******************************************************************************** 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/196/196.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10058 1.0000 500 10115 1.0000 500 10262 1.0000 500 10314 1.0000 500 10352 1.0000 500 11438 1.0000 500 11747 1.0000 500 12011 1.0000 500 1283 1.0000 500 22095 1.0000 500 22096 1.0000 500 22464 1.0000 500 22785 1.0000 500 22940 1.0000 500 2333 1.0000 500 23437 1.0000 500 23697 1.0000 500 23740 1.0000 500 23747 1.0000 500 24212 1.0000 500 25158 1.0000 500 25162 1.0000 500 25173 1.0000 500 2519 1.0000 500 25248 1.0000 500 25314 1.0000 500 25363 1.0000 500 2543 1.0000 500 261132 1.0000 500 261431 1.0000 500 261734 1.0000 500 261908 1.0000 500 262129 1.0000 500 262874 1.0000 500 263653 1.0000 500 263873 1.0000 500 264268 1.0000 500 264647 1.0000 500 264833 1.0000 500 269060 1.0000 500 269183 1.0000 500 269341 1.0000 500 269988 1.0000 500 28410 1.0000 500 29867 1.0000 500 31223 1.0000 500 31609 1.0000 500 32022 1.0000 500 36572 1.0000 500 3946 1.0000 500 7953 1.0000 500 8129 1.0000 500 8262 1.0000 500 8703 1.0000 500 8964 1.0000 500 8990 1.0000 500 9581 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/196/196.seqs.fa -oc motifs/196 -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= 57 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= 28500 N= 57 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.228 G 0.238 T 0.275 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.228 G 0.238 T 0.275 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 41 llr = 430 E-value = 8.8e-015 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 23366:871573:6436:641 pos.-specific C 545228:284:3a32718327 probability G 11121:2:1::3:11:12:1: matrix T 211:11:1::3:::312:231 bits 2.1 1.9 * 1.7 * 1.5 * Relative 1.3 ** * * Entropy 1.1 ** * * * (15.1 bits) 0.9 ****** * * * * 0.6 ****** ** * ** * 0.4 * ********* ** **** * 0.2 ********************* 0.0 --------------------- Multilevel CCCAACAACAACCAACACAAC consensus TAAGC G CTA CTATGCT sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 269183 455 7.00e-10 TCGTCATCGT CGCAACAACCTCCAACACAAC CAAACAACTC 25158 324 2.94e-09 ACCTGCCCAG CCACACAACCTACAACACATC ACTCGTTCAT 1283 468 7.42e-09 CGTCTCAAAC CTCAACAACAAACATCACTCC ACTTATCATA 22940 420 1.05e-08 GTGAATTCCT CCCAACGAGCTCCAACACAAC CTCCAACCCC 2333 471 1.48e-08 AACTCACTTC TCCACCAACCTCCCACTCAAC TCCATCAAC 264833 420 1.10e-07 GTCTTCGTTC TCAACCAACCAACCTCTCCTC TACAGCCTAT 25248 475 5.35e-07 GGCTGTTGCC CAAACTAACCAGCACATCAAC GACCA 262129 406 6.83e-07 CCTTCCTCTC TCCACCACGATCCACCACCAC ACCCTCACTA 22785 73 6.83e-07 GAGACAATAC CAAAACGACATCCCTCTCTTC TATAATTCAA 263873 333 8.66e-07 CTCATGACAT AGCAACAACAAGCCATTCAAC GGTTGCCTTC 22096 470 1.09e-06 GCCCTACTAC AACCACAACCAACAACTGAGC GTTCATCATC 31609 204 1.37e-06 CATCAAAATC TCCAGCAACAAGCAGCACCCA ATGCCGCCGC 31223 352 1.53e-06 CTTGTGTCCG ACGATCGACAAGCAACACAAA GCCAACGAGA 29867 480 1.91e-06 AGGTGCACAC CTCAACATCACACCCCACATC 8990 468 2.13e-06 AAAAGATACG CGCGATACCCTCCACCACACC TCGTACACCA 9581 353 2.37e-06 TTGAAATGAA CAAGATACCAAGCCACCCAAC GAAAGAGAGG 23747 269 2.64e-06 GTGTGTTTTG CCGAGAAACATCCATCACATC AGAACAGCTG 261132 49 3.99e-06 AGGGTAAGCT GCAAATGAACAACACCACAAC TGAGAGCGAG 25363 281 3.99e-06 AAAGGCCCCT