******************************************************************************** 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/91/91.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 42437 1.0000 500 31980 1.0000 500 42962 1.0000 500 13383 1.0000 500 7656 1.0000 500 49107 1.0000 500 44062 1.0000 500 33705 1.0000 500 7621 1.0000 500 11608 1.0000 500 2418 1.0000 500 38777 1.0000 500 32195 1.0000 500 48083 1.0000 500 44487 1.0000 500 48520 1.0000 500 33580 1.0000 500 45355 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/91/91.seqs.fa -oc motifs/91 -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= 18 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= 9000 N= 18 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.271 C 0.236 G 0.224 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.271 C 0.236 G 0.224 T 0.269 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 8 llr = 117 E-value = 6.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::4:::1:::544:1: pos.-specific C 83::::65:41::::a probability G :8:::1:4a6:::::: matrix T 3:6aa931::466a9: bits 2.2 * * 1.9 ** * * * 1.7 ** * * * 1.5 ** * * * Relative 1.3 ** *** * *** Entropy 1.1 ** *** ** *** (21.1 bits) 0.9 ****** ** ***** 0.6 ********** ***** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CGTTTTCCGGATTTTC consensus TCA TG CTAA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 38777 246 1.79e-09 TTCGGCTCGC CGTTTTCCGGAATTTC CAGTCGTTGT 42962 119 3.68e-08 TGTAACGGCA CGTTTTACGGTTTTTC GTCCTATGGA 45355 131 6.42e-08 TCTCGGCTTG CCTTTTTCGGTTTTTC CATTTTTGGT 33705 177 7.24e-08 AGAGAATCGA TGATTTCGGCATTTTC CTGAAAATGT 48520 273 9.62e-08 GTGAGTGTAT CGATTTTGGGAAATTC TGTTCTGATT 7621 119 1.13e-07 TTGTCTCCAG CGTTTTCGGGTATTAC ATTGGATGTT 44487 475 2.69e-07 TCACATCAAC TGTTTTCTGCATATTC CAAACGCACC 48083 389 8.37e-07 GCGGCGTTGA CCATTGCCGCCTATTC CTATTCGCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38777 1.8e-09 245_[+1]_239 42962 3.7e-08 118_[+1]_366 45355 6.4e-08 130_[+1]_354 33705 7.2e-08 176_[+1]_308 48520 9.6e-08 272_[+1]_212 7621 1.1e-07 118_[+1]_366 44487 2.7e-07 474_[+1]_10 48083 8.4e-07 388_[+1]_96 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=8 38777 ( 246) CGTTTTCCGGAATTTC 1 42962 ( 119) CGTTTTACGGTTTTTC 1 45355 ( 131) CCTTTTTCGGTTTTTC 1 33705 ( 177) TGATTTCGGCATTTTC 1 48520 ( 273) CGATTTTGGGAAATTC 1 7621 ( 119) CGTTTTCGGGTATTAC 1 44487 ( 475) TGTTTTCTGCATATTC 1 48083 ( 389) CCATTGCCGCCTATTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 8730 bayes= 10.8279 E= 6.4e-001 -965 167 -965 -11 -965 8 174 -965 47 -965 -965 121 -965 -965 -965 189 -965 -965 -965 189 -965 -965 -84 170 -111 140 -965 -11 -965 108 74 -110 -965 -965 216 -965 -965 67 148 -965 88 -92 -965 48 47 -965 -965 121 47 -965 -965 121 -965 -965 -965 189 -111 -965 -965 170 -965 208 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 8 E= 6.4e-001 0.000000 0.750000 0.000000 0.250000 0.000000 0.250000 0.750000 0.000000 0.375000 0.000000 0.000000 0.625000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.125000 0.875000 0.125000 0.625000 0.000000 0.250000 0.000000 0.500000 0.375000 0.125000 0.000000 0.000000 1.000000 0.000000 0.000000 0.375000 0.625000 0.000000 0.500000 0.125000 0.000000 0.375000 0.375000 0.000000 0.000000 0.625000 0.375000 0.000000 0.000000 0.625000 0.000000 0.000000 0.000000 1.000000 0.125000 0.000000 0.000000 0.875000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][GC][TA]TTT[CT][CG]G[GC][AT][TA][TA]TTC -------------------------------------------------------------------------------- Time 2.77 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 14 sites = 11 llr = 131 E-value = 1.