******************************************************************************** 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/378/378.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1595 1.0000 500 20924 1.0000 500 22059 1.0000 500 22108 1.0000 500 24159 1.0000 500 24187 1.0000 500 24873 1.0000 500 263505 1.0000 500 34228 1.0000 500 4264 1.0000 500 693 1.0000 500 932 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/378/378.seqs.fa -oc motifs/378 -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= 12 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= 6000 N= 12 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.271 C 0.225 G 0.246 T 0.258 Background letter frequencies (from dataset with add-one prior applied): A 0.271 C 0.225 G 0.246 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 19 sites = 11 llr = 151 E-value = 3.0e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4:6:86:56772465294: pos.-specific C 6139219331:8543813a probability G :21::1121:3:1:2::4: matrix T :7:1:2:::2::1:::::: bits 2.2 * 1.9 * 1.7 * * * 1.5 * * * ** * Relative 1.3 ** * * ** * Entropy 1.1 * ** * ** * ** * (19.8 bits) 0.9 ** ** * *** * ** * 0.6 ***** ****** **** * 0.4 ******************* 0.2 ******************* 0.0 ------------------- Multilevel CTACAACAAAACCAACAAC consensus A C CC G ACC G sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 34228 475 4.84e-10 TTTTTTACCT CTACAACCAAACCCCCAAC GCAAAGG 693 478 2.02e-08 CACAGATAGA CTACCTCACAACAAACAAC TACA 932 472 2.29e-08 CAGCCTGCAG CTCCAACAATAACAACAGC ATCAGTCACA 22059 465 7.58e-08 GAATGGAGCA ATACACCAAAGCACCCAGC CAGCCAGCCA 24187 445 1.13e-07 GTGCAAGCTG CTGCAACAGAGCAAACAAC CCAACGGTCT 20924 18 1.13e-07 CGGATCTTTT ATCCAACAACAACAACAGC AACAACACCC 24159 443 3.55e-07 TACCGGAGGC CGACAACCAAACCCAACGC ACCACAAGCA 4264 121 5.67e-07 AATCTTTCGG CTCCAACGAAGCGACAACC AAAGAGTAGT 24873 310 8.75e-07 GTCTGGAGGG ACACCACCATACCAGCACC CGTGCTCTTG 263505 21 1.68e-06 ATTTGGCTAC ATACATGGCAACACGCACC AAGCGTTTGA 1595 472 1.90e-06 GATAGCGACA CGATAGCACAACTAACAAC CATCCCAACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 34228 4.8e-10 474_[+1]_7 693 2e-08 477_[+1]_4 932 2.3e-08 471_[+1]_10 22059 7.6e-08 464_[+1]_17 24187 1.1e-07 444_[+1]_37 20924 1.1e-07 17_[+1]_464 24159 3.5e-07 442_[+1]_39 4264 5.7e-07 120_[+1]_361 24873 8.7e-07 309_[+1]_172 263505 1.7e-06 20_[+1]_461 1595 1.9e-06 471_[+1]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=19 seqs=11 34228 ( 475) CTACAACCAAACCCCCAAC 1 693 ( 478) CTACCTCACAACAAACAAC 1 932 ( 472) CTCCAACAATAACAACAGC 1 22059 ( 465) ATACACCAAAGCACCCAGC 1 24187 ( 445) CTGCAACAGAGCAAACAAC 1 20924 ( 18) ATCCAACAACAACAACAGC 1 24159 ( 443) CGACAACCAAACCCAACGC 1 4264 ( 121) CTCCAACGAAGCGACAACC 1 24873 ( 310) ACACCACCATACCAGCACC 1 263505 ( 21) ATACATGGCAACACGCACC 1 1595 ( 472) CGATAGCACAACTAACAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 5784 bayes= 9.39137 E= 3.0e-004 42 150 -1010 -1010 -1010 -131 -44 150 123 28 -144 -1010 -1010 201 -1010 -150 159 -31 -1010 -1010 123 -131 -144 -50 -1010 201 -144 -1010 101 28 -44 -1010 123 28 -144 -1010 142 -131 -1010 -50 142 -1010 15 -1010 -58 186 -1010 -1010 42 101 -144 -150 123 69 -1010 -1010 101 28 -44 -1010 -58 186 -1010 -1010 175 -131 -1010 -1010 42 28 56 -1010 -1010 215 -1010 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 11 E= 3.0e-004 0.363636 0.636364 0.000000 0.000000 0.000000 0.090909 0.181818 0.727273 0.636364 0.272727 0.090909 0.000000 0.000000 0.909091 0.000000 0.090909 0.818182 0.181818 0.000000 0.000000 0.636364 0.090909 0.090909 0.181818 0.000000 0.909091 0.090909 0.000000 0.545455 0.272727 0.181818 0.000000 0.636364 0.272727 0.090909 0.000000 0.727273 0.090909 0.000000 