CTTGACATCCAACAACTCCTC TCTGATCAAC 23437 93 3.99e-06 ATTTGTTATC CACGACATCAACCGTAGCAAC GATAGGTGAA 8964 143 4.41e-06 TAGTACCGTC CAAAGCAAACAGCGACAGCAC AAACTACGCA 23697 259 4.41e-06 AACGCCGTCA AGGATCAAAAAGCAACACACC CTCTTCGAAA 25314 2 4.87e-06 C CCCCCCAACCAACCAAAGAGA CAACATGACG 263653 416 5.92e-06 TCGTGTCTCC TCCGCCGACCACCCTCTCTGC ACTTCTTTTT 261734 459 7.88e-06 CTCATTCACT TCCGACAAACAACATTACACA CCCTTCCTTC 22464 378 1.04e-05 AACTTTCTTA CAAAACAAACAACAAAGGAAT AGAGTTGGAT 28410 218 1.14e-05 GGAAAATGAA TCCCCCACCAAGCGTATCCTC TGTTCACATT 264647 70 1.14e-05 ATAGAAGAGA TCAGCCAACACACATAACAAT TTGGTGGAGG 261908 475 1.14e-05 TGATTGGGCA TATCACACCCATCATCACCTC CAGAG 32022 407 1.62e-05 ATTCTCCGGC CAACACGAGCAGCCACCGCAC CGCAACTGTA 8262 475 1.77e-05 TTTTGTCCAT CAGTACACCTACCACCACACC ACAAC 23740 479 1.77e-05 GGAGTTTTCC CCTACCACCTAACCAAAGATC C 261431 76 1.92e-05 GAGATTACCA TTCAACAACAACAAACAGACT CATTTCAATG 12011 379 2.28e-05 TGGGAGCAGA GAGGCCATCAACCCAAACTAC AAATAAGGTG 25173 479 3.98e-05 CAGATTCACA GCAAAAAACAACCACCAGAAG C 7953 115 4.30e-05 CCACCGTGAA ACAATCGAGCAGCAAAACTCA CCCGTCGGCA 36572 289 5.00e-05 CTCCAATCCA ACACACGCCATGCGTCGCCTC ACAGCCTATT 11438 145 5.39e-05 AACAGCAATA CTCAATAACATTCAGCACTAA AGGTGATCGA 264268 373 7.73e-05 GGAGGTGTTG CTCATCGTCATGCAGATCCCC CACCTCTATC 25162 205 8.29e-05 CTACACGAAC AACGACGAGATCCACACCTCC ATCAATAGTG 2543 146 1.41e-04 TTTACACTAG CAAAGCAACAAACCTTGGCTT GGCGTCAGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 269183 7e-10 454_[+1]_25 25158 2.9e-09 323_[+1]_156 1283 7.4e-09 467_[+1]_12 22940 1.1e-08 419_[+1]_60 2333 1.5e-08 470_[+1]_9 264833 1.1e-07 419_[+1]_60 25248 5.4e-07 474_[+1]_5 262129 6.8e-07 405_[+1]_74 22785 6.8e-07 72_[+1]_407 263873 8.7e-07 332_[+1]_147 22096 1.1e-06 469_[+1]_10 31609 1.4e-06 203_[+1]_276 31223 1.5e-06 351_[+1]_128 29867 1.9e-06 479_[+1] 8990 2.1e-06 467_[+1]_12 9581 2.4e-06 352_[+1]_127 23747 2.6e-06 268_[+1]_211 261132 4e-06 48_[+1]_431 25363 4e-06 280_[+1]_199 23437 4e-06 92_[+1]_387 8964 4.4e-06 142_[+1]_337 23697 4.4e-06 258_[+1]_221 25314 4.9e-06 1_[+1]_478 263653 5.9e-06 415_[+1]_64 261734 7.9e-06 458_[+1]_21 22464 1e-05 377_[+1]_102 28410 1.1e-05 217_[+1]_262 264647 1.1e-05 69_[+1]_410 261908 1.1e-05 474_[+1]_5 32022 1.6e-05 406_[+1]_73 8262 1.8e-05 474_[+1]_5 23740 1.8e-05 478_[+1]_1 261431 1.9e-05 75_[+1]_404 12011 2.3e-05 378_[+1]_101 25173 4e-05 478_[+1]_1 7953 4.3e-05 114_[+1]_365 36572 5e-05 288_[+1]_191 11438 5.4e-05 144_[+1]_335 264268 7.7e-05 372_[+1]_107 25162 8.3e-05 204_[+1]_275 2543 0.00014 145_[+1]_334 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=41 269183 ( 455) CGCAACAACCTCCAACACAAC 1 25158 ( 324) CCACACAACCTACAACACATC 1 1283 ( 468) CTCAACAACAAACATCACTCC 1 22940 ( 420) CCCAACGAGCTCCAACACAAC 1 2333 ( 471) TCCACCAACCTCCCACTCAAC 1 264833 ( 420) TCAACCAACCAACCTCTCCTC 1 25248 ( 475) CAAACTAACCAGCACATCAAC 1 262129 ( 406) TCCACCACGATCCACCACCAC 1 22785 ( 73) CAAAACGACATCCCTCTCTTC 1 263873 ( 333) AGCAACAACAAGCCATTCAAC 1 22096 ( 470) AACCACAACCAACAACTGAGC 1 31609 ( 204) TCCAGCAACAAGCAGCACCCA 1 31223 ( 352) ACGATCGACAAGCAACACAAA 1 29867 ( 480) CTCAACATCACACCCCACATC 1 8990 ( 468) CGCGATACCCTCCACCACACC 1 9581 ( 353) CAAGATACCAAGCCACCCAAC 1 23747 ( 269) CCGAGAAACATCCATCACATC 1 261132 ( 49) GCAAATGAACAACACCACAAC 1 25363 ( 281) CTTGACATCCAACAACTCCTC 