; convert-matrix -v 1 -from transfac -i $RSAT/public_html/tmp/wwwrun/2014/09/05/matrix-quality_2014-09-05.235841_QFnNnl/do562plusdo732_mmus_hnf4a_liver_meme_top_m1/matrix-quality_2014-09-05.235841_do562plusdo732_mmus_hnf4a_liver_meme_top_m1_matrix.tf -to tab -o $RSAT/public_html/tmp/wwwrun/2014/09/05/matrix-quality_2014-09-05.235841_QFnNnl/do562plusdo732_mmus_hnf4a_liver_meme_top_m1/matrix-quality_2014-09-05.235841_do562plusdo732_mmus_hnf4a_liver_meme_top_m1_matrix_info.txt -bgfile $RSAT/public_html/tmp/wwwrun/2014/09/05/matrix-quality_2014-09-05.235841_QFnNnl/matrix-quality_2014-09-05.2358412nt_upstream-noorf_Canis_familiaris_EnsEMBL-ovlp-1str.freq.gz_inclusive.tab -bg_format inclusive -return counts,frequencies,weights,info,parameters,sites,logo -logo_format png -logo_opt '-e -M -t do562plusdo732_mmus_hnf4a_liver_meme_top_m1 ' -logo_file $RSAT/public_html/tmp/wwwrun/2014/09/05/matrix-quality_2014-09-05.235841_QFnNnl/do562plusdo732_mmus_hnf4a_liver_meme_top_m1/matrix-quality_2014-09-05.235841_do562plusdo732_mmus_hnf4a_liver_meme_top_m1_logo ; Input files ; input /home/rsat/rsat/public_html/tmp/wwwrun/2014/09/05/matrix-quality_2014-09-05.235841_QFnNnl/do562plusdo732_mmus_hnf4a_liver_meme_top_m1/matrix-quality_2014-09-05.235841_do562plusdo732_mmus_hnf4a_liver_meme_top_m1_matrix.tf ; prior /home/rsat/rsat/public_html/tmp/wwwrun/2014/09/05/matrix-quality_2014-09-05.235841_QFnNnl/matrix-quality_2014-09-05.2358412nt_upstream-noorf_Canis_familiaris_EnsEMBL-ovlp-1str.freq.gz_inclusive.tab ; Input format transfac ; Output files ; output /home/rsat/rsat/public_html/tmp/wwwrun/2014/09/05/matrix-quality_2014-09-05.235841_QFnNnl/do562plusdo732_mmus_hnf4a_liver_meme_top_m1/matrix-quality_2014-09-05.235841_do562plusdo732_mmus_hnf4a_liver_meme_top_m1_matrix_info.txt ; Output format tab ; pseudo-weight 1 ; Background model ; Strand undef ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.26457 ; c 0.23303 ; g 0.23983 ; t 0.26257 a 180 31 70 44 0 320 218 301 2 14 47 5 274 76 120 c 18 13 9 123 321 22 23 1 4 15 168 317 10 75 62 g 110 284 169 105 1 9 102 39 336 122 51 9 22 144 104 t 47 27 107 83 33 4 12 14 13 204 89 24 49 60 69 // a 0.5 0.1 0.2 0.1 0.0 0.9 0.6 0.8 0.0 0.0 0.1 0.0 0.8 0.2 0.3 c 0.1 0.0 0.0 0.3 0.9 0.1 0.1 0.0 0.0 0.0 0.5 0.9 0.0 0.2 0.2 g 0.3 0.8 0.5 0.3 0.0 0.0 0.3 0.1 0.9 0.3 0.1 