******************************************************************************** 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/199/199.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 11068 1.0000 500 14140 1.0000 500 1845 1.0000 500 21126 1.0000 500 2160 1.0000 500 21911 1.0000 500 23857 1.0000 500 24318 1.0000 500 24495 1.0000 500 24527 1.0000 500 24560 1.0000 500 25128 1.0000 500 25320 1.0000 500 26224 1.0000 500 262525 1.0000 500 262751 1.0000 500 264377 1.0000 500 26706 1.0000 500 267922 1.0000 500 26868 1.0000 500 269593 1.0000 500 30075 1.0000 500 32037 1.0000 500 33649 1.0000 500 33725 1.0000 500 33777 1.0000 500 34219 1.0000 500 3649 1.0000 500 37367 1.0000 500 37861 1.0000 500 38129 1.0000 500 38945 1.0000 500 38948 1.0000 500 39157 1.0000 500 40483 1.0000 500 40962 1.0000 500 4318 1.0000 500 516 1.0000 500 5452 1.0000 500 5699 1.0000 500 7964 1.0000 500 8292 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/199/199.seqs.fa -oc motifs/199 -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= 42 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= 21000 N= 42 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.260 C 0.232 G 0.244 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.260 C 0.232 G 0.244 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 35 llr = 384 E-value = 2.7e-019 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4442:45:46:14422316:1 pos.-specific C 6417913a:3a3456357366 probability G :13::62:5::6111212:12 matrix T :1111:1:11:::1:21:231 bits 2.1 * * 1.9 * * 1.7 * * 1.5 * * * Relative 1.3 * * * Entropy 1.1 * ** * * (15.8 bits) 0.8 * *** * ** * * 0.6 * *** ***** * **** 0.4 ** *** ******** **** 0.2 *************** ***** 0.0 --------------------- Multilevel CAACCGACGACGACCCCCACC consensus ACGA AC AC CCAAGAGCTG sequence T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 26868 463 1.70e-09 ATTTCGACGA CAGCCGACGACGACCGCAACC CCCCTACCTA 33725 319 6.81e-09 TTCGAAACGA CGACCGACGACGCCGTCCACC TCTCACAGCC 37367 389 1.39e-08 ACAAGCACAT CAACCAGCAACGCCCCTCACC CATCACGGTT 5699 438 2.09e-07 ACACCATTCG ACACCGACGTCGAACAGCACC GACGGAGGAC 11068 429 2.38e-07 CCCCAACCAT ACGCCACCGACCAACCACAGC AACAACTCCT 7964 18 3.08e-07 CGGCTCACTT CGGCCGACGACGACCTTCTCG ACGAGCAGAG 24318 426 3.08e-07 CGGACGCAAC AAGACGACGACGACCCCGCTG CTCCATACAA 30075 103 3.95e-07 GCCATCTTCA CCACCGGCACCGACCGGCAGC AGTAGCTCCA 24527 432 3.95e-07 GAAACCACCG CCACCACCACCACCACACACC TGCCCCAGCA 14140 468 4.46e-07 CTGTGTCAGG CACCCGCCACCCCTCTCCATC ACATCCACCA 267922 440 5.03e-07 AACCGAAGCG CGACCGACGACGCCCGAGCCT TCCGACGCTC 262525 462 5.67e-07 ATCTGCAACA CCAACAGCAACGCAACACCCC AAACAAAGAA 26706 450 7.16e-07 CCTTCGAACA CAGCCGACGCCCGACGAGACG GACCCCAAGA 3649 421 8.99e-07 GAACGTTAAC ACACCATCACCGCACTCCTTC CAGCCGCTTC 32037 435 1.55e-06 CGAGACGTTC AGCCCGACAACCAACCCCTCT CTCTCCTCAA 38129 300 1.72e-06 CGCTACCTAC CCTCCACCGACGCCAAACACA CTACATTCAG 40483 430 1.91e-06 TTTCGATCAA CGTCCGTCGTCGGCCACCACC TGCAACGACC 264377 413 2.11e-06 