1 23437 ( 93) CACGACATCAACCGTAGCAAC 1 8964 ( 143) CAAAGCAAACAGCGACAGCAC 1 23697 ( 259) AGGATCAAAAAGCAACACACC 1 25314 ( 2) CCCCCCAACCAACCAAAGAGA 1 263653 ( 416) TCCGCCGACCACCCTCTCTGC 1 261734 ( 459) TCCGACAAACAACATTACACA 1 22464 ( 378) CAAAACAAACAACAAAGGAAT 1 28410 ( 218) TCCCCCACCAAGCGTATCCTC 1 264647 ( 70) TCAGCCAACACACATAACAAT 1 261908 ( 475) TATCACACCCATCATCACCTC 1 32022 ( 407) CAACACGAGCAGCCACCGCAC 1 8262 ( 475) CAGTACACCTACCACCACACC 1 23740 ( 479) CCTACCACCTAACCAAAGATC 1 261431 ( 76) TTCAACAACAACAAACAGACT 1 12011 ( 379) GAGGCCATCAACCCAAACTAC 1 25173 ( 479) GCAAAAAACAACCACCAGAAG 1 7953 ( 115) ACAATCGAGCAGCAAAACTCA 1 36572 ( 289) ACACACGCCATGCGTCGCCTC 1 11438 ( 145) CTCAATAACATTCAGCACTAA 1 264268 ( 373) CTCATCGTCATGCAGATCCCC 1 25162 ( 205) AACGACGAGATCCACACCTCC 1 2543 ( 146) CAAAGCAACAAACCTTGGCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 27360 bayes= 11.2282 E= 8.8e-015 -60 116 -170 -17 30 94 -129 -91 40 102 -97 -191 118 -42 -12 -349 112 9 -129 -150 -240 186 -1200 -117 155 -1200 3 -1200 140 -23 -1200 -117 -108 173 -97 -1200 99 94 -1200 -249 135 -223 -1200 9 30 58 30 -249 -340 209 -1200 -1200 124 36 -129 -1200 77 -23 -170 9 6 153 -1200 -191 118 -164 -129 -17 -1200 177 -12 -1200 112 23 -1200 -69 68 9 -170 -4 -82 168 -328 -150 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 41 E= 8.8e-015 0.170732 0.512195 0.073171 0.243902 0.317073 0.439024 0.097561 0.146341 0.341463 0.463415 0.121951 0.073171 0.585366 0.170732 0.219512 0.024390 0.560976 0.243902 0.097561 0.097561 0.048780 0.829268 0.000000 0.121951 0.756098 0.000000 0.243902 0.000000 0.682927 0.195122 0.000000 0.121951 0.121951 0.756098 0.121951 0.000000 0.512195 0.439024 0.000000 0.048780 0.658537 0.048780 0.000000 0.292683 0.317073 0.341463 0.292683 0.048780 0.024390 0.975610 0.000000 0.000000 0.609756 0.292683 0.097561 0.000000 0.439024 0.195122 0.073171 0.292683 0.268293 0.658537 0.000000 0.073171 0.585366 0.073171 0.097561 0.243902 0.000000 0.780488 0.219512 0.000000 0.560976 0.268293 0.000000 0.170732 0.414634 0.243902 0.073171 0.268293 0.146341 0.731707 0.024390 0.097561 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][CA][CA][AG][AC]C[AG]AC[AC][AT][CAG]C[AC][AT][CA][AT][CG][AC][ATC]C -------------------------------------------------------------------------------- Time 24.55 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 45 llr = 430 E-value = 3.4e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 24:63454:52:62:527121 pos.-specific C 11::2::2:12:::212::3: probability G 62925621a339357151847 matrix T 2312::34:12:121322111 bits 2.1 1.9 1.7 * * * 1.5 * * * Relative 1.3 * * * Entropy 1.1 * * * * (13.8 bits) 0.9 * * * ** * * 0.6 ** * * ** * ** * 0.4 * ***** * **** ** * 0.2 ********** ********** 0.0 --------------------- Multilevel GAGAGGATGAGGAGGAGAGGG consensus T GAATA GA GA T T C sequence G C G T T A C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 31609 261 1.17e-09 AATGACAGGT TGGAGGATGAAGAGGAGAGGG CAGTGGATTC 261734 190 8.59e-09 ATCAAAGACA GAGAGGTCGACGAGCAGAGCG GAGGCAGCTG 29867 117 1.23e-07 TGACATTACG GAGGAGGAGAGGAGGACTGAG CCTAGCAGTG 22464 268 1.23e-07 AGGGGATCTG GAGAGATTGAAGAGTAAAGGG ATGATGGTTG 32022 140 2.61e-07 CACACTGGGT GTGAGAATGGCGAGGAGTGAT GCCGCGAGGG 269341 107 2.61e-07 ACTGAAAAGT