******************************************************************************** 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/426/426.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1063 1.0000 500 18991 1.0000 500 20462 1.0000 500 22118 1.0000 500 23584 1.0000 500 24068 1.0000 500 24921 1.0000 500 27318 1.0000 500 31046 1.0000 500 31859 1.0000 500 34785 1.0000 500 3486 1.0000 500 36206 1.0000 500 36524 1.0000 500 37430 1.0000 500 37485 1.0000 500 38207 1.0000 500 38335 1.0000 500 6376 1.0000 500 6584 1.0000 500 6600 1.0000 500 735 1.0000 500 8937 1.0000 500 9321 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/426/426.seqs.fa -oc motifs/426 -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= 24 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= 12000 N= 24 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.247 C 0.255 G 0.233 T 0.265 Background letter frequencies (from dataset with add-one prior applied): A 0.247 C 0.255 G 0.233 T 0.265 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 21 llr = 270 E-value = 2.1e-015 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 3215:51139:2436238256 pos.-specific C 685575197:9847:66:842 probability G 1:3:::1:::::1::::1::1 matrix T ::1:2:7::1::::42:1:11 bits 2.1 1.9 1.7 1.5 * Relative 1.3 * * *** * Entropy 1.1 * * * ***** ** (18.5 bits) 0.8 * *** ***** ** ** 0.6 ** *** ***** ****** 0.4 ** ****************** 0.2 ********************* 0.0 --------------------- Multilevel CCCCCCTCCACCACACCACAA consensus A GATA A CAT A CC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 38207 73 1.55e-09 GCCTCTTGTC CCCCTCTCCACCACTCCAAAA CCACCAACTC 31859 477 4.95e-09 ACCGTTCTCA CCGCCATCCACCCCACAGCCA TCC 27318 14 4.95e-09 ACCGTTCTCA CCGCCATCCACCCCACAGCCA TCCGGCAAAG 34785 103 2.89e-08 CTAACCACTC CCCCCCTCCACCTTACCACAA ACAGACTCCT 735 430 3.63e-08 ACCACCTCAC CCCCCATCCAACACAACACAC ACCAGACCTC 18991 427 3.63e-08 ACCACACACA CCGACCTCAACCCCTCCACTG ACATCGACCA 6584 405 7.04e-08 TCCGTCGTCT CCGCTCTACACCACACAACCC CTGGGCAAGT 6600 455 8.71e-08 GACGGACAGC CACACCACCACCCCACTACCA CCACCGACAA 9321 307 1.60e-07 CCTCGCCCTC ACCACCGCCTCCACTCCACAC CACATCCTAC 38335 350 1.60e-07 ATCTCCTTCC ACCACATCAACCAAAACAACC ACACCGTCGT 23584 452 2.86e-07 CTACACAACC AACACACCAACCACACCACAT TACGCTCTAC 36524 475 3.13e-07 AACAACAACA ACAACAACAACAACACAACAA TAACA 37485 479 4.12e-07 CCGCTTCCCG GCTCTCTCCACACCTTCACAA C 3486 417 4.93e-07 GTCGCATCGT CCTCCCTCCTCCCATCCTCCA CAGCCACGGC 36206 84 1.15e-06 TCCCCCGCCG CCGACCGCCGCCGAACAACAA CGACGAGACA 37430 475 1.84e-06 AGCACCGCCA CCCACCTGCACACACACACAA ACAAT 8937 442 4.12e-06 ACCCAAGGAC ACAATATCAACCAAAACTCCC CCCCCCCTCC 1063 345 5.79e-06 CACGTCTACA GCCCCAAACACCCCTTCAATA CATTGTAGAA 20462 311 9.69e-06 GTGGATGTTG AACATATCAACAACATCACGT CGTCTCCTCT 24921 458 1.17e-05 CGTCCGAACA