0.181818 0.727273 0.000000 0.272727 0.000000 0.181818 0.818182 0.000000 0.000000 0.363636 0.454545 0.090909 0.090909 0.636364 0.363636 0.000000 0.000000 0.545455 0.272727 0.181818 0.000000 0.181818 0.818182 0.000000 0.000000 0.909091 0.090909 0.000000 0.000000 0.363636 0.272727 0.363636 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA]T[AC]CAAC[AC][AC]A[AG]C[CA][AC][AC]CA[AGC]C -------------------------------------------------------------------------------- Time 1.67 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 8 llr = 104 E-value = 2.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1:1::43:a:81:::: pos.-specific C 64:::14::9111::3 probability G :31:a34a:1:831a1 matrix T 348a:3::::1:69:6 bits 2.2 1.9 ** ** * 1.7 ** ** * 1.5 ** *** ** Relative 1.3 ** *** ** Entropy 1.1 ** *** ** (18.8 bits) 0.9 * *** ***** ** 0.6 * *** ********* 0.4 ***** ********** 0.2 ***** ********** 0.0 ---------------- Multilevel CCTTGACGACAGTTGT consensus TT GG G C sequence G TA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 4264 445 3.24e-09 TCAACATCTT CTTTGTCGACAGTTGT TGATTATTCG 22059 336 1.18e-07 ACCGTGGCTA CCTTGTCGACAGCTGC TGTCGGAGTG 34228 84 1.46e-07 CTGACTCTTC CTTTGGCGACCGTTGC AAGTTGTTAT 24187 340 2.36e-07 CTTCAAGTGT TCTTGGGGACAATTGT CCACTACTCC 24159 227 2.80e-07 TTAGTGCTGG CGTTGAGGAGAGGTGT TTGATACGGA 24873 390 1.39e-06 AACGAGTGGT TGATGAGGACAGTTGG TGGAAAGTCG 263505 446 2.60e-06 GTAAAGAACT ACTTGCAGACTGGTGT AAAGGTACGT 693 110 3.06e-06 GGCCGAAAGG CTGTGAAGACACTGGT TGGTTACGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4264 3.2e-09 444_[+2]_40 22059 1.2e-07 335_[+2]_149 34228 1.5e-07 83_[+2]_401 24187 2.4e-07 339_[+2]_145 24159 2.8e-07 226_[+2]_258 24873 1.4e-06 389_[+2]_95 263505 2.6e-06 445_[+2]_39 693 3.1e-06 109_[+2]_375 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=8 4264 ( 445) CTTTGTCGACAGTTGT 1 22059 ( 336) CCTTGTCGACAGCTGC 1 34228 ( 84) CTTTGGCGACCGTTGC 1 24187 ( 340) TCTTGGGGACAATTGT 1 24159 ( 227) CGTTGAGGAGAGGTGT 1 24873 ( 390) TGATGAGGACAGTTGG 1 263505 ( 446) ACTTGCAGACTGGTGT 1 693 ( 110) CTGTGAAGACACTGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 5820 bayes= 9.50482 E= 2.1e+002 -111 147 -965 -4 -965 74 2 54 -111 -965 -98 154 -965 -965 -965 196 -965 -965 202 -965 47 -85 2 -4 -12 74 61 -965 -965 -965 202 -965 188 -965 -965 -965 -965 196 -98 -965 147 -85 -965 -104 -111 -85 161 -965 -965 -85 2 128 -965 -965 -98 176 -965 -965 202 -965 -965 15 -98 128 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 8 E= 2.1e+002 0.125000 0.625000 0.000000 0.250000 0.000000 0.375000 0.250000 0.375000 0.125000 0.000000 0.125000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.375000 0.125000 0.250000 0.250000 0.250000 0.375000 0.375000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.875000 0.125000 0.000000 0.750000 0.125000 0.000000 0.125000 0.125000 0.125000 0.750000 0.000000 0.000000 0.125000 0.250000 0.625000 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.125000 0.625000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT][CTG]TTG[AGT][CGA]GACAG[TG]TG[TC] -------------------------------------------------------------------------------- Time 3.09 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 12 llr = 134 E-value = 1.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 43:::31:24a335:7 pos.