GTGAAGGTGGGGAGGCGAGTG CTTTCCCTCC 2543 250 4.00e-07 TCAGAGTTCA TTGACGAAGATGAGTAGAGAG ATGGGATGTT 9581 165 4.60e-07 GGGGACCGCC GAGGGAATGAAGGTGTCAGAG GGATGTGGTT 8990 392 6.04e-07 AGCAGTGCAT TTGTCGATGACGAGGTCAGGG TGAAGTGGAA 3946 436 8.97e-07 TCGTGGCAGA GTGGAAAAGCTGAGGAAAGAG GGCTGGCGAA 25162 408 1.49e-06 GACGCTGATC GCGACGACGACGAAGGGTGCG AGAGAGACAC 23437 183 1.89e-06 GTTATAATGA GAGAAATAGATGTGGAGATAG AATCACAGCA 10115 146 1.89e-06 TATTTGAATG ATGAAATGGGGGAGGACAGCG GGAGTCTGTA 269060 35 2.70e-06 GTATGGGAAG GAGTGGAAGAAGGTGGCTGCG AGGGTCAAGA 261908 90 3.79e-06 GGCTGGTAGG ACGACGGAGTGGGGGTGAGGG GGAGGATCTT 22785 164 4.23e-06 CGTTGAGCTA GAGAGGTTGTGGACGAGAAGG ACATCAATGT 264647 125 5.26e-06 TTGCACCATC GAGAGAGCGGCGAGGCAGGAG GCGACGGTGC 23697 156 5.86e-06 GGGACGGTTG GGGGAAGAGATGATGAGAGAC CTAACAACAC 263873 399 9.82e-06 CGTTGCATTA GTGTAGAAGCGGAGGAAAGGC ATCGGTTGGC 1283 242 9.82e-06 TAGTCCAAGT AGGACGGTGATCAGCAGAGGG GTGGCTATTG 11747 13 9.82e-06 AGATGGTATT CTGAGGATGACGGGGGCAAGG AACAACGCAA 7953 314 1.46e-05 GGTCGGCAGC GAGAGGAAGCAGAGCCAGGAG AAGGTGGATT 23747 145 1.76e-05 ACCGAATCCT TTGAGAGAGAGGGATAGAGTG TACCATCAGT 24212 370 2.32e-05 GATGTGCAGC GAGAGGTAGAAGAACTCATCT TTAAAGACAG 10058 227 2.32e-05 TTCGCGATTA GAGGGGTCAGAGATGAGAGGA ATAGCGATGG 10262 195 2.54e-05 GCCGTCCTCG CGGGAGAAGGTGAGCATAGCA GGAACCACAC 8262 42 3.04e-05 TTTCCCCAGT GATTGGATGAAGAGATGAGAG ATGGTGGTAT 22095 116 3.04e-05 CTAGTGCCAA AGGAAGACGAGGATGCCTGGA CATCAGACGT 11438 217 3.32e-05 TATGAGTGGG GGGGCAGTGGCGTGGCTTGCG GTAGCGTGGC 25314 172 3.62e-05 GATTTGTACA GAGGCGGCGTTGATGTGTTGG TCGGTGCAGG 28410 3 4.66e-05 TC GAGGGTTTGAGGGTGAAAGCT GCGTTGTCGC 263653 116 4.66e-05 GTATTAGGGA GAGGAATAGGAGAATGTTGCG TCAACAGCAA 10352 6 4.66e-05 ACGAG TAGAAGATGGCCGAGTTAGAG GTCGAATGAG 36572 92 5.06e-05 TCTTCTTGTG GGGAGGGTGGGGAGCTATTCT TCCTGTCGTC 262874 91 5.06e-05 TGCACCATGA ACGAGAGTGTTGGAGATTGCG TCGACTAGTT 25173 269 5.06e-05 GCGTGAGGGA ATGAAATTGACGGTCCGAGGA ATGCCGGAAG 261132 82 5.50e-05 AGAGCGAGTT CTGACGAAAATGATGGTAGCG AGGCTGATGT 25248 33 5.50e-05 TCCAGCTTTT GGGAGATGGACGTGGTGGGGA TTAGCTACTG 261431 197 7.00e-05 TCTGGGTACT TAGACAATGGAAGAGATAGCG TTGAGCTTCG 10314 51 7.00e-05 GTAGCACCGA CGTAGGTAGGAGAAGTGAGCT TCGCTAAACA 262129 234 8.84e-05 GGCGAGAGAG GCTGAGACGATGATGTTTGGG AGTTCCCGCT 22096 239 1.03e-04 TGAGTGACAG TGGTCAATGAGGACGGGAACG AGCAATTAAA 25363 317 1.28e-04 TCAACCTCAA GTGAGAAGGGTGGATAGATTG ATAGTATTGA 264268 350 1.38e-04 AATGAGAGCC AAGTGGATGCGGGGGAGGTGT TGCTCATCGT 25158 127 1.71e-04 AGGAAGGCTT TTGTAGTAGTGGTAGTGAGGA GCATGCTCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31609 1.2e-09 260_[+2]_219 261734 8.6e-09 189_[+2]_290 29867 1.2e-07 116_[+2]_363 22464 1.2e-07 267_[+2]_212 32022 2.6e-07 139_[+2]_340 269341 2.6e-07 106_[+2]_373 2543 4e-07 249_[+2]_230 9581 4.6e-07 164_[+2]_315 8990 6e-07 391_[+2]_88 3946 9e-07 435_[+2]_44 25162 1.5e-06 407_[+2]_72 23437 1.9e-06 182_[+2]_297 10115 1.9e-06 145_[+2]_334 269060 2.7e-06 34_[+2]_445 261908 3.8e-06 89_[+2]_390 22785 4.2e-06 163_[+2]_316 264647 5.3e-06 124_[+2]_355 23697 5.9e-06 155_[+2]_324 263873 9.8e-06 398_[+2]_81 1283 9.8e-06 241_[+2]_238 11747 9.8e-06 12_[+2]_467 7953 1.5e-05 313_[+2]_166 23747 1.8e-05 144_[+2]_335 24212 2.3e-05 369_[+2]_110 10058 2.3e-05 226_[+2]_253 10262 2.5e-05 194_[+2]_285 8262 3e-05 41_[+2]_438 22095 3e-05 