CATCCATCCATCGATCAACCG ACGATATCAA 6376 469 1.24e-05 TCTGTACCTT CCGCACCCAACCCCTTGAAAA CATCGACGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38207 1.6e-09 72_[+1]_407 31859 5e-09 476_[+1]_3 27318 5e-09 13_[+1]_466 34785 2.9e-08 102_[+1]_377 735 3.6e-08 429_[+1]_50 18991 3.6e-08 426_[+1]_53 6584 7e-08 404_[+1]_75 6600 8.7e-08 454_[+1]_25 9321 1.6e-07 306_[+1]_173 38335 1.6e-07 349_[+1]_130 23584 2.9e-07 451_[+1]_28 36524 3.1e-07 474_[+1]_5 37485 4.1e-07 478_[+1]_1 3486 4.9e-07 416_[+1]_63 36206 1.1e-06 83_[+1]_396 37430 1.8e-06 474_[+1]_5 8937 4.1e-06 441_[+1]_38 1063 5.8e-06 344_[+1]_135 20462 9.7e-06 310_[+1]_169 24921 1.2e-05 457_[+1]_22 6376 1.2e-05 468_[+1]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=21 38207 ( 73) CCCCTCTCCACCACTCCAAAA 1 31859 ( 477) CCGCCATCCACCCCACAGCCA 1 27318 ( 14) CCGCCATCCACCCCACAGCCA 1 34785 ( 103) CCCCCCTCCACCTTACCACAA 1 735 ( 430) CCCCCATCCAACACAACACAC 1 18991 ( 427) CCGACCTCAACCCCTCCACTG 1 6584 ( 405) CCGCTCTACACCACACAACCC 1 6600 ( 455) CACACCACCACCCCACTACCA 1 9321 ( 307) ACCACCGCCTCCACTCCACAC 1 38335 ( 350) ACCACATCAACCAAAACAACC 1 23584 ( 452) AACACACCAACCACACCACAT 1 36524 ( 475) ACAACAACAACAACACAACAA 1 37485 ( 479) GCTCTCTCCACACCTTCACAA 1 3486 ( 417) CCTCCCTCCTCCCATCCTCCA 1 36206 ( 84) CCGACCGCCGCCGAACAACAA 1 37430 ( 475) CCCACCTGCACACACACACAA 1 8937 ( 442) ACAATATCAACCAAAACTCCC 1 1063 ( 345) GCCCCAAACACCCCTTCAATA 1 20462 ( 311) AACATATCAACAACATCACGT 1 24921 ( 458) CATCCATCCATCGATCAACCG 1 6376 ( 469) CCGCACCCAACCCCTTGAAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 11520 bayes= 9.40226 E= 2.1e-015 21 128 -129 -1104 -38 167 -1104 -1104 -138 90 30 -89 94 104 -1104 -1104 -237 148 -1104 -15 94 104 -1104 -1104 -79 -142 -129 133 -138 175 -228 -1104 43 139 -1104 -1104 179 -1104 -228 -148 -237 183 -1104 -247 -38 167 -1104 -1104 79 75 -129 -247 21 139 -1104 -247 121 -242 -1104 52 -38 128 -1104 -48 21 128 -228 -247 171 -1104 -129 -148 -38 167 -1104 -1104 94 58 -228 -148 121 -10 -129 -148 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 21 E= 2.1e-015 0.285714 0.619048 0.095238 0.000000 0.190476 0.809524 0.000000 0.000000 0.095238 0.476190 0.285714 0.142857 0.476190 0.523810 0.000000 0.000000 0.047619 0.714286 0.000000 0.238095 0.476190 0.523810 0.000000 0.000000 0.142857 0.095238 0.095238 0.666667 0.095238 0.857143 0.047619 0.000000 0.333333 0.666667 0.000000 0.000000 0.857143 0.000000 0.047619 0.095238 0.047619 0.904762 0.000000 0.047619 0.190476 0.809524 0.000000 0.000000 0.428571 0.428571 0.095238 0.047619 0.285714 0.666667 0.000000 0.047619 0.571429 0.047619 0.000000 0.380952 0.190476 0.619048 0.000000 0.190476 0.285714 0.619048 0.047619 0.047619 0.809524 0.000000 0.095238 0.095238 0.190476 0.809524 0.000000 0.000000 0.476190 0.380952 0.047619 0.095238 0.571429 0.238095 0.095238 0.095238 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA]C[CG][CA][CT][CA]TC[CA]ACC[AC][CA][AT]C[CA]AC[AC][AC] -------------------------------------------------------------------------------- Time 5.31 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 24 llr = 253 E-value = 2.6e-013 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :2:::2:1:::1::3: pos.