CCTTCCACAA CAACCGACGACGGCTTCGACG GCTCTCAAAC 25320 284 2.34e-06 CAGGGCAATG CAACTGCCAACCAACCTCCTC CCTGCCGACG 8292 433 3.46e-06 CATCGCCGGA CTACCAACGACCGACGACTTC CCCATAAGTT 5452 244 4.59e-06 TTTGGATACG CCGCTGCCGACGAAGACGACG AGCGGCGAAG 24495 382 4.59e-06 AGCTACCCGA CAGCCCACAGCCCACAACACC ACGAAGGGTA 21126 447 6.03e-06 CCGACCACCG CAGCGACCACCGACCGCGACG GCGGTGCGCT 1845 477 6.59e-06 CAATCTCTTC ATACCAACACCCCACACAATC ACC 33777 154 1.40e-05 AACGCCACAT CCGTCGGCACCGAAACCACTC AGACGTCACC 269593 351 1.64e-05 CGAGTATTGA AATACGTCAACCCCAACGACG AGCAAGAGAT 516 263 1.77e-05 TTCCATTCTC CCAACCGCAACGATCCGCCTC CATCGATCGA 40962 99 2.06e-05 CTATTGGAAG AAGACGACGACGAGGTGCACT GAATCTCCAC 38945 466 2.22e-05 ATAACTACCG AACCCATCTACCCACCTCCTC TCTCCTCCCT 38948 443 2.38e-05 GCAAAATTTG ACTCCAACGCCATCCTCCTTC CTTTTCGTCG 4318 428 2.56e-05 TATTGGAAGT AATACAACGCCGACGTCCAGT TCACCAGGCT 24560 317 2.56e-05 CTCTGTCGCT ACCCTGCCTACGCCGGCCCTC AGAGCAGAGC 34219 97 2.76e-05 GCTTCCCTTT CCGTCGACGACGAGAGCACCG CCATCATTGG 26224 478 3.64e-05 CTTCCACAAC AACACACCAACACCACACACA CA 33649 438 6.53e-05 TCCCCGCCTT CCGACGGCGTCCGTACACTTC TTCTTTTCCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 26868 1.7e-09 462_[+1]_17 33725 6.8e-09 318_[+1]_161 37367 1.4e-08 388_[+1]_91 5699 2.1e-07 437_[+1]_42 11068 2.4e-07 428_[+1]_51 7964 3.1e-07 17_[+1]_462 24318 3.1e-07 425_[+1]_54 30075 3.9e-07 102_[+1]_377 24527 3.9e-07 431_[+1]_48 14140 4.5e-07 467_[+1]_12 267922 5e-07 439_[+1]_40 262525 5.7e-07 461_[+1]_18 26706 7.2e-07 449_[+1]_30 3649 9e-07 420_[+1]_59 32037 1.5e-06 434_[+1]_45 38129 1.7e-06 299_[+1]_180 40483 1.9e-06 429_[+1]_50 264377 2.1e-06 412_[+1]_67 25320 2.3e-06 283_[+1]_196 8292 3.5e-06 432_[+1]_47 5452 4.6e-06 243_[+1]_236 24495 4.6e-06 381_[+1]_98 21126 6e-06 446_[+1]_33 1845 6.6e-06 476_[+1]_3 33777 1.4e-05 153_[+1]_326 269593 1.6e-05 350_[+1]_129 516 1.8e-05 262_[+1]_217 40962 2.1e-05 98_[+1]_381 38945 2.2e-05 465_[+1]_14 38948 2.4e-05 442_[+1]_37 4318 2.6e-05 427_[+1]_52 24560 2.6e-05 316_[+1]_163 34219 2.8e-05 96_[+1]_383 26224 3.6e-05 477_[+1]_2 33649 6.5e-05 437_[+1]_42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=35 26868 ( 463) CAGCCGACGACGACCGCAACC 1 33725 ( 319) CGACCGACGACGCCGTCCACC 1 37367 ( 389) CAACCAGCAACGCCCCTCACC 1 5699 ( 438) ACACCGACGTCGAACAGCACC 1 11068 ( 429) ACGCCACCGACCAACCACAGC 1 7964 ( 18) CGGCCGACGACGACCTTCTCG 1 24318 ( 426) AAGACGACGACGACCCCGCTG 1 30075 ( 103) CCACCGGCACCGACCGGCAGC 1 24527 ( 432) CCACCACCACCACCACACACC 1 14140 ( 468) CACCCGCCACCCCTCTCCATC 1 267922 ( 440) CGACCGACGACGCCCGAGCCT 1 262525 ( 462) CCAACAGCAACGCAACACCCC 1 26706 ( 450) CAGCCGACGCCCGACGAGACG 1 3649 ( 421) ACACCATCACCGCACTCCTTC 1 32037 ( 435) AGCCCGACAACCAACCCCTCT 1 38129 ( 300) CCTCCACCGACGCCAAACACA 1 40483 ( 430) CGTCCGTCGTCGGCCACCACC 1 264377 ( 413) CAACCGACGACGGCTTCGACG 1 25320 ( 284) CAACTGCCAACCAACCTCCTC 1 8292 ( 433) CTACCAACGACCGACGACTTC 1 5452 ( 244) CCGCTGCCGACGAAGACGACG 1 24495 ( 382) CAGCCCACAGCCCACAACACC 1 21126 ( 447) CAGCGACCACCGACCGCGACG 1 