******************************************************************************** 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/393/393.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 43211 1.0000 500 54619 1.0000 500 21039 1.0000 500 36847 1.0000 500 13470 1.0000 500 2037 1.0000 500 28743 1.0000 500 5156 1.0000 500 47924 1.0000 500 29958 1.0000 500 39993 1.0000 500 49355 1.0000 500 16032 1.0000 500 49568 1.0000 500 6402 1.0000 500 2032 1.0000 500 50345 1.0000 500 16904 1.0000 500 50416 1.0000 500 33198 1.0000 500 17115 1.0000 500 50614 1.0000 500 8521 1.0000 500 44473 1.0000 500 34422 1.0000 500 11198 1.0000 500 11559 1.0000 500 3015 1.0000 500 3137 1.0000 500 12234 1.0000 500 43158 1.0000 500 43345 1.0000 500 36662 1.0000 500 47745 1.0000 500 49309 1.0000 500 36221 1.0000 500 46293 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/393/393.seqs.fa -oc motifs/393 -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= 37 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= 18500 N= 37 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.249 C 0.267 G 0.235 T 0.249 Background letter frequencies (from dataset with add-one prior applied): A 0.249 C 0.267 G 0.235 T 0.249 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 23 llr = 253 E-value = 2.4e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 44:69:3:a:9:11a: pos.-specific C 257::644:a:313:8 probability G ::32:1:5::16:4:: matrix T 3::21331::::81:2 bits 2.1 * * 1.9 ** * 1.7 ** * 1.5 * ** * Relative 1.3 * *** ** Entropy 1.0 * *** * ** (15.9 bits) 0.8 * * *** * ** 0.6 ***** ****** ** 0.4 ************ ** 0.2 **************** 0.0 ---------------- Multilevel ACCAACCGACAGTGAC consensus TAGG TAC C C T sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 3015 102 1.20e-07 TTGTACCCTA CCCTACCGACAGTGAC ACCATTCCGA 13470 240 2.18e-07 GATACAGCTG TACAAGTGACAGTGAC ACAGAGAGTC 2032 286 2.51e-07 GGGCTAGAAG ACCGAGCGACAGTGAC TTTCTCAGTC 16904 428 5.48e-07 ATAGGTAGTC AACAACAGACATTGAC ACACGTACGC 46293 308 6.16e-07 CCTCATCCCA ACGAACCCACACTTAC AGCAGTTTAC 36221 317 6.16e-07 CCTCATCCCA ACGAACCCACACTTAC AGCAGTTTAC 50345 22 7.87e-07 CCTTTTCTCT CACAACAGACAGCGAC TTGTTTTGCG 49355 20 7.87e-07 CCTTTTCTCT CACAACAGACAGCGAC TTGTTTTGCG 44473 251 1.10e-06 CCGATAGTAT TCCAACTCACGGTCAC GGTCACAACC 16032 111 1.10e-06 ACTCCAATTT TATAACTGACAGTGAC TAAAAAACTC 3137 43 1.38e-06 ACACGCGGCG CCGAATCCACACTCAC AGTCCTGCGG 29958 389 2.54e-06 GGTGTGTGTG AACAATACACACACAC ACATTCACAA 49568 129 4.43e-06 TCCTGGGGAA AAAGACAGACACTGAC GGATGGCTTC 17115 101 6.25e-06 ATGTAAAACC ACGGATTTACAGTCAC CAACCGCTAC 5156 418 6.78e-06 TTACCCCAGC AGCATCCCACACTGAC GGTACAAGAT 8521 330 7.36e-06 GCGGAACGAC