******************************************************************************** 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/33/33.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10183 1.0000 500 10185 1.0000 500 11146 1.0000 500 11474 1.0000 500 14147 1.0000 500 1634 1.0000 500 20584 1.0000 500 21585 1.0000 500 21957 1.0000 500 22208 1.0000 500 22372 1.0000 500 2270 1.0000 500 23043 1.0000 500 2345 1.0000 500 23953 1.0000 500 25488 1.0000 500 2597 1.0000 500 261451 1.0000 500 261572 1.0000 500 262553 1.0000 500 263365 1.0000 500 264013 1.0000 500 264603 1.0000 500 267963 1.0000 500 270206 1.0000 500 27048 1.0000 500 30960 1.0000 500 35561 1.0000 500 36669 1.0000 500 36858 1.0000 500 38312 1.0000 500 39754 1.0000 500 4070 1.0000 500 4463 1.0000 500 4465 1.0000 500 4871 1.0000 500 5186 1.0000 500 5220 1.0000 500 5428 1.0000 500 5502 1.0000 500 5504 1.0000 500 5576 1.0000 500 6015 1.0000 500 6029 1.0000 500 6361 1.0000 500 7695 1.0000 500 9051 1.0000 500 9087 1.0000 500 9878 1.0000 500 9903 1.0000 500 bd308 1.0000 500 ThpsCp022 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/33/33.seqs.fa -oc motifs/33 -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= 52 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= 26000 N= 52 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.229 G 0.233 T 0.280 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.229 G 0.233 T 0.280 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 41 llr = 421 E-value = 1.1e-014 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 5174:64:54132263:32:1 pos.-specific C 3713812a138:45:283:94 probability G :11::31:3::7:333:31:4 matrix T 11132:3::31:4::221712 bits 2.1 1.9 * 1.7 * * 1.5 * * Relative 1.3 * * * * Entropy 1.1 * * ** * * (14.8 bits) 0.9 * * ** * * * 0.6 ** ** * ** ** * ** 0.4 ****** ******** * ** 0.2 ****** ******** ***** 0.0 --------------------- Multilevel ACAACAACAACGCCAGCCTCG consensus C C GT GC ATGGA GA C sequence T T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 6015 118 5.68e-09 GCCGAGGTTC ACATCATCATCGTGAGCGTCG TCGGTGGTGT 2270 478 8.43e-09 AAGGAACAAT TCAACAACGACGACAACCTCC AC 4465 470 2.50e-08 AAGATCACCT CCACCATCAACATCAGCTTCG AGGAAACATC 5576 464 1.39e-07 ACCTTGTCCA ACAACAACCACAACGTCATCC GTCGTCACAC 261451 463 1.39e-07 TGGGCACCCC TCATCATCGTCGCGATCGTCG GAGCCATATT 10183 471 2.12e-07 CGCCTCCAAT ACAACGCCACCGCCACTCTCT GCCACCACC 21957 247 4.12e-07 GCTGCCGTCG ACATCGACATCAACGGCATCT CCATTGGCAT 5428 424 6.01e-07 CAAACAACAA CCATCAACATCGTGGACCTTC ACTAACTACG 23953 472 6.01e-07 GAGTCAACAT TCAACATCAACATGGGCTTCG GTCCCCCT 261572 449 7.68e-07 TTGACGTTGA CTAACGACGCCACGAACATCG TCGCTTGTCC 5186 358 1.10e-06 CCATCAAAAG ATATCAACGACGCAATCAACC ATAAAGCAAA 23043 161 1.23e-06 ATCGTTGGAG AGATCGTCACCGCCGATGTCG TCGTTATTGG 1634 397 1.23e-06 TTGTCTTCAT CAATCCACACCACCAACGTCC