******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.8.1 (Release date: Tue Feb 7 14:03:40 EST 2012) 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= seqs_100.fasta ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1 1.0000 20 2 1.0000 20 3 1.0000 20 4 1.0000 20 5 1.0000 20 6 1.0000 20 7 1.0000 20 8 1.0000 20 9 1.0000 20 10 1.0000 20 11 1.0000 20 12 1.0000 20 13 1.0000 20 14 1.0000 20 15 1.0000 20 16 1.0000 20 17 1.0000 20 18 1.0000 20 19 1.0000 20 20 1.0000 20 21 1.0000 20 22 1.0000 20 23 1.0000 20 24 1.0000 20 25 1.0000 20 26 1.0000 20 27 1.0000 20 28 1.0000 20 29 1.0000 20 30 1.0000 20 31 1.0000 20 32 1.0000 20 33 1.0000 20 34 1.0000 20 35 1.0000 20 36 1.0000 20 37 1.0000 20 38 1.0000 20 39 1.0000 20 40 1.0000 20 41 1.0000 20 42 1.0000 20 43 1.0000 20 44 1.0000 20 45 1.0000 20 46 1.0000 20 47 1.0000 20 48 1.0000 20 49 1.0000 20 50 1.0000 20 51 1.0000 20 52 1.0000 20 53 1.0000 20 54 1.0000 20 55 1.0000 20 56 1.0000 20 57 1.0000 20 58 1.0000 20 59 1.0000 20 60 1.0000 20 61 1.0000 20 62 1.0000 20 63 1.0000 20 64 1.0000 20 65 1.0000 20 66 1.0000 20 67 1.0000 20 68 1.0000 20 69 1.0000 20 70 1.0000 20 71 1.0000 20 72 1.0000 20 73 1.0000 20 74 1.0000 20 75 1.0000 20 76 1.0000 20 77 1.0000 20 78 1.0000 20 79 1.0000 20 80 1.0000 20 81 1.0000 20 82 1.0000 20 83 1.0000 20 84 1.0000 20 85 1.0000 20 86 1.0000 20 87 1.0000 20 88 1.0000 20 89 1.0000 20 90 1.0000 20 91 1.0000 20 92 1.0000 20 93 1.0000 20 94 1.0000 20 95 1.0000 20 96 1.0000 20 97 1.0000 20 98 1.0000 20 99 1.0000 20 100 1.0000 20 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme seqs_100.fasta -dna -oc . -nostatus -time 7200 -maxsize 60000 -mod zoops -nmotifs 3 -minw 6 -maxw 7 -revcomp model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 6 maxw= 7 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 100 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= 2000 N= 100 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.315 C 0.185 G 0.185 T 0.315 Background letter frequencies (from dataset with add-one prior applied): A 0.314 C 0.186 G 0.186 T 0.314 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 7 sites = 94 llr = 549 E-value = 1.3e-075 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 7118:22 pos.