-specific C :62:8:37:::41112 probability G :187:81:86:37392 matrix T 6:132:63:::::2:: bits 2.2 1.9 * 1.7 * * 1.5 * * * Relative 1.3 * * * * Entropy 1.1 **** **** * (16.1 bits) 0.9 ****** **** * * 0.6 ****** **** * ** 0.4 ************* ** 0.2 **************** 0.0 ---------------- Multilevel TCGGCGTCGGACGAGA consensus AA T ACT A GAG sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 4264 267 2.62e-09 CCTCATTACG TCGGCGTTGGACGAGA TTAAGTTGGA 24873 481 1.14e-08 TCAGGGTGCT ACGGCGTCGGACGTGA AATT 1595 61 5.40e-07 AACAAAACCA ACGGCATCAGAGGAGA CTCCTTCCAT 20924 347 8.44e-07 CTGGATGGTG TACGTGTCGGACGAGA CATCAGACAT 24159 414 1.56e-06 AAGTGGAAAC AAGTCGTCGGAGAAGC GATTACCGGA 693 3 1.72e-06 AG TCGGCGGTGAAGAAGA TAAGGTTGTG 932 91 5.36e-06 GAACCGAACC TCGTCGACGAAAAGGA AGGAGGATGG 22108 339 5.80e-06 TGCCGTGCTG AATGCGTCGGAAGCGA GGAAGATACT 24187 363 8.43e-06 TGTCCACTAC TCCTCGCCAAACGAGC ACTGCCCTCT 22059 20 1.04e-05 ACGATGCAGC AAGTCGTCGAACGGCG CATCGCAGCA 34228 325 2.20e-05 GTCTGAGCTG TCGGCACTGGAGCTGG CGTTGTCTTC 263505 50 3.89e-05 AAGCGTTTGA TGGGTACTGAAAGGGA GCTTGAGGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4264 2.6e-09 266_[+3]_218 24873 1.1e-08 480_[+3]_4 1595 5.4e-07 60_[+3]_424 20924 8.4e-07 346_[+3]_138 24159 1.6e-06 413_[+3]_71 693 1.7e-06 2_[+3]_482 932 5.4e-06 90_[+3]_394 22108 5.8e-06 338_[+3]_146 24187 8.4e-06 362_[+3]_122 22059 1e-05 19_[+3]_465 34228 2.2e-05 324_[+3]_160 263505 3.9e-05 49_[+3]_435 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=12 4264 ( 267) TCGGCGTTGGACGAGA 1 24873 ( 481) ACGGCGTCGGACGTGA 1 1595 ( 61) ACGGCATCAGAGGAGA 1 20924 ( 347) TACGTGTCGGACGAGA 1 24159 ( 414) AAGTCGTCGGAGAAGC 1 693 ( 3) TCGGCGGTGAAGAAGA 1 932 ( 91) TCGTCGACGAAAAGGA 1 22108 ( 339) AATGCGTCGGAAGCGA 1 24187 ( 363) TCCTCGCCAAACGAGC 1 22059 ( 20) AAGTCGTCGAACGGCG 1 34228 ( 325) TCGGCACTGGAGCTGG 1 263505 ( 50) TGGGTACTGAAAGGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 5820 bayes= 9.36712 E= 1.0e+001 62 -1023 -1023 118 30 137 -156 -1023 -1023 -43 161 -163 -1023 -1023 144 37 -1023 189 -1023 -63 -12 -1023 161 -1023 -170 15 -156 118 -1023 157 -1023 37 -70 -1023 176 -1023 62 -1023 124 -1023 188 -1023 -1023 -1023 -12 89 44 -1023 -12 -143 144 -1023 88 -143 2 -63 -1023 -143 189 -1023 130 -43 -56 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 12 E= 1.0e+001 0.416667 0.000000 0.000000 0.583333 0.333333 0.583333 0.083333 0.000000 0.000000 0.166667 0.750000 0.083333 0.000000 0.000000 0.666667 0.333333 0.000000 0.833333 0.000000 0.166667 0.250000 0.000000 0.750000 0.000000 0.083333 0.250000 0.083333 0.583333 0.000000 0.666667 0.000000 0.333333 0.166667 0.000000 0.833333 0.000000 0.416667 0.000000 0.583333 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.416667 0.333333 0.000000 0.250000 0.083333 0.666667 0.000000 0.500000 0.083333 0.250000 0.166667 0.000000 0.083333 0.916667 0.000000 0.666667 0.166667 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TA][CA]G[GT]C[GA][TC][CT]G[GA]A[CGA][GA][AG]GA -------------------------------------------------------------------------------- Time 4.71 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1595 2.42e-05 60_[+3(5.40e-07)]_395_\ [+1(1.90e-06)]_10 20924 1.96e-06 17_[+1(1.13e-07)]_310_\ [+3(8.44e-07)]_138 22059 3.63e-09 19_[+3(1.04e-05)]_300_\ [+2(1.18e-07)]_113_[+1(7.58e-08)]_17 22108 1.33e-02 338_[+3(5.80e-06)]_146 24159 5.85e-09 226_[+2(2.80e-07)]_171_\ [+3(1.56e-06)]_13_[+1(3.55e-07)]_39 24187 8.19e-09 87_[+3(6.24e-05)]_236_\ [+2(2.36e-07)]_7_[+3(8.43e-06)]_66_[+1(1.13e-07)]_37 24873 6.28e-10 309_[+1(8.75e-07)]_61_\ [+2(1.39e-06)]_75_[+3(1.14e-08)]_4 263505 3.37e-06 20_[+1(1.68e-06)]_10_[+3(3.89e-05)]_\ 380_[+2(2.60e-06)]_39 34228 8.10e-11 83_[+2(1.46e-07)]_92_[+2(8.33e-06)]_\ 117_[+3(2.20e-05)]_134_[+1(4.84e-10)]_7 4264 3.56e-13 120_[+1(5.67e-07)]_19_\ [+3(2.46e-05)]_92_[+3(2.62e-09)]_162_[+2(3.24e-09)]_40 693 4.12e-09 2_[+3(1.72e-06)]_91_[+2(3.06e-06)]_\ 352_[+1(2.02e-08)]_4 932 4.28e-06 20_[+3(7.51e-05)]_54_[+3(5.36e-06)]_\ 365_[+1(2.29e-08)]_10 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************