******************************************************************************** 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/213/213.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1011 1.0000 500 11165 1.0000 500 11575 1.0000 500 11779 1.0000 500 1553 1.0000 500 17214 1.0000 500 20933 1.0000 500 21371 1.0000 500 21978 1.0000 500 22792 1.0000 500 23817 1.0000 500 2553 1.0000 500 25724 1.0000 500 262271 1.0000 500 263848 1.0000 500 30659 1.0000 500 31785 1.0000 500 33343 1.0000 500 34211 1.0000 500 35518 1.0000 500 37662 1.0000 500 38121 1.0000 500 39141 1.0000 500 40713 1.0000 500 4130 1.0000 500 42475 1.0000 500 42577 1.0000 500 4270 1.0000 500 4704 1.0000 500 4783 1.0000 500 5902 1.0000 500 6692 1.0000 500 7597 1.0000 500 7704 1.0000 500 8303 1.0000 500 8353 1.0000 500 889 1.0000 500 904 1.0000 500 9388 1.0000 500 9459 1.0000 500 9855 1.0000 500 9947 1.0000 500 bd1879 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/213/213.seqs.fa -oc motifs/213 -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= 43 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= 21500 N= 43 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.266 C 0.238 G 0.229 T 0.267 Background letter frequencies (from dataset with add-one prior applied): A 0.266 C 0.238 G 0.229 T 0.267 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 38 llr = 366 E-value = 4.5e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 12:::522:1:11:411211 pos.-specific C 22:12:2:221:212:::23 probability G 44:382:7137318257166 matrix T 22a5:47174266124272: bits 2.1 1.9 1.7 * 1.5 * Relative 1.3 * * Entropy 1.1 * * * * * (13.9 bits) 0.9 * * * * * ** * 0.6 *** *** ** * ***** 0.4 ******* **** ***** 0.2 ************** ***** 0.0 -------------------- Multilevel GGTTGATGTTGTTGAGGTGG consensus TA G T CGTG CTT C sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 21371 218 2.00e-11 GCTTTCGACC GGTTGATGTTGTTGGGGTGG GTGCCGAGGA 2553 138 2.14e-08 CAGATCCCAT GGTTGATGTTGTTGATGGCG ATGAAAGTTG 9388 2 1.41e-07 T AGTTGGTGTGGTTGTTTTGG GTAAGGCGAG 23817 99 1.87e-07 TGTCTGACGA GGTTGATGTTGGTGGTGTAC TACTGCTACG 40713 188 2.82e-07 CCGCGACGGT GTTGCTTGTGGTTGTGGTTG AATCGACGGC 6692 87 5.46e-07 TGAACTCAGC GGTTGATGGCTGCGCTGTGG TATTGATTCA 263848 312 6.20e-07 CGTAAGGGGA GATGGATACGGTGGCGGTGG AATCTCGTCT 37662 11 7.04e-07 ATGATGAGTT GGTTGAAGTGTATGATGTCG ATGGTGGACG 22792 293 1.15e-06 AGGGTGGCGG TCTTCATGTTGGAGAGGTGC GTTGTGATTG 4130 376 1.29e-06 GTGGGAAGGA TATTGATATGGTTGATGACG CAAGCGACTT 34211 345 2.57e-06 TAGTTCTGAT TCTCCTTGTGGTGGTGGTGG TCAAAGACAG 4704 