-specific C 1:::::1 probability G 199:a73 matrix T 1::1:15 bits 2.4 * 2.2 * 1.9 * 1.7 ** * Relative 1.5 ** * Entropy 1.2 ** ** (8.4 bits) 1.0 ** ** 0.7 ***** 0.5 ****** 0.2 ******* 0.0 ------- Multilevel AGGAGGT consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------- 100 + 3 3.71e-05 TT AGGAGGT TTTGGAAATC 96 + 9 3.71e-05 CTATTTCA AGGAGGT TATGT 93 + 9 3.71e-05 TTAAGCGA AGGAGGT GTAAA 92 + 9 3.71e-05 TGTAGTGG AGGAGGT TAAAC 90 + 6 3.71e-05 AGCAT AGGAGGT GTTTTTAT 85 + 9 3.71e-05 TTTTTTAC AGGAGGT GGTTC 76 + 8 3.71e-05 ATAAATG AGGAGGT GGAAAG 71 + 7 3.71e-05 ATTTCA AGGAGGT AGATTTT 66 + 10 3.71e-05 TTTTAGTAA AGGAGGT TCTT 65 + 9 3.71e-05 TAGATAAC AGGAGGT GATTT 57 + 7 3.71e-05 CCTCTT AGGAGGT GATTTTT 52 + 3 3.71e-05 TT AGGAGGT TTTGGAAATC 43 + 13 3.71e-05 AATTCTCAGA AGGAGGT G 37 + 7 3.71e-05 TACATA AGGAGGT AGAAAAT 17 + 9 3.71e-05 AAGTCCAG AGGAGGT ATAAT 15 + 6 3.71e-05 GAATA AGGAGGT AGATAGGC 1 + 9 3.71e-05 ATGGGCTT AGGAGGT CATAT 36 + 9 5.90e-05 GTTCATGC AGGAGGG TTACT 21 + 9 5.90e-05 TTTAGTAT AGGAGGG ATTAA 16 + 9 5.90e-05 GAGTTTTA AGGAGGG AGAAG 99 + 10 1.18e-04 TAAATTTTT AGGAGGA TTAT 81 + 7 1.18e-04 TGTTTA AGGAGGA GGATGCA 72 - 8 1.18e-04 ATAAAA AGGAGGA TAGGGAG 56 + 9 1.18e-04 TTAAGATA AGGAGGA GATTT 53 + 6 1.18e-04 TTCAA GGGAGGT GGTGAATT 50 + 9 1.18e-04 AAACTTAC GGGAGGT GTAAA 48 + 7 1.18e-04 TATTGA AGGAGGA ATATAAC 39 + 8 1.18e-04 CAGATTT AGGAGGA CAATAA 29 + 7 1.18e-04 TTTTAA GGGAGGT GTGGTAA 23 + 8 1.18e-04 TAAGTTA AGGAGGA AAGACC 20 + 13 1.18e-04 TTTTTAAGGG GGGAGGT A 6 + 9 1.18e-04 GAGGATTA GGGAGGT ATTAA 68 + 9 1.53e-04 CCTTGTGG AGGAGGC TTGTG 47 + 5 1.53e-04 TCAA AGGAGGC GGTGTTCAA 42 + 8 1.53e-04 GAATAAA AGGAGGC TGTCTT 45 + 12 1.90e-04 GAAGAAAAGA AGGTGGT TG 9 - 14 1.90e-04 . AGGTGGT AAAGAGTGAA 78 + 6 3.12e-04 TTTTT TGGAGGT GATTTTTC 77 + 9 3.12e-04 TAACGGAA AGGAGAT GATTC 10 + 8 3.34e-04 AAATTTG CGGAGGT TGTGAA 98 + 6 4.14e-04 TTTGA AGGAGAG GTTTTAGC 95 + 8 4.14e-04 AGTTGAA AGGAGAG AAGATT 87 + 6 4.14e-04 ACTTA AGGAGAG GATAGTAA 54 - 9 4.14e-04 ACAAA AGGAGAG CTCATTCA 38 + 8 4.14e-04 AAGTTAT TGGAGGG GTATTT 28 + 10 4.14e-04 TTTTAAGTG AGGAGAG AAAA 24 + 5 4.14e-04 AATA AGGAGAG TGTATAGTT 62 + 7 4.40e-04 TGTGCA GGGAGGC TAGATAA 5 + 9 4.62e-04 TAAAGAAT AGGGGGT CAAAA 83 + 7 8.83e-04 TTTCGA AGGAGTG TATTTTA 80 + 9 8.83e-04 TAAAAGAA AGGAGAA GAGCT 70 + 9 8.83e-04 AATAGACA GGGAGAT GGAAC 61 + 8 8.83e-04 ATTAAAA AAGAGGT GTTTAC 55 + 8 8.83e-04 TGGCAGA AAGAGGT GAAAGC 46 + 7 8.83e-04 AACTTC TGGAGGA CATAAAA 44 + 9 8.83e-04 TTAATGAG AAGAGGT GTTTT 11 + 8 8.83e-04 CATATAA AAGAGGT GAAATA 3 + 6 8.83e-04 AAAAT AAGAGGT GTTTTTTA 2 + 9 8.83e-04 TCAAAAAC AGGAGTG AAAAA 67 + 8 1.01e-03 AATTGTA AGAAGGT GATAAA 18 + 9 1.01e-03 TGTCAGAG AGAAGGT GTGAC 64 + 7 1.20e-03 TTTAAC TGGAGGC GGAAACT 51 + 2 1.20e-03 A AGAAGGG TTTTCTAGAC 41 + 9 