******************************************************************************** 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/64/64.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 9011 1.0000 500 42822 1.0000 500 42864 1.0000 500 51422 1.0000 500 47096 1.0000 500 21369 1.0000 500 47614 1.0000 500 52285 1.0000 500 48196 1.0000 500 43646 1.0000 500 43693 1.0000 500 7164 1.0000 500 49316 1.0000 500 40647 1.0000 500 10437 1.0000 500 50514 1.0000 500 34096 1.0000 500 36252 1.0000 500 43074 1.0000 500 33876 1.0000 500 44912 1.0000 500 47050 1.0000 500 44299 1.0000 500 54749 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/64/64.seqs.fa -oc motifs/64 -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= 24 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= 12000 N= 24 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.276 C 0.229 G 0.221 T 0.274 Background letter frequencies (from dataset with add-one prior applied): A 0.276 C 0.229 G 0.221 T 0.273 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 23 llr = 213 E-value = 1.3e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :39:5::3a416 pos.-specific C 12:a:::2:131 probability G :5:::a14:43: matrix T 9:1:5:9:::33 bits 2.2 * * 2.0 * * 1.7 * * 1.5 * ** ** * Relative 1.3 * ** ** * Entropy 1.1 * ** ** * (13.3 bits) 0.9 * ***** * 0.7 ******* * * 0.4 ********** * 0.2 ********** * 0.0 ------------ Multilevel TGACAGTGAATA consensus A T A GCT sequence C C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 40647 313 6.45e-08 TCCACTACCT TGACAGTGAGTA GTTTTTGTGA 49316 300 6.33e-07 TAAAGCTGTA TGACTGTGAGGA AATTCCCGCT 54749 109 1.47e-06 TAAATTTCAT TGACAGTGAATT CAGCAATATC 43693 141 2.18e-06 CTTCCAACCC TGACAGTAAAGA GAAATAGAGA 43074 257 5.85e-06 TATGTTATAC TGACTGTGAAAA TGGGAAAACT 33876 423 7.72e-06 ATTTGCACGT TGACAGTGAGAT GCCTATGAGC 36252 312 9.47e-06 GCTTTTATTG TGACTGTCAACT GTCGGTTCCA 47050 305 1.14e-05 CGTTAAAAAA TAACTGTAAATA TAGTCGAGTC 21369 145 1.14e-05 TGTTCTTAAC TAACTGTAAGCA TTTTACTTAC 44299 195 1.40e-05 TAAATTACAT TGACTGTGACCT ACCTAATTTT 44912 112 1.40e-05 ACCAAGTCAC TGACTGTGACCT ACAATCTATT 43646 428 1.55e-05 ATGTCATTTC TCACAGTCAAGA TCAGCCCCTG 42864 352 1.74e-05 ACAGGTGCAT TAACAGTAAATT TTGGCCATAA 47096 440 2.04e-05 CGGAGGAGAG TCACAGTCAGTT AGTCCGACAT 9011 75 2.60e-05 TATGAAAATC TGTCAGTGAGTA GGCATATATC 42822 248 4.00e-05 CAATTTGCAT TAACTGTAAAAT TGAATTGTAC 52285 176 5.02e-05 AACGCAAGAT TCACTGTAAATC GTAGGTGCTG 50514 372 5.89e-05 AAACGAGTAC CAACTGTGAACA AAGCACTTGC 47614 217 5.89e-05 TCGATAGAGC TCACAGTCAGGC CTTTTAAAAT 48196 255 1.01e-04 ATCGAGTTCC TCACAGTCATGA AGAACGCCCA 34096 196 1.39e-04 AAACCTGGTA CAACAGTAACTA GGGTTTGTGG 7164 279 1.65e-04 CATTGAATTG TGTCAGGAAGCA TTTGAACTTG 10437 109 1.72e-04 TGTCATTGAT TGACTGGGGGGA GGGGAATTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 40647 6.4e-08 312_[+1]_176 49316 6.3e-07 299_[+1]_189 54749 1.5e-06 108_[+1]_380 43693 2.2e-06 140_[+1]_348 43074 5.9e-06 256_[+1]_232 33876 7.7e-06 422_[+1]_66 36252 