******************************************************************************** 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/460/460.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1549 1.0000 500 1701 1.0000 500 1833 1.0000 500 5713 1.0000 500 8182 1.0000 500 bd1079 1.0000 500 bd518 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/460/460.seqs.fa -oc motifs/460 -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= 7 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= 3500 N= 7 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.274 C 0.218 G 0.262 T 0.246 Background letter frequencies (from dataset with add-one prior applied): A 0.274 C 0.218 G 0.262 T 0.246 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 4 llr = 94 E-value = 7.3e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A a:3:a::a8:a:3aa3:a3a: pos.-specific C ::8a::8::8:38::8a:::: probability G :3:::::::3::::::::3:: matrix T :8:::a3:3::8::::::5:a bits 2.2 * * 2.0 * *** * * ** ** ** 1.8 * *** * * ** ** ** 1.5 * *** * * ** ** ** Relative 1.3 * ****** ********* ** Entropy 1.1 ****************** ** (34.0 bits) 0.9 ****************** ** 0.7 ****************** ** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel ATCCATCAACATCAACCATAT consensus GA T TG CA A A sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- bd1079 79 1.83e-13 TCTCTCCACC ATCCATCAACATCAACCATAT CATATATACA 8182 79 1.83e-13 TCTCTCCACC ATCCATCAACATCAACCATAT CATATATACA 1833 111 2.72e-11 AAGCAACCAG ATACATCAACATCAAACAGAT CAATACAGAG 1701 127 2.14e-10 CCCTCACCGC AGCCATTATGACAAACCAAAT GGATGCAACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1079 1.8e-13 78_[+1]_401 8182 1.8e-13 78_[+1]_401 1833 2.7e-11 110_[+1]_369 1701 2.1e-10 126_[+1]_353 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=4 bd1079 ( 79) ATCCATCAACATCAACCATAT 1 8182 ( 79) ATCCATCAACATCAACCATAT 1 1833 ( 111) ATACATCAACATCAAACAGAT 1 1701 ( 127) AGCCATTATGACAAACCAAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3360 bayes= 9.71253 E= 7.3e-003 187 -865 -865 -865 -865 -865 -7 161 -13 178 -865 -865 -865 219 -865 -865 187 -865 -865 -865 -865 -865 -865 202 -865 178 -865 2 187 -865 -865 -865 145 -865 -865 2 -865 178 -7 -865 187 -865 -865 -865 -865 20 -865 161 -13 178 -865 -865 187 -865 -865 -865 187 -865 -865 -865 -13 178 -865 -865 -865 219 -865 -865 187 -865 -865 -865 -13 -865 -7 102 187 -865 -865 -865 -865 -865 -865 202 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 7.3e-003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.250000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.250000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[TG][CA]CAT[CT]A[AT][CG]A[TC][CA]AA[CA]CA[TAG]AT -------------------------------------------------------------------------------- Time 0.45 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 6 llr = 110 E-value = 5.5e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 28a:a572757::::2:3:5: pos.-specific C 82:7:527232a8:a:2283a probability G :::3::22:::::2::7:2:: matrix T ::::::::222:28:825:2: bits 2.2 * * * 2.0 * * * * * 1.8 * * * * * 1.5 * * * ** * * * Relative 1.3 *** * ***** * * Entropy 1.1 ****** ***** * * (26.3 bits) 0.9 ****** * ***** * * 0.7 ********* ******* * * 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CAACAAACAAACCTCTGTCAC consensus G C C A C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- bd1079 454 1.16e-12 CCTCTTCATT CAACACACAAACCTCTGACAC GAGACGAAAG 8182 454 1.16e-12 CCTCTTCATT CAACACACAAACCTCTGACAC GAGACGAAAG 5713 340 1.10e-08 TCATGTCCCC CAACACGCTTCCCTCTCTCTC GGCTGTGTCT 1833 429 1.49e-08 ATACGCCGTG CCACAACAACTCCTCTTTCCC ACGTCGTCGG bd518 393 1.77e-08 CTATGCTTTT AAAGAAAGACACCTCAGCCCC TGTCCCAATC 1701 34 1.77e-08 AGCTCAGCAT CAAGAAACCAACTGCTGTGAC TGTAAACACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1079 1.2e-12 453_[+2]_26 8182 1.2e-12 453_[+2]_26 5713 1.1e-08 339_[+2]_140 1833 1.5e-08 428_[+2]_51 bd518 1.8e-08 392_[+2]_87 1701 1.8e-08 33_[+2]_446 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=6 bd1079 ( 454) CAACACACAAACCTCTGACAC 1 8182 ( 454) CAACACACAAACCTCTGACAC 1 5713 ( 340) CAACACGCTTCCCTCTCTCTC 1 1833 ( 