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1 ********************************************************************************
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2 MEME - Motif discovery tool
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3 ********************************************************************************
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4 MEME version 4.11.0 (Release date: Thu Nov 26 17:48:49 2015 +1000)
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5
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6 For further information on how to interpret these results or to get
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7 a copy of the MEME software please access http://meme-suite.org .
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8
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9 This file may be used as input to the MAST algorithm for searching
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10 sequence databases for matches to groups of motifs. MAST is available
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11 for interactive use and downloading at http://meme-suite.org .
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12 ********************************************************************************
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13
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14
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15 ********************************************************************************
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16 REFERENCE
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17 ********************************************************************************
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18 If you use this program in your research, please cite:
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19
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20 Timothy L. Bailey and Charles Elkan,
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21 "Fitting a mixture model by expectation maximization to discover
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22 motifs in biopolymers", Proceedings of the Second International
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23 Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
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24 AAAI Press, Menlo Park, California, 1994.
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25 ********************************************************************************
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26
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27
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28 ********************************************************************************
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29 TRAINING SET
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30 ********************************************************************************
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31 DATAFILE=
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32 ALPHABET= ACDEFGHIKLMNPQRSTVWY
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33 Sequence name Weight Length Sequence name Weight Length
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34 ------------- ------ ------ ------------- ------ ------
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35 chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50
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36 chr21_28217753_28217803_ 1.0000 50 chr21_31710037_31710087_ 1.0000 50
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37 chr21_31744582_31744632_ 1.0000 50 chr21_31768316_31768366_ 1.0000 50
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38 chr21_31914206_31914256_ 1.0000 50 chr21_31933633_31933683_ 1.0000 50
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39 chr21_31962741_31962791_ 1.0000 50 chr21_31964683_31964733_ 1.0000 50
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40 chr21_31973364_31973414_ 1.0000 50 chr21_31992870_31992920_ 1.0000 50
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41 chr21_32185595_32185645_ 1.0000 50 chr21_32202076_32202126_ 1.0000 50
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42 chr21_32253899_32253949_ 1.0000 50 chr21_32410820_32410870_ 1.0000 50
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43 chr21_36411748_36411798_ 1.0000 50 chr21_37838750_37838800_ 1.0000 50
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44 chr21_45705687_45705737_ 1.0000 50 chr21_45971413_45971463_ 1.0000 50
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45 chr21_45978668_45978718_ 1.0000 50 chr21_45993530_45993580_ 1.0000 50
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46 chr21_46020421_46020471_ 1.0000 50 chr21_46031920_46031970_ 1.0000 50
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47 chr21_46046964_46047014_ 1.0000 50 chr21_46057197_46057247_ 1.0000 50
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48 chr21_46086869_46086919_ 1.0000 50 chr21_46102103_46102153_ 1.0000 50
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49 chr21_47517957_47518007_ 1.0000 50 chr21_47575506_47575556_ 1.0000 50
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50 ********************************************************************************
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51
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52 ********************************************************************************
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53 COMMAND LINE SUMMARY
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54 ********************************************************************************
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55 This information can also be useful in the event you wish to report a
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56 problem with the MEME software.