9.5e-06 311_[+1]_177 47050 1.1e-05 304_[+1]_184 21369 1.1e-05 144_[+1]_344 44299 1.4e-05 194_[+1]_294 44912 1.4e-05 111_[+1]_377 43646 1.6e-05 427_[+1]_61 42864 1.7e-05 351_[+1]_137 47096 2e-05 439_[+1]_49 9011 2.6e-05 74_[+1]_414 42822 4e-05 247_[+1]_241 52285 5e-05 175_[+1]_313 50514 5.9e-05 371_[+1]_117 47614 5.9e-05 216_[+1]_272 48196 0.0001 254_[+1]_234 34096 0.00014 195_[+1]_293 7164 0.00017 278_[+1]_210 10437 0.00017 108_[+1]_380 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=23 40647 ( 313) TGACAGTGAGTA 1 49316 ( 300) TGACTGTGAGGA 1 54749 ( 109) TGACAGTGAATT 1 43693 ( 141) TGACAGTAAAGA 1 43074 ( 257) TGACTGTGAAAA 1 33876 ( 423) TGACAGTGAGAT 1 36252 ( 312) TGACTGTCAACT 1 47050 ( 305) TAACTGTAAATA 1 21369 ( 145) TAACTGTAAGCA 1 44299 ( 195) TGACTGTGACCT 1 44912 ( 112) TGACTGTGACCT 1 43646 ( 428) TCACAGTCAAGA 1 42864 ( 352) TAACAGTAAATT 1 47096 ( 440) TCACAGTCAGTT 1 9011 ( 75) TGTCAGTGAGTA 1 42822 ( 248) TAACTGTAAAAT 1 52285 ( 176) TCACTGTAAATC 1 50514 ( 372) CAACTGTGAACA 1 47614 ( 217) TCACAGTCAGGC 1 48196 ( 255) TCACAGTCATGA 1 34096 ( 196) CAACAGTAACTA 1 7164 ( 279) TGTCAGGAAGCA 1 10437 ( 109) TGACTGGGGGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 11736 bayes= 9.3955 E= 1.3e-006 -1117 -140 -1117 174 -8 -8 124 -1117 172 -1117 -1117 -165 -1117 212 -1117 -1117 92 -1117 -1117 81 -1117 -1117 218 -1117 -1117 -1117 -134 174 33 -8 98 -1117 179 -1117 -234 -1117 65 -81 83 -265 -108 19 24 35 103 -140 -1117 35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 23 E= 1.3e-006 0.000000 0.086957 0.000000 0.913043 0.260870 0.217391 0.521739 0.000000 0.913043 0.000000 0.000000 0.086957 0.000000 1.000000 0.000000 0.000000 0.521739 0.000000 0.000000 0.478261 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.086957 0.913043 0.347826 0.217391 0.434783 0.000000 0.956522 0.000000 0.043478 0.000000 0.434783 0.130435 0.391304 0.043478 0.130435 0.260870 0.260870 0.347826 0.565217 0.086957 0.000000 0.347826 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[GAC]AC[AT]GT[GAC]A[AG][TCG][AT] -------------------------------------------------------------------------------- Time 4.59 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 10 llr = 125 E-value = 2.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::32:512:2::::: pos.-specific C 712::2::::::8:: probability G 1:442::2:3a:2a8 matrix T 29148396a5:a::2 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 CTGGTATTTTGTCGG consensus T ATGT A G G T sequence CA C G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 47614 343 2.78e-08 GTGATTCGGG CTATTTTTTTGTCGG AAGACATCAT 34096 117 1.27e-07 CCGTTCATTT CTGATATATTGTCGG CCTCCATCGT 21369 417 1.87e-07 GCAGTGAATG CTGTTCTTTTGTGGG GCAACCAAAC 9011 446 3.06e-07 TCGGAACAAC CTTTTATGTTGTCGG AAACTATTTC 10437 478 3.82e-07 CAGGAGTCCG CCAGTATTTGGTCGG TTCGACCC 44912 355 9.19e-07 TGCTCACAAA TTCGTTTGTTGTCGG AGCCTTGTGG 44299 102 1.42e-06 TGCCCTTTCC CTGAGATTTGGTCGT ACCAATATTA 7164 200 1.42e-06 CACTTCCAGG GTGGGATTTAGTCGG