******************************************************************************** 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/189/189.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10230 1.0000 500 1135 1.0000 500 11801 1.0000 500 25575 1.0000 500 270367 1.0000 500 27776 1.0000 500 36263 1.0000 500 37377 1.0000 500 4454 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/189/189.seqs.fa -oc motifs/189 -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 0.252 C 0.232 G 0.253 T 0.263 Background letter frequencies (from dataset with add-one prior applied): A 0.252 C 0.232 G 0.253 T 0.263 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 6 llr = 114 E-value = 1.2e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :a:7:a:8:::3255:7287: pos.-specific C 8:825:82aaa:722728:35 probability G 2:2:5:2::::7:33:::::5 matrix T :::2::::::::2::32:2:: bits 2.1 *** 1.9 * * *** 1.7 * * *** 1.5 *** ** *** * Relative 1.3 *** ****** ** Entropy 1.1 *** ******** * **** (27.5 bits) 0.8 ************* ****** 0.6 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CACACACACCCGCAACACAAC consensus G A GGT CG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 37377 407 2.81e-12 GCCAGATAGA CACAGACACCCGCGGCACAAC TGCATCATCT 270367 456 2.81e-12 GCCAGATAGA CACAGACACCCGCGGCACAAC TGCATCATCT 1135 335 6.85e-10 TTCCTGTCTT CACAGAGACCCGAAATACAAG CGTCCAGCAT 10230 246 1.69e-09 CCTCTACCAC CACCCACACCCGCAACCAACG CAACCACCAT 11801 480 1.32e-08 CTCCAGCCAG CACACACACCCATCATTCTCG 36263 471 1.57e-08 ATACTATCTT GAGTCACCCCCACACCACAAC ACATCAATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37377 2.8e-12 406_[+1]_73 270367 2.8e-12 455_[+1]_24 1135 6.8e-10 334_[+1]_145 10230 1.7e-09 245_[+1]_234 11801 1.3e-08 479_[+1] 36263 1.6e-08 470_[+1]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=6 37377 ( 407) CACAGACACCCGCGGCACAAC 1 270367 ( 456) CACAGACACCCGCGGCACAAC 1 1135 ( 335) CACAGAGACCCGAAATACAAG 1 10230 ( 246) CACCCACACCCGCAACCAACG 1 11801 ( 480) CACACACACCCATCATTCTCG 1 36263 ( 471) GAGTCACCCCCACACCACAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 4320 bayes= 10.5905 E= 1.2e-003 -923 184 -60 -923 199 -923 -923 -923 -923 184 -60 -923 140 -48 -923 -65 -923 111 98 -923 199 -923 -923 -923 -923 184 -60 -923 172 -48 -923 -923 -923 210 -923 -923 -923 210 -923 -923 -923 210 -923 -923 40 -923 140 -923 -60 152 -923 -65 99 -48 40 -923 99 -48 40 -923 -923 152 -923 34 140 -48 -923 -65 -60 184 -923 -923 172 -923 -923 -65 140 52 -923 -923 -923 111 98 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6 E= 1.2e-003 0.000000 0.833333 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.666667 0.166667 0.000000 0.166667 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.833333 0.166667 0.000000 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 0.333333 0.000000 0.666667 0.000000 0.166667 0.666667 0.000000 0.166667 0.500000 0.166667 0.333333 0.000000 0.500000 0.166667 0.333333 0.000000 0.000000 0.666667 0.000000 0.333333 0.666667 0.166667 0.000000 0.166667 0.166667 0.833333 0.000000 0.000000 0.833333 0.000000 0.000000 0.166667 0.666667 0.333333 0.000000 0.000000 0.000000 0.500000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CACA[CG]ACACCC[GA]C[AG][AG][CT]ACA[AC][CG] -------------------------------------------------------------------------------- Time 1.03 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 19 sites = 6 llr = 108 E-value = 4.8e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 2a:22:5:22::72:::a2 pos.