******************************************************************************** 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/164/164.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1086 1.0000 500 21885 1.0000 500 22696 1.0000 500 24902 1.0000 500 25499 1.0000 500 263355 1.0000 500 268447 1.0000 500 268546 1.0000 500 269780 1.0000 500 33973 1.0000 500 35017 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/164/164.seqs.fa -oc motifs/164 -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 0.275 C 0.254 G 0.206 T 0.265 Background letter frequencies (from dataset with add-one prior applied): A 0.275 C 0.254 G 0.206 T 0.265 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 11 llr = 112 E-value = 1.3e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1:a519a:7835 pos.-specific C 18:29::a3162 probability G 7::::1:::1:4 matrix T 12:3::::::1: bits 2.3 2.1 * 1.8 * ** 1.6 * * ** Relative 1.4 ** **** Entropy 1.1 ** ****** (14.7 bits) 0.9 *** ****** 0.7 *** ******* 0.5 ************ 0.2 ************ 0.0 ------------ Multilevel GCAACAACAACA consensus T C AG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 24902 300 1.78e-07 TTTTGACAAA GCAACAACAACG TGTCAACTCG 33973 489 1.78e-06 ATTAACGCCA GCAACAACAAAC 35017 489 3.62e-06 TCTCCTGCTG TCAACAACAACG 268546 346 3.62e-06 CCGATGCTAC CCAACAACAACA GCAGCAGCAT 21885 335 5.58e-06 ACACTTGAAA GCATCAACAATA GATAGTCGAC 22696 414 1.30e-05 AAAATCAGCG GTAACAACCAAA TCTCTCATTT 1086 212 1.30e-05 AGACGTCCAG ACACCAACAACA TTGCATCTTG 268447 97 1.50e-05 ACCGCGAGAG GCACCAACCAAC ACGTCATCGA 269780 64 1.59e-05 GATTGATACC GTAACAACACCG TGCAAAAGAT 25499 184 2.09e-05 CATATTCTGA GCATAAACCACG TTGATTCGTA 263355 108 3.27e-05 CTCAACCATG GCATCGACAGCA GACCCATCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24902 1.8e-07 299_[+1]_189 33973 1.8e-06 488_[+1] 35017 3.6e-06 488_[+1] 268546 3.6e-06 345_[+1]_143 21885 5.6e-06 334_[+1]_154 22696 1.3e-05 413_[+1]_75 1086 1.3e-05 211_[+1]_277 268447 1.5e-05 96_[+1]_392 269780 1.6e-05 63_[+1]_425 25499 2.1e-05 183_[+1]_305 263355 3.3e-05 107_[+1]_381 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=11 24902 ( 300) GCAACAACAACG 1 33973 ( 489) GCAACAACAAAC 1 35017 ( 489) TCAACAACAACG 1 268546 ( 346) CCAACAACAACA 1 21885 ( 335) GCATCAACAATA 1 22696 ( 414) GTAACAACCAAA 1 1086 ( 212) ACACCAACAACA 1 268447 ( 97) GCACCAACCAAC 1 269780 ( 64) GTAACAACACCG 1 25499 ( 184) GCATAAACCACG 1 263355 ( 108) GCATCGACAGCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5379 bayes= 8.93074 E= 1.3e+001 -160 -148 182 -154 -1010 169 -1010 -54 186 -1010 -1010 -1010 99 -48 -1010 4 -160 184 -1010 -1010 172 -1010 -118 -1010 186 -1010 -1010 -1010 -1010 198 -1010 -1010 140 10 -1010 -1010 157 -148 -118 -1010 -1 132 -1010 -154 72 -48 82 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 11 E= 1.3e+001 0.090909 0.090909 0.727273 0.090909 0.000000 0.818182 0.000000 0.181818 1.000000 0.000000 0.000000 0.000000 0.545455 0.181818 0.000000 0.272727 0.090909 0.909091 0.000000 0.000000 0.909091 0.000000 0.090909 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.727273 0.272727 0.000000 0.000000 0.818182 0.090909 0.090909 0.000000 0.272727 0.636364 0.000000 0.090909 0.454545 0.181818 0.363636 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GCA[AT]CAAC[AC]A[CA][AG] -------------------------------------------------------------------------------- Time 1.37 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 11 llr = 111 E-value = 5.8e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :66::::41::: pos.