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57
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58 command: meme
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59
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60 model: mod= zoops nmotifs= 1 evt= inf
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61 object function= E-value of product of p-values
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62 width: minw= 8 maxw= 50
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63 width: wg= 11 ws= 1 endgaps= yes
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64 nsites: minsites= 2 maxsites= 30 wnsites= 0.8
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65 theta: spmap= pam spfuzz= 120
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66 global: substring= yes branching= no wbranch= no
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67 em: prior= megap b= 7500 maxiter= 50
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68 distance= 1e-05
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69 data: n= 1500 N= 30 shuffle= -1
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70
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71 sample: seed= 0 ctfrac= -1 maxwords= -1
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72 Dirichlet mixture priors file: prior30.plib
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73 Letter frequencies in dataset:
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74 A 0.294 C 0.231 D 0.000 E 0.000 F 0.000 G 0.257 H 0.000 I 0.000 K 0.000
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75 L 0.000 M 0.000 N 0.000 P 0.000 Q 0.000 R 0.000 S 0.000 T 0.217 V 0.000
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76 W 0.000 Y 0.000
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77 Background letter frequencies (from dataset with add-one prior applied):
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78 A 0.291 C 0.229 D 0.001 E 0.001 F 0.001 G 0.255 H 0.001 I 0.001 K 0.001
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79 L 0.001 M 0.001 N 0.001 P 0.001 Q 0.001 R 0.001 S 0.001 T 0.215 V 0.001
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80 W 0.001 Y 0.001
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81 ********************************************************************************
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82
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83
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84 ********************************************************************************
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85 MOTIF 1 MEME width = 11 sites = 25 llr = 239 E-value = 2.4e-011
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86 ********************************************************************************
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87 --------------------------------------------------------------------------------
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88 Motif 1 Description
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89 --------------------------------------------------------------------------------
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90 Simplified A 2323:a:a8a8
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91 pos.-specific C ::3::::::::
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92 probability D :::::::::::
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93 matrix E :::::::::::
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94 F :::::::::::
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95 G 7746::::::1
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96 H :::::::::::
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97 I :::::::::::
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98 K :::::::::::
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99 L :::::::::::
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100 M :::::::::::
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101 N :::::::::::
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102 P :::::::::::
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103 Q :::::::::::
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104 R :::::::::::
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105 S :::::::::::
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106 T 1:2:a:a:2::
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107 V :::::::::::
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108 W :::::::::::
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109 Y :::::::::::
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110
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111 bits 10.6
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112 9.5
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113 8.5
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114 7.4
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115 Relative 6.3
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116 Entropy 5.3
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117 (13.8 bits) 4.2
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118 3.2
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119 2.1 * **
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120 1.1 ** ********
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121 0.0 -----------
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122
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123 Multilevel GGGGTATAAAA
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124 consensus AACA T
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125 sequence
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126
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127
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128 --------------------------------------------------------------------------------
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129
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130 --------------------------------------------------------------------------------
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131 Motif 1 sites sorted by position p-value
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132 --------------------------------------------------------------------------------
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133 Sequence name Start P-value Site
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134 ------------- ----- --------- -----------
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135 chr21_46046964_46047014_ 13 1.06e-06 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC
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136 chr21_46057197_46057247_ 37 3.41e-06 ACAGGCCCTG GGCATATAAAA GCC