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::8171::944:: pos.-specific C 211:9::::15:1: probability G ::32::914:238: matrix T 896::3:96::41a bits 2.2 1.9 * 1.7 * * * 1.5 * * ** * * Relative 1.3 ** ** ** * ** Entropy 1.1 ** ******* ** (17.1 bits) 0.9 ** ******* ** 0.6 ********** ** 0.4 ************** 0.2 ************** 0.0 -------------- Multilevel TTTACAGTTACAGT consensus G T G AT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------- 33705 385 2.92e-08 GAAAGAAAAG TTTACAGTTAAAGT TTCCAATTTA 42437 311 1.74e-07 TCACAGGTAA TTTGCAGTTACGGT AGAGGCTGGC 44062 175 2.07e-07 ACAAGGAGCG TTGACAGTGAAAGT TCACTCTCCC 33580 277 3.60e-07 TATTGCATAA TTGACAGTGAGAGT GAGTGAAAAA 49107 223 1.09e-06 AACACTTTTA TTTACAGTTAAGTT TAAAATTGGC 48083 352 1.40e-06 TAGCAAACAC TTTACTGGTACTGT TGCTACCTAG 48520 257 1.80e-06 TGAAAATTGA CTGACAGTGAGTGT ATCGATTTTG 32195 251 2.14e-06 TTTTTTCCTT TCTACTGTTAATGT ACGCTCACTG 42962 383 6.00e-06 AGTTGTTGTG CTTACTGTTACGCT TTAGCGTCGC 31980 409 6.00e-06 ACAGTTAGCA TTCACAATGACTGT TAATAAAACT 7656 426 1.26e-05 TATACCTCTG TTTGAAGTTCCAGT TGATACGGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 33705 2.9e-08 384_[+2]_102 42437 1.7e-07 310_[+2]_176 44062 2.1e-07 174_[+2]_312 33580 3.6e-07 276_[+2]_210 49107 1.1e-06 222_[+2]_264 48083 1.4e-06 351_[+2]_135 48520 1.8e-06 256_[+2]_230 32195 2.1e-06 250_[+2]_236 42962 6e-06 382_[+2]_104 31980 6e-06 408_[+2]_78 7656 1.3e-05 425_[+2]_61 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=14 seqs=11 33705 ( 385) TTTACAGTTAAAGT 1 42437 ( 311) TTTGCAGTTACGGT 1 44062 ( 175) TTGACAGTGAAAGT 1 33580 ( 277) TTGACAGTGAGAGT 1 49107 ( 223) TTTACAGTTAAGTT 1 48083 ( 352) TTTACTGGTACTGT 1 48520 ( 257) CTGACAGTGAGTGT 1 32195 ( 251) TCTACTGTTAATGT 1 42962 ( 383) CTTACTGTTACGCT 1 31980 ( 409) TTCACAATGACTGT 1 7656 ( 426) TTTGAAGTTCCAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 8766 bayes= 9.99195 E= 1.4e+000 -1010 -38 -1010 160 -1010 -137 -1010 176 -1010 -137 28 124 159 -1010 -30 -1010 -157 194 -1010 -1010 142 -1010 -1010 2 -157 -1010 202 -1010 -1010 -1010 -130 176 -1010 -1010 70 124 175 -137 -1010 -1010 42 94 -30 -1010 42 -1010 28 43 -1010 -137 187 -156 -1010 -1010 -1010 189 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 11 E= 1.4e+000 0.000000 0.181818 0.000000 0.818182 0.000000 0.090909 0.000000 0.909091 0.000000 0.090909 0.272727 0.636364 0.818182 0.000000 0.181818 0.000000 0.090909 0.909091 0.000000 0.000000 0.727273 0.000000 0.000000 0.272727 0.090909 0.000000 0.909091 0.000000 0.000000 0.000000 0.090909 0.909091 0.000000 0.000000 0.363636 0.636364 0.909091 0.090909 0.000000 0.000000 0.363636 0.454545 0.181818 0.000000 0.363636 0.000000 0.272727 0.363636 0.000000 0.090909 0.818182 0.090909 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TT[TG]AC[AT]GT[TG]A[CA][ATG]GT -------------------------------------------------------------------------------- Time 6.02 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 14 llr = 139 E-value = 1.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 12:1:11:::99 pos.