0.0 0.1 0.4 0.3 t 0.1 0.1 0.3 0.2 0.1 0.0 0.0 0.0 0.0 0.6 0.3 0.1 0.1 0.2 0.2 // a 0.6 -1.1 -0.3 -0.8 -5.9 1.2 0.8 1.2 -3.7 -1.9 -0.7 -2.9 1.1 -0.2 0.2 c -1.5 -1.8 -2.2 0.4 1.4 -1.3 -1.3 -4.2 -3.0 -1.7 0.7 1.3 -2.1 -0.1 -0.3 g 0.3 1.2 0.7 0.2 -4.2 -2.2 0.2 -0.8 1.4 0.4 -0.5 -2.2 -1.3 0.5 0.2 t -0.7 -1.2 0.1 -0.1 -1.0 -3.1 -2.0 -1.9 -2.0 0.8 -0.0 -1.3 -0.6 -0.4 -0.3 // a 0.3 -0.1 -0.1 -0.1 -0.0 1.1 0.5 1.0 -0.0 -0.1 -0.1 -0.0 0.8 -0.0 0.1 c -0.1 -0.1 -0.1 0.1 1.2 -0.1 -0.1 -0.0 -0.0 -0.1 0.3 1.2 -0.1 -0.0 -0.1 g 0.1 1.0 0.3 0.1 -0.0 -0.1 0.1 -0.1 1.3 0.1 -0.1 -0.1 -0.1 0.2 0.1 t -0.1 -0.1 0.0 -0.0 -0.1 -0.0 -0.1 -0.1 -0.1 0.4 -0.0 -0.1 -0.1 -0.1 -0.1 // ; Sites 355 >site_0 AGGTCAAAGTCCAGA >site_1 AGGGCAAAGTCCAGG >site_2 AGGCCAGAGTCCAGA >site_3 AGGGCAGAGTCCAGA >site_4 AGTGCAAAGTCCAGC >site_5 AGTCCAGAGTCCAGA >site_6 AGGCCAAAGGCCAAA >site_7 GGGGCAGAGTCCAGA >site_8 GGGGCAGAGTCCAGA >site_9 AGTCCAAAGTTCAGT >site_10 TGGTCAAAGTCCAGA >site_11 GGGTCAGAGTCCAGA >site_12 AGGTCAGAGTTCAGA >site_13 AGGGCAGAGTCCAAG >site_14 AGGTCAGAGTCCACA >site_15 GGTTCAAAGTCCAAA >site_16 AGGCCAAAGGTCAAA >site_17 GGGGCAGAGTCCAGG >site_18 AGGCCAAAGTTCACT >site_19 GGGGCAAAGGTCAGA >site_20 AGGTCAAAGGGCAGA >site_21 AGGACAGAGTCCAGG >site_22 AGGGCAAAGGGCAGG >site_23 GGTGCAAAGTCCATG >site_24 AGGCCAGAGGCCAGC >site_25 AGGTCAAAGGACAGG >site_26 GGGGCAGAGTTCAGG >site_27 AGTCCAAGGTCCAGA >site_28 AGGTCAGAGTCCACT >site_29 AGGCCAAAGGACAGC >site_30 TGGCCAAAGGCCAAA >site_31 GGTACAAAGTTCAGA >site_32 AGGGCAAAGGACAGC >site_33 AGTTCAAAGTACAAG >site_34 GGTTCAGAGTTCAGA >site_35 TGTACAAAGTCCAGA >site_36 AGGCCAAGGTCCAAA >site_37 GGGCCAAAGTGCAAG >site_38 AGGGCAAAGGGCAGC >site_39 AGGGCAAAGGACAAG >site_40 AGGGCAGAGGGCAGA >site_41 AGTCCAAAGGACAGC >site_42 AGGCCAGAGGGCAGG >site_43 AGTCCAAAGGACAGC >site_44 AGAGCAAAGGTCAGC >site_45 AGGTCAAGGGCCAGA >site_46 TGGCCAAAGTTCATG >site_47 TGATCAAAGGCCAGA >site_48 AGGGCAGAGGTCAAG >site_49 GGTGCAGAGGTCAGA >site_50 AGTCTAAAGTCCAAA >site_51 AGGTCAGAGTCCTGG >site_52 GGGGCAAAGGGCAAA >site_53 AGAACAAAGGCCACA >site_54 AGGGCAAAGTTCTCA >site_55 AGGCCAAATTCCAGA >site_56 AGGCCAAAGCTCAGA >site_57 AGTACAGAGTCCATG >site_58 TGGTCAGAGGCCAGG >site_59 GGGGCAAAGGGCAGC >site_60 AGGCTAAAGTCCATG >site_61 GGGACAAAGGTCAGT >site_62 GGGGCACAGTCCAGG >site_63 AGTCCCAAGTCCAGG >site_64 AGGGCAGAGGGCAGT >site_65 GGAGCAAAGGACAGA >site_66 