1845 ( 477) ATACCAACACCCCACACAATC 1 33777 ( 154) CCGTCGGCACCGAAACCACTC 1 269593 ( 351) AATACGTCAACCCCAACGACG 1 516 ( 263) CCAACCGCAACGATCCGCCTC 1 40962 ( 99) AAGACGACGACGAGGTGCACT 1 38945 ( 466) AACCCATCTACCCACCTCCTC 1 38948 ( 443) ACTCCAACGCCATCCTCCTTC 1 4318 ( 428) AATACAACGCCGACGTCCAGT 1 24560 ( 317) ACCCTGCCTACGCCGGCCCTC 1 34219 ( 97) CCGTCGACGACGAGAGCACCG 1 26224 ( 478) AACACACCAACACCACACACA 1 33649 ( 438) CCGACGGCGTCCGTACACTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 20160 bayes= 9.99036 E= 2.7e-019 51 144 -1177 -1177 62 79 -77 -221 51 -70 49 -88 -19 162 -1177 -221 -1177 193 -309 -162 51 -202 123 -1177 81 15 -51 -121 -1177 211 -1177 -1177 72 -1177 107 -221 120 30 -309 -162 -1177 211 -1177 -1177 -160 44 130 -1177 72 79 -77 -320 51 107 -209 -162 -19 137 -77 -320 -38 56 -10 -21 13 107 -109 -121 -119 156 -29 -1177 113 15 -1177 -62 -1177 130 -151 38 -219 137 -10 -121 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 35 E= 2.7e-019 0.371429 0.628571 0.000000 0.000000 0.400000 0.400000 0.142857 0.057143 0.371429 0.142857 0.342857 0.142857 0.228571 0.714286 0.000000 0.057143 0.000000 0.885714 0.028571 0.085714 0.371429 0.057143 0.571429 0.000000 0.457143 0.257143 0.171429 0.114286 0.000000 1.000000 0.000000 0.000000 0.428571 0.000000 0.514286 0.057143 0.600000 0.285714 0.028571 0.085714 0.000000 1.000000 0.000000 0.000000 0.085714 0.314286 0.600000 0.000000 0.428571 0.400000 0.142857 0.028571 0.371429 0.485714 0.057143 0.085714 0.228571 0.600000 0.142857 0.028571 0.200000 0.342857 0.228571 0.228571 0.285714 0.485714 0.114286 0.114286 0.114286 0.685714 0.200000 0.000000 0.571429 0.257143 0.000000 0.171429 0.000000 0.571429 0.085714 0.342857 0.057143 0.600000 0.228571 0.114286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA][AC][AG][CA]C[GA][AC]C[GA][AC]C[GC][AC][CA][CA][CGTA][CA][CG][AC][CT][CG] -------------------------------------------------------------------------------- Time 14.64 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 32 llr = 319 E-value = 6.2e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :3::1::::::131:1 pos.-specific C 111::112::1:2:1: probability G 9::9545624772338 matrix T :791554286324661 bits 2.1 1.9 1.7 * 1.5 * ** Relative 1.3 * ** * Entropy 1.1 * ** ** (14.4 bits) 0.8 **** **** * 0.6 ************ *** 0.4 ************ *** 0.2 ************ *** 0.0 ---------------- Multilevel GTTGGTGGTTGGTTTG consensus A TGT GT AGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 21911 130 1.28e-08 GTTGACTTGA GTTGGGGGTTGGTTGG TTGTCATGGA 25128 243 8.67e-08 GGCAAGATTT GTTGTGTGTTTGTTTG GTGTATCAGA 30075 341 1.21e-07 TGTGGCGAAG GTTGGGTGTGGGGGTG TTTGAATTTT 40962 215 5.55e-07 GTGCATTTAG GTTGGTTGTGCGTTTG GCTGAATCTA 8292 59 6.35e-07 GTGGAGAGAG GTTGATGGTTGGATGG CCACGGAGAC 1845 271 8.26e-07 GCGTTATTCT GTTGTTTGTTGGAGTT GGAGGGGACG 25320 41 9.38e-07 AGAAGCTTTT GTTGGTGGTTGGCTGA GTGAAGGCAG 23857 170 1.36e-06 ATTGTGTACT GTCGGTGGGTGGTTTG GAGGCCTTTC 267922 242 1.94e-06 GTCGTAAAGA