193 3.20e-06 ACCCTGCCTA GGTGGACGTCGTTCCTGTTG CAACGTCCTA 35518 41 3.56e-06 GTCCTTGGGA GTTGGATATGGTCGATTAGG AGGCCTCCAA 9855 453 4.41e-06 CCGTGGAAGA CGTCATTGTTGTTGGTGTGC GCATTTTTGC 7597 73 5.43e-06 TTTGGTTGAA TGTTGTTGTTGTTTCGATGC CGTCTCTATA 4270 183 6.01e-06 GAATCGTTTT GCTTGTTGTCCTTGCCGTGC ACGTATCGTT 8303 35 6.65e-06 CATATGAATT GGTGGATGGATGTGATGACG ACGATGCAGA 42577 292 8.13e-06 CATCAGTTGG ATTGGATTTGGTTGTGTTGC GAAGGTGTGG 42475 14 9.89e-06 AAGAAAGAAT GTTGTTTGTTGTTTGGGTGG AGAGGAAGGA 262271 331 1.20e-05 TGCTTTCCTT TGTGGATGTTGGAGGATTGC CCTGGCTGAG 9947 178 1.90e-05 ATGTGCTGGA TCTTGTCGCCTTCGTTGTGC CTACAATCAT 7704 141 1.90e-05 ATGAATAAAG CATGGGAGGCTTTGAGGAGG AAAGGTAGGT 21978 156 2.49e-05 TTTGAACTCG CATTGATACCGATGATGTGA AGCACTTCCG 17214 157 2.49e-05 TTTGAACTCG CATTGATACCGATGATGTGA AGCACTTCCG 8353 206 2.72e-05 CCAAAAAACT TATTCGAGTTGGTGAGTTTG GTATTACAAT 1553 67 3.23e-05 CTGTGTCAGG ACTCGTTTGGTTTGCTGTGG TTCAGGCTCC 30659 4 3.82e-05 TTG TGTCGGTGCAGGAGCTGTTG TTGCAGTCCT 1011 183 4.51e-05 GTGCACGCGA CGTTGATTTTGGAGCGGGCC AAGCCGACGC 9459 62 5.30e-05 TGGATATTCC AGTTGAAGCACTTGAGTAGG TCGTCTACGA 20933 263 6.22e-05 ATGAAGTGCC CTTCGTAGTGTTTGGAGAGG AGGAGGAAAT 25724 353 7.28e-05 GAAGAGCGAA CATGGACGCATGAGAGGTTG CATATGCAGC 11575 336 7.28e-05 GTAGTGAGAA CGTTGTCGTGCTTACGGTGA AAATTTCAAA bd1879 366 8.48e-05 CAAATTTTGT GTTGGGAGTTGTCCAGGACG CGAAGGTGCA 4783 286 1.06e-04 GGGTGCGAAC GATTGTAGGTCTGGTGATGG AAGACCGCTG 11165 411 1.14e-04 GAAAGCAGCT GCTGCGTGTTGGCGTGTGTG CACCAACGCG 889 299 1.42e-04 TTGTACGTTG GCTGCTCATGTTTGGTGTAC ATCACTGCCT 5902 72 1.42e-04 AGAAAAGATG GGGTGTCGTGGACTAGGTGC ACGGAGCCAT 39141 293 2.15e-04 TAGTAAAAGT TTTTGTTACTGGGGTTTGGC CGACACCTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21371 2e-11 217_[+1]_263 2553 2.1e-08 137_[+1]_343 9388 1.4e-07 1_[+1]_479 23817 1.9e-07 98_[+1]_382 40713 2.8e-07 187_[+1]_293 6692 5.5e-07 86_[+1]_394 263848 6.2e-07 311_[+1]_169 37662 7e-07 10_[+1]_470 22792 1.1e-06 292_[+1]_188 4130 1.3e-06 375_[+1]_105 34211 2.6e-06 344_[+1]_136 4704 3.2e-06 192_[+1]_288 35518 3.6e-06 40_[+1]_440 9855 4.4e-06 452_[+1]_28 7597 5.4e-06 72_[+1]_408 4270 6e-06 182_[+1]_298 8303 6.7e-06 34_[+1]_446 42577 8.1e-06 291_[+1]_189 42475 9.9e-06 13_[+1]_467 262271 1.2e-05 330_[+1]_150 9947 1.9e-05 177_[+1]_303 7704 1.9e-05 140_[+1]_340 21978 2.5e-05 155_[+1]_325 17214 2.5e-05 156_[+1]_324 8353 2.7e-05 205_[+1]_275 1553 3.2e-05 66_[+1]_414 30659 3.8e-05 3_[+1]_477 1011 4.5e-05 182_[+1]_298 9459 5.3e-05 61_[+1]_419 20933 6.2e-05 262_[+1]_218 25724 7.3e-05 352_[+1]_128 11575 7.3e-05 335_[+1]_145 bd1879 