-specific C ::::2331:::::::: probability G 26237426:58:3a38 matrix T 82871252a5198:52 bits 2.1 1.9 * 1.7 * * 1.5 * * * Relative 1.3 * * ** * Entropy 1.1 * * * **** * (15.2 bits) 0.8 * *** ****** * 0.6 * *** ****** * 0.4 ***** ********** 0.2 ***** ********** 0.0 ---------------- Multilevel TGTTGGTGTGGTTGTG consensus GAGG CCT T G AT sequence AG G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 38335 2 7.02e-08 A TGGTGTTGTTGTTGTG TGGTGCGGCA 8937 298 2.66e-07 TTTGTGGCTC TGTTGGTGTTATTGTG TACAAGATCT 23584 97 3.06e-07 CCCGTCTTCG TGTTGCCGTTGTTGGT GTTGCGTGAG 31859 334 3.49e-07 AAATGGTGCG TTTTGATTTTGTTGTG TCCGAGGCCG 1063 265 3.49e-07 CTGTTTGTTT GGTGGTCGTGGTTGTG TGCGTCGTTA 37485 279 4.50e-07 GTTGTTTTTT AGTTGCTGTTGTTGTG GCTTCTTCCT 37430 51 5.08e-07 GCTCATGGTT TGTTTGCTTGGTTGTG TTGTCTGTTG 6376 261 1.99e-06 TGCGGGGTGC TGTAGACGTTGTTGGG GGAATCTTTT 24921 210 1.99e-06 TCGTCATGGT TGTGCGGGTGGTGGAG GTAAATTTAC 18991 53 2.69e-06 ATGGATCGAC GATTGTGGTGGTGGTG TTGGAGGCAC 9321 23 2.97e-06 GAGGTGCATC TTTGGATGTGGTGGTT TGATAGAAGT 20462 148 3.61e-06 CGTTCGTTGT GTTTGGTGTTGATGGG TACGATACTG 36206 366 4.36e-06 GAGCTTGAAA TGGTGGTTTGTTGGTG GAACGATCAC 735 337 4.78e-06 GGCGTTTTTA TCTTGGTCTTGTGGTG CTTCAGGCGG 6584 291 4.78e-06 GTTCCTCGTC TGTTCGTGTTGTTCAG GACAGTGTGA 38207 152 5.23e-06 ATTGCTGTGT TGTTGCGCTGTTTGAG AATACGTTCT 27318 295 5.73e-06 ACGTTGTCAG TATTGCCGTGGAGGGG CCTCCTCCTC 31046 247 1.04e-05 AAGCACGTCT TGTGTCTGTCGTTGGG TGCGGATTGT 3486 96 1.23e-05 GATGGGAAGG TAGGGAGGTGGTTGAT ATGTGGTTGA 34785 398 2.79e-05 CATCTTGATC TGTTGATATGTTTGTA TGAATATCAG 36524 222 4.18e-05 ATGTTCGCGC GTGTGGCTTGGATGAG AGAAGACGAC 24068 20 5.06e-05 AAGATCTCCG TGTGTTGATGGTTGGT CTAAGACAAA 6600 290 6.86e-05 CACCGTCGAA TATGCCCTGTGTTGTG GGCGAACAAT 22118 311 7.28e-05 CGCAAAGAGC GAGTCGTCTTGTTGAT CAAATTAGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 38335 7e-08 1_[+2]_483 8937 2.7e-07 297_[+2]_187 23584 3.1e-07 96_[+2]_388 31859 3.5e-07 333_[+2]_151 1063 3.5e-07 264_[+2]_220 37485 4.5e-07 278_[+2]_206 37430 5.1e-07 50_[+2]_434 6376 2e-06 260_[+2]_224 24921 2e-06 209_[+2]_275 18991 2.7e-06 52_[+2]_432 9321 3e-06 22_[+2]_462 20462 3.6e-06 147_[+2]_337 36206 4.4e-06 365_[+2]_119 735 4.8e-06 336_[+2]_148 6584 4.8e-06 290_[+2]_194 38207 5.2e-06 151_[+2]_333 27318 5.7e-06 294_[+2]_190 31046 1e-05 246_[+2]_238 3486 1.2e-05 95_[+2]_389 34785 2.8e-05 397_[+2]_87 36524 4.2e-05 221_[+2]_263 24068 5.1e-05 19_[+2]_465 6600 