115_[+2]_364 11438 3.3e-05 216_[+2]_263 25314 3.6e-05 171_[+2]_308 28410 4.7e-05 2_[+2]_477 263653 4.7e-05 115_[+2]_364 10352 4.7e-05 5_[+2]_474 36572 5.1e-05 91_[+2]_388 262874 5.1e-05 90_[+2]_389 25173 5.1e-05 268_[+2]_211 261132 5.5e-05 81_[+2]_398 25248 5.5e-05 32_[+2]_447 261431 7e-05 196_[+2]_283 10314 7e-05 50_[+2]_429 262129 8.8e-05 233_[+2]_246 22096 0.0001 238_[+2]_241 25363 0.00013 316_[+2]_163 264268 0.00014 349_[+2]_130 25158 0.00017 126_[+2]_353 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=45 31609 ( 261) TGGAGGATGAAGAGGAGAGGG 1 261734 ( 190) GAGAGGTCGACGAGCAGAGCG 1 29867 ( 117) GAGGAGGAGAGGAGGACTGAG 1 22464 ( 268) GAGAGATTGAAGAGTAAAGGG 1 32022 ( 140) GTGAGAATGGCGAGGAGTGAT 1 269341 ( 107) GTGAAGGTGGGGAGGCGAGTG 1 2543 ( 250) TTGACGAAGATGAGTAGAGAG 1 9581 ( 165) GAGGGAATGAAGGTGTCAGAG 1 8990 ( 392) TTGTCGATGACGAGGTCAGGG 1 3946 ( 436) GTGGAAAAGCTGAGGAAAGAG 1 25162 ( 408) GCGACGACGACGAAGGGTGCG 1 23437 ( 183) GAGAAATAGATGTGGAGATAG 1 10115 ( 146) ATGAAATGGGGGAGGACAGCG 1 269060 ( 35) GAGTGGAAGAAGGTGGCTGCG 1 261908 ( 90) ACGACGGAGTGGGGGTGAGGG 1 22785 ( 164) GAGAGGTTGTGGACGAGAAGG 1 264647 ( 125) GAGAGAGCGGCGAGGCAGGAG 1 23697 ( 156) GGGGAAGAGATGATGAGAGAC 1 263873 ( 399) GTGTAGAAGCGGAGGAAAGGC 1 1283 ( 242) AGGACGGTGATCAGCAGAGGG 1 11747 ( 13) CTGAGGATGACGGGGGCAAGG 1 7953 ( 314) GAGAGGAAGCAGAGCCAGGAG 1 23747 ( 145) TTGAGAGAGAGGGATAGAGTG 1 24212 ( 370) GAGAGGTAGAAGAACTCATCT 1 10058 ( 227) GAGGGGTCAGAGATGAGAGGA 1 10262 ( 195) CGGGAGAAGGTGAGCATAGCA 1 8262 ( 42) GATTGGATGAAGAGATGAGAG 1 22095 ( 116) AGGAAGACGAGGATGCCTGGA 1 11438 ( 217) GGGGCAGTGGCGTGGCTTGCG 1 25314 ( 172) GAGGCGGCGTTGATGTGTTGG 1 28410 ( 3) GAGGGTTTGAGGGTGAAAGCT 1 263653 ( 116) GAGGAATAGGAGAATGTTGCG 1 10352 ( 6) TAGAAGATGGCCGAGTTAGAG 1 36572 ( 92) GGGAGGGTGGGGAGCTATTCT 1 262874 ( 91) ACGAGAGTGTTGGAGATTGCG 1 25173 ( 269) ATGAAATTGACGGTCCGAGGA 1 261132 ( 82) CTGACGAAAATGATGGTAGCG 1 25248 ( 33) GGGAGATGGACGTGGTGGGGA 1 261431 ( 197) TAGACAATGGAAGAGATAGCG 1 10314 ( 51) CGTAGGTAGGAGAAGTGAGCT 1 262129 ( 234) GCTGAGACGATGATGTTTGGG 1 22096 ( 239) TGGTCAATGAGGACGGGAACG 1 25363 ( 317) GTGAGAAGGGTGGATAGATTG 1 264268 ( 350) AAGTGGATGCGGGGGAGGTGT 1 25158 ( 127) TTGTAGTAGTGGTAGTGAGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 27360 bayes= 9.62525 E= 3.4e-007 -73 -136 128 -63 63 -136 -10 7 -1214 -1214 197 -204 122 -1214 4 -82 27 -4 97 -1214 55 -1214 133 -363 85 -1214 4 7 46 -55 -184 62 -254 -1214 200 -1214 99 -136 28 -131 -8 -4 28 -17 -353 -236 197 -1214 132 -1214 16 -163 -22 -236 110 -31 -353 -55 158 -131 85 -78 -84 -5 -73 -36 104 -63 137 -1214 -142 -17 -195 -1214 175 -105 -8 55 58 -204 -95 -236 153 -105 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 45 E= 3.4e-007 0.155556 0.088889 0.577778 0.177778 0.400000 0.088889 0.222222 0.288889 0.000000 0.000000 0.933333 0.066667 0.600000 0.000000 0.244444 0.155556 0.311111 0.222222 0.466667 0.000000 0.377778 0.000000 0.600000 0.022222 0.466667 0.000000 0.244444 0.288889 0.355556 0.155556 0.066667 0.422222 0.044444 0.000000 0.955556 0.000000 0.511111 0.088889 0.288889 0.111111 0.244444 0.222222 0.288889 0.244444 0.022222 0.044444 0.933333 0.000000 0.644444 0.000000 0.266667 0.088889 0.222222 0.044444 0.511111 0.222222 0.022222 0.155556 0.711111 0.111111 0.466667 0.133333 