GATGAGGGTTGGTTGG GAGACGTTTT 7964 138 6.34e-06 TGGTGCCGGC GTTGGGGCGTGGCGGG TTGTCCAACG 4318 177 6.34e-06 CGGAGGAGGC CATGGTGGTTTGTGTG GAGGAGGAGA 24527 240 7.00e-06 AAGTGGTTTG GTTTTGCGTGGGCTTG TAGCCCGATC 14140 32 7.00e-06 GCTCATTTGT GCTGTGGGTTTGCGTG GCTACAAATG 33725 53 7.72e-06 ACTCAGCTCC GTCGGTGGTGGTGGTG GTGAGCCCGA 21126 24 7.72e-06 AGCTCCCAGT CATGTTGCTGGGATTG GTTGGAGGAC 33649 248 8.49e-06 TGTTTGAGTT GTTGTTGTTGGTATCG CTCATGGTGA 32037 209 9.33e-06 CATTGTGAAT GTTGGTGGTGTTTGTT AGATGGCTGT 24318 22 1.02e-05 AGAATGGGGA GTTGTGGTTGTGTGTT CTTGGATAGA 5699 192 1.23e-05 TGATGGTGGT GATGGTGGTGGTGATG GTGCTTTGAA 26868 187 1.23e-05 CATTGCCTCT GTTGTCCGTTGGATCG TATTAGCATA 269593 223 1.34e-05 GTATCAATCA GTTGTTGATTGAATTG GAATCGTTGA 2160 126 1.90e-05 TTTGATACGT GATGTGTTTGTGTTCG GAAATGATGA 37861 29 2.25e-05 GGTGTGCCGT GTTGGTTCGTGGACTG TTGTTGAAGC 39157 280 2.44e-05 CAATACCCCA GTTGTTCGTTGGGATA TCGGACAGTG 3649 63 2.64e-05 GTCGTCGTCT GATTTGTCTTTGTTTG CAGCGTTCAT 33777 407 2.64e-05 CTTCTTTTCG GTTGGTTCTGCTTTGG ACCTCTCCCT 34219 428 3.35e-05 TGGGGTGAGT GTCGGCTGTTGGATTA TGCAATTGCA 262751 6 3.35e-05 GGTAG CTTGTTTGGTGGTTGT CAACATTGTT 262525 83 5.23e-05 GGTGTTCTGA GCTTTTTGTGTGAGTG CAGATGACGC 5452 388 6.01e-05 GAGATTCTGC GATGGGCTTTGACTGG TGACGGAACA 40483 318 6.90e-05 GTTCCAACGT GTTGTGTTGGGTGTTA CGTGCTGCCG 38948 4 9.57e-05 GGA GATGGGGTGGGAGGGG TGATTGGGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 21911 1.3e-08 129_[+2]_355 25128 8.7e-08 242_[+2]_242 30075 1.2e-07 340_[+2]_144 40962 5.6e-07 214_[+2]_270 8292 6.4e-07 58_[+2]_426 1845 8.3e-07 270_[+2]_214 25320 9.4e-07 40_[+2]_444 23857 1.4e-06 169_[+2]_315 267922 1.9e-06 241_[+2]_243 7964 6.3e-06 137_[+2]_347 4318 6.3e-06 176_[+2]_308 24527 7e-06 239_[+2]_245 14140 7e-06 31_[+2]_453 33725 7.7e-06 52_[+2]_432 21126 7.7e-06 23_[+2]_461 33649 8.5e-06 247_[+2]_237 32037 9.3e-06 208_[+2]_276 24318 1e-05 21_[+2]_463 5699 1.2e-05 191_[+2]_293 26868 1.2e-05 186_[+2]_298 269593 1.3e-05 222_[+2]_262 2160 1.9e-05 125_[+2]_359 37861 2.2e-05 28_[+2]_456 39157 2.4e-05 279_[+2]_205 3649 2.6e-05 62_[+2]_422 33777 2.6e-05 406_[+2]_78 34219 3.3e-05 427_[+2]_57 262751 3.3e-05 5_[+2]_479 262525 5.2e-05 82_[+2]_402 5452 6e-05 387_[+2]_97 40483 6.9e-05 317_[+2]_167 38948 9.6e-05 3_[+2]_481 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=32 21911 ( 130) GTTGGGGGTTGGTTGG 1 25128 ( 243) GTTGTGTGTTTGTTTG 1 30075 ( 341) GTTGGGTGTGGGGGTG 1 40962 ( 215) GTTGGTTGTGCGTTTG 1 8292 ( 59) GTTGATGGTTGGATGG 1 1845 ( 271) GTTGTTTGTTGGAGTT 1 25320 ( 41) GTTGGTGGTTGGCTGA 1 23857 ( 170) GTCGGTGGGTGGTTTG 1 267922 ( 242) GATGAGGGTTGGTTGG 1 7964 ( 138) GTTGGGGCGTGGCGGG 1 4318 ( 177) CATGGTGGTTTGTGTG 1 24527 ( 240) GTTTTGCGTGGGCTTG 1 14140 ( 32) GCTGTGGGTTTGCGTG 1 33725 ( 53) GTCGGTGGTGGTGGTG 1 21126 ( 24) CATGTTGCTGGGATTG 1 33649 ( 248) GTTGTTGTTGGTATCG 1 32037 ( 209) GTTGGTGGTGTTTGTT 1 24318 ( 22) GTTGTGGTTGTGTGTT 1 5699 ( 192) GATGGTGGTGGTGATG 1 26868 ( 187) GTTGTCCGTTGGATCG 1 269593 ( 223) GTTGTTGATTGAATTG 1 2160 ( 