AACAATCCACAATCAT CAAAAAATGG 50614 32 8.64e-06 TATATTGCAT TCGTATTCACAGTCAT CTTGAGAAAG 43158 439 1.01e-05 ACTGTCTCAG TCGAACCGACTGTAAC GTTACAGTAA 54619 268 1.01e-05 TACGTATGTT TCCTTCCCACAGACAC GCTTACACCG 47745 287 1.09e-05 TCGGAGGATG GACGACAGACGGTGAC TGTAACGTGG 50416 189 1.56e-05 CACGAATCGA CCCAATTTACAGTTAT TGCGTTTCTT 39993 417 1.68e-05 CGAGCATCGT ACCTTGCCACAGTCAT TCCCTACGCG 49309 203 3.00e-05 AGTCGTCGTG TACGACAGACACAAAT AGCAATATTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3015 1.2e-07 101_[+1]_383 13470 2.2e-07 239_[+1]_245 2032 2.5e-07 285_[+1]_199 16904 5.5e-07 427_[+1]_57 46293 6.2e-07 307_[+1]_177 36221 6.2e-07 316_[+1]_168 50345 7.9e-07 21_[+1]_463 49355 7.9e-07 19_[+1]_465 44473 1.1e-06 250_[+1]_234 16032 1.1e-06 110_[+1]_374 3137 1.4e-06 42_[+1]_442 29958 2.5e-06 388_[+1]_96 49568 4.4e-06 128_[+1]_356 17115 6.3e-06 100_[+1]_384 5156 6.8e-06 417_[+1]_67 8521 7.4e-06 329_[+1]_155 50614 8.6e-06 31_[+1]_453 43158 1e-05 438_[+1]_46 54619 1e-05 267_[+1]_217 47745 1.1e-05 286_[+1]_198 50416 1.6e-05 188_[+1]_296 39993 1.7e-05 416_[+1]_68 49309 3e-05 202_[+1]_282 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=23 3015 ( 102) CCCTACCGACAGTGAC 1 13470 ( 240) TACAAGTGACAGTGAC 1 2032 ( 286) ACCGAGCGACAGTGAC 1 16904 ( 428) AACAACAGACATTGAC 1 46293 ( 308) ACGAACCCACACTTAC 1 36221 ( 317) ACGAACCCACACTTAC 1 50345 ( 22) CACAACAGACAGCGAC 1 49355 ( 20) CACAACAGACAGCGAC 1 44473 ( 251) TCCAACTCACGGTCAC 1 16032 ( 111) TATAACTGACAGTGAC 1 3137 ( 43) CCGAATCCACACTCAC 1 29958 ( 389) AACAATACACACACAC 1 49568 ( 129) AAAGACAGACACTGAC 1 17115 ( 101) ACGGATTTACAGTCAC 1 5156 ( 418) AGCATCCCACACTGAC 1 8521 ( 330) AACAATCCACAATCAT 1 50614 ( 32) TCGTATTCACAGTCAT 1 43158 ( 439) TCGAACCGACTGTAAC 1 54619 ( 268) TCCTTCCCACAGACAC 1 47745 ( 287) GACGACAGACGGTGAC 1 50416 ( 189) CCCAATTTACAGTTAT 1 39993 ( 417) ACCTTGCCACAGTCAT 1 49309 ( 203) TACGACAGACACAAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 17945 bayes= 10.0089 E= 2.4e-006 80 -30 -243 29 80 97 -243 -1117 -252 129 15 -251 129 -1117 -11 -52 180 -1117 -1117 -93 -1117 119 -85 7 29 70 -1117 7 -1117 70 102 -151 200 -1117 -1117 -1117 -1117 191 -1117 -1117 180 -1117 -144 -251 -252 19 137 -251 -93 -162 -1117 165 -152 38 88 -93 200 -1117 -1117 -1117 -1117 155 -1117 -19 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 23 E= 2.4e-006 0.434783 0.217391 0.043478 0.304348 0.434783 0.521739 0.043478 0.000000 0.043478 0.652174 0.260870 0.043478 0.608696 0.000000 0.217391 0.173913 0.869565 0.000000 0.000000 0.130435 0.000000 0.608696 0.130435 0.260870 0.304348 0.434783 0.000000 0.260870 0.000000 0.434783 0.478261 0.086957 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.869565 