429) CCACAACAACTCCTCTTTCCC 1 bd518 ( 393) AAAGAAAGACACCTCAGCCCC 1 1701 ( 34) CAAGAAACCAACTGCTGTGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3360 bayes= 9.57485 E= 5.5e-003 -71 193 -923 -923 160 -39 -923 -923 187 -923 -923 -923 -923 161 35 -923 187 -923 -923 -923 87 120 -923 -923 128 -39 -65 -923 -71 161 -65 -923 128 -39 -923 -56 87 61 -923 -56 128 -39 -923 -56 -923 220 -923 -923 -923 193 -923 -56 -923 -923 -65 176 -923 220 -923 -923 -71 -923 -923 176 -923 -39 134 -56 28 -39 -923 102 -923 193 -65 -923 87 61 -923 -56 -923 220 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 5.5e-003 0.166667 0.833333 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.666667 0.166667 0.166667 0.000000 0.166667 0.666667 0.166667 0.000000 0.666667 0.166667 0.000000 0.166667 0.500000 0.333333 0.000000 0.166667 0.666667 0.166667 0.000000 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.000000 0.166667 0.833333 0.000000 1.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.833333 0.000000 0.166667 0.666667 0.166667 0.333333 0.166667 0.000000 0.500000 0.000000 0.833333 0.166667 0.000000 0.500000 0.333333 0.000000 0.166667 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CAA[CG]A[AC]ACA[AC]ACCTCTG[TA]C[AC]C -------------------------------------------------------------------------------- Time 0.86 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 7 llr = 82 E-value = 6.3e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1::3:::4:991 pos.-specific C :3:3:::3a::9 probability G ::93:a:::::: matrix T 9711a:a3:11: bits 2.2 * 2.0 *** * 1.8 *** * 1.5 *** * * Relative 1.3 *** *** **** Entropy 1.1 *** *** **** (16.8 bits) 0.9 *** *** **** 0.7 *** *** **** 0.4 *** ******** 0.2 *** ******** 0.0 ------------ Multilevel TTGATGTACAAC consensus C C C sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ bd1079 240 1.85e-07 CGAGAGTGTG TTGGTGTACAAC CATATTTTCC 8182 240 1.85e-07 CGAGAGTGTG TTGGTGTACAAC CATATTTTCC 1833 395 9.07e-07 ACTAATTGCT TCGCTGTTCAAC ATTGACGGGA 5713 214 2.09e-06 CAAGCCGCCA TTTCTGTCCAAC AAATGTCCCT 1549 157 2.99e-06 AAGGTTGGGA TTGATGTTCTAC CGTCGATGTG bd518 52 7.97e-06 TCGTCGGTCC TCGTTGTACAAA TCAAAGCAAA 1701 198 1.09e-05 GAGCCTTTGG ATGATGTCCATC TGACGTCCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- bd1079 1.9e-07 239_[+3]_249 8182 1.9e-07 239_[+3]_249 1833 9.1e-07 394_[+3]_94 5713 2.1e-06 213_[+3]_275 1549 3e-06 156_[+3]_332 bd518 8e-06 51_[+3]_437 1701 1.1e-05 197_[+3]_291 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=7 bd1079 ( 240) TTGGTGTACAAC 1 8182 ( 240) TTGGTGTACAAC 1 1833 ( 395) TCGCTGTTCAAC 1 5713 ( 214) TTTCTGTCCAAC 1 1549 ( 157) TTGATGTTCTAC 1 bd518 ( 52) TCGTTGTACAAA 1 1701 ( 198) ATGATGTCCATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 3423 bayes= 8.93074 E= 6.3e-001 -94 -945 -945 180 -945 39 -945 154 -945 -945 171 -78 6 39 12 -78 -945 -945 -945 202 -945 -945 193 -945 -945 -945 -945 202 65 39 -945 22 -945 220 -945 -945 165 -945 -945 -78 165 -945 -945 -78 -94 197 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 6.3e-001 0.142857 0.000000 0.000000 0.857143 0.000000 0.285714 0.000000 0.714286 0.000000 0.000000 0.857143 0.142857 0.285714 0.285714 0.285714 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.428571 0.285714 0.000000 0.285714 0.000000 1.000000 0.000000 0.000000 0.857143 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.142857 0.142857 0.857143 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[TC]G[ACG]TGT[ACT]CAAC -------------------------------------------------------------------------------- Time 1.25 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1549 1.09e-03 156_[+3(2.99e-06)]_236_\ [+2(9.71e-05)]_75 1701 2.68e-12 33_[+2(1.77e-08)]_72_[+1(2.14e-10)]_\ 50_[+3(1.09e-05)]_291 1833 3.12e-14 110_[+1(2.72e-11)]_263_\ [+3(9.07e-07)]_22_[+2(1.49e-08)]_51 5713 2.53e-07 213_[+3(2.09e-06)]_114_\ [+2(1.10e-08)]_140 8182 6.65e-21 78_[+1(1.83e-13)]_140_\ [+3(1.85e-07)]_202_[+2(1.16e-12)]_26 bd1079 6.65e-21 78_[+1(1.83e-13)]_140_\ [+3(1.85e-07)]_202_[+2(1.16e-12)]_26 bd518 4.16e-06 51_[+3(7.97e-06)]_329_\ [+2(1.77e-08)]_87 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************