8.5e-05 365_[+1]_115 4783 0.00011 285_[+1]_195 11165 0.00011 410_[+1]_70 889 0.00014 298_[+1]_182 5902 0.00014 71_[+1]_409 39141 0.00021 292_[+1]_188 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=38 21371 ( 218) GGTTGATGTTGTTGGGGTGG 1 2553 ( 138) GGTTGATGTTGTTGATGGCG 1 9388 ( 2) AGTTGGTGTGGTTGTTTTGG 1 23817 ( 99) GGTTGATGTTGGTGGTGTAC 1 40713 ( 188) GTTGCTTGTGGTTGTGGTTG 1 6692 ( 87) GGTTGATGGCTGCGCTGTGG 1 263848 ( 312) GATGGATACGGTGGCGGTGG 1 37662 ( 11) GGTTGAAGTGTATGATGTCG 1 22792 ( 293) TCTTCATGTTGGAGAGGTGC 1 4130 ( 376) TATTGATATGGTTGATGACG 1 34211 ( 345) TCTCCTTGTGGTGGTGGTGG 1 4704 ( 193) GGTGGACGTCGTTCCTGTTG 1 35518 ( 41) GTTGGATATGGTCGATTAGG 1 9855 ( 453) CGTCATTGTTGTTGGTGTGC 1 7597 ( 73) TGTTGTTGTTGTTTCGATGC 1 4270 ( 183) GCTTGTTGTCCTTGCCGTGC 1 8303 ( 35) GGTGGATGGATGTGATGACG 1 42577 ( 292) ATTGGATTTGGTTGTGTTGC 1 42475 ( 14) GTTGTTTGTTGTTTGGGTGG 1 262271 ( 331) TGTGGATGTTGGAGGATTGC 1 9947 ( 178) TCTTGTCGCCTTCGTTGTGC 1 7704 ( 141) CATGGGAGGCTTTGAGGAGG 1 21978 ( 156) CATTGATACCGATGATGTGA 1 17214 ( 157) CATTGATACCGATGATGTGA 1 8353 ( 206) TATTCGAGTTGGTGAGTTTG 1 1553 ( 67) ACTCGTTTGGTTTGCTGTGG 1 30659 ( 4) TGTCGGTGCAGGAGCTGTTG 1 1011 ( 183) CGTTGATTTTGGAGCGGGCC 1 9459 ( 62) AGTTGAAGCACTTGAGTAGG 1 20933 ( 263) CTTCGTAGTGTTTGGAGAGG 1 25724 ( 353) CATGGACGCATGAGAGGTTG 1 11575 ( 336) CGTTGTCGTGCTTACGGTGA 1 bd1879 ( 366) GTTGGGAGTTGTCCAGGACG 1 4783 ( 286) GATTGTAGGTCTGGTGATGG 1 11165 ( 411) GCTGCGTGTTGGCGTGTGTG 1 889 ( 299) GCTGCTCATGTTTGGTGTAC 1 5902 ( 72) GGGTGTCGTGGACTAGGTGC 1 39141 ( 293) TTTTGTTACTGGGGTTTGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 20683 bayes= 9.28073 E= 4.5e-006 -134 -18 97 -17 -34 -37 88 -53 -1189 -1189 -312 187 -1189 -86 58 98 -334 -59 179 -334 83 -1189 -53 47 -53 -59 -1189 130 -53 -1189 169 -176 -1189 -18 -80 130 -134 -37 58 47 -1189 -118 153 -17 -134 -1189 34 118 -102 -59 -112 118 -334 -218 188 -176 47 -1 -31 -34 -234 -318 105 75 -234 -1189 169 -34 -53 -1189 -112 141 -234 -59 147 -76 -175 41 140 -1189 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 38 E= 4.5e-006 0.105263 0.210526 0.447368 0.236842 0.210526 0.184211 0.421053 0.184211 0.000000 0.000000 0.026316 0.973684 0.000000 0.131579 0.342105 0.526316 0.026316 0.157895 0.789474 0.026316 0.473684 0.000000 0.157895 0.368421 0.184211 0.157895 0.000000 0.657895 0.184211 0.000000 0.736842 0.078947 0.000000 0.210526 0.131579 0.657895 0.105263 0.184211 0.342105 0.368421 0.000000 0.105263 0.657895 0.236842 0.105263 0.000000 0.289474 0.605263 0.131579 0.157895 0.105263 0.605263 0.026316 0.052632 