TGTTCAAAGGTCAGG >site_67 GTGCCAAAGTCCAGT >site_68 GGTGTAAAGTCCAGG >site_69 GGACCAAAGTGCAAG >site_70 TGGGCAAAGGTCATA >site_71 ATTCCAAAGTCCAAG >site_72 ATTGCAAAGTCCACA >site_73 AGGGCAGAGGGCAAG >site_74 AGGTCAGAGGACAGC >site_75 AAGGCAAAGTCCACT >site_76 AGGTCAAGGTCCACT >site_77 AGAGCAAAGTCCTAG >site_78 GGTCCAAAGACCAGA >site_79 AGGTCAAGGTCCACC >site_80 AGACTAAAGTCCACA >site_81 GAGTCAAAGTCCAAG >site_82 AGAACAAAGGTCAAG >site_83 GGAACAGAGTCCAAA >site_84 AGAGCAAGGTCCAAG >site_85 AGGCCAAATTCCACA >site_86 AGGGCAAGGTGCAGT >site_87 CGGGCAAAGTCCATT >site_88 GGAACAGAGTCCAGC >site_89 GTGTCAGAGTCCAGA >site_90 AGTGCCAAGTCCAGC >site_91 AGTCCAAAGTACTGT >site_92 AGTCCAAAGTTCTCT >site_93 GGACCAGAGGACAGA >site_94 TGACCAAAGGTCACA >site_95 GGGGCCAAGTCCAGT >site_96 AGACCAAAGGCCTAG >site_97 AGGCTAAAGGTCAGC >site_98 GGGTTAAAGTCCATG >site_99 GGTGCAAAGGTCTGA >site_100 AGGACAAAGTCTACA >site_101 AGGTCAGAGGACACT >site_102 AGTCCAAAGTTCGGT >site_103 AGGCCAGAGTCTAAG >site_104 AGGACAAAGTCTACA >site_105 TAGCCAAAGTCCAGC >site_106 GGGGCAGAGTCCTAG >site_107 GGGTCAGAGTACACT >site_108 AGAGCAAAGTCCTTT >site_109 AGACCAGAGGGCATA >site_110 GGGTCAAAGCTCAGG >site_111 AGGACACAGTCCACG >site_112 AGGGCACAGGGCAGA >site_113 GGTACAAAGGGCAAA >site_114 GAGCCAGAGTCCACA >site_115 AGGGCAAAGTCGACA >site_116 AGTTCACAGTCCATT >site_117 TGTTCAAAGTGCAAC >site_118 AGAGCAAGGTTCATA >site_119 GGTCCAGAGGCCTGG >site_120 AGAGCAGAGGACAAG >site_121 AGGACAGAGGGCAAG >site_122 GAGTCAAAGTACAGG >site_123 GGAGCAAGGTCCAAG >site_124 AGAGCAGGGTCCAGT >site_125 GGTGCAAGGTACAGG >site_126 AATCCAAAGGGCAGG >site_127 GGTCTAAAGTTCATA >site_128 GGGCCAAAGAGCAGA >site_129 GGTTCAAAGTCTAAG >site_130 AGGGCACAGGCCACC >site_131 ACTCCAAAGTTCAAA >site_132 AGGGCAAAGTCCCTG >site_133 GGTCCACAGTCCACT >site_134 TGGGCAGAGTCCTAA >site_135 AGGGCAAAGCTCACT >site_136 GGGTCAGAGTACTGA >site_137 TGTTCAGAGGTCACA >site_138 GGACCAGAGGGCAGT >site_139 AGTGCAAAGATCAAG >site_140 AAGCCAAAGGTCAAC >site_141 GGGACACAGTCCACA >site_142 AGTTCAGAGGCCTTA >site_143 GGTCCAAAGCTCAGT >site_144 AGGTCAGAGTCCCGG >site_145 AGTCCAAAGTGTAGC >site_146 GGGTCAGAGGGCAAC >site_147 CAGTCAAAGTCCAGA >site_148 AGGACAAGGGTCACA >site_149 AGGCCAGAGGCTACG >site_150 AGAGCAAGGTACACA >site_151 GTTCCAAAGTTCATG >site_152 TGACCAAAGTCCTCG >site_153 GGGTTAGAGTCCATG >site_154 AGGCCAGGGTTCACC >site_155 AGTCCAATGGTCAGG >site_156 GGGTTAGAGTCCATG >site_157 ACACCAAAGTCCACG >site_158 GAACCAGAGTCCAAA >site_159 GGTCCATAGTACAGA >site_160 GGGACAAAGGGCTGA >site_161 AATCCAAAGGGCATA >site_162 GGTTCCAAGTTCAGT >site_163 AGTTTAGAGTTCATG >site_164 AGGGCAAATTGCACA >site_165 AAATCAGAGGCCAAA >site_166 GTACCAGAGTCCAGC >site_167 GGTACCAAGTTCAGA >site_168 AGTCCAAAGTCTTGT >site_169 GGCACAAAGTCCACA >site_170 GGTCCAAGGGGCAAA >site_171 ACTCCAAAGTTCAAC >site_172 GGAGCAAAGTACTTA >site_173 AGAGCAAAGGTCTCC >site_174 AGGCTAGAGGTCAAT >site_175 AGGTCTAAGTCCACA >site_176 TGTGCACAGTACAGA >site_177 AGTATAGAGTACAGA >site_178 AGGTCAAAGTTAAGT >site_179 AGTCCAAAGGATAAG >site_180 GCTGCAAAGTCCATT >site_181 TGTCCAAGGTACACA >site_182 AGTCTACAGTTCAGG >site_183 TGATCCAAGTCCAAA >site_184 AGCTCAGAGGCCATG >site_185 AGGGTAGAGGGCATA >site_186 TGAGCAAGGTCCACC >site_187 AGATCAAAGAACACA >site_188 AGAGCAGAGAGCAGA >site_189 AGGGCAAAGGGGAGG >site_190 ATTCCAAAGTCTAGC >site_191 AGGGCAGAGTCTTGT >site_192 CGTCCAGGGTCCAGG >site_193 AGAGCAAAGTACCGG >site_194 GGTCCAAAGTCGACC >site_195 GGTACAAGGTGCAAG >site_196 GGAACAGAGTACATC >site_197 GCACCAAAGGTCAGG >site_198 GAGCCAAAGTCCTCC >site_199 TGTGCATAGTTCAAA >site_200 GGTGCACAGGACACA >site_201 CGGGCAAATTCCAGG >site_202 AGTCCGAAGGTCAAG >site_203 CGACCAAAGTCCTTG >site_204 ATGTCACAGGCCAGT >site_205 GGTGCAAATGTCAGT >site_206 TGGGTAAAGTCCTAG >site_207 TGTCCAATGTCCATT >site_208 TGTTCAAGGTACATG >site_209 CAGTCAAAGTCCATT >site_210 ATTCCAGGGTCCACA >site_211 TGTCCAAAGCACAGC >site_212 TGAGCAAAGTCCGCT >site_213 AGGCTCAAGTTCAGC >site_214 GGACCAGAGCTCACA >site_215 AGGACATAGGGCAAA >site_216 TGGCCAAATGTCAGT >site_217 AACCCAAAGGTCAGA >site_218 AGGACAAAGAGCATT >site_219 GGATCAGTGTCCAGC >site_220 GGACCCGAGTCCACT >site_221 TGAGCAAGGTTCATC >site_222 GGTTTAAAGTTCTGC >site_223 AAGTCCAAGGCCAGC >site_224 GGAACAAAGATCACA >site_225 GGGCTGAAGTCCAGA >site_226 AAGGCAAAGGGCTGT >site_227 TGTCCCAAGGTCATA >site_228 GTGCCAAGGTCCATC >site_229 AGAATAGAGTTCATG >site_230 TAGTCAAAGTCCTCG >site_231 AGCACAAAGGGCACA >site_232 GTCCCAAAGTCCACA >site_233 AGGACAAAGTCTTAC >site_234 AGGCCAGTGTACACC >site_235 TGAGCAAAGGGTAGA >site_236 TGATCAAAGGCTATG >site_237 TGAGCAGGGTGCAGG >site_238 AGAGCAAAATCCAAA >site_239 AGGTCCCAGGTCAGG >site_240 ACTCTAAAGGCCAGT >site_241 GGAGCACAGTCCTTG >site_242 GGTACACAGGACACA >site_243 GAGACAAAGTCCTCT >site_244 AGTCCAGAGCACTGA >site_245 GTGCCAAGGTGCACA >site_246 AGTCCAATGTCCTTC >site_247 AGTGCAAAGAGCTGC >site_248 ATGACACAGTTCAGC >site_249 TAGTCAAGGTCCAAT >site_250 CGGGCAAAGGTCTTT >site_251 GGGTCGAAGGGCAAA >site_252 ATGCCCAAGTTCAAC >site_253 AGTCCAAAGGGCCCT >site_254 CAGTCAGAGTCCACT >site_255 AGTTCAAATCCCAGT >site_256 GGGGTCAAGGTCAGG >site_257 GGGACACGGTCCATG >site_258 GCACCAAGGTCCAGT >site_259 AGGTTACAGGCCTGA >site_260 AGGTCATAGTCTATT >site_261 GGACCAAAGTCTGGT >site_262 AGTGTGGAGTCCAGA >site_263 ACTCCAGAGTCCGGG >site_264 AGGTTGAAGTCCATG >site_265 AGGTTAAAGTCGAAT >site_266 AGGGCAGAGGCGTGG >site_267 AGTTCAGAGGTTTGG >site_268 GTGCCCGAGTCCAGC >site_269 TGGGCAAAGCTCGGA >site_270 ATTACAAAGGTCTGC >site_271 AGGGCATTGTCCATG >site_272 TGGCCAGAGGACTTC >site_273 GATCCACAGTGCAGT >site_274 GCTCCAAAGGGCACC >site_275 AAGCCAGGGGGCAGT >site_276 TGGTCAGTGGTCACA >site_277 GTGTCAATGGCCAGT >site_278 AGGACAAAGGCTGGC >site_279 GGAACAAAGTTCCCG >site_280 GGGTCAAAGAGCTTA >site_281 GTTCCAAAGTCCGTC >site_282 GCAACAGAGTACAGA >site_283 GGGCCAGTGTTCTGT >site_284 TGTGCAATGTCCTTA >site_285 TGGCCAAAGGGGAAG >site_286 AGACCAATGGACTGA >site_287 AGTCCAAAAGTCAAG >site_288 AATGCCGAGGCCAAG >site_289 CAGTCAGAGGCCATT >site_290 GGGCCTAAGCCCAGA >site_291 AGGGCAGAGACCGCT >site_292 AAGACAGAGTCTAAT >site_293 CAGACAAAGTACATG >site_294 AGAGCCAAGTCCGTT >site_295 GGCTCCAAGTCCAAT >site_296 GGGTCAGAGTGCCTT >site_297 TGGTCAGAGTTCCCT >site_298 ACTTCATAGTTCAAA >site_299 AGTCCAATGTTCGAT >site_300 GGATCAGAGACCGGA >site_301 AGGCCAAGGTCTTTC >site_302 ACTCCAAGGTACAAT >site_303 AGGTCTAGGGCCAGT >site_304 GTTCCAAAGCTCATT >site_305 AGCTCAAAGATCAAC >site_306 GGGGTAAAGTACGAC >site_307 ATTCCCAAGGCCTGG >site_308 GGGTCAAAGGTGTGT >site_309 GGGGCATAGGTCTCT >site_310 ATGCCACAGCCCAGC >site_311 AGCACACAGGACAGA >site_312 ACAGCAAGGTACATA >site_313 ATTCCAGATTCCACC >site_314 TGGGCATAGTCCGTG >site_315 GGGCCGAAGGCCTCC >site_316 GGGTCAATGTATAAA >site_317 GATCCCAAGGGCAAA >site_318 TGTGCAGAGTTAATG >site_319 TAACCAAAGTCCGCC >site_320 GGGGCAAAGTCAGCG >site_321 CGATCAAAGGTCGAT >site_322 AGTGTAAATTGCATC >site_323 AGATCAAGGTTGAAC >site_324 TAAGTAGAGGTCAGA >site_325 CGGGCAGAGAGCACC >site_326 AGGGCGAAGTCCCTC >site_327 AGGGCATATGCCTGG >site_328 ATTGCATGGTTCAAA >site_329 AGAGTAAACGCCACA >site_330 AGACCCGATTTCAAG >site_331 AGAGCAGAGAGTATA >site_332 AGGTCAGGCGCCAAG >site_333 TGTACAAAGGAAAAA >site_334 AATGCAAAGGTAAAT >site_335 