AATAACACAA 2345 412 1.38e-06 TGCACAACAC ACACTATCATAGTCGGCCTCC ACAACCATCA 22208 419 1.38e-06 GCCTGAGTTC TGACCAACACCGTCATCTTCC ATAATCGTCG 263365 384 1.72e-06 CCCAACACCC AACACGTCGCCGCCGACGTCG ATATGACAGC 11474 386 3.64e-06 CGAGCAAAGA ACAATGGCGTCGTCAGCCACA CACGTAACGC 262553 297 4.03e-06 CTATCCCGAG ACGCTCACGACGTCATCATCC CACCTTTGCA 10185 32 4.03e-06 CACCGCATGA TCACCACCACCGCCTGCAACC CTCCCTCTCG 6029 121 5.44e-06 AGAGCATATC CCAACATCATTGTAGCCGACC CTTCACCACT 36669 397 6.00e-06 TGTCTTGAAC GGTACAACGACGCCGACCTCC GGATCGGCGT 267963 104 7.27e-06 CCCTCGCCTC TCTCTACCATCGCAATCGTCG CGAATGGAAC 21585 254 8.78e-06 CCAGCTGGCA CCAACGACGACGCAGCCAGTG ATGTTTTGCA 264013 2 9.64e-06 T CGATCAGCACCAAGAGTATCG CTGTTTGATG 4070 353 1.06e-05 GTGACTTCTG CCACAGGCCACGCAAGCAACG CTACCAACAC 30960 347 1.51e-05 AGCAAAGATA CAACCATCACAGTGGCCCTCT TCCCTTGTTC 36858 410 1.65e-05 TCAAATACGC CCACCGCCCACGCACCCGACC GACCCCCCTC 2597 244 1.96e-05 GGCATGACTG CCAACAGCAAGGAAAGCGGCG GTGGTGACGA 38312 179 2.13e-05 TTTGCATAAA ACTCCATCAACGCGGCTGTTT AGAAAACTCC 7695 461 2.52e-05 GCTCTGTTTG CCCCCACCGACACCGATCTTC CCAATCAAAT 264603 271 2.52e-05 TATTTCTGGA ACGACATCATCTACACTCTCG TGCCAATGTT 20584 429 2.52e-05 CCCTTCTCCG ACATCTACCCTGCCAACCTCA CCCAACACGC 5504 259 2.73e-05 CAAAGGTGGG ATGATGACGTCGTGAGCGTCT CGGGATAGCG 6361 300 2.96e-05 GAAATTGAGA ACACTGCCATCGCAAATCACA AATCACAAAT 4463 466 3.21e-05 GCCCGTCACC ACTTCAGCGCTACCACCCACT CTGATTCCAT 27048 41 3.77e-05 ACAATACGAG ACCAACACCACATCAACCTCC AAGCATAGTC 25488 125 3.77e-05 TCTTGTGCAG CCATCAATCACATCAGCAGCT CGACACGGAT 5220 139 4.40e-05 CTTGGATGAG AAGTCATCAAAGTCATTGTCG CTCGCCATTC 9051 337 4.75e-05 GATAAATCAC AAACTTGCGCCGACGGCCACG CCGTGCGCGA 22372 474 6.41e-05 TTTCCCTTTA ACTACAACTACAAGATCTACC TGCACC 9903 409 1.78e-04 CTTGCCCTGA CTTATGCTGACGTGAGCATCG TTGCTTCCGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6015 5.7e-09 117_[+1]_362 2270 8.4e-09 477_[+1]_2 4465 2.5e-08 469_[+1]_10 5576 1.4e-07 463_[+1]_16 261451 1.4e-07 462_[+1]_17 10183 2.1e-07 470_[+1]_9 21957 4.1e-07 246_[+1]_233 5428 6e-07 423_[+1]_56 23953 6e-07 471_[+1]_8 261572 7.7e-07 448_[+1]_31 5186 1.1e-06 357_[+1]_122 23043 1.2e-06 160_[+1]_319 1634 1.2e-06 396_[+1]_83 2345 1.4e-06 411_[+1]_68 22208 1.4e-06 418_[+1]_61 263365 1.7e-06 383_[+1]_96 11474 3.6e-06 385_[+1]_94 262553 4e-06 296_[+1]_183 10185 4e-06 31_[+1]_448 6029 5.4e-06 120_[+1]_359 36669 6e-06 396_[+1]_83 267963 7.3e-06 103_[+1]_376 21585 8.8e-06 253_[+1]_226 264013 9.6e-06 1_[+1]_478 4070 1.1e-05 352_[+1]_127 30960 1.5e-05 346_[+1]_133 36858 1.6e-05 409_[+1]_70 2597 2e-05 243_[+1]_236 38312 2.1e-05 178_[+1]_301 7695 2.5e-05 460_[+1]_19 264603 2.5e-05 270_[+1]_209 20584 2.5e-05 428_[+1]_51 5504 2.7e-05 258_[+1]_221 6361 3e-05 299_[+1]_180 4463 3.2e-05 465_[+1]_14 27048 3.8e-05 40_[+1]_439 25488 3.8e-05 124_[+1]_355 5220 4.4e-05 138_[+1]_341 9051 