0.842105 0.078947 0.368421 0.236842 0.184211 0.210526 0.052632 0.026316 0.473684 0.447368 0.052632 0.000000 0.736842 0.210526 0.184211 0.000000 0.105263 0.710526 0.052632 0.157895 0.631579 0.157895 0.078947 0.315789 0.605263 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GTC][GA]T[TG]G[AT]TG[TC][TG][GT][TG]TG[ACT][GT][GT]TG[GC] -------------------------------------------------------------------------------- Time 14.86 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 27 llr = 295 E-value = 7.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :5443123:373166:94:22 pos.-specific C 9235:76147:3931a1:911 probability G 1:2:21:14:1211:::::15 matrix T :31:51151113::3::6163 bits 2.1 1.9 * 1.7 * 1.5 * * * Relative 1.3 * * ** * Entropy 1.1 * * ** * (15.7 bits) 0.9 * * ** * ** * 0.6 * * ** ** ******* 0.4 ** **** *** ******* 0.2 *********** ********* 0.0 --------------------- Multilevel CAACTCCTCCAACAACATCTG consensus TCAA AAGA C CT A AT sequence G T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 21978 401 2.51e-12 ATCGCTACGC CAAATCCTGCACCAACATCTG CCGTCGGCGA 17214 402 2.51e-12 ATCGCTACGC CAAATCCTGCACCAACATCTG CCGTCGGCGA 30659 374 2.14e-08 GATTTTGCCC CTACGCCTCCAGCAACATCGA CACCTCCCCG 9388 395 4.16e-07 ACGACGAAAT CCCATCCCGCAACCTCAACGG AAGACACCAA 5902 369 4.16e-07 AGTAACTTCT CTGATACTCAAACGACAACTG CACCATATCT 31785 42 4.67e-07 ATCTCACTAC CACCACCATCAGCACCATCAG CCTGAGTGGT 11779 173 8.17e-07 CCGACCGACA CCCCACCACCAGCCTCCTCTT AGTGTCTGCA 4783 414 1.13e-06 TCCTCTGAAA CTCATCATGTATCAACATCTC TTCTCTTATT 33343 473 1.25e-06 CTCATTTTCA CTGAACCACCGCCAACAACGA AGCAATC 35518 68 1.39e-06 AGGAGGCCTC CAACTCAACATTCAACATCCG TCCAGAGAAG 42475 62 2.51e-06 GTTGGGATTA CATATCATACATCATCATCTA TTGGATCAAA 7597 46 3.66e-06 TAGTTGATGC CACCGCATGAGCCATCATTTG GTTGAATGTT 8303 384 4.01e-06 CCGTTTTCGG CAACACTTGAAACCACACCTA GCCAAAGAGG 4270 38 4.39e-06 ATAAACCAAA CTGAATCATCATCAACATCAT GTCTACCGCA 38121 264 4.81e-06 CAGCGGCAAA CAGCTCTAGCATCATTATCAG CCCATCGATA 9459 242 5.74e-06 GAGATCCGTA CAAATGAGGAAACGACATCTT GGCTGTTTCT 34211 67 6.26e-06 GACTCGGTGG CAACGGCATCACCCCCATCAG CTGAGAGAGA 263848 65 9.54e-06 CATCTAATAT TACCTCTCCAAACAACAACTT GGAGTATGAT 20933 454 1.12e-05 GCATTGTTCA GTAATTCTGCATCAACAACAC ATCTATCTCA 42577 119 1.22e-05 ATCTAACCCA CCACTCCTCCGGCCACCTTCG CAGCAGTTTC 22792 378 1.22e-05 AGAGGCTCTA CTTCAACTGTAACCTCAACTT TTCAACTTCA 262271 44 1.42e-05 CGTACAGGCG CTCCTCCTCATCGGTCAACTT TTTACTCTCT 889 91 2.24e-05 TCCGAACCAA CACTGCCACCAGCGACCATTG CCTCGTCTTT 1553 390 2.60e-05 TCCAAATACT CCGAGCACCCACAAACAACAA CCCCTCGTCC 11575 141 2.60e-05 