0.133333 0.266667 0.155556 0.177778 0.488889 0.177778 0.666667 0.000000 0.088889 0.244444 0.066667 0.000000 0.800000 0.133333 0.244444 0.333333 0.355556 0.066667 0.133333 0.044444 0.688889 0.133333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[ATG]G[AG][GAC][GA][ATG][TA]G[AG][GATC]G[AG][GAT]G[AT]G[AT]G[GCA]G -------------------------------------------------------------------------------- Time 48.06 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 33 llr = 334 E-value = 1.7e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::1:::1::1:2::1: pos.-specific C 371:a24831814336 probability G 1::1::2:::12:22: matrix T 6389:83278156544 bits 2.1 * 1.9 * 1.7 * 1.5 * Relative 1.3 *** * Entropy 1.1 * *** * * * (14.6 bits) 0.9 ***** **** * * 0.6 ****** **** * * 0.4 ****** **** ** * 0.2 **************** 0.0 ---------------- Multilevel TCTTCTCCTTCTTTTC consensus CT TTC ACCCT sequence G G GG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 36572 22 4.59e-08 TCAGCTGCCT TCTTCTTCTTCTTCTT CTTCTTCTTC 262129 390 1.02e-07 CTCTCTTCCT TCTTCTCCTTCCTCTC TCCACCACGA 11438 432 2.39e-07 ACGGTTGATT TCTTCTCTTTCATTTC TCGCTGCTCT 261132 397 3.29e-07 CGTCTGTTTC TCTGCTGCTTCTTTTC GCTACGAAGA 22464 443 3.29e-07 GTCATTGATA TTTTCTGCTTCTCTTT GTAATACTGA 25314 246 5.13e-07 CGCTGTACAA CCTTCTGCCTCGTCTC ATGCTTTGCA 261734 485 7.80e-07 ACACACCCTT CCTTCTGCTTCCTTGC 10352 361 1.90e-06 TTTGACCATA TCTTCTCCTTATTTCC TGCTGAGCCT 31609 18 2.41e-06 GTCCAATGTC TCCTCTCCTTCACTGT AACTTAGTAA 22785 245 2.70e-06 CTACGGAGGC CCTTCTGCTTCTGCTC GGCACATCAT 263873 94 4.19e-06 ACACAGGCGG TCTTCTATTTCTTTGT TGCGGCTCGC 25363 230 4.19e-06 TTCTTTTCAT TCTTCTCCATCTTGGC TGAGGCGTTT 264833 286 4.66e-06 TTAGAGGACT CTTTCTCTTTCGTCTT TCAAATGAAT 262874 459 4.66e-06 TGCCAAGAGC TCTGCTGCCTCTCGCC TCGATGCTTT 22096 404 5.73e-06 TTTTCTTCAA CTCTCTTCTTCATTTT GACGAAGCTG 2519 273 7.00e-06 TCTCTCTCTA TTCTCTTCCTCTCTCT GCTCTCTCCC 10058 471 7.71e-06 GGTTCTTTCG TTTTCCCCTCCTTCCC GTACGAGTTA 269183 101 8.49e-06 GGACACCTGC TCCTCTCCCTGTCCTC TGAGCTTCAA 22940 378 8.49e-06 AATTGTCACA CCATCTACTTCATTTT CAGATCTCAA 8703 168 1.02e-05 GAGTATGTAT TCATCTTCTTCGCTAT CACCATTGGC 3946 417 1.23e-05 TCCTTGAGTT GTTTCTTCTTCGTGGC AGAGTGGAAA 8964 418 1.34e-05 ACAACGGTAT CTATCTCCCTCTCCAC CCAGCGACCT 261431 386 1.60e-05 ACCAATCTTA CTTTCTACTACACTCC AAGGGCATCA 31223 259 1.90e-05 TGTCCGTCAC TTTTCTTCCACGTGGC AAGTAAGGGA 9581 474 3.07e-05 ATCTCGTGTG CCTTCTCTTTGCCGTC GCCGCCACAT 8990 22 3.31e-05 CCATTTGTGT TCTTCCCTTTGTTGGC CATGCTTAGT 264647 353 3.31e-05 CAATTATCAC CCTTCTGCTATGTCTC TTAGTGACTC 2543 20 3.31e-05 CAAAGTACTT TCTTCTCTCTTTCCCT CATACTTATT 23740 264 3.31e-05 TTCAGCACTC GCTGCTTCCTCATTTT GTTTTGGCTT 8129 472 3.57e-05 CTGCGGCAAA TCATCCTCCACTCTCC TCCGATGCTC 28410 165 4.14e-05 CCTAAAAATC ATTTCCTCTTCGCTCC TGCAGCATCT 269988 436 5.49e-05 CCATCAAATT CCTGCCTCTCCTCGCC ACACGCCAGT 32022 305 5.87e-05 GTCCATCTTT TTTTCTCTTCCATTAT TTTTAAGACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36572 4.6e-08 21_[+3]_463 262129 1e-07 389_[+3]_95 11438 2.4e-07 431_[+3]_53 261132 3.3e-07 396_[+3]_88 22464 3.3e-07 442_[+3]_42 25314 5.1e-07 245_[+3]_239 261734 7.8e-07 484_[+3] 10352 1.9e-06 360_[+3]_124 31609 2.4e-06 17_[+3]_467 22785 2.7e-06 244_[+3]_240 263873 4.2e-06 93_[+3]_391 25363 4.2e-06 229_[+3]_255 264833 4.7e-06 285_[+3]_199 