0.000000 0.086957 0.043478 0.043478 0.304348 0.608696 0.043478 0.130435 0.086957 0.000000 0.782609 0.086957 0.347826 0.434783 0.130435 1.000000 0.000000 0.000000 0.000000 0.000000 0.782609 0.000000 0.217391 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [ATC][CA][CG][AG]A[CT][CAT][GC]ACA[GC]T[GC]A[CT] -------------------------------------------------------------------------------- Time 11.58 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 15 llr = 208 E-value = 1.8e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :1:111:23725:1::::::: pos.-specific C 55622:11:1:21:a184111 probability G 31::41475:6181:::1::: matrix T 2347385:312118:925999 bits 2.1 1.9 * 1.7 ** * 1.5 ** *** Relative 1.3 * *** *** Entropy 1.0 * * ***** *** (20.0 bits) 0.8 ** * * * ***** *** 0.6 ** *** ** ********* 0.4 * ** ****** ********* 0.2 ********************* 0.0 --------------------- Multilevel CCCTGTTGGAGAGTCTCTTTT consensus GTTCT GAA AC TC sequence T C T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 50345 452 1.18e-09 TTCTTCAGCA GCCTCTGGTAGAGTCTTTTTT CGTCTACAAA 49355 452 1.18e-09 TTCTTCAGCA GCCTCTGGTAGAGTCTTTTTT CGTCTACAAA 46293 46 1.19e-08 CGATTCCTCT CCCCGTGAAAAAGTCTCTTTT GTTTCGTGTT 36221 66 1.19e-08 CGATTCCTCT CCCCGTGAAAAAGTCTCTTTT GTTTCGGGTT 5156 388 1.67e-08 CCGCTTCCTG CTCTGTTGGCGACTCTCCTTT TACCCCAGCA 2037 468 1.03e-07 ATCCACGAAT CCCTTTGCGAGTGTCCCCTTT GTTGTTCAAA 29958 122 1.62e-07 TGACAACACT GTTCGTTGGATGTTCTCCTTT TTGGTTGGAC 50416 452 2.28e-07 GCACGCACAC CTCTTTGGGAGCGACTCTCTC TCTCTCTCTG 44473 52 2.48e-07 TAGGCCAGCG CTTTGGTGTTGGGTCTTTTTT GTGTTCGAGC 50614 415 3.45e-07 ATCCCTGATC GCCTGACCGAGAGTCTCGTTT TCCCTCGATT 21039 387 4.37e-07 GCCAGTGTTC TATTCTTGTAGTGTCTCTTCT CCCCGTAGGT 6402 442 5.94e-07 CTGCTAGCCG CCTTTGTGGATCGACTCTTTC TCAACGGTGC 43158 156 6.40e-07 CATTAAAGTG TGTTATTAGAGAGTCTCCCTT GAACAATGAC 34422 83 2.19e-06 TTATACGAAC TTTATTTGACTATTCTCCTTT GGGTAAGAAC 16904 294 2.98e-06 ACCATGGCGG GACTTTCGATACGGCTCCTTT TTCCCTCTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50345 1.2e-09 451_[+2]_28 49355 1.2e-09 451_[+2]_28 46293 1.2e-08 45_[+2]_434 36221 1.2e-08 65_[+2]_414 5156 1.7e-08 387_[+2]_92 2037 1e-07 467_[+2]_12 29958 1.6e-07 121_[+2]_358 50416 2.3e-07 451_[+2]_28 44473 2.5e-07 51_[+2]_428 50614 3.4e-07 414_[+2]_65 21039 4.4e-07 386_[+2]_93 6402 5.9e-07 441_[+2]_38 43158 6.4e-07 155_[+2]_324 34422 2.2e-06 82_[+2]_397 16904 3e-06 293_[+2]_186 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=15 50345 ( 452) GCCTCTGGTAGAGTCTTTTTT 1 49355 ( 452) GCCTCTGGTAGAGTCTTTTTT 1 46293 ( 46) CCCCGTGAAAAAGTCTCTTTT 1 36221 ( 66) CCCCGTGAAAAAGTCTCTTTT 1 5156 ( 388) CTCTGTTGGCGACTCTCCTTT 1 2037 ( 