126) GATGTGTTTGTGTTCG 1 37861 ( 29) GTTGGTTCGTGGACTG 1 39157 ( 280) GTTGTTCGTTGGGATA 1 3649 ( 63) GATTTGTCTTTGTTTG 1 33777 ( 407) GTTGGTTCTGCTTTGG 1 34219 ( 428) GTCGGCTGTTGGATTA 1 262751 ( 6) CTTGTTTGGTGGTTGT 1 262525 ( 83) GCTTTTTGTGTGAGTG 1 5452 ( 388) GATGGGCTTTGACTGG 1 40483 ( 318) GTTGTGTTGGGTGTTA 1 38948 ( 4) GATGGGGTGGGAGGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 20370 bayes= 10.6352 E= 6.2e-008 -1164 -131 189 -1164 -6 -189 -1164 138 -1164 -131 -1164 178 -1164 -1164 189 -149 -206 -1164 94 83 -1164 -189 73 101 -1164 -89 103 51 -305 -57 136 -49 -1164 -1164 -38 162 -1164 -1164 84 109 -1164 -189 149 -8 -147 -1164 156 -49 11 -57 -38 51 -206 -289 36 117 -1164 -131 20 124 -106 -1164 162 -108 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 32 E= 6.2e-008 0.000000 0.093750 0.906250 0.000000 0.250000 0.062500 0.000000 0.687500 0.000000 0.093750 0.000000 0.906250 0.000000 0.000000 0.906250 0.093750 0.062500 0.000000 0.468750 0.468750 0.000000 0.062500 0.406250 0.531250 0.000000 0.125000 0.500000 0.375000 0.031250 0.156250 0.625000 0.187500 0.000000 0.000000 0.187500 0.812500 0.000000 0.000000 0.437500 0.562500 0.000000 0.062500 0.687500 0.250000 0.093750 0.000000 0.718750 0.187500 0.281250 0.156250 0.187500 0.375000 0.062500 0.031250 0.312500 0.593750 0.000000 0.093750 0.281250 0.625000 0.125000 0.000000 0.750000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[TA]TG[GT][TG][GT]GT[TG][GT]G[TA][TG][TG]G -------------------------------------------------------------------------------- Time 28.78 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 41 llr = 376 E-value = 6.5e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :6:482:a2425:7226:51 pos.-specific C 1:2::1::::121:1112:2 probability G 7:66249:655171261525 matrix T 141::2::111211411323 bits 2.1 1.9 * 1.7 ** 1.5 ** Relative 1.3 * ** Entropy 1.1 * ** (13.2 bits) 0.8 ** ** ** ** 0.6 ***** **** ** * 0.4 ***** **** ** * ** 0.2 ************** ***** 0.0 -------------------- Multilevel GAGGAGGAGGGAGATGAGAG consensus TCA T AA AA TTT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 262751 173 3.86e-10 GGCCGTGGAT GAGAATGAGAGAGAGGAGAG AGCGATGATC 21126 47 4.63e-08 TTGGTTGGAG GACGATGAGTGAGAGGAGAG CGCCATGGTT 33649 297 2.20e-07 GAGGACGAGA GACGACGAGAGTGAAGGGAG CAACTGGTGT 26706 225 2.20e-07 GGGAAGTGTG GAGAGGGAGAGAGGTGTGAG TCCCAGCTGA 30075 295 2.94e-07 CGGTGGGTGG TTGGAGGAGGGAGAAGAGCG TCATCGTCGG 267922 113 5.89e-07 TGGAATGTTT CAGGAGGAGAGTGATCAGAC TGGCCCTTCG 37367 127 1.13e-06 AGGCCACGGC GAGGAGGAAGGCGGCGAGTT TCATCATCGT 4318 193 2.11e-06 GGTTTGTGTG GAGGAGGAGAGAGTCTCGAT CCCCGTCTGG 38129 123 2.11e-06 CGCCACGGCA GAGAGAGAAAAAGAAGAGAC TTCGTTCCGG 24527 180 2.68e-06 GCCACCTCAT GTTGACGAGAGAGATAAGCG ACGACGACGA 23857 99 3.01e-06 TGTTGATGCC GATGAGGAGGTAGATGGCGT TTAGAGCCTG 38945 233 3.38e-06 ATACTTCATG TTGGATGAGAGAGATGTTGT TCAGCGGCGA 24318 240 5.31e-06 GAGTAGTCAG CTGAGAGAGAGAGAAAATAG GTCGGTGTTG 516 44 6.60e-06 AACACGACGG GAGAGAGAGCGCGATGCGAG AGCGAGGTTG 