TTTTCAAATTACAAA >site_336 TGTGTACGGTCCATA >site_337 TGGGGAAAGTACAAG >site_338 GGTTCTAAGTTCTAC >site_339 TGATTAAAGGTTATG >site_340 AGTACGGAGGCCGGG >site_341 GTAGTAAAGTCCGAG >site_342 GGTACATAGTCCCTG >site_343 CGGCCATAGCCCACC >site_344 AGCCCAGAGTAGACG >site_345 GTGCCCGAGTCTAGC >site_346 AAAATAAAGTTTAGT >site_347 CTACCAAAGGTCGCA >site_348 CGGCCAGGGGTCCGG >site_349 CGAGCAGACGCCACG >site_350 GGTCCACCGGTCACG >site_351 AGGGCAGTGCGCGCG >site_352 CGTCCAAATCCCGAA >site_353 AGGTCGCGGTACTCG >site_354 CGAACCGACGCCGCG ; ; Matrix parameters ; Columns 15 ; Rows 4 ; Alphabet a|c|g|t ; Prior a:0.264573486852274|c:0.233031168150323|g:0.239829744535815|t:0.262565600461588 ; program transfac ; matrix.nb 1 ; accession do562+do732_mmus_hnf4a_liver_meme_top_m1 ; AC do562+do732_mmus_hnf4a_liver_meme_top_m1 ; id do562+do732_mmus_hnf4a_liver_meme_top_m1 ; name do562plusdo732_mmus_hnf4a_liver_meme_top_m1 ; description rGksCArAGkyCAgr ; statistical_basis 355 sequences ; sites 355 ; min.prior 0.233031 ; alphabet.size 4 ; max.bits 2 ; total.information 7.96487 ; information.per.column 0.530991 ; max.possible.info.per.col 1.45658 ; consensus.strict aGgcCAaAGtcCAga ; consensus.strict.rc TCTGGACTTTGGCCT ; consensus.IUPAC rGksCArAGkcCAgr ; consensus.IUPAC.rc YCTGGMCTYTGSMCY ; consensus.regexp [ag]G[gt][cg]CA[ag]AG[gt]cCAg[ag] ; consensus.regexp.rc [CT]CTGG[AC]CT[CT]TG[CG][AC]C[CT] ; residues.content.crude.freq a:0.3196|c:0.2218|g:0.3018|t:0.1568 ; G+C.content.crude.freq 0.523568 ; residues.content.corrected.freq a:0.3195|c:0.2218|g:0.3016|t:0.1571 ; G+C.content.corrected.freq 0.523426 ; min(P(S|M)) 2.77433e-24 ; max(P(S|M)) 0.000674304 ; proba_range 0.000674304 ; Wmin -33.6 ; Wmax 13.6 ; Wrange 47.2 ; logo file:/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/05/matrix-quality_2014-09-05.235841_QFnNnl/do562plusdo732_mmus_hnf4a_liver_meme_top_m1//matrix-quality_2014-09-05.235841_do562plusdo732_mmus_hnf4a_liver_meme_top_m1_logo_m1.png ; logo file:/home/rsat/rsat/public_html/tmp/wwwrun/2014/09/05/matrix-quality_2014-09-05.235841_QFnNnl/do562plusdo732_mmus_hnf4a_liver_meme_top_m1//matrix-quality_2014-09-05.235841_do562plusdo732_mmus_hnf4a_liver_meme_top_m1_logo_m1_rc.png ; Host name rsat ; Job started 2014-09-06.000938 ; Job done 2014-09-06.000938 ; Seconds 0.3 ; user 0.3 ; system 0.03 ; cuser 0.33 ; csystem 0.01