4.8e-05 336_[+1]_143 22372 6.4e-05 473_[+1]_6 9903 0.00018 408_[+1]_71 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=41 6015 ( 118) ACATCATCATCGTGAGCGTCG 1 2270 ( 478) TCAACAACGACGACAACCTCC 1 4465 ( 470) CCACCATCAACATCAGCTTCG 1 5576 ( 464) ACAACAACCACAACGTCATCC 1 261451 ( 463) TCATCATCGTCGCGATCGTCG 1 10183 ( 471) ACAACGCCACCGCCACTCTCT 1 21957 ( 247) ACATCGACATCAACGGCATCT 1 5428 ( 424) CCATCAACATCGTGGACCTTC 1 23953 ( 472) TCAACATCAACATGGGCTTCG 1 261572 ( 449) CTAACGACGCCACGAACATCG 1 5186 ( 358) ATATCAACGACGCAATCAACC 1 23043 ( 161) AGATCGTCACCGCCGATGTCG 1 1634 ( 397) CAATCCACACCACCAACGTCC 1 2345 ( 412) ACACTATCATAGTCGGCCTCC 1 22208 ( 419) TGACCAACACCGTCATCTTCC 1 263365 ( 384) AACACGTCGCCGCCGACGTCG 1 11474 ( 386) ACAATGGCGTCGTCAGCCACA 1 262553 ( 297) ACGCTCACGACGTCATCATCC 1 10185 ( 32) TCACCACCACCGCCTGCAACC 1 6029 ( 121) CCAACATCATTGTAGCCGACC 1 36669 ( 397) GGTACAACGACGCCGACCTCC 1 267963 ( 104) TCTCTACCATCGCAATCGTCG 1 21585 ( 254) CCAACGACGACGCAGCCAGTG 1 264013 ( 2) CGATCAGCACCAAGAGTATCG 1 4070 ( 353) CCACAGGCCACGCAAGCAACG 1 30960 ( 347) CAACCATCACAGTGGCCCTCT 1 36858 ( 410) CCACCGCCCACGCACCCGACC 1 2597 ( 244) CCAACAGCAAGGAAAGCGGCG 1 38312 ( 179) ACTCCATCAACGCGGCTGTTT 1 7695 ( 461) CCCCCACCGACACCGATCTTC 1 264603 ( 271) ACGACATCATCTACACTCTCG 1 20584 ( 429) ACATCTACCCTGCCAACCTCA 1 5504 ( 259) ATGATGACGTCGTGAGCGTCT 1 6361 ( 300) ACACTGCCATCGCAAATCACA 1 4463 ( 466) ACTTCAGCGCTACCACCCACT 1 27048 ( 41) ACCAACACCACATCAACCTCC 1 25488 ( 125) CCATCAATCACATCAGCAGCT 1 5220 ( 139) AAGTCATCAAAGTCATTGTCG 1 9051 ( 337) AAACTTGCGCCGACGGCCACG 1 22372 ( 474) ACTACAACTACAAGATCTACC 1 9903 ( 409) CTTATGCTGACGTGAGCATCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 24960 bayes= 9.52642 E= 1.1e-014 92 58 -325 -94 -108 158 -125 -152 140 -165 -125 -94 59 47 -1200 6 -240 172 -1200 -52 118 -165 33 -252 59 -42 -67 6 -1200 205 -1200 -252 92 -65 55 -352 76 35 -1200 -6 -182 186 -325 -193 18 -1200 155 -352 -40 94 -1200 39 -40 123 21 -1200 124 -323 55 -352 5 -23 55 -52 -1200 181 -1200 -52 5 58 33 -152 -8 -1200 -167 129 -1200 198 -1200 -152 -182 68 75 -71 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 41 E= 1.1e-014 0.487805 0.341463 0.024390 0.146341 0.121951 0.682927 0.097561 0.097561 0.682927 0.073171 0.097561 0.146341 0.390244 0.317073 0.000000 0.292683 0.048780 0.756098 0.000000 0.195122 0.585366 0.073171 0.292683 0.048780 0.390244 0.170732 0.146341 0.292683 0.000000 0.951220 0.000000 0.048780 0.487805 0.146341 0.341463 0.024390 0.439024 0.292683 0.000000 0.268293 0.073171 0.829268 0.024390 0.073171 0.292683 0.000000 0.682927 0.024390 0.195122 0.439024 0.000000 0.365854 0.195122 0.536585 0.268293 0.000000 0.609756 0.024390 0.341463 0.024390 0.268293 0.195122 0.341463 0.195122 0.000000 0.804878 0.000000 0.195122 0.268293 0.341463 0.292683 0.097561 0.243902 