269593 396 6.60e-06 CATCCATTGA GAGAACGAGGGCAACAAGAT CGACAGTACC 8292 37 7.35e-06 CGGTCGGTGA GATGAAGATGGGGTGGAGAG AGGTTGATGG 3649 220 9.09e-06 CCACGTAAGG CAGGAGGAGGGAAATATTAT TTATTTCGAG 7964 204 1.24e-05 GTTGTGTGAT TTGGAGGATGGTGATGTTGG TCTCTCGTCT 262525 1 1.24e-05 . GAGGAAGAGGTTGATTATTA GGAATGCAAT 33777 234 1.37e-05 GTTGGTTAAA GTAGAGGAAAGTGAGGTGTG TGATGCGATC 1845 107 1.37e-05 GATGAAAGCT GTGGACGAAGAGCATGAGTT TGGTGTATGA 26868 69 1.84e-05 TGAGGATTGT GAGTATGAAGCAGATGATGG ATGTCAGAAT 39157 192 2.23e-05 AAGAGAAGGA CTGGAAGAGGTCGTCGACAG CCCACGGCTT 32037 316 2.23e-05 TGTCGGTCAA GAGGAGGAGAAGGGCACTTG TCCCTGTCAT 40483 187 2.70e-05 AGTTTGTAGC GAGAAGAAGGATGAAGGCTG GGATGATGGA 21911 37 2.96e-05 GAAGTTTAAG GAGAAGGATGTATTGGAGTT GATAAAGGGA 264377 237 3.89e-05 TGAAAGTGCT GTCGAGGACGAAGAGACGTT GTAGTTGAGG 34219 368 5.53e-05 GAAATCGCTG GAGAGTGAAGCCGAGGCCAT TGTCTCAGAG 33725 157 5.53e-05 CCTAGCGGTA GAGGAGCAGTACCAAGAGAG AAGGTGTTCG 24495 316 5.53e-05 TGGATGCCGT GGCAAGGAGGGCTAGGAGGC TGATTGGGCT 11068 105 5.53e-05 ATTGCGAGCC GTTGACGAGGGAGAAAGTGA AAGGCTGAGT 25320 199 8.41e-05 TAAAATGTCA TTGAAGGAGGGAGCAAAGTA ATTTACAAAA 5452 284 1.16e-04 GTGAGACGAA GTCAGTGAAAAAGATTGCAG ACAGCGGCTA 40962 404 1.25e-04 GCTCGAAATG GACGATGAGACGTATCCCAG ATGTGTCCAG 26224 78 1.25e-04 CACTGCCAAA GTAGATGACGAATATGATAC AATGAGGAAA 38948 401 1.46e-04 AGTGTGTAAC GACAAAGATATGGTCGATAC AACGGCATCA 14140 64 1.83e-04 AATGCCAAGA TATGACGAGAGACAATTGAT CACGAATGCC 25128 291 2.44e-04 GAGATTATGA CACAAAGAGAAGTGTAACAG TTGTCGTGTT 24560 182 2.44e-04 CTCTCTGGGT GACAAGAAAATAGGGGATAA CGTAGTGATA 5699 150 3.00e-04 GCTTGTGGAT GTGAGTGATTGTGATGGTGC TGCTGCTGCT 2160 241 3.00e-04 GATCCTTGTA CTGAAGGAGACCCATCACTC AATACTGTGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 262751 3.9e-10 172_[+3]_308 21126 4.6e-08 46_[+3]_434 33649 2.2e-07 296_[+3]_184 26706 2.2e-07 224_[+3]_256 30075 2.9e-07 294_[+3]_186 267922 5.9e-07 112_[+3]_368 37367 1.1e-06 126_[+3]_354 4318 2.1e-06 192_[+3]_288 38129 2.1e-06 122_[+3]_358 24527 2.7e-06 179_[+3]_301 23857 3e-06 98_[+3]_382 38945 3.4e-06 232_[+3]_248 24318 5.3e-06 239_[+3]_241 516 6.6e-06 43_[+3]_437 269593 6.6e-06 395_[+3]_85 8292 7.4e-06 36_[+3]_444 3649 9.1e-06 219_[+3]_261 7964 1.2e-05 203_[+3]_277 262525 1.2e-05 [+3]_480 33777 1.4e-05 233_[+3]_247 1845 1.4e-05 106_[+3]_374 26868 1.8e-05 68_[+3]_412 39157 2.2e-05 191_[+3]_289 32037 2.2e-05 315_[+3]_165 40483 2.7e-05 186_[+3]_294 21911 3e-05 36_[+3]_444 264377 3.9e-05 236_[+3]_244 34219 5.5e-05 367_[+3]_113 33725 5.5e-05 156_[+3]_324 24495 5.5e-05 315_[+3]_165 11068 5.5e-05 104_[+3]_376 25320 8.4e-05 198_[+3]_282 5452 0.00012 283_[+3]_197 40962 0.00013 403_[+3]_77 26224 0.00013 77_[+3]_403 38948 0.00015 400_[+3]_80 14140 0.00018 63_[+3]_417 25128 0.00024 290_[+3]_190 24560 0.00024 181_[+3]_299 5699 0.0003 149_[+3]_331 2160 0.0003 240_[+3]_240 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=41 262751 ( 173) GAGAATGAGAGAGAGGAGAG 1 21126 ( 47) GACGATGAGTGAGAGGAGAG 1 33649 ( 297) GACGACGAGAGTGAAGGGAG 