ATTGTCATGG CCAAGATGTCAGCCTCAACTT CGGATGCCAG 25724 295 3.21e-05 TACACGGCAA GAACTCCTGCTTGAACCACGG GGACCATGGC 904 34 3.45e-05 ATATGTACTG CTTCAACGCCGAACACATCTG ACGCACGAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21978 2.5e-12 400_[+2]_79 17214 2.5e-12 401_[+2]_78 30659 2.1e-08 373_[+2]_106 9388 4.2e-07 394_[+2]_85 5902 4.2e-07 368_[+2]_111 31785 4.7e-07 41_[+2]_438 11779 8.2e-07 172_[+2]_307 4783 1.1e-06 413_[+2]_66 33343 1.2e-06 472_[+2]_7 35518 1.4e-06 67_[+2]_412 42475 2.5e-06 61_[+2]_418 7597 3.7e-06 45_[+2]_434 8303 4e-06 383_[+2]_96 4270 4.4e-06 37_[+2]_442 38121 4.8e-06 263_[+2]_216 9459 5.7e-06 241_[+2]_238 34211 6.3e-06 66_[+2]_413 263848 9.5e-06 64_[+2]_415 20933 1.1e-05 453_[+2]_26 42577 1.2e-05 118_[+2]_361 22792 1.2e-05 377_[+2]_102 262271 1.4e-05 43_[+2]_436 889 2.2e-05 90_[+2]_389 1553 2.6e-05 389_[+2]_90 11575 2.6e-05 140_[+2]_339 25724 3.2e-05 294_[+2]_185 904 3.4e-05 33_[+2]_446 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=27 21978 ( 401) CAAATCCTGCACCAACATCTG 1 17214 ( 402) CAAATCCTGCACCAACATCTG 1 30659 ( 374) CTACGCCTCCAGCAACATCGA 1 9388 ( 395) CCCATCCCGCAACCTCAACGG 1 5902 ( 369) CTGATACTCAAACGACAACTG 1 31785 ( 42) CACCACCATCAGCACCATCAG 1 11779 ( 173) CCCCACCACCAGCCTCCTCTT 1 4783 ( 414) CTCATCATGTATCAACATCTC 1 33343 ( 473) CTGAACCACCGCCAACAACGA 1 35518 ( 68) CAACTCAACATTCAACATCCG 1 42475 ( 62) CATATCATACATCATCATCTA 1 7597 ( 46) CACCGCATGAGCCATCATTTG 1 8303 ( 384) CAACACTTGAAACCACACCTA 1 4270 ( 38) CTGAATCATCATCAACATCAT 1 38121 ( 264) CAGCTCTAGCATCATTATCAG 1 9459 ( 242) CAAATGAGGAAACGACATCTT 1 34211 ( 67) CAACGGCATCACCCCCATCAG 1 263848 ( 65) TACCTCTCCAAACAACAACTT 1 20933 ( 454) GTAATTCTGCATCAACAACAC 1 42577 ( 119) CCACTCCTCCGGCCACCTTCG 1 22792 ( 378) CTTCAACTGTAACCTCAACTT 1 262271 ( 44) CTCCTCCTCATCGGTCAACTT 1 889 ( 91) CACTGCCACCAGCGACCATTG 1 1553 ( 390) CCGAGCACCCACAAACAACAA 1 11575 ( 141) CCAAGATGTCAGCCTCAACTT 1 25724 ( 295) GAACTCCTGCTTGAACCACGG 1 904 ( 34) CTTCAACGCCGAACACATCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 20640 bayes= 10.146 E= 7.5e-002 -1140 190 -162 -285 85 -36 -1140 32 61 31 -30 -126 74 112 -1140 -285 -4 -1140 -4 96 -85 156 -162 -185 -26 140 -1140 -85 15 -110 -104 85 -284 77 83 -85 -4 148 -1140 -185 148 -1140 -63 -126 -4 12 -4 -4 -184 184 -162 -1140 106 31 -63 -1140 124 -168 -1140 15 -1140 201 -1140 -285 168 -69 -1140 -1140 61 -268 -1140 106 -1140 190 -1140 -126 -26 -168 -63 106 -52 -168 107 -4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 27 E= 7.5e-002 0.000000 0.888889 0.074074 0.037037 0.481481 0.185185 0.000000 