0.000000 0.073171 0.682927 0.000000 0.902439 0.000000 0.097561 0.073171 0.365854 0.390244 0.170732 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [AC]CA[ACT]C[AG][AT]C[AG][ACT]C[GA][CT][CG][AG][GA]C[CGA][TA]C[GC] -------------------------------------------------------------------------------- Time 23.63 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 17 llr = 227 E-value = 1.2e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 142:::2:21:21:122154: pos.-specific C 83::86:84:a6185449129 probability G 235113:11::2::142:12: matrix T :129118149::923131421 bits 2.1 * 1.9 * 1.7 * * 1.5 * * * * * Relative 1.3 ** ** ** ** * * Entropy 1.1 * ** ** ** ** * * (19.3 bits) 0.9 * ***** ***** * * 0.6 * ****** ***** * * 0.4 * ****** ***** * ** * 0.2 **************** ** * 0.0 --------------------- Multilevel CAGTCCTCCTCCTCCCCCAAC consensus CA G T TGT TG sequence GT T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 36669 227 2.03e-10 TTTTGATCAT CCGTCCTCCACCTCCCCCAAC CAAGTCTACA 270206 461 2.03e-10 TTTTGATCAT CCGTCCTCCACCTCCCCCAAC CAAGTCTACA 1634 40 4.09e-09 TCCTTCCATT CAGTGCTCTTCCTCCGTCAGC CGCTTGCTTG 6015 461 1.22e-07 ACCATTCCCC CGGTCGTCGTCGTCCGTCGTC AGTCCTAACA 2270 333 1.78e-07 GGGTCGTCGT CGGTCGTCTTCGTTGGCCTTC GTGAAATGAG 25488 271 2.13e-07 TCGAAGTACA CCTTCCTCCTCCCTTCCCTGC CTCAAATCAA 11146 453 2.55e-07 ACTCCTGCCG CTGTCGTCATCATCACGCAAC TTCATTTCAC 2597 469 2.79e-07 GTACTGCCTT CATTCCAGTTCCTCCAACACC AGAAGAGCAA 5186 471 3.94e-07 TCTCTGAACA CAGTTCACATCATCCACCACC ATCGCCATC 9051 365 5.07e-07 ACGCCGTGCG CGATCTTGCTCCTCACTCTCC TCGACCTCCA 14147 81 5.97e-07 CTTGAAGTCC CAATCCTTTTCCTCCGACAAT TTGTTTGTCT 5502 451 7.01e-07 TGACTTCTGG GGTTCCTCTTCCTCTGGTTGC CGGGGAGTCC 2345 472 7.59e-07 TACAAACATC ACATCCTCATCATCGGTCAGC CAGCAATA 10183 446 8.88e-07 TTTGACGCCC CGATCTACCTCCTCTCGCCTC CAATACAACG 263365 414 1.04e-06 GATATGACAG CCGGCGTCGTCCACTCTCTAC TTCCGCTACA 261451 28 1.04e-06 CGTACGTGGA GATTCCTCCTCCTCCTCATTC TACTATGAAC 11474 282 3.70e-06 ACTTTTATTA GAGTTGTCTTCGTTTAACAAC TTACTACACT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36669 2e-10 226_[+2]_253 270206 2e-10 460_[+2]_19 1634 4.1e-09 39_[+2]_440 6015 1.2e-07 460_[+2]_19 2270 1.8e-07 332_[+2]_147 25488 2.1e-07 270_[+2]_209 11146 2.6e-07 452_[+2]_27 2597 2.8e-07 468_[+2]_11 5186 3.9e-07 470_[+2]_9 9051 5.1e-07 364_[+2]_115 14147 6e-07 80_[+2]_399 5502 7e-07 450_[+2]_29 2345 7.6e-07 471_[+2]_8 10183 8.9e-07 445_[+2]_34 263365 1e-06 413_[+2]_66 261451 1e-06 27_[+2]_452 11474 3.7e-06 281_[+2]_198 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=17 36669 ( 227) CCGTCCTCCACCTCCCCCAAC 1 270206 ( 461) CCGTCCTCCACCTCCCCCAAC 1 1634 ( 40) CAGTGCTCTTCCTCCGTCAGC 1 6015 ( 461) CGGTCGTCGTCGTCCGTCGTC 1 2270 ( 333) CGGTCGTCTTCGTTGGCCTTC 1 25488 ( 271) CCTTCCTCCTCCCTTCCCTGC 1 11146 ( 453) CTGTCGTCATCATCACGCAAC 1 2597 ( 