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137 chr21_45971413_45971463_ 10 3.41e-06 CAGGCCCTG GGCATATAAAA GCCCCAGCAG
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138 chr21_31964683_31964733_ 14 3.41e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC
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139 chr21_45993530_45993580_ 8 4.00e-06 CCAAGGA GGAGTATAAAA GCCCCACAAA
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140 chr21_32202076_32202126_ 14 5.01e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC
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141 chr21_46031920_46031970_ 16 6.06e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC
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142 chr21_32410820_32410870_ 22 8.67e-06 AATCACTGAG GATGTATAAAA GTCCCAGGGA
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143 chr21_32185595_32185645_ 19 8.67e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT
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144 chr21_31992870_31992920_ 17 8.67e-06 CACTATTGAA GATGTATAAAA TTTCATTTGC
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145 chr21_46020421_46020471_ 3 1.21e-05 GA GACATATAAAA GCCAACATCC
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146 chr21_47517957_47518007_ 33 1.59e-05 CCGGCGGGGC GGGGTATAAAG GGGGCGG
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147 chr21_45978668_45978718_ 5 1.59e-05 CAGA GGGGTATAAAG GTTCCGACCA
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148 chr21_31914206_31914256_ 16 1.68e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG
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149 chr21_32253899_32253949_ 20 2.03e-05 CACCAGCAAG GATATATAAAA GCTCAGGAGT
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150 chr21_31744582_31744632_ 13 3.06e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC
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151 chr21_19617074_19617124_ 40 3.06e-05 CCTCGGGACG TGGGTATATAA
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152 chr21_45705687_45705737_ 38 3.82e-05 CGTGGTCGCG GGGGTATAACA GC
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153 chr21_31768316_31768366_ 1 3.82e-05 . AACGTATATAA ATGGTCCTGT
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154 chr21_47575506_47575556_ 31 4.02e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG
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155 chr21_26934381_26934431_ 28 5.52e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG
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156 chr21_31710037_31710087_ 15 5.94e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC
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157 chr21_36411748_36411798_ 23 6.78e-05 AGTTTCAGTT GGCATCtaaaa attatataac
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158 chr21_31933633_31933683_ 3 2.08e-04 TC AGAGTATATAT AAATGTTCCT
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159 chr21_31962741_31962791_ 14 4.05e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC
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160 --------------------------------------------------------------------------------
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161
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162 --------------------------------------------------------------------------------
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163 Motif 1 block diagrams
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164 --------------------------------------------------------------------------------
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165 SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
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166 ------------- ---------------- -------------
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167 chr21_46046964_46047014_ 1.1e-06 12_[1]_27
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168 chr21_46057197_46057247_ 3.4e-06 36_[1]_3
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169 chr21_45971413_45971463_ 3.4e-06 9_[1]_30
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170 chr21_31964683_31964733_ 3.4e-06 13_[1]_26
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171 chr21_45993530_45993580_ 4e-06 7_[1]_32
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172 chr21_32202076_32202126_ 5e-06 13_[1]_26
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173 chr21_46031920_46031970_ 6.1e-06 15_[1]_24
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174 chr21_32410820_32410870_ 8.7e-06 21_[1]_18
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175 chr21_32185595_32185645_ 8.7e-06 18_[1]_21
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176 chr21_31992870_31992920_ 8.7e-06 16_[1]_23
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177 chr21_46020421_46020471_ 1.2e-05 2_[1]_37
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178 chr21_47517957_47518007_ 1.6e-05 32_[1]_7
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179 chr21_45978668_45978718_ 1.6e-05 4_[1]_35
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180 chr21_31914206_31914256_ 1.7e-05 15_[1]_24
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181 chr21_32253899_32253949_ 2e-05 19_[1]_20
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182 chr21_31744582_31744632_ 3.1e-05 12_[1]_27
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183 chr21_19617074_19617124_ 3.1e-05 39_[1]
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184 chr21_45705687_45705737_ 3.8e-05 37_[1]_2
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185 chr21_31768316_31768366_ 3.8e-05 [1]_39
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186 chr21_47575506_47575556_ 4e-05 30_[1]_9
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187 chr21_26934381_26934431_ 5.5e-05 27_[1]_12
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188 chr21_31710037_31710087_ 5.9e-05 14_[1]_25
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189 chr21_36411748_36411798_ 6.8e-05 22_[1]_17
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190 chr21_31933633_31933683_ 0.00021 2_[1]_37
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191 chr21_31962741_31962791_ 0.0004 13_[1]_26
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192 --------------------------------------------------------------------------------
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193
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194 --------------------------------------------------------------------------------
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195 Motif 1 in BLOCKS format
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196 --------------------------------------------------------------------------------
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197 BL MOTIF 1 width=11 seqs=25