0.333333 0.407407 0.296296 0.185185 0.111111 0.444444 0.518519 0.000000 0.037037 0.259259 0.000000 0.222222 0.518519 0.148148 0.703704 0.074074 0.074074 0.222222 0.629630 0.000000 0.148148 0.296296 0.111111 0.111111 0.481481 0.037037 0.407407 0.407407 0.148148 0.259259 0.666667 0.000000 0.074074 0.740741 0.000000 0.148148 0.111111 0.259259 0.259259 0.222222 0.259259 0.074074 0.851852 0.074074 0.000000 0.555556 0.296296 0.148148 0.000000 0.629630 0.074074 0.000000 0.296296 0.000000 0.962963 0.000000 0.037037 0.851852 0.148148 0.000000 0.000000 0.407407 0.037037 0.000000 0.555556 0.000000 0.888889 0.000000 0.111111 0.222222 0.074074 0.148148 0.555556 0.185185 0.074074 0.481481 0.259259 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[AT][AC][CA][TAG]C[CA][TA][CG][CA]A[ACTG]C[AC][AT]CA[TA]C[TA][GT] -------------------------------------------------------------------------------- Time 28.86 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 17 llr = 221 E-value = 5.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 8:66:7822343512114:85 pos.-specific C ::221:1:12223::4:::1: probability G 1a1293178244184:55a:5 matrix T 1:::::11:411114641:11 bits 2.1 * * 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 AGAAGAAGGTGGAGGTGGGAA consensus CC G AAAC TCTA G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 904 258 4.13e-10 GTGGGATGGA AGCAGAAGGCGGAGTCGGGAG GTGGACCAGT 40713 300 3.56e-09 GTGAAGAGCT AGAAGATGGTGAAGGTGGGAA AGGAGTTGAG 39141 174 5.49e-09 GAGAGCAGTG AGCAGAAGGAGGCGATTAGAA GGACTCATCC 22792 347 8.34e-09 ATGGTTGGGA AGAAGAAGGGGGAAGTGAGAG AGAGGCTCTA 4704 256 1.24e-07 TTGTCGAATG AGACGAAGGTACGGTTGTGAG TACCAAATAT 7704 18 2.72e-07 GGTGCAACGA AGCCGAAGGATGAGTTTGGTG ACGAACTTCG 37662 78 2.72e-07 GAATAAATGA GGAAGGAGGAACCGTCGGGCG ATGTGATGAT 20933 283 2.98e-07 TTTGGAGAGG AGGAGGAAATAAAGGCGGGAA ATCTTTGGGC 263848 413 4.69e-07 ACTACGAACC AGACGAATCCGAAGTTTGGAG AGCCTACGTG 5902 132 9.21e-07 GCCGAGTTTG AGAAGGAGATAGAGATATGAA GGATTGGGAG 30659 170 9.21e-07 CGATGCGGAG AGAAGACAGACAAGACTAGAA ACAGGACGGC 9855 182 1.72e-06 GTTGGATGGA GGAGGGAGGTGGATGAGAGAA AAGGCAGTAC 42475 34 1.72e-06 GTTTGGGTGG AGAGGAAGGAATCGTTTAGTT GGGATTACAT 8353 125 2.14e-06 GACACGAGCT AGGACAAGGGGTTGTCTGGAG AAAGAAGATT 42577 182 2.30e-06 CGAGGGACGT TGAGGAGAGCCGCGGTGGGAG TCTTCTTGGT 11165 48 2.65e-06 TTATTGTCAA AGAAGAGGGGACCTGCTAGCA AATCAATTCA 34211 250 3.50e-06 GGCTCGTTAA AGCCGGATATCATGGTGAGAA GGAGAGACAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 904 4.1e-10 257_[+3]_222 40713 3.6e-09 299_[+3]_180 39141 5.5e-09 173_[+3]_306 