1.21e-03 AAAATGGA CGGAGGC TTTCT 97 + 11 1.38e-03 ATTATACGAG AGGTGAT AAT 82 + 12 1.38e-03 TATTCTTTTG AGGTGAT AC 73 + 10 1.38e-03 TTTAAGGAT AGGTGAT ACGC 69 + 11 1.38e-03 AGCATGTGGT AGGTGAT TAA 60 + 7 1.47e-03 AAGTGA AGGGGGA ACATATA 14 + 9 1.47e-03 AGAATATG AGGGGGA ATTGT 75 + 9 1.71e-03 TAAATGAA AGGAGTA TATAC 63 + 11 1.71e-03 TTCTTAAGTG AGGTGAG AGA 33 + 5 1.71e-03 TTGT AGGTGAG AGTTGTTTT 49 + 8 2.04e-03 CATAAAT GGGAGTG AAGTAA 26 + 5 2.04e-03 AAGA AGCAGGA ACTTGCGCC 84 + 7 2.43e-03 GATAAA GGAAGGG AAAATTT 13 + 13 2.43e-03 TGTGCTTTCA GGGCGGG G 91 + 11 2.54e-03 TTTTAATCGA AGGTGTT AAA 58 + 11 3.07e-03 GATAATGAAA GGGTGAT GTA 19 + 3 3.07e-03 AG TGGTGGA GTATATAAAG 74 + 8 3.26e-03 GGCTAAA GTGAGGG ATATAT 88 + 8 3.85e-03 CCTGGAT TGGAGTG ATGGAA 22 + 7 3.85e-03 TAAGAA AGTAGGT TATGGCG 89 + 2 4.62e-03 T TGCAGGG AAAAGCAAGG 86 + 7 5.35e-03 ATTTGA GCGAGGT GCTTAAG 79 + 9 5.93e-03 TAACTGGA CGGTGAT TTTTA 12 - 4 5.93e-03 CCCCCAAAAA TTGAGGG CTT 4 + 8 5.93e-03 TCATAAA GTGAGGA ATTTAA 40 - 2 8.44e-03 GGAAAATAAC AAAAGGT A 27 - 5 8.74e-03 AATCCGTTT CGGCGGA TTTT 7 + 7 9.41e-03 ATAAAA TAGAGGC AAAAGCC 35 - 7 1.27e-02 TTAATTG AGCAGTA TCAATT 25 + 1 1.27e-02 . ATAAGGG CAAATGCCCT 30 - 14 1.35e-02 . CGCTGGG ACGATATAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 100 3.7e-05 2_[+1]_11 96 3.7e-05 8_[+1]_5 93 3.7e-05 8_[+1]_5 92 3.7e-05 8_[+1]_5 90 3.7e-05 5_[+1]_8 85 3.7e-05 8_[+1]_5 76 3.7e-05 7_[+1]_6 71 3.7e-05 6_[+1]_7 66 3.7e-05 9_[+1]_4 65 3.7e-05 8_[+1]_5 57 3.7e-05 6_[+1]_7 52 3.7e-05 2_[+1]_11 43 3.7e-05 12_[+1]_1 37 3.7e-05 6_[+1]_7 17 3.7e-05 8_[+1]_5 15 3.7e-05 5_[+1]_8 1 3.7e-05 8_[+1]_5 36 5.9e-05 8_[+1]_5 21 5.9e-05 8_[+1]_5 16 5.9e-05 8_[+1]_5 99 0.00012 9_[+1]_4 81 0.00012 6_[+1]_7 72 0.00012 7_[-1]_6 56 0.00012 8_[+1]_5 53 0.00012 5_[+1]_8 50 0.00012 8_[+1]_5 48 0.00012 6_[+1]_7 39 0.00012 7_[+1]_6 29 0.00012 6_[+1]_7 23 0.00012 7_[+1]_6 20 0.00012 12_[+1]_1 6 0.00012 8_[+1]_5 68 0.00015 8_[+1]_5 47 0.00015 4_[+1]_9 42 0.00015 7_[+1]_6 45 0.00019 11_[+1]_2 9 0.00019 13_[-1] 78 0.00031 5_[+1]_8 77 0.00031 8_[+1]_5 10 0.00033 7_[+1]_6 98 0.00041 5_[+1]_8 95 0.00041 7_[+1]_6 87 0.00041 5_[+1]_8 54 0.00041 8_[-1]_5 38 0.00041 7_[+1]_6 28 0.00041 9_[+1]_4 24 0.00041 4_[+1]_9 62 0.00044 6_[+1]_7 5 0.00046 8_[+1]_5 83 0.00088 6_[+1]_7 80 0.00088 8_[+1]_5 70 0.00088 8_[+1]_5 61 0.00088 7_[+1]_6 55 0.00088 7_[+1]_6 46 0.00088 6_[+1]_7 44 0.00088 8_[+1]_5 11 0.00088 7_[+1]_6 3 0.00088 5_[+1]_8 2 0.00088 8_[+1]_5 67 0.001 7_[+1]_6 18 0.001 8_[+1]_5 64 0.0012 6_[+1]_7 51 