469) CATTCCAGTTCCTCCAACACC 1 5186 ( 471) CAGTTCACATCATCCACCACC 1 9051 ( 365) CGATCTTGCTCCTCACTCTCC 1 14147 ( 81) CAATCCTTTTCCTCCGACAAT 1 5502 ( 451) GGTTCCTCTTCCTCTGGTTGC 1 2345 ( 472) ACATCCTCATCATCGGTCAGC 1 10183 ( 446) CGATCTACCTCCTCTCGCCTC 1 263365 ( 414) CCGGCGTCGTCCACTCTCTAC 1 261451 ( 28) GATTCCTCCTCCTCCTCATTC 1 11474 ( 282) GAGTTGTCTTCGTTTAACAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 24960 bayes= 11.314 E= 1.2e-003 -213 174 -40 -1073 45 36 34 -225 -13 -1073 119 -25 -1073 -1073 -198 175 -1073 185 -198 -125 -1073 136 34 -125 -55 -1073 -1073 156 -1073 185 -98 -225 -55 62 -98 33 -113 -1073 -1073 166 -1073 213 -1073 -1073 -55 150 -40 -1073 -213 -196 -1073 166 -1073 185 -1073 -66 -113 104 -98 7 -55 85 60 -225 -55 62 -40 7 -213 195 -1073 -225 103 -196 -198 33 45 -38 2 -25 -1073 204 -1073 -225 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 17 E= 1.2e-003 0.058824 0.764706 0.176471 0.000000 0.352941 0.294118 0.294118 0.058824 0.235294 0.000000 0.529412 0.235294 0.000000 0.000000 0.058824 0.941176 0.000000 0.823529 0.058824 0.117647 0.000000 0.588235 0.294118 0.117647 0.176471 0.000000 0.000000 0.823529 0.000000 0.823529 0.117647 0.058824 0.176471 0.352941 0.117647 0.352941 0.117647 0.000000 0.000000 0.882353 0.000000 1.000000 0.000000 0.000000 0.176471 0.647059 0.176471 0.000000 0.058824 0.058824 0.000000 0.882353 0.000000 0.823529 0.000000 0.176471 0.117647 0.470588 0.117647 0.294118 0.176471 0.411765 0.352941 0.058824 0.176471 0.352941 0.176471 0.294118 0.058824 0.882353 0.000000 0.058824 0.529412 0.058824 0.058824 0.352941 0.352941 0.176471 0.235294 0.235294 0.000000 0.941176 0.000000 0.058824 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- C[ACG][GAT]TC[CG]TC[CT]TCCTC[CT][CG][CT]C[AT][AGT]C -------------------------------------------------------------------------------- Time 45.98 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 33 llr = 344 E-value = 7.3e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :4241115225342152321: pos.-specific C :12::::1::111::1:1::: probability G a245576377243583853:9 matrix T :42242422:222311:1591 bits 2.1 * 1.9 * 1.7 * 1.5 * * Relative 1.3 * * * ** Entropy 1.1 * * * * ** (15.0 bits) 0.9 * ** ** * * ** 0.6 * * ** ** * * ** 0.4 * **** ** ******** 0.2 ** ****************** 0.0 --------------------- Multilevel GAGGGGGAGGAGAGGAGGTTG consensus TTAT TG A AGT GAAG sequence A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 6015 52 4.76e-13 TCCGATATAG GTGGGGGAGGAGAGGAGGTTG TCGCCTCCGG 261572 160 2.25e-08 GAGGAGGCAA GAGGTGGAAGTGAGGAGATTG TATCCACTAT 20584 267 4.28e-08 GTCGGCCGTG GAGAGTGAGGAGAGGTGGGTG GATGTTGGTA 30960 96 1.05e-07 TGGCCTTTTG GGCAGGGAGGAGGAGAGTTTG TAGGCTGTTG 23043 35 4.54e-07 GCGTATCGAA GAGAGGTGGGATTTGAGGGAG GGATCGTCGA 2270 282 6.55e-07 CTGGTGCTTT GGGTGGGTGAATGGGGGGTTG CTGGTTGCAA 