22792 8.3e-09 346_[+3]_133 4704 1.2e-07 255_[+3]_224 7704 2.7e-07 17_[+3]_462 37662 2.7e-07 77_[+3]_402 20933 3e-07 282_[+3]_197 263848 4.7e-07 412_[+3]_67 5902 9.2e-07 131_[+3]_348 30659 9.2e-07 169_[+3]_310 9855 1.7e-06 181_[+3]_298 42475 1.7e-06 33_[+3]_446 8353 2.1e-06 124_[+3]_355 42577 2.3e-06 181_[+3]_298 11165 2.7e-06 47_[+3]_432 34211 3.5e-06 249_[+3]_230 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=17 904 ( 258) AGCAGAAGGCGGAGTCGGGAG 1 40713 ( 300) AGAAGATGGTGAAGGTGGGAA 1 39141 ( 174) AGCAGAAGGAGGCGATTAGAA 1 22792 ( 347) AGAAGAAGGGGGAAGTGAGAG 1 4704 ( 256) AGACGAAGGTACGGTTGTGAG 1 7704 ( 18) AGCCGAAGGATGAGTTTGGTG 1 37662 ( 78) GGAAGGAGGAACCGTCGGGCG 1 20933 ( 283) AGGAGGAAATAAAGGCGGGAA 1 263848 ( 413) AGACGAATCCGAAGTTTGGAG 1 5902 ( 132) AGAAGGAGATAGAGATATGAA 1 30659 ( 170) AGAAGACAGACAAGACTAGAA 1 9855 ( 182) GGAGGGAGGTGGATGAGAGAA 1 42475 ( 34) AGAGGAAGGAATCGTTTAGTT 1 8353 ( 125) AGGACAAGGGGTTGTCTGGAG 1 42577 ( 182) TGAGGAGAGCCGCGGTGGGAG 1 11165 ( 48) AGAAGAGGGGACCTGCTAGCA 1 34211 ( 250) AGCCGGATATCATGGTGAGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 20640 bayes= 11.0397 E= 5.4e-001 163 -1073 -96 -218 -1073 -1073 213 -1073 128 -2 -96 -1073 114 -2 -37 -1073 -1073 -202 204 -1073 141 -1073 36 -1073 152 -202 -96 -218 -59 -1073 163 -118 -59 -202 174 -1073 14 -43 -37 40 41 -43 85 -218 14 -43 85 -118 99 30 -196 -118 -218 -1073 185 -118 -59 -1073 85 63 -218 57 -1073 114 -218 -1073 121 63 63 -1073 104 -118 -1073 -1073 213 -1073 152 -102 -1073 -118 82 -1073 104 -218 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 17 E= 5.4e-001 0.823529 0.000000 0.117647 0.058824 0.000000 0.000000 1.000000 0.000000 0.647059 0.235294 0.117647 0.000000 0.588235 0.235294 0.176471 0.000000 0.000000 0.058824 0.941176 0.000000 0.705882 0.000000 0.294118 0.000000 0.764706 0.058824 0.117647 0.058824 0.176471 0.000000 0.705882 0.117647 0.176471 0.058824 0.764706 0.000000 0.294118 0.176471 0.176471 0.352941 0.352941 0.176471 0.411765 0.058824 0.294118 0.176471 0.411765 0.117647 0.529412 0.294118 0.058824 0.117647 0.058824 0.000000 0.823529 0.117647 0.176471 0.000000 0.411765 0.411765 0.058824 0.352941 0.000000 0.588235 0.058824 0.000000 0.529412 0.411765 0.411765 0.000000 0.470588 0.117647 0.000000 0.000000 1.000000 0.000000 0.764706 0.117647 0.000000 0.117647 0.470588 0.000000 0.470588 0.058824 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- AG[AC][AC]G[AG]AGG[TA][GA][GA][AC]G[GT][TC][GT][GA]GA[AG] -------------------------------------------------------------------------------- Time 