******************************************************************************** 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/281/281.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 22976 1.0000 500 32880 1.0000 500 4051 1.0000 500 6627 1.0000 500 7022 1.0000 500 bd1792 1.0000 500 bd1944 1.0000 500 bd753 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/281/281.seqs.fa -oc motifs/281 -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= 8 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= 4000 N= 8 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.248 C 0.215 G 0.271 T 0.266 Background letter frequencies (from dataset with add-one prior applied): A 0.248 C 0.215 G 0.271 T 0.266 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 8 llr = 136 E-value = 6.4e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::::::111:18:88549a pos.-specific C :814:53::::341:1313:: probability G :11:94:a:9:8::9:::31: matrix T a186118:9:9:5111:41:: bits 2.2 2.0 * * 1.8 * * * 1.6 * * ** Relative 1.3 * * **** * * ** Entropy 1.1 ** ** ****** * * ** (24.6 bits) 0.9 ***** ****** **** ** 0.7 ****************** ** 0.4 ****************** ** 0.2 ********************* 0.0 --------------------- Multilevel TCTTGCTGTGTGTAGAAAAAA consensus C GC CC CTC sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- bd753 229 3.67e-13 CGTTCCATCC TCTTGCTGTGTGTAGAAAAAA GGAGTTGTAG bd1792 87 3.67e-13 CGTTCCATCC TCTTGCTGTGTGTAGAAAAAA GGAGTTGTAG 4051 144 3.67e-13 CGTGGCAACC TCTTGCTGTGTGTAGAAAAAA GGAGTTGTAG 32880 53 2.41e-08 CCCAACACCA TCCCGTCGTGAGCAGAAACAA CTCTCTCGAT bd1944 148 3.17e-08 TGAGTGTGTT TCTCGGTGAGTGCCGACCGAA AGATTCCTTG 6627 61 9.36e-08 CGTCTCAAGT TCTCGGCGTGTCTATCCTTAA AAATTTCGGG 7022 389 1.16e-07 GTGGTATTTA TGTTTCTGTGTGCTGAATGGA TTAGTGTGTT 22976 281 3.82e-07 TGTGTTTGTG TTGTGGTGTATCAAGTATCAA TAACGCAACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd753 3.7e-13 228_[+1]_251 bd1792 3.7e-13 86_[+1]_393 4051 3.7e-13 143_[+1]_336 32880 2.4e-08 52_[+1]_427 bd1944 3.2e-08 147_[+1]_332 6627 9.4e-08 60_[+1]_419 7022 1.2e-07 388_[+1]_91 22976 3.8e-07 280_[+1]_199 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=8 bd753 ( 229) TCTTGCTGTGTGTAGAAAAAA 1 bd1792 ( 87) TCTTGCTGTGTGTAGAAAAAA 1 4051 ( 144) TCTTGCTGTGTGTAGAAAAAA 1 32880 ( 53) TCCCGTCGTGAGCAGAAACAA 1 bd1944 ( 148) TCTCGGTGAGTGCCGACCGAA 1 6627 ( 61) TCTCGGCGTGTCTATCCTTAA 1 7022 ( 389) TGTTTCTGTGTGCTGAATGGA 1 22976 ( 281) TTGTGGTGTATCAAGTATCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3840 bayes= 8.90388 E= 6.4e-006 -965 -965 -965 191 -965 180 -112 -109 -965 -78 -112 149 -965 80 -965 123 -965 -965 169 -109 -965 122 47 -109 -965 22 -965 149 -965 -965 188 -965 -99 -965 -965 172 -99 -965 169 -965 -99 -965 -965 172 -965 22 147 -965 -99 80 -965 91 160 -78 -965 -109 -965 -965 169 -109 160 -78 -965 -109 160 22 -965 -965 101 -78 -965 50 60 22 -12 -109 182 -965 -112 -965 201 -965 -965 -965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 6.4e-006 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.125000 0.125000 0.000000 0.125000 0.125000 0.750000 0.000000 0.375000 0.000000 0.625000 0.000000 0.000000 0.875000 0.125000 0.000000 0.500000 0.375000 0.125000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.125000 0.000000 0.000000 0.875000 0.125000 0.000000 0.875000 0.000000 0.125000 0.000000 0.000000 0.875000 0.000000 0.250000 0.750000 0.000000 0.125000 0.375000 0.000000 0.500000 0.750000 0.125000 0.000000 0.125000 0.000000 0.000000 0.875000 0.125000 0.750000 0.125000 0.000000 0.125000 0.750000 0.250000 0.000000 0.000000 0.500000 0.125000 0.000000 0.375000 0.375000 0.250000 0.250000 0.125000 0.875000 0.000000 0.125000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TCT[TC]G[CG][TC]GTGT[GC][TC]AGA[AC][AT][ACG]AA -------------------------------------------------------------------------------- Time 0.56 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 5 llr = 90 E-value = 6.4e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 2:6:::6::4:::::: pos.