AGTAATCGTC 49316 78 5.23e-06 TGACATCGAG CTATTTATTAGTGGG ACAAATATGC 47096 109 6.09e-06 AGGACGTCGC TTCGTCTATGGTCGT GGATGCCACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47614 2.8e-08 342_[+2]_143 34096 1.3e-07 116_[+2]_369 21369 1.9e-07 416_[+2]_69 9011 3.1e-07 445_[+2]_40 10437 3.8e-07 477_[+2]_8 44912 9.2e-07 354_[+2]_131 44299 1.4e-06 101_[+2]_384 7164 1.4e-06 199_[+2]_286 49316 5.2e-06 77_[+2]_408 47096 6.1e-06 108_[+2]_377 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=10 47614 ( 343) CTATTTTTTTGTCGG 1 34096 ( 117) CTGATATATTGTCGG 1 21369 ( 417) CTGTTCTTTTGTGGG 1 9011 ( 446) CTTTTATGTTGTCGG 1 10437 ( 478) CCAGTATTTGGTCGG 1 44912 ( 355) TTCGTTTGTTGTCGG 1 44299 ( 102) CTGAGATTTGGTCGT 1 7164 ( 200) GTGGGATTTAGTCGG 1 49316 ( 78) CTATTTATTAGTGGG 1 47096 ( 109) TTCGTCTATGGTCGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 11664 bayes= 10.4383 E= 2.3e+002 -997 161 -114 -45 -997 -120 -997 172 12 -20 86 -145 -47 -997 86 55 -997 -997 -14 155 85 -20 -997 13 -146 -997 -997 172 -47 -997 -14 113 -997 -997 -997 187 -47 -997 44 87 -997 -997 218 -997 -997 -997 -997 187 -997 180 -14 -997 -997 -997 218 -997 -997 -997 186 -45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 10 E= 2.3e+002 0.000000 0.700000 0.100000 0.200000 0.000000 0.100000 0.000000 0.900000 0.300000 0.200000 0.400000 0.100000 0.200000 0.000000 0.400000 0.400000 0.000000 0.000000 0.200000 0.800000 0.500000 0.200000 0.000000 0.300000 0.100000 0.000000 0.000000 0.900000 0.200000 0.000000 0.200000 0.600000 0.000000 0.000000 0.000000 1.000000 0.200000 0.000000 0.300000 0.500000 0.000000 0.000000 1.000000 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 0.000000 0.800000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT]T[GAC][GTA][TG][ATC]T[TAG]T[TGA]GT[CG]G[GT] -------------------------------------------------------------------------------- Time 9.26 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 9 llr = 122 E-value = 3.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 4::613::a83:917: pos.-specific C :1:2:1::::471::: probability G ::2:22aa:213::3a matrix T 698273::::1::9:: bits 2.2 ** * 2.0 *** * 1.7 *** * 1.5 *** * Relative 1.3 * *** *** * Entropy 1.1 ** **** ***** (19.5 bits) 0.9 *** **** ***** 0.7 *** * **** ***** 0.4 ***** **** ***** 0.2 ***** ********** 0.0 ---------------- Multilevel TTTATAGGAACCATAG consensus A GCGT GAG G sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 47614 398 9.39e-09 CGCAGTATGG ATTATAGGAACGATAG TCTTGTTGCT 52285 482 1.21e-08 GGACTCTATG TTTTTAGGAACCATAG AAG 54749 142 2.37e-08 AATCAGATAT ATTATGGGAAACATGG GGGGTCATTC 49316 104 2.85e-08 CAAATATGCT TTTATTGGAAGCATAG AAAATCCTCC 7164 131 7.05e-07 GACGCTTTGC TTTCGGGGAGCGATGG GCTGAAAAGA 51422 485 8.05e-07 TTTTTTCTTC TCTCGTGGAAACATAG 43074 394 1.05e-06 GTTTGGGCTT TTGATAGGAGCCCTGG GGAAGGAAGC 48196 2 1.19e-06 A ATGAATGGAATCATAG TCCGAATATT 10437 24 1.90e-06 TGTGCTCTGT ATTTTCGGAAAGAAAG ACTGCACAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47614 