42.67 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1011 1.38e-01 182_[+1(4.51e-05)]_298 11165 2.15e-03 47_[+3(2.65e-06)]_432 11575 1.14e-02 140_[+2(2.60e-05)]_174_\ [+1(7.28e-05)]_145 11779 1.52e-02 66_[+2(4.23e-05)]_85_[+2(8.17e-07)]_\ 307 1553 2.05e-03 66_[+1(3.23e-05)]_303_\ [+2(2.60e-05)]_90 17214 1.29e-09 156_[+1(2.49e-05)]_225_\ [+2(2.51e-12)]_78 20933 3.94e-06 262_[+1(6.22e-05)]_[+3(2.98e-07)]_\ 150_[+2(1.12e-05)]_26 21371 4.32e-07 38_[+1(8.13e-06)]_159_\ [+1(2.00e-11)]_206_[+1(4.51e-05)]_37 21978 1.29e-09 155_[+1(2.49e-05)]_225_\ [+2(2.51e-12)]_79 22792 4.38e-09 109_[+3(9.51e-05)]_162_\ [+1(1.15e-06)]_34_[+3(8.34e-09)]_10_[+2(1.22e-05)]_102 23817 4.95e-04 98_[+1(1.87e-07)]_382 2553 5.56e-05 137_[+1(2.14e-08)]_343 25724 5.60e-03 294_[+2(3.21e-05)]_37_\ [+1(7.28e-05)]_128 262271 2.15e-03 43_[+2(1.42e-05)]_266_\ [+1(1.20e-05)]_150 263848 8.06e-08 64_[+2(9.54e-06)]_226_\ [+1(6.20e-07)]_81_[+3(4.69e-07)]_67 30659 2.42e-08 3_[+1(3.82e-05)]_146_[+3(9.21e-07)]_\ 183_[+2(2.14e-08)]_106 31785 9.15e-03 41_[+2(4.67e-07)]_438 33343 9.10e-03 472_[+2(1.25e-06)]_7 34211 1.23e-06 66_[+2(6.26e-06)]_73_[+1(4.51e-05)]_\ 69_[+3(3.50e-06)]_74_[+1(2.57e-06)]_136 35518 7.80e-05 40_[+1(3.56e-06)]_7_[+2(1.39e-06)]_\ 412 37662 1.07e-06 10_[+1(7.04e-07)]_47_[+3(2.72e-07)]_\ 61_[+1(6.73e-05)]_321 38121 6.11e-03 263_[+2(4.81e-06)]_216 39141 2.42e-05 173_[+3(5.49e-09)]_306 40713 2.90e-08 187_[+1(2.82e-07)]_55_\ [+3(6.08e-07)]_16_[+3(3.56e-09)]_180 4130 6.36e-03 375_[+1(1.29e-06)]_105 42475 9.62e-07 13_[+1(9.89e-06)]_[+3(1.72e-06)]_7_\ [+2(2.51e-06)]_418 42577 4.30e-06 118_[+2(1.22e-05)]_42_\ [+3(2.30e-06)]_89_[+1(8.13e-06)]_189 4270 1.40e-04 37_[+2(4.39e-06)]_124_\ [+1(6.01e-06)]_298 4704 4.22e-06 192_[+1(3.20e-06)]_43_\ [+3(1.24e-07)]_224 4783 1.33e-04 306_[+3(9.85e-05)]_86_\ [+2(1.13e-06)]_66 5902 1.16e-06 131_[+3(9.21e-07)]_216_\ [+2(4.16e-07)]_111 6692 3.22e-03 86_[+1(5.46e-07)]_394 7597 3.41e-04 45_[+2(3.66e-06)]_6_[+1(5.43e-06)]_\ 408 7704 1.06e-04 17_[+3(2.72e-07)]_102_\ [+1(1.90e-05)]_340 8303 2.52e-05 34_[+1(6.65e-06)]_329_\ [+2(4.01e-06)]_96 8353 2.24e-04 124_[+3(2.14e-06)]_60_\ [+1(2.72e-05)]_275 889 1.26e-02 90_[+2(2.24e-05)]_389 904 4.95e-07 33_[+2(3.45e-05)]_203_\ [+3(4.13e-10)]_222 9388 2.39e-06 1_[+1(1.41e-07)]_373_[+2(4.16e-07)]_\ 85 9459 2.50e-03 61_[+1(5.30e-05)]_160_\ [+2(5.74e-06)]_238 9855 1.78e-04 181_[+3(1.72e-06)]_250_\ [+1(4.41e-06)]_28 9947 6.84e-02 177_[+1(1.90e-05)]_303 bd1879 1.16e-01 365_[+1(8.48e-05)]_115 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************