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198 chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1
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199 chr21_46057197_46057247_ ( 37) GGCATATAAAA 1
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200 chr21_45971413_45971463_ ( 10) GGCATATAAAA 1
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201 chr21_31964683_31964733_ ( 14) GGCATATAAAA 1
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202 chr21_45993530_45993580_ ( 8) GGAGTATAAAA 1
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203 chr21_32202076_32202126_ ( 14) GAGGTATAAAA 1
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204 chr21_46031920_46031970_ ( 16) AGGGTATAAAA 1
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205 chr21_32410820_32410870_ ( 22) GATGTATAAAA 1
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206 chr21_32185595_32185645_ ( 19) GGGATATATAA 1
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207 chr21_31992870_31992920_ ( 17) GATGTATAAAA 1
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208 chr21_46020421_46020471_ ( 3) GACATATAAAA 1
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209 chr21_47517957_47518007_ ( 33) GGGGTATAAAG 1
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210 chr21_45978668_45978718_ ( 5) GGGGTATAAAG 1
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211 chr21_31914206_31914256_ ( 16) AGAGTATAAAA 1
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212 chr21_32253899_32253949_ ( 20) GATATATAAAA 1
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213 chr21_31744582_31744632_ ( 13) AGCATATATAA 1
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214 chr21_19617074_19617124_ ( 40) TGGGTATATAA 1
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215 chr21_45705687_45705737_ ( 38) GGGGTATAACA 1
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216 chr21_31768316_31768366_ ( 1) AACGTATATAA 1
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217 chr21_47575506_47575556_ ( 31) AGCGTATAAAG 1
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218 chr21_26934381_26934431_ ( 28) GAGTTATAAAA 1
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219 chr21_31710037_31710087_ ( 15) TGAGTATATAA 1
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220 chr21_36411748_36411798_ ( 23) GGCATCTAAAA 1
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221 chr21_31933633_31933683_ ( 3) AGAGTATATAT 1
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222 chr21_31962741_31962791_ ( 14) GTTGGATAAAA 1
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223 //
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224
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225 --------------------------------------------------------------------------------
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226
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227 --------------------------------------------------------------------------------
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228 Motif 1 position-specific scoring matrix
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229 --------------------------------------------------------------------------------
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230 log-odds matrix: alength= 20 w= 11 n= 1200 bayes= 5.33554 E= 2.4e-011
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231 -32 -680 91 77 7 138 -20 55 64 107 11 150 142 72 87 396 -148 221 -140 -36
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232 -11 -680 89 76 7 137 -21 55 63 107 10 149 141 71 87 396 -239 220 -140 -36
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233 -79 41 4 21 -7 44 -62 42 -5 99 0 99 138 52 42 399 -46 223 -173 -68
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234 11 -677 48 47 -2 127 -43 46 27 101 3 124 138 60 62 397 -235 220 -160 -55
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235 -596 -820 12 -21 -53 -267 -74 37 16 44 -37 98 31 9 19 319 212 127 -193 -95
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236 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8
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237 -838 -990 -89 -149 -151 -841 -161 -117 -113 -66 -209 -68 -69 -129 -91 111 221 -55 -255 -173
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238 176 -858 -79 -103 -115 -717 -148 -95 -108 -17 -162 -61 -12 -95 -69 193 -737 52 -240 -153
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239 134 -686 0 16 -12 -553 -68 44 -8 96 -9 88 124 41 36 384 11 216 -177 -71
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240 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8
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241 147 -614 89 129 93 -121 12 160 113 217 108 144 144 111 125 447 -241 332 -81 22
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242 --------------------------------------------------------------------------------
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243
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244 --------------------------------------------------------------------------------
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245 Motif 1 position-specific probability matrix
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246 --------------------------------------------------------------------------------
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247 letter-probability matrix: alength= 20 w= 11 nsites= 25 E= 2.4e-011
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248 0.240000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.080000 0.000000 0.000000 0.000000
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249 0.280000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000
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250 0.160000 0.320000 0.000000 0.000000 0.000000 0.360000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.160000 0.000000 0.000000 0.000000
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251 0.320000 0.000000 0.000000 0.000000 0.000000 0.640000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000
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252 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.960000 0.000000 0.000000 0.000000
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253 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
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254 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000
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255 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
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256 0.760000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.240000 0.000000 0.000000 0.000000
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257 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