-specific C 82:2a:::a:a2::aa probability G :828:::::4:::::: matrix T ::2::a4a:2:8aa:: bits 2.2 * * * ** 2.0 ** ** * **** 1.8 ** ** * **** 1.6 * ** ** * **** Relative 1.3 ** *** ** ****** Entropy 1.1 ** ****** ****** (25.9 bits) 0.9 ** ****** ****** 0.7 ********* ****** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CGAGCTATCACTTTCC consensus ACGC T G C sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 4051 323 1.47e-10 CTGCTCGGGG CGAGCTATCACTTTCC CCTTCCATTT bd753 433 3.08e-10 CTGCTTGGGA CGAGCTATCGCTTTCC TTCCATTTTC bd1792 265 3.08e-10 GATCTCGGGA CGAGCTATCGCTTTCC TTCCATTCTC 32880 484 1.51e-08 GCGGAAGATA AGGGCTTTCACTTTCC A 6627 460 3.62e-08 CCTCCCTCAT CCTCCTTTCTCCTTCC CTCTTGTCAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4051 1.5e-10 322_[+2]_162 bd753 3.1e-10 432_[+2]_52 bd1792 3.1e-10 264_[+2]_220 32880 1.5e-08 483_[+2]_1 6627 3.6e-08 459_[+2]_25 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=5 4051 ( 323) CGAGCTATCACTTTCC 1 bd753 ( 433) CGAGCTATCGCTTTCC 1 bd1792 ( 265) CGAGCTATCGCTTTCC 1 32880 ( 484) AGGGCTTTCACTTTCC 1 6627 ( 460) CCTCCTTTCTCCTTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 3880 bayes= 9.84989 E= 6.4e-004 -31 189 -897 -897 -897 -10 156 -897 127 -897 -44 -41 -897 -10 156 -897 -897 222 -897 -897 -897 -897 -897 191 127 -897 -897 59 -897 -897 -897 191 -897 222 -897 -897 69 -897 56 -41 -897 222 -897 -897 -897 -10 -897 159 -897 -897 -897 191 -897 -897 -897 191 -897 222 -897 -897 -897 222 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 5 E= 6.4e-004 0.200000 0.800000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.600000 0.000000 0.200000 0.200000 0.000000 0.200000 0.800000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.600000 0.000000 0.000000 0.400000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.400000 0.000000 0.400000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CA][GC][AGT][GC]CT[AT]TC[AGT]C[TC]TTCC -------------------------------------------------------------------------------- Time 1.08 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 5 llr = 87 E-value = 3.0e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2::4:::a:68aa88: pos.-specific C :8:62:a:24::::2: probability G :2a:::::::2::2:a matrix T 8:::8a::8::::::: bits 2.2 * 2.0 *** ** 1.8 * *** ** * 1.6 * *** ** * Relative 1.3 ** ***** ****** Entropy 1.1 **************** (25.2 bits) 0.9 **************** 0.7 **************** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel TCGCTTCATAAAAAAG consensus AG AC CCG GC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- bd753 457 2.11e-10 CCTTCCATTT TCGCTTCATAAAAAAG GTAAGCTTCT bd1792 289 2.11e-10 CCTTCCATTC TCGCTTCATAAAAAAG GTAAGCTTCT 4051 349 2.11e-10 CCTTCCATTT TCGCTTCATAAAAAAG GTAAGCCAAA 6627 150 4.80e-08 ATTTGAAGGA AGGATTCACCAAAAAG AGTGTTTAAG 32880 458 7.25e-08 TTTCTCAAAG TCGACTCATCGAAGCG GCGGAAGATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd753 2.1e-10 456_[+3]_28 bd1792 2.1e-10 288_[+3]_196 4051 2.1e-10 348_[+3]_136 6627 4.8e-08 149_[+3]_335 32880 7.2e-08 457_[+3]_27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=5 bd753 ( 457) TCGCTTCATAAAAAAG 1 bd1792 ( 289) TCGCTTCATAAAAAAG 1 4051 ( 349) TCGCTTCATAAAAAAG 1 6627 ( 150) AGGATTCACCAAAAAG 1 32880 ( 458) TCGACTCATCGAAGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 3880 bayes= 9.84989 E= 3.0e-002 -31 -897 -897 159 -897 189 -44 -897 -897 -897 188 -897 69 148 -897 -897 -897 -10 -897 159 -897 -897 -897 191 -897 222 -897 -897 201 -897 -897 -897 -897 -10 -897 159 127 90 -897 -897 169 -897 -44 -897 201 -897 -897 -897 201 -897 -897 -897 169 -897 -44 -897 169 -10 -897 -897 -897 -897 188 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 5 E= 3.0e-002 0.200000 0.000000 0.000000 0.800000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.600000 0.400000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TA][CG]G[CA][TC]TCA[TC][AC][AG]AA[AG][AC]G -------------------------------------------------------------------------------- Time 1.69 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22976 1.96e-03 280_[+1(3.82e-07)]_199 32880 1.76e-12 52_[+1(2.41e-08)]_384_\ [+3(7.25e-08)]_10_[+2(1.51e-08)]_1 4051 2.02e-21 143_[+1(3.67e-13)]_75_\ [+1(9.94e-05)]_62_[+2(1.47e-10)]_10_[+3(2.11e-10)]_136 6627 9.79e-12 60_[+1(9.36e-08)]_68_[+3(4.80e-08)]_\ 294_[+2(3.62e-08)]_25 7022 1.36e-03 388_[+1(1.16e-07)]_91 bd1792 4.12e-21 86_[+1(3.67e-13)]_75_[+1(1.81e-07)]_\ 61_[+2(3.08e-10)]_8_[+3(2.11e-10)]_196 bd1944 3.85e-04 147_[+1(3.17e-08)]_332 bd753 4.12e-21 97_[+1(8.72e-05)]_110_\ [+1(3.67e-13)]_96_[+1(1.81e-07)]_66_[+2(3.08e-10)]_8_[+3(2.11e-10)]_28 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************