1 26706 ( 225) GAGAGGGAGAGAGGTGTGAG 1 30075 ( 295) TTGGAGGAGGGAGAAGAGCG 1 267922 ( 113) CAGGAGGAGAGTGATCAGAC 1 37367 ( 127) GAGGAGGAAGGCGGCGAGTT 1 4318 ( 193) GAGGAGGAGAGAGTCTCGAT 1 38129 ( 123) GAGAGAGAAAAAGAAGAGAC 1 24527 ( 180) GTTGACGAGAGAGATAAGCG 1 23857 ( 99) GATGAGGAGGTAGATGGCGT 1 38945 ( 233) TTGGATGAGAGAGATGTTGT 1 24318 ( 240) CTGAGAGAGAGAGAAAATAG 1 516 ( 44) GAGAGAGAGCGCGATGCGAG 1 269593 ( 396) GAGAACGAGGGCAACAAGAT 1 8292 ( 37) GATGAAGATGGGGTGGAGAG 1 3649 ( 220) CAGGAGGAGGGAAATATTAT 1 7964 ( 204) TTGGAGGATGGTGATGTTGG 1 262525 ( 1) GAGGAAGAGGTTGATTATTA 1 33777 ( 234) GTAGAGGAAAGTGAGGTGTG 1 1845 ( 107) GTGGACGAAGAGCATGAGTT 1 26868 ( 69) GAGTATGAAGCAGATGATGG 1 39157 ( 192) CTGGAAGAGGTCGTCGACAG 1 32037 ( 316) GAGGAGGAGAAGGGCACTTG 1 40483 ( 187) GAGAAGAAGGATGAAGGCTG 1 21911 ( 37) GAGAAGGATGTATTGGAGTT 1 264377 ( 237) GTCGAGGACGAAGAGACGTT 1 34219 ( 368) GAGAGTGAAGCCGAGGCCAT 1 33725 ( 157) GAGGAGCAGTACCAAGAGAG 1 24495 ( 316) GGCAAGGAGGGCTAGGAGGC 1 11068 ( 105) GTTGACGAGGGAGAAAGTGA 1 25320 ( 199) TTGAAGGAGGGAGCAAAGTA 1 5452 ( 284) GTCAGTGAAAAAGATTGCAG 1 40962 ( 404) GACGATGAGACGTATCCCAG 1 26224 ( 78) GTAGATGACGAATATGATAC 1 38948 ( 401) GACAAAGATATGGTCGATAC 1 14140 ( 64) TATGACGAGAGACAATTGAT 1 25128 ( 291) CACAAAGAGAAGTGTAACAG 1 24560 ( 182) GACAAGAAAATAGGGGATAA 1 5699 ( 150) GTGAGTGATTGTGATGGTGC 1 2160 ( 241) CTGAAGGAGACCCATCACTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 20202 bayes= 9.22084 E= 6.5e-007 -1200 -66 158 -111 123 -1200 -332 47 -241 -8 132 -111 67 -1200 120 -343 167 -1200 -52 -1200 -42 -66 85 -26 -241 -325 192 -1200 194 -1200 -1200 -1200 -42 -225 138 -111 75 -325 92 -185 -25 -125 114 -85 91 -25 -74 -63 -241 -125 158 -111 149 -325 -100 -111 -25 -66 -15 65 -25 -166 132 -143 111 -66 -74 -85 -1200 -25 107 15 104 -225 -52 -11 -142 -44 92 2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 41 E= 6.5e-007 0.000000 0.146341 0.731707 0.121951 0.609756 0.000000 0.024390 0.365854 0.048780 0.219512 0.609756 0.121951 0.414634 0.000000 0.560976 0.024390 0.829268 0.000000 0.170732 0.000000 0.195122 0.146341 0.439024 0.219512 0.048780 0.024390 0.926829 0.000000 1.000000 0.000000 0.000000 0.000000 0.195122 0.048780 0.634146 0.121951 0.439024 0.024390 0.463415 0.073171 0.219512 0.097561 0.536585 0.146341 0.487805 0.195122 0.146341 0.170732 0.048780 0.097561 0.731707 0.121951 0.731707 0.024390 0.121951 0.121951 0.219512 0.146341 0.219512 0.414634 0.219512 0.073171 0.609756 0.097561 0.560976 0.146341 0.146341 0.146341 0.000000 0.195122 0.512195 0.292683 0.536585 0.048780 0.170732 0.243902 0.097561 0.170732 0.463415 0.268293 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[AT][GC][GA]A[GT]GAG[GA][GA]AGA[TAG][GA]A[GT][AT][GT] -------------------------------------------------------------------------------- Time 42.63 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11068 7.54e-05 104_[+3(5.53e-05)]_304_\ [+1(2.38e-07)]_51 14140 9.50e-06 31_[+2(7.00e-06)]_420_\ [+1(4.46e-07)]_12 1845 