468) CCCTTTGCGAGTGTCCCCTTT 1 29958 ( 122) GTTCGTTGGATGTTCTCCTTT 1 50416 ( 452) CTCTTTGGGAGCGACTCTCTC 1 44473 ( 52) CTTTGGTGTTGGGTCTTTTTT 1 50614 ( 415) GCCTGACCGAGAGTCTCGTTT 1 21039 ( 387) TATTCTTGTAGTGTCTCTTCT 1 6402 ( 442) CCTTTGTGGATCGACTCTTTC 1 43158 ( 156) TGTTATTAGAGAGTCTCCCTT 1 34422 ( 83) TTTATTTGACTATTCTCCTTT 1 16904 ( 294) GACTTTCGATACGGCTCCTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 17760 bayes= 10.1332 E= 1.8e-002 -1055 81 50 -31 -90 81 -182 42 -1055 117 -1055 69 -190 -42 -1055 156 -190 -42 76 42 -190 -1055 -82 169 -1055 -100 76 91 -32 -100 150 -1055 10 -1055 99 10 156 -100 -1055 -90 -32 -1055 135 -31 110 -42 -82 -90 -1055 -200 176 -90 -90 -1055 -182 169 -1055 191 -1055 -1055 -1055 -200 -1055 191 -1055 158 -1055 -31 -1055 58 -182 110 -1055 -100 -1055 180 -1055 -200 -1055 191 -1055 -100 -1055 180 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 15 E= 1.8e-002 0.000000 0.466667 0.333333 0.200000 0.133333 0.466667 0.066667 0.333333 0.000000 0.600000 0.000000 0.400000 0.066667 0.200000 0.000000 0.733333 0.066667 0.200000 0.400000 0.333333 0.066667 0.000000 0.133333 0.800000 0.000000 0.133333 0.400000 0.466667 0.200000 0.133333 0.666667 0.000000 0.266667 0.000000 0.466667 0.266667 0.733333 0.133333 0.000000 0.133333 0.200000 0.000000 0.600000 0.200000 0.533333 0.200000 0.133333 0.133333 0.000000 0.066667 0.800000 0.133333 0.133333 0.000000 0.066667 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.066667 0.000000 0.933333 0.000000 0.800000 0.000000 0.200000 0.000000 0.400000 0.066667 0.533333 0.000000 0.133333 0.000000 0.866667 0.000000 0.066667 0.000000 0.933333 0.000000 0.133333 0.000000 0.866667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CGT][CT][CT][TC][GTC]T[TG][GA][GAT]A[GAT][AC]GTCT[CT][TC]TTT -------------------------------------------------------------------------------- Time 23.08 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 16 llr = 212 E-value = 3.2e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :3313163294:4:313:346 pos.-specific C 853::93:8:58:::11a231 probability G :1397::6:11164:6::43: matrix T 311:::211::1:6726:113 bits 2.1 1.9 * 1.7 * * * 1.5 * * * * Relative 1.3 *** * * Entropy 1.0 * *** * **** * (19.1 bits) 0.8 * *** *** **** * 0.6 * *************** * 0.4 ** *************** * 0.2 ** ****************** 0.0 --------------------- Multilevel CCCGGCAGCACCGTTGTCGAA consensus TAG A CA A AGA A ACT sequence A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 50345 83 3.26e-10 CCATCGTGAA CACGGCAGCAACGTAGTCGGA GCGGAATTTG 49355 81 3.26e-10 CCATCGTGAA CACGGCAGCAACGTAGTCGGA GCGGAATTTG 11559 134 4.56e-09 TAGGTAGTGG CCGGGCCACACCGGTGACGGA ACTTGCCAAA 11198 