-specific C 8:553a:8:2a7382aa:8 probability G ::2:2::2::::::::::: matrix T ::333:5:87:3::8:::: bits 2.1 * * ** 1.9 * * * *** 1.7 * * * *** 1.5 ** * * * * **** Relative 1.3 ** * ** * ****** Entropy 1.1 ** **** ********* (25.9 bits) 0.8 ** **** ********* 0.6 **** ************** 0.4 **** ************** 0.2 **** ************** 0.0 ------------------- Multilevel CACCCCACTTCCACTCCAC consensus TTT T TC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 37377 433 2.88e-11 ACAACTGCAT CATCTCACTTCCACTCCAC AACCAGCCTC 270367 482 2.88e-11 ACAACTGCAT CATCTCACTTCCACTCCAC 27776 471 2.71e-09 TCTTGAGGCC CACTCCTGTCCCACTCCAC TTAAACGCAT 4454 470 1.71e-08 ACCACCTCTG AAGACCACTTCTCCTCCAC AACTACAACA 36263 190 1.90e-08 GAACATAAAA CACTGCTCAACTCCTCCAC CTGTCCTACC 11801 113 1.90e-08 CGTGATACTG CACCACTCTTCCAACCCAA GTCAGGCACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37377 2.9e-11 432_[+2]_49 270367 2.9e-11 481_[+2] 27776 2.7e-09 470_[+2]_11 4454 1.7e-08 469_[+2]_12 36263 1.9e-08 189_[+2]_292 11801 1.9e-08 112_[+2]_369 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=19 seqs=6 37377 ( 433) CATCTCACTTCCACTCCAC 1 270367 ( 482) CATCTCACTTCCACTCCAC 1 27776 ( 471) CACTCCTGTCCCACTCCAC 1 4454 ( 470) AAGACCACTTCTCCTCCAC 1 36263 ( 190) CACTGCTCAACTCCTCCAC 1 11801 ( 113) CACCACTCTTCCAACCCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 4338 bayes= 10.5965 E= 4.8e-004 -60 184 -923 -923 199 -923 -923 -923 -923 111 -60 34 -60 111 -923 34 -60 52 -60 34 -923 210 -923 -923 99 -923 -923 93 -923 184 -60 -923 -60 -923 -923 166 -60 -48 -923 134 -923 210 -923 -923 -923 152 -923 34 140 52 -923 -923 -60 184 -923 -923 -923 -48 -923 166 -923 210 -923 -923 -923 210 -923 -923 199 -923 -923 -923 -60 184 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 6 E= 4.8e-004 0.166667 0.833333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.166667 0.333333 0.166667 0.500000 0.000000 0.333333 0.166667 0.333333 0.166667 0.333333 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.833333 0.166667 0.000000 0.166667 0.000000 0.000000 0.833333 0.166667 0.166667 0.000000 0.666667 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.666667 0.333333 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 0.000000 0.166667 0.000000 0.833333 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.833333 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- CA[CT][CT][CT]C[AT]CTTC[CT][AC]CTCCAC -------------------------------------------------------------------------------- Time 1.91 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 19 sites = 7 llr = 116 E-value = 1.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::3::1::a993:443a: pos.