-specific C 11:::1::44:: probability G 1:::55:166:1 matrix T 77a95399::1: bits 2.2 1.9 * 1.7 * 1.5 ** * * Relative 1.3 ** ** *** Entropy 1.1 *** ****** (14.3 bits) 0.9 **** ****** 0.6 ***** ****** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTTTGGTTGGAA consensus A TT CC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 48520 196 7.01e-08 CTCCAACGTC TTTTGGTTGGAA CAACCAGACT 48083 109 7.01e-08 AAAGCGTTGG TTTTGGTTGGAA TTCGCGACAC 45355 150 1.95e-06 GTTTTTCCAT TTTTGGTTGGAG AGCGTGATCA 31980 380 2.50e-06 AACGACCGAT TTTTTCTTCGAA CTAGCTCACA 42962 463 5.15e-06 CCATCCAAAA CTTTTTTTGGAA CAAACAGGAC 7656 451 1.14e-05 GATACGGAAT TTTTTGTTCGTA GTCTTGGCCA 33705 411 1.21e-05 CCAATTTAAG TTTTGGATGCAA AGTACGGTGG 44487 206 1.55e-05 TTGTTTAAGT GTTTTTTTCGAA TTTGGGGCCG 2418 123 1.81e-05 TCGATCCCGA TATTTCTTCCAA GAGATTGCTA 49107 81 2.81e-05 ACAAGAGCAT TTTATTTTGCAA TGCAGATCAA 32195 162 3.21e-05 GACGAATAGG TTTTTATGCGAA TGATCAATGT 44062 45 3.21e-05 GCTTTCGAAC AATTGTTTGGAA TAAAGAGAGA 13383 63 3.47e-05 AGCAGCCCCC TCTTGGTTGCAG TACGGAGGAC 11608 160 6.40e-05 CCGTTGCTGC CATTGGTGCCAA TTTTGGAAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 48520 7e-08 195_[+3]_293 48083 7e-08 108_[+3]_380 45355 1.9e-06 149_[+3]_339 31980 2.5e-06 379_[+3]_109 42962 5.2e-06 462_[+3]_26 7656 1.1e-05 450_[+3]_38 33705 1.2e-05 410_[+3]_78 44487 1.6e-05 205_[+3]_283 2418 1.8e-05 122_[+3]_366 49107 2.8e-05 80_[+3]_408 32195 3.2e-05 161_[+3]_327 44062 3.2e-05 44_[+3]_444 13383 3.5e-05 62_[+3]_426 11608 6.4e-05 159_[+3]_329 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=14 48520 ( 196) TTTTGGTTGGAA 1 48083 ( 109) TTTTGGTTGGAA 1 45355 ( 150) TTTTGGTTGGAG 1 31980 ( 380) TTTTTCTTCGAA 1 42962 ( 463) CTTTTTTTGGAA 1 7656 ( 451) TTTTTGTTCGTA 1 33705 ( 411) TTTTGGATGCAA 1 44487 ( 206) GTTTTTTTCGAA 1 2418 ( 123) TATTTCTTCCAA 1 49107 ( 81) TTTATTTTGCAA 1 32195 ( 162) TTTTTATGCGAA 1 44062 ( 45) AATTGTTTGGAA 1 13383 ( 63) TCTTGGTTGCAG 1 11608 ( 160) CATTGGTGCCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 8802 bayes= 10.5177 E= 1.4e+002 -192 -72 -165 141 -34 -172 -1045 141 -1045 -1045 -1045 189 -192 -1045 -1045 179 -1045 -1045 116 89 -192 -72 116 9 -192 -1045 -1045 179 -1045 -1045 -65 167 -1045 86 135 -1045 -1045 60 152 -1045 178 -1045 -1045 -191 166 -1045 -65 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 14 E= 1.4e+002 0.071429 0.142857 0.071429 0.714286 0.214286 0.071429 0.000000 0.714286 0.000000 0.000000 0.000000 1.000000 0.071429 0.000000 0.000000 0.928571 0.000000 0.000000 0.500000 0.500000 0.071429 0.142857 0.500000 0.285714 0.071429 0.000000 0.000000 0.928571 0.000000 0.000000 0.142857 0.857143 0.000000 0.428571 0.571429 0.000000 0.000000 0.357143 0.642857 0.000000 0.928571 0.000000 0.000000 0.071429 0.857143 0.000000 0.142857 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[TA]TT[GT][GT]TT[GC][GC]AA -------------------------------------------------------------------------------- Time 8.85 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42437 3.05e-03 310_[+2(1.74e-07)]_176 31980 1.66e-04 379_[+3(2.50e-06)]_17_\ [+2(6.00e-06)]_78 42962 3.71e-08 118_[+1(3.68e-08)]_248_\ [+2(6.00e-06)]_66_[+3(5.15e-06)]_26 13383 7.65e-02 62_[+3(3.47e-05)]_426 7656 1.64e-03 425_[+2(1.26e-05)]_11_\ [+3(1.14e-05)]_38 49107 2.51e-04 80_[+3(2.81e-05)]_130_\ [+2(1.09e-06)]_55_[+2(2.30e-06)]_195 44062 1.39e-04 44_[+3(3.21e-05)]_118_\ [+2(2.07e-07)]_312 33705 1.12e-09 176_[+1(7.24e-08)]_192_\ [+2(2.92e-08)]_12_[+3(1.21e-05)]_78 7621 1.09e-03 118_[+1(1.13e-07)]_366 11608 9.42e-02 159_[+3(6.40e-05)]_329 2418 6.57e-02 122_[+3(1.81e-05)]_366 38777 3.89e-05 245_[+1(1.79e-09)]_239 32195 6.05e-04 161_[+3(3.21e-05)]_77_\ [+2(2.14e-06)]_236 48083 3.29e-09 108_[+3(7.01e-08)]_23_\ [+3(7.96e-05)]_196_[+2(1.40e-06)]_23_[+1(8.37e-07)]_96 44487 3.63e-05 205_[+3(1.55e-05)]_257_\ [+1(2.69e-07)]_10 48520 5.62e-10 195_[+3(7.01e-08)]_49_\ [+2(1.80e-06)]_2_[+1(9.62e-08)]_9_[+3(9.74e-05)]_191 33580 4.56e-04 226_[+2(1.70e-06)]_36_\ [+2(3.60e-07)]_117_[+2(9.12e-06)]_79 45355 2.76e-06 130_[+1(6.42e-08)]_3_[+3(1.95e-06)]_\ 339 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************