369 3.04e-08 CAGCTACCAC CAAGGCCGAACCGTTGACCAA TCGTTTGCGG 46293 386 9.47e-08 AGATCCATCC CGTGGCTGCAACATTGACACA GCAGTGCACA 36221 386 9.47e-08 AGATCCATCC CGTGGCTGCAACATTGACACA GCAGTGCACA 13470 165 2.80e-07 TCGGTTCACA CCGGACAAAACGATTTTCGAA CGTTATGTAA 54619 88 3.36e-07 TGATGGCTGT TCCGGCAGCAACAGTATCAAC AACAACAATC 3015 404 8.44e-07 TGCCGCTACC CCGGGATACACCGTTGCCGGT CGACCGCGAC 16904 345 1.23e-06 CGATTGTGAT TCGGACAGCAGCAGTTTCTAA AAATATCGAA 16032 206 1.23e-06 TCGGTTCGTG CCCGGCAGTACCGTATACACC CCACGATAAT 33198 466 1.43e-06 TGTATTCAGA CAAGACAGAGCCATTCTCAAA GCTAGCAAGC 8521 405 2.02e-06 ATCCACGGCT TCGAGCAACACGGGTGCCGAT GGAAGGGCGT 2032 479 2.16e-06 GCGATCCCTA CCAAGCCTCACCGGAGTCCAT T 36662 449 2.31e-06 CCGTACCTTG CAAGACCGCAATGGACTCGCA GCTCCTGCCA 50614 324 2.99e-06 AAAGCTTCTT TTCGACAACAACATTGTCCTT CAACTATCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 50345 3.3e-10 82_[+3]_397 49355 3.3e-10 80_[+3]_399 11559 4.6e-09 133_[+3]_346 11198 3e-08 368_[+3]_111 46293 9.5e-08 385_[+3]_94 36221 9.5e-08 385_[+3]_94 13470 2.8e-07 164_[+3]_315 54619 3.4e-07 87_[+3]_392 3015 8.4e-07 403_[+3]_76 16904 1.2e-06 344_[+3]_135 16032 1.2e-06 205_[+3]_274 33198 1.4e-06 465_[+3]_14 8521 2e-06 404_[+3]_75 2032 2.2e-06 478_[+3]_1 36662 2.3e-06 448_[+3]_31 50614 3e-06 323_[+3]_156 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=16 50345 ( 83) CACGGCAGCAACGTAGTCGGA 1 49355 ( 81) CACGGCAGCAACGTAGTCGGA 1 11559 ( 134) CCGGGCCACACCGGTGACGGA 1 11198 ( 369) CAAGGCCGAACCGTTGACCAA 1 46293 ( 386) CGTGGCTGCAACATTGACACA 1 36221 ( 386) CGTGGCTGCAACATTGACACA 1 13470 ( 165) CCGGACAAAACGATTTTCGAA 1 54619 ( 88) TCCGGCAGCAACAGTATCAAC 1 3015 ( 404) CCGGGATACACCGTTGCCGGT 1 16904 ( 345) TCGGACAGCAGCAGTTTCTAA 1 16032 ( 206) CCCGGCAGTACCGTATACACC 1 33198 ( 466) CAAGACAGAGCCATTCTCAAA 1 8521 ( 405) TCGAGCAACACGGGTGCCGAT 1 2032 ( 479) CCAAGCCTCACCGGAGTCCAT 1 36662 ( 449) CAAGACCGCAATGGACTCGCA 1 50614 ( 324) TTCGACAACAACATTGTCCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 17760 bayes= 10.8525 E= 3.2e-001 -1064 149 -1064 1 33 91 -91 -199 0 23 41 -99 -99 -1064 189 -1064 33 -1064 155 -1064 -199 181 -1064 -1064 117 -9 -1064 -41 33 -1064 141 -199 -41 149 -1064 -199 191 -1064 -191 -1064 81 91 -191 -1064 -1064 161 -91 -199 81 -1064 126 -1064 -1064 -1064 67 133 33 -1064 -1064 147 -199 -109 141 -41 33 -109 -1064 118 -1064 191 -1064 -1064 33 -51 89 -199 81 -9 9 -199 133 -109 -1064 1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 16 E= 3.2e-001 0.000000 0.750000 0.000000 0.250000 0.312500 0.500000 0.125000 0.062500 0.250000 0.312500 0.312500 0.125000 0.125000 0.000000 0.875000 0.000000 0.312500 0.000000 0.687500 0.000000 0.062500 0.937500 0.000000 0.000000 