0.0012 1_[+1]_12 41 0.0012 8_[+1]_5 97 0.0014 10_[+1]_3 82 0.0014 11_[+1]_2 73 0.0014 9_[+1]_4 69 0.0014 10_[+1]_3 60 0.0015 6_[+1]_7 14 0.0015 8_[+1]_5 75 0.0017 8_[+1]_5 63 0.0017 10_[+1]_3 33 0.0017 4_[+1]_9 49 0.002 7_[+1]_6 26 0.002 4_[+1]_9 84 0.0024 6_[+1]_7 13 0.0024 12_[+1]_1 91 0.0025 10_[+1]_3 58 0.0031 10_[+1]_3 19 0.0031 2_[+1]_11 74 0.0033 7_[+1]_6 88 0.0039 7_[+1]_6 22 0.0039 6_[+1]_7 89 0.0046 1_[+1]_12 86 0.0054 6_[+1]_7 79 0.0059 8_[+1]_5 12 0.0059 3_[-1]_10 4 0.0059 7_[+1]_6 40 0.0084 1_[-1]_12 27 0.0087 4_[-1]_9 7 0.0094 6_[+1]_7 35 0.013 6_[-1]_7 25 0.013 [+1]_13 30 0.014 13_[-1] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=7 seqs=94 100 ( 3) AGGAGGT 1 96 ( 9) AGGAGGT 1 93 ( 9) AGGAGGT 1 92 ( 9) AGGAGGT 1 90 ( 6) AGGAGGT 1 85 ( 9) AGGAGGT 1 76 ( 8) AGGAGGT 1 71 ( 7) AGGAGGT 1 66 ( 10) AGGAGGT 1 65 ( 9) AGGAGGT 1 57 ( 7) AGGAGGT 1 52 ( 3) AGGAGGT 1 43 ( 13) AGGAGGT 1 37 ( 7) AGGAGGT 1 17 ( 9) AGGAGGT 1 15 ( 6) AGGAGGT 1 1 ( 9) AGGAGGT 1 36 ( 9) AGGAGGG 1 21 ( 9) AGGAGGG 1 16 ( 9) AGGAGGG 1 99 ( 10) AGGAGGA 1 81 ( 7) AGGAGGA 1 72 ( 8) AGGAGGA 1 56 ( 9) AGGAGGA 1 53 ( 6) GGGAGGT 1 50 ( 9) GGGAGGT 1 48 ( 7) AGGAGGA 1 39 ( 8) AGGAGGA 1 29 ( 7) GGGAGGT 1 23 ( 8) AGGAGGA 1 20 ( 13) GGGAGGT 1 6 ( 9) GGGAGGT 1 68 ( 9) AGGAGGC 1 47 ( 5) AGGAGGC 1 42 ( 8) AGGAGGC 1 45 ( 12) AGGTGGT 1 9 ( 14) AGGTGGT 1 78 ( 6) TGGAGGT 1 77 ( 9) AGGAGAT 1 10 ( 8) CGGAGGT 1 98 ( 6) AGGAGAG 1 95 ( 8) AGGAGAG 1 87 ( 6) AGGAGAG 1 54 ( 9) AGGAGAG 1 38 ( 8) TGGAGGG 1 28 ( 10) AGGAGAG 1 24 ( 5) AGGAGAG 1 62 ( 7) GGGAGGC 1 5 ( 9) AGGGGGT 1 83 ( 7) AGGAGTG 1 80 ( 9) AGGAGAA 1 70 ( 9) GGGAGAT 1 61 ( 8) AAGAGGT 1 55 ( 8) AAGAGGT 1 46 ( 7) TGGAGGA 1 44 ( 9) AAGAGGT 1 11 ( 8) AAGAGGT 1 3 ( 6) AAGAGGT 1 2 ( 9) AGGAGTG 1 67 ( 8) AGAAGGT 1 18 ( 9) AGAAGGT 1 64 ( 7) TGGAGGC 1 51 ( 2) AGAAGGG 1 41 ( 9) CGGAGGC 1 97 ( 11) AGGTGAT 1 82 ( 12) AGGTGAT 1 73 ( 10) AGGTGAT 1 69 ( 11) AGGTGAT 1 60 ( 7) AGGGGGA 1 14 ( 9) AGGGGGA 1 75 ( 9) AGGAGTA 1 63 ( 11) AGGTGAG 1 33 ( 5) AGGTGAG 1 49 ( 8) GGGAGTG 1 26 ( 5) AGCAGGA 1 84 ( 7) GGAAGGG 1 13 ( 13) GGGCGGG 1 91 ( 11) AGGTGTT 1 58 ( 11) GGGTGAT 1 19 ( 3) TGGTGGA 1 74 ( 8) GTGAGGG 1 88 ( 8) TGGAGTG 1 22 ( 7) AGTAGGT 1 89 ( 2) TGCAGGG 1 86 ( 7) GCGAGGT 1 79 ( 9) CGGTGAT 1 12 ( 4) TTGAGGG 1 4 ( 8) GTGAGGA 1 40 ( 2) AAAAGGT 1 27 ( 5) CGGCGGA 1 7 ( 7) TAGAGGC 1 35 ( 7) AGCAGTA 1 25 ( 1) ATAAGGG 1 30 ( 14) CGCTGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 1400 bayes= 4.24793 E= 1.3e-075 116 -180 -32 -171 -208 -412 223 -288 -230 -212 225 -488 136 -312 -254 -118 -1320 -1320 243 -1320 -80 -1320 200 -208 -80 -132 46 64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 94 E= 1.3e-075 0.702128 0.053191 0.148936 0.095745 0.074468 0.010638 0.872340 0.042553 0.063830 0.042553 0.882979 0.010638 0.808511 0.021277 0.031915 0.138298 0.000000 0.000000 1.000000 0.000000 0.180851 0.000000 0.744681 0.074468 0.180851 0.074468 0.255319 0.489362 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- AGGAGG[TG] -------------------------------------------------------------------------------- Time 0.68 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 7 sites = 2 llr = 19 E-value = 8.3e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :5::::: pos.-specific C a:::::: probability G :::a:aa matrix T :5a:a:: bits 2.4 * * ** 2.2 * * ** 1.9 * * ** 1.7 * ***** Relative 1.5 * ***** Entropy 1.2 * ***** (13.7 bits) 1.0 * ***** 0.7 ******* 0.5 ******* 0.2 ******* 0.0 ------- Multilevel CATGTGG consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------- 69 + 3 7.41e-05 AG CATGTGG TAGGTGATTA 68 + 2 7.41e-05 C CTTGTGG AGGAGGCTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 69 7.4e-05 2_[+2]_11 68 7.4e-05 1_[+2]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=7 seqs=2 69 ( 3) CATGTGG 1 68 ( 2) CTTGTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 1400 bayes= 9.44915 E= 8.3e+004 -765 242 -765 -765 67 -765 -765 67 -765 -765 -765 166 -765 -765 242 -765 -765 -765 -765 166 -765 -765 242 -765 -765 -765 242 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 2 E= 8.3e+004 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[AT]TGTGG -------------------------------------------------------------------------------- Time 1.08 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 7 sites = 2 llr = 19 E-value = 8.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::aaa:: pos.-specific C ::::::a probability G aa::::: matrix T :::::a: bits 2.4 ** * 2.2 ** * 1.9 ** * 1.7 ******* Relative 1.5 ******* Entropy 1.2 ******* (14.0 bits) 1.0 ******* 0.7 ******* 0.5 ******* 0.2 ******* 0.0 ------- Multilevel GGAAATC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ------- 100 + 13 6.26e-05 AGGAGGTTTT GGAAATC T 52 + 13 6.26e-05 AGGAGGTTTT GGAAATC T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 100 6.3e-05 12_[+3]_1 52 6.3e-05 12_[+3]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=7 seqs=2 100 ( 13) GGAAATC 1 52 ( 13) GGAAATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 