-specific C 9::6:23:47:: probability G :::::4:::::: matrix T 1444a57653aa bits 2.3 2.1 1.8 * ** 1.6 * * ** Relative 1.4 * * ** Entropy 1.1 * * * *** (14.5 bits) 0.9 ***** ** *** 0.7 ***** ****** 0.5 ************ 0.2 ************ 0.0 ------------ Multilevel CAACTTTTTCTT consensus TTT GCACT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 268447 481 3.96e-07 CCATCACCGA CAACTTTTCCTT GACCCTTG 35017 400 7.85e-07 CTCCTTTTTA CTACTTTTTCTT ATCAACGTGG 269780 251 9.96e-07 ACATTGTGTC CAATTGTTTCTT CTAATGATGT 1086 37 3.49e-06 CCGTCTACAT CTACTTTATCTT TGTCTCATGA 24902 58 1.15e-05 GGTTTCTAGT CATCTGTTCTTT TTTACTTTTT 268546 414 1.27e-05 CGCTTCTTCT CATCTCTATCTT CCCTCAACGA 263355 435 1.61e-05 CACAACTCCC CTTCTTCTCCTT CCATCTCCCT 33973 114 2.07e-05 GGAATTGCTG CAATTGCACCTT CAGTGTGGAT 25499 111 3.79e-05 TTACAACCTA CTTTTTTTACTT GATCCAATCC 22696 340 3.79e-05 CCATTGAGGG TAACTGTTTTTT TTTCCATCCG 21885 102 5.61e-05 TCTCTTTTGC CAATTCCATTTT CCATTTGCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 268447 4e-07 480_[+2]_8 35017 7.9e-07 399_[+2]_89 269780 1e-06 250_[+2]_238 1086 3.5e-06 36_[+2]_452 24902 1.2e-05 57_[+2]_431 268546 1.3e-05 413_[+2]_75 263355 1.6e-05 434_[+2]_54 33973 2.1e-05 113_[+2]_375 25499 3.8e-05 110_[+2]_378 22696 3.8e-05 339_[+2]_149 21885 5.6e-05 101_[+2]_387 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=11 268447 ( 481) CAACTTTTCCTT 1 35017 ( 400) CTACTTTTTCTT 1 269780 ( 251) CAATTGTTTCTT 1 1086 ( 37) CTACTTTATCTT 1 24902 ( 58) CATCTGTTCTTT 1 268546 ( 414) CATCTCTATCTT 1 263355 ( 435) CTTCTTCTCCTT 1 33973 ( 114) CAATTGCACCTT 1 25499 ( 111) CTTTTTTTACTT 1 22696 ( 340) TAACTGTTTTTT 1 21885 ( 102) CAATTCCATTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5379 bayes= 8.93074 E= 5.8e+001 -1010 184 -1010 -154 121 -1010 -1010 46 121 -1010 -1010 46 -1010 132 -1010 46 -1010 -1010 -1010 192 -1010 -48 82 78 -1010 10 -1010 146 40 -1010 -1010 126 -160 52 -1010 104 -1010 152 -1010 4 -1010 -1010 -1010 192 -1010 -1010 -1010 192 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 11 E= 5.8e+001 0.000000 0.909091 0.000000 0.090909 0.636364 0.000000 0.000000 0.363636 0.636364 0.000000 0.000000 0.363636 0.000000 0.636364 0.000000 0.363636 0.000000 0.000000 0.000000 1.000000 0.000000 0.181818 0.363636 0.454545 0.000000 0.272727 0.000000 0.727273 0.363636 0.000000 0.000000 0.636364 0.090909 0.363636 0.000000 0.545455 0.000000 0.727273 0.000000 0.272727 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[AT][AT][CT]T[TG][TC][TA][TC][CT]TT -------------------------------------------------------------------------------- Time 2.69 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 8 llr = 91 E-value = 6.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:6a:::3:::1 pos.