0.562500 0.250000 0.000000 0.187500 0.312500 0.000000 0.625000 0.062500 0.187500 0.750000 0.000000 0.062500 0.937500 0.000000 0.062500 0.000000 0.437500 0.500000 0.062500 0.000000 0.000000 0.812500 0.125000 0.062500 0.437500 0.000000 0.562500 0.000000 0.000000 0.000000 0.375000 0.625000 0.312500 0.000000 0.000000 0.687500 0.062500 0.125000 0.625000 0.187500 0.312500 0.125000 0.000000 0.562500 0.000000 1.000000 0.000000 0.000000 0.312500 0.187500 0.437500 0.062500 0.437500 0.250000 0.250000 0.062500 0.625000 0.125000 0.000000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT][CA][CGA]G[GA]C[AC][GA]CA[CA]C[GA][TG][TA]G[TA]C[GA][ACG][AT] -------------------------------------------------------------------------------- Time 34.34 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 43211 7.74e-01 500 54619 8.94e-05 87_[+3(3.36e-07)]_129_\ [+3(1.65e-05)]_9_[+1(1.01e-05)]_217 21039 1.76e-03 386_[+2(4.37e-07)]_93 36847 1.64e-01 500 13470 2.31e-06 164_[+3(2.80e-07)]_54_\ [+1(2.18e-07)]_245 2037 1.04e-03 467_[+2(1.03e-07)]_12 28743 8.59e-01 500 5156 2.56e-06 387_[+2(1.67e-08)]_9_[+1(6.78e-06)]_\ 67 47924 4.67e-02 500 29958 5.17e-06 121_[+2(1.62e-07)]_246_\ [+1(2.54e-06)]_96 39993 1.82e-02 416_[+1(1.68e-05)]_68 49355 2.57e-14 19_[+1(7.87e-07)]_45_[+3(3.26e-10)]_\ 350_[+2(1.18e-09)]_28 16032 3.33e-05 110_[+1(1.10e-06)]_79_\ [+3(1.23e-06)]_274 49568 1.14e-02 128_[+1(4.43e-06)]_356 6402 1.53e-03 441_[+2(5.94e-07)]_38 2032 1.07e-05 285_[+1(2.51e-07)]_177_\ [+3(2.16e-06)]_1 50345 2.57e-14 21_[+1(7.87e-07)]_45_[+3(3.26e-10)]_\ 348_[+2(1.18e-09)]_28 16904 6.07e-08 195_[+1(8.16e-05)]_82_\ [+2(2.98e-06)]_30_[+3(1.23e-06)]_62_[+1(5.48e-07)]_57 50416 7.30e-05 188_[+1(1.56e-05)]_247_\ [+2(2.28e-07)]_28 33198 5.59e-03 465_[+3(1.43e-06)]_14 17115 3.66e-02 100_[+1(6.25e-06)]_384 50614 2.35e-07 31_[+1(8.64e-06)]_276_\ [+3(2.99e-06)]_70_[+2(3.45e-07)]_65 8521 1.66e-04 329_[+1(7.36e-06)]_59_\ [+3(2.02e-06)]_75 44473 2.77e-06 51_[+2(2.48e-07)]_178_\ [+1(1.10e-06)]_234 34422 1.88e-02 82_[+2(2.19e-06)]_397 11198 5.15e-04 368_[+3(3.04e-08)]_111 11559 1.32e-04 133_[+3(4.56e-09)]_346 3015 3.63e-06 101_[+1(1.20e-07)]_286_\ [+3(8.44e-07)]_76 3137 9.25e-04 42_[+1(1.38e-06)]_355_\ [+2(4.19e-05)]_66 12234 3.16e-01 500 43158 7.97e-05 155_[+2(6.40e-07)]_262_\ [+1(1.01e-05)]_46 43345 7.77e-01 500 36662 4.12e-03 448_[+3(2.31e-06)]_31 47745 3.43e-03 233_[+3(7.32e-05)]_32_\ [+1(1.09e-05)]_198 49309 1.46e-01 202_[+1(3.00e-05)]_282 36221 3.78e-11 65_[+2(1.19e-08)]_230_\ [+1(6.16e-07)]_53_[+3(9.47e-08)]_94 46293 3.78e-11 45_[+2(1.19e-08)]_241_\ [+1(6.16e-07)]_62_[+3(9.47e-08)]_94 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************