261451 265 1.05e-06 GGCCGGGGAT GTGTTGTTGGATTTGGGGTTG GCGAATGAGT 5502 286 1.64e-06 GGTGATTGAA GTGGTTGATGTTGGGAGATTG GAGGAAGGAG 4463 95 1.64e-06 GGAAAGTCTC GTTGGGGAGAGAAGGAGATTT CTCGTGCACT 35561 185 1.64e-06 AGTGCTTGCA GTAGTGGAGGTGCAGGGCTTG GCAACGTTCA 36858 241 3.09e-06 CGTCTTCGAA GATGAGTCGGCTTGGAGGTTG GCTGTAAATG 4465 250 3.42e-06 TGTCGACGTT GACATGTTGGTAGCGAGGGTG AACTCCAAAG 2345 127 3.42e-06 GCGCCGGCCG GTTGGGTGGAGAGGGAACGTG GATGTTATCC 262553 139 4.61e-06 CAACTGCATC GTCAGGGTGGTGAGTTGGGTG ACAAATTAGT 6029 478 5.08e-06 TACCCTCCTA GATGTATAGCAAGGGAGAGTG AC 5186 47 5.08e-06 AAGTGTCAGC GACGGGGATGACATGGAGATG GATAATGATG 264013 145 6.75e-06 AGACGACGGA GGGGAGGGAGGAAGGAGATAG TGCTTGATGA 10185 236 6.75e-06 GGAGCCTAGG GAGAGGGTTGTGGTGCGGATG ATTGTGGTGC 5428 197 7.41e-06 TTGATAGACG GTGTTGGGTGGAGTGAAAGTG ACTGATGATG 5576 181 8.13e-06 GCTGTCGTTC GTTTAGTAGAAAATGAGAATG ATATCGTTGA 11146 362 8.13e-06 GAGAAGGAGC GAAGGGGAGGGCTTGAGGTTA CATCGTGTCA 6361 358 9.74e-06 CGTTTTGCTT GTTGTGGAGGAACATGGTGTG CAATCCTTCC 21585 55 9.74e-06 CACAAGTAAT GCAAGGTAGAGGAGGGGATAG GTGGACAGCC 4871 30 1.16e-05 ACGATGTGTC GACAGAAAGGCGAGGGGTGTG GTCAACGCTT 38312 101 1.38e-05 AAGCCGAAAA GAAGGTTGGAAGGGTCGGTTG TCGGTTTCTG 2597 142 2.11e-05 CGCGGTTGTG GCGATGGTAGAGAGGAAGTTT CTCCTATGAA 22208 20 2.47e-05 GATATGAGAT GTAATGGGTGATGAAGGAGTG AATGCAAGCG 4070 240 2.68e-05 GTCACAAAGT GAAGTGTGGAAATGATGGATG AGTTGAATGA 21957 357 3.38e-05 ACATGGTCGC GTCGTTAGAAAGAAGGGGTTG GCAGTTGGCG 5504 281 4.24e-05 TGAGCGTCTC GGGATAGCGGAGTTGAAGTAG ACACGTTTAA 14147 354 4.24e-05 TTTTGAACTT GGTTGTTGTGAATTGAAGTTG AACCTATGGT 11474 63 6.53e-05 GACTAGGGCC GATGCATAGGCGAAGAGTATG ACGCTATTGT 39754 362 7.50e-05 CTATCGGGCT GAAAAGGGAGCACGGGACGTG GCTTTTTGTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6015 4.8e-13 51_[+3]_428 261572 2.3e-08 159_[+3]_320 20584 4.3e-08 266_[+3]_213 30960 1e-07 95_[+3]_384 23043 4.5e-07 34_[+3]_445 2270 6.6e-07 281_[+3]_198 261451 1e-06 264_[+3]_215 5502 1.6e-06 285_[+3]_194 4463 1.6e-06 94_[+3]_385 35561 1.6e-06 184_[+3]_295 36858 3.1e-06 240_[+3]_239 4465 3.4e-06 249_[+3]_230 2345 3.4e-06 126_[+3]_353 262553 4.6e-06 138_[+3]_341 6029 5.1e-06 477_[+3]_2 5186 5.1e-06 46_[+3]_433 264013 6.8e-06 144_[+3]_335 10185 6.8e-06 235_[+3]_244 5428 7.4e-06 196_[+3]_283 5576 8.1e-06 180_[+3]_299 11146 8.1e-06 361_[+3]_118 6361 9.7e-06 357_[+3]_122 21585 9.7e-06 54_[+3]_425 4871 1.2e-05 29_[+3]_450 38312 1.4e-05 100_[+3]_379 2597 2.1e-05 141_[+3]_338 22208 2.5e-05 19_[+3]_460 4070 2.7e-05 239_[+3]_240 21957 3.4e-05 356_[+3]_123 5504 4.2e-05 280_[+3]_199 14147 4.2e-05 353_[+3]_126 11474 6.5e-05 62_[+3]_417 39754 7.5e-05 361_[+3]_118 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=33 6015 ( 52) GTGGGGGAGGAGAGGAGGTTG 1 261572 ( 160) GAGGTGGAAGTGAGGAGATTG 1 20584 ( 267) GAGAGTGAGGAGAGGTGGGTG 1 30960 ( 96) GGCAGGGAGGAGGAGAGTTTG 