-specific C 3a::::::34a4 probability G :::::3a:8::4 matrix T 6:4:a8:8:6:1 bits 2.3 * 2.1 * * * 1.8 * ** * * 1.6 * ** * * Relative 1.4 * ** * * * Entropy 1.1 * ****** * (16.5 bits) 0.9 ********** 0.7 *********** 0.5 *********** 0.2 ************ 0.0 ------------ Multilevel TCAATTGTGTCC consensus C T G ACC G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 22696 137 5.57e-08 CTTTGAACCA TCAATTGTGTCG TAGACTCGAA 269780 201 2.97e-07 AAAAAAGATC TCAATTGTGCCC TCGTTTCCTA 33973 366 1.42e-06 GCATTTTTTG TCAATGGTGCCC CTTCATCCCG 268447 42 1.88e-06 GAAAATAATT CCAATGGTGTCG ACACAATAAT 21885 471 6.98e-06 GGTTGTTTGG TCTATTGACTCG TTTCATAGGC 1086 254 7.51e-06 CAAGTAGATG TCTATTGAGTCT TTTGTAGGAT 24902 327 8.77e-06 ACTCGTCTCC ACAATTGTGTCA TCGATACACC 25499 448 9.39e-06 TTTATCCTCT CCTATTGTCCCC TATGGACACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22696 5.6e-08 136_[+3]_352 269780 3e-07 200_[+3]_288 33973 1.4e-06 365_[+3]_123 268447 1.9e-06 41_[+3]_447 21885 7e-06 470_[+3]_18 1086 7.5e-06 253_[+3]_235 24902 8.8e-06 326_[+3]_162 25499 9.4e-06 447_[+3]_41 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=8 22696 ( 137) TCAATTGTGTCG 1 269780 ( 201) TCAATTGTGCCC 1 33973 ( 366) TCAATGGTGCCC 1 268447 ( 42) CCAATGGTGTCG 1 21885 ( 471) TCTATTGACTCG 1 1086 ( 254) TCTATTGAGTCT 1 24902 ( 327) ACAATTGTGTCA 1 25499 ( 448) CCTATTGTCCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5379 bayes= 9.39098 E= 6.5e+001 -114 -2 -965 124 -965 198 -965 -965 118 -965 -965 50 186 -965 -965 -965 -965 -965 -965 192 -965 -965 28 150 -965 -965 228 -965 -14 -965 -965 150 -965 -2 186 -965 -965 56 -965 124 -965 198 -965 -965 -114 56 86 -108 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 8 E= 6.5e+001 0.125000 0.250000 0.000000 0.625000 0.000000 1.000000 0.000000 0.000000 0.625000 0.000000 0.000000 0.375000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.250000 0.750000 0.000000 0.000000 0.375000 0.000000 0.625000 0.000000 1.000000 0.000000 0.000000 0.125000 0.375000 0.375000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TC]C[AT]AT[TG]G[TA][GC][TC]C[CG] -------------------------------------------------------------------------------- Time 3.94 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1086 6.47e-06 36_[+2(3.49e-06)]_163_\ [+1(1.30e-05)]_30_[+3(7.51e-06)]_235 21885 3.31e-05 101_[+2(5.61e-05)]_221_\ [+1(5.58e-06)]_124_[+3(6.98e-06)]_18 22696 6.73e-07 136_[+3(5.57e-08)]_191_\ [+2(3.79e-05)]_62_[+1(1.30e-05)]_75 24902 4.62e-07 57_[+2(1.15e-05)]_230_\ [+1(1.78e-07)]_15_[+3(8.77e-06)]_162 25499 9.63e-05 110_[+2(3.79e-05)]_61_\ [+1(2.09e-05)]_252_[+3(9.39e-06)]_41 263355 5.70e-03 107_[+1(3.27e-05)]_315_\ [+2(1.61e-05)]_54 268447 3.00e-07 41_[+3(1.88e-06)]_43_[+1(1.50e-05)]_\ 372_[+2(3.96e-07)]_8 268546 6.83e-04 345_[+1(3.62e-06)]_56_\ [+2(1.27e-05)]_75 269780 1.37e-07 63_[+1(1.59e-05)]_125_\ [+3(2.97e-07)]_38_[+2(9.96e-07)]_183_[+3(5.82e-05)]_43 33973 1.21e-06 113_[+2(2.07e-05)]_240_\ [+3(1.42e-06)]_111_[+1(1.78e-06)] 35017 2.05e-05 399_[+2(7.85e-07)]_77_\ [+1(3.62e-06)] -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************