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258 0.840000 0.000000 0.000000 0.000000 0.000000 0.120000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000
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259 --------------------------------------------------------------------------------
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260
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261 --------------------------------------------------------------------------------
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262 Motif 1 regular expression
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263 --------------------------------------------------------------------------------
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264 [GA][GA][GC][GA]TATA[AT]AA
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265 --------------------------------------------------------------------------------
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266
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267
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268
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269
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270 Time
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271
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272 ********************************************************************************
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273
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274
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275 ********************************************************************************
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276 SUMMARY OF MOTIFS
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277 ********************************************************************************
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278
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279 --------------------------------------------------------------------------------
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280 Combined block diagrams: non-overlapping sites with p-value < 0.0001
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281 --------------------------------------------------------------------------------
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282 SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
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283 ------------- ---------------- -------------
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284 chr21_19617074_19617124_ 1.22e-03 39_[1(3.06e-05)]
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285 chr21_26934381_26934431_ 2.21e-03 27_[1(5.52e-05)]_12
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286 chr21_28217753_28217803_ 7.29e-01 50
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287 chr21_31710037_31710087_ 2.37e-03 14_[1(5.94e-05)]_25
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288 chr21_31744582_31744632_ 1.22e-03 12_[1(3.06e-05)]_27
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289 chr21_31768316_31768366_ 1.53e-03 [1(3.82e-05)]_39
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290 chr21_31914206_31914256_ 6.70e-04 15_[1(1.68e-05)]_24
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291 chr21_31933633_31933683_ 1.81e-03 4_[1(4.54e-05)]_35
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292 chr21_31962741_31962791_ 1.61e-02 50
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293 chr21_31964683_31964733_ 1.36e-04 13_[1(3.41e-06)]_26
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294 chr21_31973364_31973414_ 1.99e-01 50
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295 chr21_31992870_31992920_ 3.47e-04 16_[1(8.67e-06)]_23
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296 chr21_32185595_32185645_ 3.47e-04 18_[1(8.67e-06)]_21
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297 chr21_32202076_32202126_ 2.01e-04 13_[1(5.01e-06)]_26
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298 chr21_32253899_32253949_ 8.11e-04 19_[1(2.03e-05)]_20
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299 chr21_32410820_32410870_ 3.47e-04 21_[1(8.67e-06)]_18
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300 chr21_36411748_36411798_ 2.71e-03 22_[1(6.78e-05)]_17
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301 chr21_37838750_37838800_ 8.23e-02 50
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302 chr21_45705687_45705737_ 1.53e-03 37_[1(3.82e-05)]_2
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303 chr21_45971413_45971463_ 1.36e-04 9_[1(3.41e-06)]_30
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304 chr21_45978668_45978718_ 6.37e-04 4_[1(1.59e-05)]_35
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305 chr21_45993530_45993580_ 1.60e-04 7_[1(4.00e-06)]_32
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306 chr21_46020421_46020471_ 4.83e-04 2_[1(1.21e-05)]_37
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307 chr21_46031920_46031970_ 2.43e-04 15_[1(6.06e-06)]_24
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308 chr21_46046964_46047014_ 4.26e-05 12_[1(1.06e-06)]_27
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309 chr21_46057197_46057247_ 1.36e-04 36_[1(3.41e-06)]_3
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310 chr21_46086869_46086919_ 4.30e-02 50
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311 chr21_46102103_46102153_ 4.30e-02 50
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312 chr21_47517957_47518007_ 6.37e-04 32_[1(1.59e-05)]_7
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313 chr21_47575506_47575556_ 1.61e-03 30_[1(4.02e-05)]_9
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314 --------------------------------------------------------------------------------
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315
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316 ********************************************************************************
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317
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318
|
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319 ********************************************************************************
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320 Stopped because requested number of motifs (1) found.
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321 ********************************************************************************
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322
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323 CPU:
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324
|
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325 ********************************************************************************
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