1 23043 ( 35) GAGAGGTGGGATTTGAGGGAG 1 2270 ( 282) GGGTGGGTGAATGGGGGGTTG 1 261451 ( 265) GTGTTGTTGGATTTGGGGTTG 1 5502 ( 286) GTGGTTGATGTTGGGAGATTG 1 4463 ( 95) GTTGGGGAGAGAAGGAGATTT 1 35561 ( 185) GTAGTGGAGGTGCAGGGCTTG 1 36858 ( 241) GATGAGTCGGCTTGGAGGTTG 1 4465 ( 250) GACATGTTGGTAGCGAGGGTG 1 2345 ( 127) GTTGGGTGGAGAGGGAACGTG 1 262553 ( 139) GTCAGGGTGGTGAGTTGGGTG 1 6029 ( 478) GATGTATAGCAAGGGAGAGTG 1 5186 ( 47) GACGGGGATGACATGGAGATG 1 264013 ( 145) GGGGAGGGAGGAAGGAGATAG 1 10185 ( 236) GAGAGGGTTGTGGTGCGGATG 1 5428 ( 197) GTGTTGGGTGGAGTGAAAGTG 1 5576 ( 181) GTTTAGTAGAAAATGAGAATG 1 11146 ( 362) GAAGGGGAGGGCTTGAGGTTA 1 6361 ( 358) GTTGTGGAGGAACATGGTGTG 1 21585 ( 55) GCAAGGTAGAGGAGGGGATAG 1 4871 ( 30) GACAGAAAGGCGAGGGGTGTG 1 38312 ( 101) GAAGGTTGGAAGGGTCGGTTG 1 2597 ( 142) GCGATGGTAGAGAGGAAGTTT 1 22208 ( 20) GTAATGGGTGATGAAGGAGTG 1 4070 ( 240) GAAGTGTGGAAATGATGGATG 1 21957 ( 357) GTCGTTAGAAAGAAGGGGTTG 1 5504 ( 281) GGGATAGCGGAGTTGAAGTAG 1 14147 ( 354) GGTTGTTGTGAATTGAAGTTG 1 11474 ( 63) GATGCATAGGCGAAGAGTATG 1 39754 ( 362) GAAAAGGGAGCACGGGACGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 24960 bayes= 10.3282 E= 7.3e-003 -1169 -1169 210 -1169 72 -192 -62 38 -28 -33 64 -21 49 -1169 106 -88 -109 -292 97 49 -109 -1169 164 -88 -209 -1169 131 38 81 -192 38 -62 -77 -1169 152 -62 -9 -292 164 -1169 100 -92 -36 -62 37 -192 87 -62 61 -133 38 -40 -51 -292 115 -4 -209 -1169 187 -162 108 -192 38 -162 -28 -1169 176 -1169 8 -133 115 -121 -77 -1169 52 88 -109 -1169 -1169 165 -309 -1169 197 -221 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 33 E= 7.3e-003 0.000000 0.000000 1.000000 0.000000 0.424242 0.060606 0.151515 0.363636 0.212121 0.181818 0.363636 0.242424 0.363636 0.000000 0.484848 0.151515 0.121212 0.030303 0.454545 0.393939 0.121212 0.000000 0.727273 0.151515 0.060606 0.000000 0.575758 0.363636 0.454545 0.060606 0.303030 0.181818 0.151515 0.000000 0.666667 0.181818 0.242424 0.030303 0.727273 0.000000 0.515152 0.121212 0.181818 0.181818 0.333333 0.060606 0.424242 0.181818 0.393939 0.090909 0.303030 0.212121 0.181818 0.030303 0.515152 0.272727 0.060606 0.000000 0.848485 0.090909 0.545455 0.060606 0.303030 0.090909 0.212121 0.000000 0.787879 0.000000 0.272727 0.090909 0.515152 0.121212 0.151515 0.000000 0.333333 0.515152 0.121212 0.000000 0.000000 0.878788 0.030303 0.000000 0.909091 0.060606 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[AT][GTA][GA][GT]G[GT][AG]G[GA]A[GA][AGT][GT]G[AG][GA][GA][TG]TG -------------------------------------------------------------------------------- Time 67.24 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10183 5.17e-06 445_[+2(8.88e-07)]_4_[+1(2.12e-07)]_\ 9 10185 2.28e-04 31_[+1(4.03e-06)]_137_\ [+3(4.24e-05)]_25_[+3(6.75e-06)]_244 11146 1.16e-05 361_[+3(8.13e-06)]_70_\ [+2(2.55e-07)]_27 11474 1.41e-05 