262874 4.7e-06 458_[+3]_26 22096 5.7e-06 403_[+3]_81 2519 7e-06 272_[+3]_212 10058 7.7e-06 470_[+3]_14 269183 8.5e-06 100_[+3]_384 22940 8.5e-06 377_[+3]_107 8703 1e-05 167_[+3]_317 3946 1.2e-05 416_[+3]_68 8964 1.3e-05 417_[+3]_67 261431 1.6e-05 385_[+3]_99 31223 1.9e-05 258_[+3]_226 9581 3.1e-05 473_[+3]_11 8990 3.3e-05 21_[+3]_463 264647 3.3e-05 352_[+3]_132 2543 3.3e-05 19_[+3]_465 23740 3.3e-05 263_[+3]_221 8129 3.6e-05 471_[+3]_13 28410 4.1e-05 164_[+3]_320 269988 5.5e-05 435_[+3]_49 32022 5.9e-05 304_[+3]_180 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=33 36572 ( 22) TCTTCTTCTTCTTCTT 1 262129 ( 390) TCTTCTCCTTCCTCTC 1 11438 ( 432) TCTTCTCTTTCATTTC 1 261132 ( 397) TCTGCTGCTTCTTTTC 1 22464 ( 443) TTTTCTGCTTCTCTTT 1 25314 ( 246) CCTTCTGCCTCGTCTC 1 261734 ( 485) CCTTCTGCTTCCTTGC 1 10352 ( 361) TCTTCTCCTTATTTCC 1 31609 ( 18) TCCTCTCCTTCACTGT 1 22785 ( 245) CCTTCTGCTTCTGCTC 1 263873 ( 94) TCTTCTATTTCTTTGT 1 25363 ( 230) TCTTCTCCATCTTGGC 1 264833 ( 286) CTTTCTCTTTCGTCTT 1 262874 ( 459) TCTGCTGCCTCTCGCC 1 22096 ( 404) CTCTCTTCTTCATTTT 1 2519 ( 273) TTCTCTTCCTCTCTCT 1 10058 ( 471) TTTTCCCCTCCTTCCC 1 269183 ( 101) TCCTCTCCCTGTCCTC 1 22940 ( 378) CCATCTACTTCATTTT 1 8703 ( 168) TCATCTTCTTCGCTAT 1 3946 ( 417) GTTTCTTCTTCGTGGC 1 8964 ( 418) CTATCTCCCTCTCCAC 1 261431 ( 386) CTTTCTACTACACTCC 1 31223 ( 259) TTTTCTTCCACGTGGC 1 9581 ( 474) CCTTCTCTTTGCCGTC 1 8990 ( 22) TCTTCCCTTTGTTGGC 1 264647 ( 353) CCTTCTGCTATGTCTC 1 2543 ( 20) TCTTCTCTCTTTCCCT 1 23740 ( 264) GCTGCTTCCTCATTTT 1 8129 ( 472) TCATCCTCCACTCTCC 1 28410 ( 165) ATTTCCTCTTCGCTCC 1 269988 ( 436) CCTGCCTCTCCTCGCC 1 32022 ( 305) TTTTCTCTTCCATTAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 27645 bayes= 10.4757 E= 1.7e-005 -309 55 -197 106 -1169 154 -1169 28 -109 -91 -1169 146 -1169 -1169 -97 167 -1169 213 -1169 -1169 -1169 -59 -1169 162 -150 79 -17 14 -1169 179 -1169 -38 -309 26 -1169 134 -109 -133 -1169 152 -309 184 -139 -218 -28 -133 -17 82 -1169 79 -297 106 -1169 41 -17 82 -150 26 -17 62 -1169 148 -1169 40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 33 E= 1.7e-005 0.030303 0.333333 0.060606 0.575758 0.000000 0.666667 0.000000 0.333333 0.121212 0.121212 0.000000 0.757576 0.000000 0.000000 0.121212 0.878788 0.000000 1.000000 0.000000 0.000000 0.000000 0.151515 0.000000 0.848485 0.090909 0.393939 0.212121 0.303030 0.000000 0.787879 0.000000 0.212121 0.030303 0.272727 0.000000 0.696970 0.121212 0.090909 0.000000 0.787879 0.030303 0.818182 0.090909 0.060606 0.212121 0.090909 0.212121 0.484848 0.000000 0.393939 0.030303 0.575758 0.000000 0.303030 0.212121 0.484848 0.090909 0.272727 0.212121 0.424242 0.000000 0.636364 0.000000 0.363636 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TC][CT]TTCT[CTG][CT][TC]TC[TAG][TC][TCG][TCG][CT] -------------------------------------------------------------------------------- Time 70.63 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10058 2.56e-03 226_[+2(2.32e-05)]_223_\ [+3(7.71e-06)]_14 10115 4.40e-03 145_[+2(1.89e-06)]_334 10262 2.77e-02 194_[+2(2.54e-05)]_285 10314 2.35e-01 50_[+2(7.00e-05)]_429 10352 1.31e-03 5_[+2(4.66e-05)]_334_[+3(1.90e-06)]_\ 124 11438 7.51e-06 144_[+1(5.39e-05)]_51_\ [+2(3.32e-05)]_194_[+3(2.39e-07)]_53 11747 5.02e-02 12_[+2(9.82e-06)]_467 