9.4e-09 397_[+3]_87 52285 1.2e-08 481_[+3]_3 54749 2.4e-08 141_[+3]_343 49316 2.8e-08 103_[+3]_381 7164 7e-07 130_[+3]_354 51422 8e-07 484_[+3] 43074 1e-06 393_[+3]_91 48196 1.2e-06 1_[+3]_483 10437 1.9e-06 23_[+3]_461 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=9 47614 ( 398) ATTATAGGAACGATAG 1 52285 ( 482) TTTTTAGGAACCATAG 1 54749 ( 142) ATTATGGGAAACATGG 1 49316 ( 104) TTTATTGGAAGCATAG 1 7164 ( 131) TTTCGGGGAGCGATGG 1 51422 ( 485) TCTCGTGGAAACATAG 1 43074 ( 394) TTGATAGGAGCCCTGG 1 48196 ( 2) ATGAATGGAATCATAG 1 10437 ( 24) ATTTTCGGAAAGAAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 11640 bayes= 11.1843 E= 3.2e+001 69 -982 -982 102 -982 -104 -982 170 -982 -982 1 151 101 -5 -982 -30 -131 -982 1 128 27 -104 1 29 -982 -982 218 -982 -982 -982 218 -982 185 -982 -982 -982 149 -982 1 -982 27 95 -99 -130 -982 154 59 -982 168 -104 -982 -982 -131 -982 -982 170 127 -982 59 -982 -982 -982 218 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 9 E= 3.2e+001 0.444444 0.000000 0.000000 0.555556 0.000000 0.111111 0.000000 0.888889 0.000000 0.000000 0.222222 0.777778 0.555556 0.222222 0.000000 0.222222 0.111111 0.000000 0.222222 0.666667 0.333333 0.111111 0.222222 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.777778 0.000000 0.222222 0.000000 0.333333 0.444444 0.111111 0.111111 0.000000 0.666667 0.333333 0.000000 0.888889 0.111111 0.000000 0.000000 0.111111 0.000000 0.000000 0.888889 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TA]T[TG][ACT][TG][ATG]GGA[AG][CA][CG]AT[AG]G -------------------------------------------------------------------------------- Time 13.90 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9011 1.13e-04 74_[+1(2.60e-05)]_359_\ [+2(3.06e-07)]_40 42822 1.19e-01 247_[+1(4.00e-05)]_241 42864 1.19e-01 351_[+1(1.74e-05)]_137 51422 2.77e-03 484_[+3(8.05e-07)] 47096 8.06e-04 108_[+2(6.09e-06)]_316_\ [+1(2.04e-05)]_49 21369 2.44e-05 144_[+1(1.14e-05)]_260_\ [+2(1.87e-07)]_69 47614 6.89e-10 216_[+1(5.89e-05)]_114_\ [+2(2.78e-08)]_40_[+3(9.39e-09)]_87 52285 7.54e-06 175_[+1(5.02e-05)]_22_\ [+1(4.64e-05)]_260_[+3(1.21e-08)]_3 48196 1.36e-03 1_[+3(1.19e-06)]_483 43646 8.44e-02 427_[+1(1.55e-05)]_61 43693 6.22e-03 140_[+1(2.18e-06)]_348 7164 3.25e-06 130_[+3(7.05e-07)]_53_\ [+2(1.42e-06)]_286 49316 3.74e-09 77_[+2(5.23e-06)]_11_[+3(2.85e-08)]_\ 180_[+1(6.33e-07)]_189 40647 2.98e-04 312_[+1(6.45e-08)]_176 10437 2.52e-06 23_[+3(1.90e-06)]_438_\ [+2(3.82e-07)]_8 50514 1.12e-01 371_[+1(5.89e-05)]_117 34096 1.60e-04 116_[+2(1.27e-07)]_369 36252 5.75e-02 311_[+1(9.47e-06)]_177 43074 4.49e-05 256_[+1(5.85e-06)]_125_\ [+3(1.05e-06)]_91 33876 2.36e-02 422_[+1(7.72e-06)]_66 44912 7.43e-05 111_[+1(1.40e-05)]_231_\ [+2(9.19e-07)]_131 47050 6.84e-02 304_[+1(1.14e-05)]_184 44299 2.35e-04 101_[+2(1.42e-06)]_78_\ [+1(1.40e-05)]_20_[+1(1.90e-05)]_262 54749 5.69e-07 108_[+1(1.47e-06)]_21_\ [+3(2.37e-08)]_343 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************