******************************************************************************** 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/152/152.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10749 1.0000 500 23654 1.0000 500 264902 1.0000 500 264903 1.0000 500 270127 1.0000 500 5660 1.0000 500 7359 1.0000 500 9653 1.0000 500 bd906 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/152/152.seqs.fa -oc motifs/152 -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= 9 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= 4500 N= 9 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.252 G 0.208 T 0.282 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.252 G 0.208 T 0.282 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 4 llr = 101 E-value = 1.5e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::::5::::::a5:::::: pos.-specific C ::::::::::::5::5:aa:a probability G ::aaa::5aa:5::::a:::: matrix T aa:::a55::a55:55:::a: bits 2.3 *** ** * 2.0 *** ** * *** * 1.8 ****** *** * ***** 1.6 ****** *** * ***** Relative 1.4 ****** *** * ***** Entropy 1.1 ****** ***** * ***** (36.3 bits) 0.9 ********************* 0.7 ********************* 0.5 ********************* 0.2 ********************* 0.0 --------------------- Multilevel TTGGGTAGGGTGCAACGCCTC consensus TT TT TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 9653 109 1.39e-12 GAATGATTTT TTGGGTAGGGTGTAATGCCTC GGGCCCTCAA 10749 109 1.39e-12 GAATGATTTT TTGGGTAGGGTGTAATGCCTC GGGCCCTCAA 7359 324 1.05e-11 AATTAGTGGA TTGGGTTTGGTTCATCGCCTC TTGACTCTAT 23654 324 1.05e-11 AATTAGTGGA TTGGGTTTGGTTCATCGCCTC TTGACTCTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9653 1.4e-12 108_[+1]_371 10749 1.4e-12 108_[+1]_371 7359 1.1e-11 323_[+1]_156 23654 1.1e-11 323_[+1]_156 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=4 9653 ( 109) TTGGGTAGGGTGTAATGCCTC 1 10749 ( 109) TTGGGTAGGGTGTAATGCCTC 1 7359 ( 324) TTGGGTTTGGTTCATCGCCTC 1 23654 ( 324) TTGGGTTTGGTTCATCGCCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4320 bayes= 10.0755 E= 1.5e-004 -865 -865 -865 182 -865 -865 -865 182 -865 -865 226 -865 -865 -865 226 -865 -865 -865 226 -865 -865 -865 -865 182 96 -865 -865 82 -865 -865 126 82 -865 -865 226 -865 -865 -865 226 -865 -865 -865 -865 182 -865 -865 126 82 -865 99 -865 82 195 -865 -865 -865 96 -865 -865 82 -865 99 -865 82 -865 -865 226 -865 -865 199 -865 -865 -865 199 -865 -865 -865 -865 -865 182 -865 199 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 1.5e-004 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.500000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TTGGGT[AT][GT]GGT[GT][CT]A[AT][CT]GCCTC -------------------------------------------------------------------------------- Time 0.94 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 20 sites = 6 llr = 116 E-value = 2.3e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::3:a2:8:57::::::::: pos.-specific C :2:2::::::3:753::::7 probability G 28:8:57:a::83:::a::: matrix T 8:7::332:5:2:57a:aa3 bits 2.3 * * 2.0 * * * 1.8 * * **** 1.6 * ** * * **** Relative 1.4 ** ** ** * **** Entropy 1.1 ** ** *** *** **** (27.9 bits) 0.9 ***** ************** 0.7 ******************** 0.5 ******************** 0.2 ******************** 0.0 -------------------- Multilevel TGTGAGGAGAAGCCTTGTTC consensus A TT TC GTC T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 7359 225 1.03e-10 AGCCTGTTCA TGTGAGTAGTAGGTTTGTTC TGATTTGGTT 23654 224 1.03e-10 AGCCTGTTCC TGTGAGTAGTAGGTTTGTTC TGATTTGGTC 9653 19 1.56e-10 GGTTGGAGAT TGAGATGAGAAGCCTTGTTT TCTCTGTGTT 10749 19 1.56e-10 GGTTGGAGAT TGAGATGAGAAGCCTTGTTT TCTCTGTGTT 5660 324 1.12e-09 GGAGAGAGAA GGTGAAGAGACGCCCTGTTC CTCGTTCCGC 264902 193 1.96e-08 CAACAGCCCC TCTCAGGTGTCTCTCTGTTC AGCGTGTTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7359 1e-10 224_[+2]_256 23654 1e-10 223_[+2]_257 9653 1.6e-10 18_[+2]_462 10749 1.6e-10 18_[+2]_462 5660 1.1e-09 323_[+2]_157 264902 2e-08 192_[+2]_288 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=6 