50108 90 4.54e-10 CAGGTACGGG CTGTCACTGTGAGTTC GTTGTATAAT 38878 53 2.11e-07 TTGTCAAAAA CTCGCTCAGTGTGTTC GGATCCTGAA 45285 284 2.32e-07 GGTCGCACCG CTTTCAGAGTTAGTTC TAGAGACAAG 50485 196 2.32e-07 TTGGTGGTAG CTGGCAGTGAGTGTTC ACTGCATGCA 49613 330 2.78e-07 GACGAACGAA CTTGAACAGTGAATTC TCGTTACCTC 39430 198 3.83e-07 ACGCAAATTT ATCTCAATGTGACTTC CAAATGTCGT 47336 148 7.87e-07 GGAAGAGCCT CTGTAATTGGGACTTC AATCGCAAAA 46750 415 1.55e-06 TATTGCCAAC CTCTAAAAGTGTTTCC AGTCCACCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50108 4.5e-10 89_[+2]_395 38878 2.1e-07 52_[+2]_432 45285 2.3e-07 283_[+2]_201 50485 2.3e-07 195_[+2]_289 49613 2.8e-07 329_[+2]_155 39430 3.8e-07 197_[+2]_287 47336 7.9e-07 147_[+2]_337 46750 1.6e-06 414_[+2]_70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=8 50108 ( 90) CTGTCACTGTGAGTTC 1 38878 ( 53) CTCGCTCAGTGTGTTC 1 45285 ( 284) CTTTCAGAGTTAGTTC 1 50485 ( 196) CTGGCAGTGAGTGTTC 1 49613 ( 330) CTTGAACAGTGAATTC 1 39430 ( 198) ATCTCAATGTGACTTC 1 47336 ( 148) CTGTAATTGGGACTTC 1 46750 ( 415) CTCTAAAAGTGTTTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8245 bayes= 10.0079 E= 1.2e+003 -107 185 -965 -965 -965 -965 -965 191 -965 63 71 -9 -965 -965 71 124 51 137 -965 -965 173 -965 -965 -108 -8 63 13 -108 92 -965 -965 91 -965 -965 213 -965 -107 -965 -87 150 -965 -965 193 -108 124 -965 -965 50 -107 4 113 -108 -965 -965 -965 191 -965 -95 -965 172 -965 204 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 8 E= 1.2e+003 0.125000 0.875000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.375000 0.375000 0.250000 0.000000 0.000000 0.375000 0.625000 0.375000 0.625000 0.000000 0.000000 0.875000 0.000000 0.000000 0.125000 0.250000 0.375000 0.250000 0.125000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.125000 0.000000 0.125000 0.750000 0.000000 0.000000 0.875000 0.125000 0.625000 0.000000 0.000000 0.375000 0.125000 0.250000 0.500000 0.125000 0.000000 0.000000 0.000000 1.000000 0.000000 0.125000 0.000000 0.875000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CT[CGT][TG][CA]A[CAG][AT]GTG[AT][GC]TTC -------------------------------------------------------------------------------- Time 6.44 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 5 llr = 68 E-value = 1.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :62:a:2:8:a: pos.-specific C :26::a8:2a:2 probability G a:2a:::a:::8 matrix T :2:::::::::: bits 2.1 * * * * * 1.9 * *** * ** 1.7 * *** * ** 1.5 * *** * *** Relative 1.3 * ********* Entropy 1.1 * ********* (19.5 bits) 0.9 * ********* 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GACGACCGACAG consensus CA A C C sequence TG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 47232 274 4.58e-08 ATCCGCTAGC GACGACCGACAG CGGTGCATCA 50108 459 2.69e-07 AGCTCTATCG GACGACCGCCAG ATTGAAAACT 38878 286 3.68e-07 TAAATGGGTA GACGACAGACAG TTGTCTTCTC 47084 284 4.97e-07 TCAATCAAAC GCAGACCGACAG ATAGGGTAGG 47336 32 1.59e-06 TGCCGGTGCG GTGGACCGACAC AACCATTCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47232 4.6e-08 273_[+3]_215 50108 2.7e-07 458_[+3]_30 38878 3.7e-07 285_[+3]_203 47084 5e-07 283_[+3]_205 47336 1.6e-06 31_[+3]_457 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=5 47232 ( 274) GACGACCGACAG 1 50108 ( 459) GACGACCGCCAG 1 38878 ( 286) GACGACAGACAG 1 47084 ( 284) GCAGACCGACAG 1 47336 ( 32) GTGGACCGACAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 8313 bayes= 10.95 E= 1.7e+003 -897 -897 213 -897 118 -28 -897 -41 -40 131 -19 -897 -897 -897 213 -897 192 -897 -897 -897 -897 204 -897 -897 -40 172 -897 -897 -897 -897 213 -897 160 -28 -897 -897 -897 204 -897 -897 192 -897 -897 -897 -897 -28 180 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 5 E= 1.7e+003 0.000000 0.000000 1.000000 0.000000 0.600000 0.200000 0.000000 0.200000 0.200000 0.600000 0.200000 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 0.200000 0.800000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[ACT][CAG]GAC[CA]G[AC]CA[GC] -------------------------------------------------------------------------------- Time 9.58 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17226 3.39e-04 287_[+1(2.00e-08)]_197 32379 6.36e-01 500 8890 6.24e-01 500 47232 5.55e-04 273_[+3(4.58e-08)]_215 38878 1.93e-09 52_[+2(2.11e-07)]_217_\ [+3(3.68e-07)]_39_[+1(5.94e-07)]_80_[+2(7.76e-05)]_52 50485 4.66e-04 195_[+2(2.32e-07)]_289 45065 1.42e-02 45_[+1(2.12e-06)]_439 45283 9.99e-01 500 45285 1.16e-07 117_[+1(7.85e-05)]_150_\ [+2(2.32e-07)]_176_[+1(1.56e-08)]_9 27082 1.14e-05 189_[+1(9.04e-05)]_279_\ [+1(4.62e-09)] 46215 3.80e-01 500 39430 1.50e-06 107_[+1(5.49e-07)]_74_\ [+2(3.83e-07)]_287 47336 1.93e-05 31_[+3(1.59e-06)]_104_\ [+2(7.87e-07)]_337 46750 7.05e-05 286_[+1(2.38e-06)]_112_\ [+2(1.55e-06)]_70 47084 1.14e-05 50_[+1(6.89e-07)]_217_\ [+3(4.97e-07)]_205 49613 2.41e-06 329_[+2(2.78e-07)]_44_\ [+1(4.61e-07)]_95 50108 1.04e-11 89_[+2(4.54e-10)]_82_[+1(1.39e-06)]_\ 255_[+3(2.69e-07)]_30 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************