-specific C 9:144:119:::::1:6:: probability G :::1::17::1::9:6::: matrix T 1a916a611::1714:1:a bits 2.1 1.9 * * * ** 1.7 * * * ** 1.5 ** * **** * ** Relative 1.3 *** * **** * ** Entropy 1.1 *** ** ****** * ** (23.9 bits) 0.8 *** ** ******* * ** 0.6 *** ** ************ 0.4 *** ** ************ 0.2 ******************* 0.0 ------------------- Multilevel CTTCTTTGCAAATGAGCAT consensus AC A TAA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 37377 110 4.11e-11 ATGTGTGGTG CTTATTTGCAAATGTGCAT GTGGTGATGT 270367 159 4.11e-11 ATGTGTGGTG CTTATTTGCAAATGTGCAT GTGGTGATGT 36263 167 3.08e-09 GACATGACGC CTTTCTAGCAAATGAACAT AAAACACTGC 1135 429 9.76e-09 GTCCATTTGA CTTCCTGCCAAAAGAGCAT CGCTCCCACC 10230 9 5.35e-08 AGTACATG CTTGCTTGCAATTTAGAAT CTTGAAGGGG 4454 57 1.18e-07 CAACGTGGAC CTTCTTCTCAGATGCAAAT GCCAGGTGTA 11801 398 2.40e-07 GCACTACTGC TTCCTTTGTAAAAGTATAT TAAAAAAGGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37377 4.1e-11 109_[+3]_372 270367 4.1e-11 158_[+3]_323 36263 3.1e-09 166_[+3]_315 1135 9.8e-09 428_[+3]_53 10230 5.3e-08 8_[+3]_473 4454 1.2e-07 56_[+3]_425 11801 2.4e-07 397_[+3]_84 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=19 seqs=7 37377 ( 110) CTTATTTGCAAATGTGCAT 1 270367 ( 159) CTTATTTGCAAATGTGCAT 1 36263 ( 167) CTTTCTAGCAAATGAACAT 1 1135 ( 429) CTTCCTGCCAAAAGAGCAT 1 10230 ( 9) CTTGCTTGCAATTTAGAAT 1 4454 ( 57) CTTCTTCTCAGATGCAAAT 1 11801 ( 398) TTCCTTTGTAAAAGTATAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 4338 bayes= 9.11674 E= 1.5e-002 -945 188 -945 -88 -945 -945 -945 193 -945 -70 -945 170 18 88 -82 -88 -945 88 -945 112 -945 -945 -945 193 -82 -70 -82 112 -945 -70 150 -88 -945 188 -945 -88 199 -945 -945 -945 176 -945 -82 -945 176 -945 -945 -88 18 -945 -945 144 -945 -945 176 -88 76 -70 -945 71 76 -945 117 -945 18 130 -945 -88 199 -945 -945 -945 -945 -945 -945 193 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 7 E= 1.5e-002 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 0.000000 1.000000 0.000000 0.142857 0.000000 0.857143 0.285714 0.428571 0.142857 0.142857 0.000000 0.428571 0.000000 0.571429 0.000000 0.000000 0.000000 1.000000 0.142857 0.142857 0.142857 0.571429 0.000000 0.142857 0.714286 0.142857 0.000000 0.857143 0.000000 0.142857 1.000000 0.000000 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.857143 0.000000 0.000000 0.142857 0.285714 0.000000 0.000000 0.714286 0.000000 0.000000 0.857143 0.142857 0.428571 0.142857 0.000000 0.428571 0.428571 0.000000 0.571429 0.000000 0.285714 0.571429 0.000000 0.142857 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CTT[CA][TC]TTGCAAA[TA]G[AT][GA][CA]AT -------------------------------------------------------------------------------- Time 2.64 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10230 2.14e-10 8_[+3(5.35e-08)]_218_[+1(1.69e-09)]_\ 121_[+2(5.01e-05)]_94 1135 2.11e-10 334_[+1(6.85e-10)]_73_\ [+3(9.76e-09)]_53 11801 3.81e-12 112_[+2(1.90e-08)]_266_\ [+3(2.40e-07)]_63_[+1(1.32e-08)] 25575 3.34e-01 500 270367 6.07e-22 158_[+3(4.11e-11)]_278_\ [+1(2.81e-12)]_5_[+2(2.88e-11)] 27776 3.41e-06 470_[+2(2.71e-09)]_11 36263 7.33e-14 166_[+3(3.08e-09)]_4_[+2(1.90e-08)]_\ 262_[+1(1.57e-08)]_9 37377 6.07e-22 109_[+3(4.11e-11)]_278_\ [+1(2.81e-12)]_5_[+2(2.88e-11)]_49 4454 5.58e-08 56_[+3(1.18e-07)]_394_\ [+2(1.71e-08)]_12 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************