7 n= 1400 bayes= 9.44915 E= 8.4e+004 -765 -765 242 -765 -765 -765 242 -765 166 -765 -765 -765 166 -765 -765 -765 166 -765 -765 -765 -765 -765 -765 166 -765 242 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 7 nsites= 2 E= 8.4e+004 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- GGAAATC -------------------------------------------------------------------------------- Time 1.37 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1 3.17e-03 8_[+1(3.71e-05)]_5 2 1.74e-01 20 3 1.90e-01 20 4 2.30e-01 20 5 6.90e-02 20 6 5.21e-02 20 7 4.71e-01 20 8 2.79e-01 20 9 4.67e-02 20 10 2.32e-02 20 11 9.84e-02 20 12 3.18e-01 20 13 3.68e-02 20 14 5.74e-02 20 15 1.65e-02 5_[+1(3.71e-05)]_8 16 2.36e-02 8_[+1(5.90e-05)]_5 17 3.07e-03 8_[+1(3.71e-05)]_5 18 2.01e-01 20 19 2.16e-01 20 20 3.97e-02 20 21 2.36e-02 8_[+1(5.90e-05)]_5 22 3.00e-01 20 23 1.88e-02 20 24 1.26e-01 20 25 3.65e-01 20 26 7.22e-02 20 27 5.28e-01 20 28 7.93e-02 20 29 7.82e-03 20 30 8.46e-01 20 31 9.05e-01 20 32 9.69e-01 20 33 3.52e-01 20 34 1.00e+00 20 35 8.47e-01 20 36 4.94e-03 8_[+1(5.90e-05)]_5 37 7.44e-03 6_[+1(3.71e-05)]_7 38 9.76e-02 20 39 2.27e-02 20 40 2.56e-01 20 41 1.32e-01 20 42 3.07e-02 20 43 1.17e-02 12_[+1(3.71e-05)]_1 44 2.02e-01 20 45 3.20e-02 20 46 1.24e-02 20 47 2.76e-02 20 48 3.97e-02 20 49 3.37e-01 20 50 1.84e-02 20 51 1.38e-01 20 52 8.09e-05 2_[+1(3.71e-05)]_3_[+3(6.26e-05)]_1 53 1.84e-02 20 54 1.53e-02 20 55 8.26e-02 20 56 1.88e-02 20 57 9.24e-03 6_[+1(3.71e-05)]_7 58 4.45e-01 20 59 8.79e-01 20 60 1.52e-01 20 61 1.90e-01 20 62 6.67e-02 20 63 2.52e-01 20 64 2.40e-02 20 65 3.39e-03 8_[+1(3.71e-05)]_5 66 1.65e-02 9_[+1(3.71e-05)]_4 67 2.23e-01 20 68 6.90e-04 1_[+2(7.41e-05)]_12 69 3.17e-03 2_[+2(7.41e-05)]_11 70 7.48e-02 20 71 1.65e-02 6_[+1(3.71e-05)]_7 72 3.97e-02 20 73 2.69e-01 20 74 1.61e-01 20 75 3.78e-01 20 76 7.44e-03 7_[+1(3.71e-05)]_6 77 5.13e-02 20 78 3.39e-02 20 79 3.19e-01 20 80 2.16e-01 20 81 5.12e-02 20 82 1.10e-01 20 83 2.60e-01 20 84 2.22e-01 20 85 3.39e-03 8_[+1(3.71e-05)]_5 86 5.45e-01 20 87 4.74e-02 20 88 5.30e-01 20 89 2.39e-01 20 90 1.48e-02 5_[+1(3.71e-05)]_8 91 4.33e-01 20 92 7.44e-03 8_[+1(3.71e-05)]_5 93 1.65e-02 8_[+1(3.71e-05)]_5 94 9.86e-01 20 95 1.33e-01 20 96 9.24e-03 8_[+1(3.71e-05)]_5 97 1.63e-01 20 98 1.26e-01 20 99 4.84e-02 20 100 8.09e-05 2_[+1(3.71e-05)]_3_[+3(6.26e-05)]_1 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: cl1nweb ********************************************************************************