7359 ( 225) TGTGAGTAGTAGGTTTGTTC 1 23654 ( 224) TGTGAGTAGTAGGTTTGTTC 1 9653 ( 19) TGAGATGAGAAGCCTTGTTT 1 10749 ( 19) TGAGATGAGAAGCCTTGTTT 1 5660 ( 324) GGTGAAGAGACGCCCTGTTC 1 264902 ( 193) TCTCAGGTGTCTCTCTGTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 4329 bayes= 9.94085 E= 2.3e-004 -923 -923 -32 156 -923 -59 200 -923 37 -923 -923 124 -923 -59 200 -923 196 -923 -923 -923 -63 -923 126 24 -923 -923 168 24 169 -923 -923 -76 -923 -923 226 -923 96 -923 -923 82 137 40 -923 -923 -923 -923 200 -76 -923 140 68 -923 -923 99 -923 82 -923 40 -923 124 -923 -923 -923 182 -923 -923 226 -923 -923 -923 -923 182 -923 -923 -923 182 -923 140 -923 24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 2.3e-004 0.000000 0.000000 0.166667 0.833333 0.000000 0.166667 0.833333 0.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.166667 0.833333 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.500000 0.333333 0.000000 0.000000 0.666667 0.333333 0.833333 0.000000 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.666667 0.333333 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- TG[TA]GA[GT][GT]AG[AT][AC]G[CG][CT][TC]TGTT[CT] -------------------------------------------------------------------------------- Time 1.87 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 4 llr = 91 E-value = 3.1e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::a3::8::::::35:::::: pos.-specific C a::38:3::3::3858a3a:8 probability G :a:53a:aa8a:3::::5::: matrix T :::::::::::a5::3:3:a3 bits 2.3 * * ** * 2.0 *** * ** * * * 1.8 *** * ** ** * ** 1.6 *** * ** ** * ** Relative 1.4 *** ** ***** * ** Entropy 1.1 *** ******** * ** *** (32.8 bits) 0.9 *** ******** **** *** 0.7 ************ ******** 0.5 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CGAGCGAGGGGTTCACCGCTC consensus AG C C CACT C T sequence C G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 9653 358 1.72e-13 GGCAAGAGGT CGAGCGAGGGGTTCCCCGCTC CAGCAAACAC 10749 358 1.72e-13 GGCAAGAGGT CGAGCGAGGGGTTCCCCGCTC CAGCAAACAC 264902 375 2.57e-10 TCACCAACAT CGACGGCGGCGTCCACCCCTC TGATGAAACT 5660 111 2.74e-10 AAGGATCAAC CGAACGAGGGGTGAATCTCTT CCCTTCCCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9653 1.7e-13 357_[+3]_122 10749 1.7e-13 357_[+3]_122 264902 2.6e-10 374_[+3]_105 5660 2.7e-10 110_[+3]_369 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=4 9653 ( 358) CGAGCGAGGGGTTCCCCGCTC 1 10749 ( 358) CGAGCGAGGGGTTCCCCGCTC 1 264902 ( 375) CGACGGCGGCGTCCACCCCTC 1 5660 ( 111) CGAACGAGGGGTGAATCTCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4320 bayes= 10.0755 E= 3.1e-002 -865 199 -865 -865 -865 -865 226 -865 195 -865 -865 -865 -4 -1 126 -865 -865 157 26 -865 -865 -865 226 -865 154 -1 -865 -865 -865 -865 226 -865 -865 -865 226 -865 -865 -1 184 -865 -865 -865 226 -865 -865 -865 -865 182 -865 -1 26 82 -4 157 -865 -865 96 99 -865 -865 -865 157 -865 -17 -865 199 -865 -865 -865 -1 126 -17 -865 199 -865 -865 -865 -865 -865 182 -865 157 -865 -17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 3.1e-002 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.250000 0.500000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.250000 0.500000 0.250000 0.750000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.500000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CGA[GAC][CG]G[AC]GG[GC]GT[TCG][CA][AC][CT]C[GCT]CT[CT] -------------------------------------------------------------------------------- Time 2.77 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10749 7.91e-24 18_[+2(1.56e-10)]_70_[+1(1.39e-12)]_\ 228_[+3(1.72e-13)]_122 23654 1.43e-13 223_[+2(1.03e-10)]_80_\ [+1(1.05e-11)]_156 264902 3.58e-10 192_[+2(1.96e-08)]_162_\ [+3(2.57e-10)]_105 264903 6.45e-01 500 270127 5.26e-01 500 5660 2.34e-11 110_[+3(2.74e-10)]_192_\ [+2(1.12e-09)]_157 7359 1.10e-13 224_[+2(1.03e-10)]_79_\ [+1(1.05e-11)]_156 9653 7.91e-24 18_[+2(1.56e-10)]_70_[+1(1.39e-12)]_\ 228_[+3(1.72e-13)]_122 bd906 5.97e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************