62_[+3(6.53e-05)]_198_\ [+2(3.70e-06)]_83_[+1(3.64e-06)]_94 14147 2.69e-04 80_[+2(5.97e-07)]_252_\ [+3(4.24e-05)]_126 1634 1.87e-07 39_[+2(4.09e-09)]_13_[+2(9.83e-06)]_\ 302_[+1(1.23e-06)]_83 20584 2.82e-05 266_[+3(4.28e-08)]_141_\ [+1(2.52e-05)]_51 21585 6.73e-04 54_[+3(9.74e-06)]_178_\ [+1(8.78e-06)]_226 21957 5.18e-05 246_[+1(4.12e-07)]_89_\ [+3(3.38e-05)]_123 22208 6.25e-05 19_[+3(2.47e-05)]_378_\ [+1(1.38e-06)]_61 22372 1.00e-01 473_[+1(6.41e-05)]_6 2270 5.17e-11 32_[+1(5.95e-05)]_56_[+1(2.52e-05)]_\ 151_[+3(6.55e-07)]_30_[+2(1.78e-07)]_124_[+1(8.43e-09)]_2 23043 4.92e-06 34_[+3(4.54e-07)]_66_[+1(9.83e-05)]_\ 18_[+1(1.23e-06)]_319 2345 1.02e-07 126_[+3(3.42e-06)]_264_\ [+1(1.38e-06)]_39_[+2(7.59e-07)]_8 23953 4.14e-03 471_[+1(6.01e-07)]_8 25488 1.47e-04 124_[+1(3.77e-05)]_125_\ [+2(2.13e-07)]_209 2597 2.32e-06 87_[+3(7.50e-05)]_33_[+3(2.11e-05)]_\ 81_[+1(1.96e-05)]_204_[+2(2.79e-07)]_11 261451 5.57e-09 27_[+2(1.04e-06)]_216_\ [+3(1.05e-06)]_177_[+1(1.39e-07)]_17 261572 6.17e-07 120_[+3(6.09e-05)]_18_\ [+3(2.25e-08)]_268_[+1(7.68e-07)]_31 262553 1.15e-04 138_[+3(4.61e-06)]_137_\ [+1(4.03e-06)]_183 263365 4.39e-05 383_[+1(1.72e-06)]_9_[+2(1.04e-06)]_\ 66 264013 3.21e-04 1_[+1(9.64e-06)]_122_[+3(6.75e-06)]_\ 335 264603 3.85e-02 270_[+1(2.52e-05)]_209 267963 1.99e-02 103_[+1(7.27e-06)]_376 270206 1.45e-06 460_[+2(2.03e-10)]_19 27048 1.34e-01 40_[+1(3.77e-05)]_439 30960 1.80e-05 95_[+3(1.05e-07)]_63_[+3(4.24e-05)]_\ 146_[+1(1.51e-05)]_133 35561 1.17e-02 184_[+3(1.64e-06)]_295 36669 2.75e-08 226_[+2(2.03e-10)]_149_\ [+1(6.00e-06)]_20_[+2(2.43e-05)]_42 36858 8.10e-04 240_[+3(3.09e-06)]_148_\ [+1(1.65e-05)]_70 38312 2.96e-03 69_[+3(9.80e-05)]_10_[+3(1.38e-05)]_\ 57_[+1(2.13e-05)]_301 39754 2.46e-01 361_[+3(7.50e-05)]_118 4070 3.00e-03 239_[+3(2.68e-05)]_92_\ [+1(1.06e-05)]_127 4463 3.39e-04 94_[+3(1.64e-06)]_123_\ [+3(5.28e-05)]_53_[+3(4.24e-05)]_132_[+1(3.21e-05)]_14 4465 5.91e-07 249_[+3(3.42e-06)]_199_\ [+1(2.50e-08)]_10 4871 2.21e-02 29_[+3(1.16e-05)]_450 5186 6.49e-08 46_[+3(5.08e-06)]_290_\ [+1(1.10e-06)]_92_[+2(3.94e-07)]_9 5220 9.08e-02 138_[+1(4.40e-05)]_341 5428 5.35e-06 196_[+3(7.41e-06)]_206_\ [+1(6.01e-07)]_56 5502 2.55e-05 285_[+3(1.64e-06)]_144_\ [+2(7.01e-07)]_29 5504 3.23e-03 258_[+1(2.73e-05)]_1_[+3(4.24e-05)]_\ 199 5576 1.31e-05 180_[+3(8.13e-06)]_262_\ [+1(1.39e-07)]_16 6015 3.82e-17 51_[+3(4.76e-13)]_45_[+1(5.68e-09)]_\ 57_[+1(5.53e-05)]_74_[+2(2.20e-05)]_149_[+2(1.22e-07)]_19 6029 2.30e-04 120_[+1(5.44e-06)]_336_\ [+3(5.08e-06)]_2 6361 3.40e-03 299_[+1(2.96e-05)]_37_\ [+3(9.74e-06)]_122 7695 4.44e-02 460_[+1(2.52e-05)]_19 9051 1.18e-04 336_[+1(4.75e-05)]_7_[+2(5.07e-07)]_\ 115 9087 7.70e-01 500 9878 5.47e-01 500 9903 2.50e-01 500 bd308 9.77e-01 500 ThpsCp022 9.77e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************