1.60e-06 106_[+3(1.37e-05)]_144_\ [+2(8.26e-07)]_190_[+1(6.59e-06)]_3 21126 6.45e-08 23_[+2(7.72e-06)]_7_[+3(4.63e-08)]_\ 13_[+2(3.62e-05)]_312_[+1(4.76e-05)]_18_[+1(6.03e-06)]_33 2160 2.74e-02 125_[+2(1.90e-05)]_359 21911 5.21e-06 36_[+3(2.96e-05)]_73_[+2(1.28e-08)]_\ 355 23857 6.64e-05 98_[+3(3.01e-06)]_51_[+2(1.36e-06)]_\ 315 24318 4.16e-07 21_[+2(1.02e-05)]_38_[+1(8.54e-06)]_\ 143_[+3(5.31e-06)]_166_[+1(3.08e-07)]_54 24495 1.68e-03 315_[+3(5.53e-05)]_46_\ [+1(4.59e-06)]_98 24527 1.99e-07 179_[+3(2.68e-06)]_40_\ [+2(7.00e-06)]_176_[+1(3.95e-07)]_48 24560 3.95e-02 316_[+1(2.56e-05)]_163 25128 3.38e-04 118_[+2(2.07e-05)]_108_\ [+2(8.67e-08)]_242 25320 3.55e-06 40_[+2(9.38e-07)]_142_\ [+3(8.41e-05)]_65_[+1(2.34e-06)]_196 26224 3.08e-02 477_[+1(3.64e-05)]_2 262525 6.59e-06 [+3(1.24e-05)]_62_[+2(5.23e-05)]_\ 363_[+1(5.67e-07)]_18 262751 2.00e-07 5_[+2(3.35e-05)]_151_[+3(3.86e-10)]_\ 47_[+3(4.49e-07)]_241 264377 1.21e-03 236_[+3(3.89e-05)]_156_\ [+1(2.11e-06)]_67 26706 3.50e-06 224_[+3(2.20e-07)]_205_\ [+1(7.16e-07)]_30 267922 1.93e-08 112_[+3(5.89e-07)]_109_\ [+2(1.94e-06)]_182_[+1(5.03e-07)]_18_[+1(3.40e-05)]_1 26868 1.32e-08 68_[+3(1.84e-05)]_98_[+2(1.23e-05)]_\ 260_[+1(1.70e-09)]_17 269593 2.24e-05 222_[+2(1.34e-05)]_112_\ [+1(1.64e-05)]_24_[+3(6.60e-06)]_85 30075 6.25e-10 102_[+1(3.95e-07)]_17_\ [+1(5.08e-05)]_26_[+1(2.85e-06)]_42_[+2(9.57e-05)]_28_[+3(2.94e-07)]_5_\ [+2(1.23e-05)]_5_[+2(1.21e-07)]_119_[+1(4.59e-06)]_4 32037 5.92e-06 73_[+2(4.52e-05)]_119_\ [+2(9.33e-06)]_91_[+3(2.23e-05)]_99_[+1(1.55e-06)]_45 33649 2.47e-06 110_[+2(3.10e-05)]_121_\ [+2(8.49e-06)]_33_[+3(2.20e-07)]_121_[+1(6.53e-05)]_42 33725 8.39e-08 52_[+2(7.72e-06)]_88_[+3(5.53e-05)]_\ 142_[+1(6.81e-09)]_5_[+1(3.46e-06)]_135 33777 6.66e-05 153_[+1(1.40e-05)]_59_\ [+3(1.37e-05)]_153_[+2(2.64e-05)]_78 34219 4.80e-04 96_[+1(2.76e-05)]_250_\ [+3(5.53e-05)]_40_[+2(3.35e-05)]_57 3649 4.13e-06 62_[+2(2.64e-05)]_141_\ [+3(9.09e-06)]_181_[+1(8.99e-07)]_59 37367 6.19e-07 126_[+3(1.13e-06)]_242_\ [+1(1.39e-08)]_91 37861 1.11e-01 28_[+2(2.25e-05)]_456 38129 4.17e-05 122_[+3(2.11e-06)]_124_\ [+1(4.46e-05)]_12_[+1(1.72e-06)]_104_[+1(3.17e-05)]_55 38945 4.48e-04 232_[+3(3.38e-06)]_213_\ [+1(2.22e-05)]_14 38948 2.24e-03 3_[+2(9.57e-05)]_423_[+1(2.38e-05)]_\ 37 39157 2.03e-03 191_[+3(2.23e-05)]_68_\ [+2(2.44e-05)]_205 40483 4.85e-05 186_[+3(2.70e-05)]_111_\ [+2(6.90e-05)]_96_[+1(1.91e-06)]_50 40962 1.76e-05 98_[+1(2.06e-05)]_95_[+2(5.55e-07)]_\ 89_[+2(2.86e-05)]_165 4318 6.25e-06 176_[+2(6.34e-06)]_[+3(2.11e-06)]_\ 215_[+1(2.56e-05)]_52 516 8.70e-04 43_[+3(6.60e-06)]_199_\ [+1(1.77e-05)]_217 5452 3.18e-04 243_[+1(4.59e-06)]_123_\ [+2(6.01e-05)]_97 5699 1.21e-05 140_[+2(7.88e-05)]_35_\ [+2(1.23e-05)]_31_[+2(3.62e-05)]_183_[+1(2.09e-07)]_42 7964 5.80e-07 17_[+1(3.08e-07)]_99_[+2(6.34e-06)]_\ 50_[+3(1.24e-05)]_277 8292 4.04e-07 36_[+3(7.35e-06)]_2_[+2(6.35e-07)]_\ 358_[+1(3.46e-06)]_47 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************