12011 5.77e-02 378_[+1(2.28e-05)]_101 1283 9.79e-07 241_[+2(9.82e-06)]_162_\ [+1(5.80e-05)]_22_[+1(7.42e-09)]_12 22095 6.73e-02 115_[+2(3.04e-05)]_364 22096 1.07e-05 403_[+3(5.73e-06)]_50_\ [+1(1.09e-06)]_10 22464 1.44e-08 240_[+2(4.66e-05)]_6_[+2(1.23e-07)]_\ 89_[+1(1.04e-05)]_44_[+3(3.29e-07)]_42 22785 2.09e-07 72_[+1(6.83e-07)]_70_[+2(4.23e-06)]_\ 60_[+3(2.70e-06)]_240 22940 2.58e-06 30_[+1(2.68e-05)]_326_\ [+3(8.49e-06)]_26_[+1(1.05e-08)]_60 2333 1.63e-04 288_[+1(2.68e-05)]_161_\ [+1(1.48e-08)]_9 23437 8.78e-05 92_[+1(3.99e-06)]_69_[+2(1.89e-06)]_\ 297 23697 4.50e-04 155_[+2(5.86e-06)]_82_\ [+1(4.41e-06)]_221 23740 2.63e-03 263_[+3(3.31e-05)]_199_\ [+1(1.77e-05)]_1 23747 7.37e-04 102_[+1(7.73e-05)]_21_\ [+2(1.76e-05)]_103_[+1(2.64e-06)]_211 24212 1.47e-01 369_[+2(2.32e-05)]_110 25158 6.93e-06 323_[+1(2.94e-09)]_156 25162 7.23e-04 204_[+1(8.29e-05)]_104_\ [+2(3.94e-05)]_57_[+2(1.49e-06)]_72 25173 6.12e-03 268_[+2(5.06e-05)]_189_\ [+1(3.98e-05)]_1 2519 3.48e-02 239_[+3(8.14e-05)]_17_\ [+3(7.00e-06)]_212 25248 4.29e-04 32_[+2(5.50e-05)]_421_\ [+1(5.35e-07)]_5 25314 1.89e-06 1_[+1(4.87e-06)]_149_[+2(3.62e-05)]_\ 53_[+3(5.13e-07)]_239 25363 3.08e-05 229_[+3(4.19e-06)]_35_\ [+1(3.99e-06)]_199 2543 2.72e-05 19_[+3(3.31e-05)]_214_\ [+2(4.00e-07)]_230 261132 1.54e-06 48_[+1(3.99e-06)]_12_[+2(5.50e-05)]_\ 294_[+3(3.29e-07)]_88 261431 2.30e-04 75_[+1(1.92e-05)]_100_\ [+2(7.00e-05)]_168_[+3(1.60e-05)]_99 261734 2.13e-09 189_[+2(8.59e-09)]_248_\ [+1(7.88e-06)]_5_[+3(7.80e-07)] 261908 4.78e-04 89_[+2(3.79e-06)]_364_\ [+1(1.14e-05)]_5 262129 1.65e-07 233_[+2(8.84e-05)]_135_\ [+3(1.02e-07)]_[+1(6.83e-07)]_74 262874 2.54e-03 90_[+2(5.06e-05)]_347_\ [+3(4.66e-06)]_26 263653 9.41e-04 115_[+2(4.66e-05)]_279_\ [+1(5.92e-06)]_64 263873 8.24e-07 93_[+3(4.19e-06)]_223_\ [+1(8.66e-07)]_45_[+2(9.82e-06)]_81 264268 5.55e-02 372_[+1(7.73e-05)]_107 264647 2.94e-05 69_[+1(1.14e-05)]_34_[+2(5.26e-06)]_\ 75_[+3(8.14e-05)]_116_[+3(3.31e-05)]_132 264833 8.25e-06 285_[+3(4.66e-06)]_118_\ [+1(1.10e-07)]_60 269060 2.75e-02 34_[+2(2.70e-06)]_63_[+2(7.57e-05)]_\ 361 269183 1.80e-07 100_[+3(8.49e-06)]_338_\ [+1(7.00e-10)]_25 269341 4.69e-04 106_[+2(2.61e-07)]_30_\ [+2(8.18e-05)]_322 269988 8.71e-02 435_[+3(5.49e-05)]_49 28410 2.34e-04 2_[+2(4.66e-05)]_141_[+3(4.14e-05)]_\ 37_[+1(1.14e-05)]_262 29867 7.68e-06 116_[+2(1.23e-07)]_47_\ [+2(4.60e-07)]_274_[+1(1.91e-06)] 31223 2.54e-04 258_[+3(1.90e-05)]_77_\ [+1(1.53e-06)]_128 31609 1.88e-10 17_[+3(2.41e-06)]_23_[+3(7.71e-06)]_\ 131_[+1(1.37e-06)]_36_[+2(1.17e-09)]_219 32022 4.64e-06 139_[+2(2.61e-07)]_62_\ [+2(1.46e-05)]_61_[+3(5.87e-05)]_86_[+1(1.62e-05)]_73 36572 2.34e-06 21_[+3(4.59e-08)]_54_[+2(5.06e-05)]_\ 133_[+3(9.21e-05)]_27_[+1(5.00e-05)]_191 3946 1.24e-04 416_[+3(1.23e-05)]_3_[+2(8.97e-07)]_\ 44 7953 3.51e-03 114_[+1(4.30e-05)]_178_\ [+2(1.46e-05)]_166 8129 1.24e-01 471_[+3(3.57e-05)]_13 8262 4.74e-03 41_[+2(3.04e-05)]_412_\ [+1(1.77e-05)]_5 8703 5.91e-02 167_[+3(1.02e-05)]_317 8964 1.01e-03 142_[+1(4.41e-06)]_254_\ [+3(1.34e-05)]_67 8990 9.64e-07 21_[+3(3.31e-05)]_354_\ [+2(6.04e-07)]_2_[+2(8.84e-05)]_32_[+1(2.13e-06)]_12 9581 7.76e-07 164_[+2(4.60e-07)]_167_\ [+1(2.37e-06)]_100_[+3(3.07e-05)]_11 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************