6.9e-05 289_[+2]_195 22118 7.3e-05 310_[+2]_174 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=24 38335 ( 2) TGGTGTTGTTGTTGTG 1 8937 ( 298) TGTTGGTGTTATTGTG 1 23584 ( 97) TGTTGCCGTTGTTGGT 1 31859 ( 334) TTTTGATTTTGTTGTG 1 1063 ( 265) GGTGGTCGTGGTTGTG 1 37485 ( 279) AGTTGCTGTTGTTGTG 1 37430 ( 51) TGTTTGCTTGGTTGTG 1 6376 ( 261) TGTAGACGTTGTTGGG 1 24921 ( 210) TGTGCGGGTGGTGGAG 1 18991 ( 53) GATTGTGGTGGTGGTG 1 9321 ( 23) TTTGGATGTGGTGGTT 1 20462 ( 148) GTTTGGTGTTGATGGG 1 36206 ( 366) TGGTGGTTTGTTGGTG 1 735 ( 337) TCTTGGTCTTGTGGTG 1 6584 ( 291) TGTTCGTGTTGTTCAG 1 38207 ( 152) TGTTGCGCTGTTTGAG 1 27318 ( 295) TATTGCCGTGGAGGGG 1 31046 ( 247) TGTGTCTGTCGTTGGG 1 3486 ( 96) TAGGGAGGTGGTTGAT 1 34785 ( 398) TGTTGATATGTTTGTA 1 36524 ( 222) GTGTGGCTTGGATGAG 1 24068 ( 20) TGTGTTGATGGTTGGT 1 6600 ( 290) TATGCCCTGTGTTGTG 1 22118 ( 311) GAGTCGTCTTGTTGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 11640 bayes= 9.36712 E= 2.6e-013 -257 -1123 -16 150 -25 -261 133 -67 -1123 -1123 -16 158 -257 -1123 33 133 -1123 -61 161 -108 -25 -3 69 -67 -1123 19 -16 92 -157 -103 133 -35 -1123 -1123 -248 185 -1123 -261 110 79 -257 -1123 184 -108 -98 -1123 -1123 172 -1123 -1123 10 150 -1123 -261 204 -1123 2 -1123 10 92 -257 -1123 169 -35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 24 E= 2.6e-013 0.041667 0.000000 0.208333 0.750000 0.208333 0.041667 0.583333 0.166667 0.000000 0.000000 0.208333 0.791667 0.041667 0.000000 0.291667 0.666667 0.000000 0.166667 0.708333 0.125000 0.208333 0.250000 0.375000 0.166667 0.000000 0.291667 0.208333 0.500000 0.083333 0.125000 0.583333 0.208333 0.000000 0.000000 0.041667 0.958333 0.000000 0.041667 0.500000 0.458333 0.041667 0.000000 0.833333 0.125000 0.125000 0.000000 0.000000 0.875000 0.000000 0.000000 0.250000 0.750000 0.000000 0.041667 0.958333 0.000000 0.250000 0.000000 0.250000 0.500000 0.041667 0.000000 0.750000 0.208333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG][GA][TG][TG]G[GCA][TCG][GT]T[GT]GT[TG]G[TAG][GT] -------------------------------------------------------------------------------- Time 10.37 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 19 llr = 230 E-value = 2.5e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 5:472154223271:611:11 pos.-specific C 29415914626728a:19618 probability G :11:::31261111:22:33: matrix T 3:13312211::1::27:151 bits 2.1 1.9 * 1.7 * * * 1.5 * * * * Relative 1.3 * * ** * * Entropy 1.1 * * * ** * * (17.5 bits) 0.8 * * * **** * * 0.6 ** * * ********* * 0.4 ** *** *********** * 0.2 ********************* 0.0 --------------------- Multilevel ACAACCAACGCCACCATCCTC consensus T CTT GC CAA G GG sequence A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 3486 476 1.20e-10 AACAATACAC TCCACCACCGCCACCATCGGC ACCA 27318 104 1.15e-08 CGACGGACGC ACCATCATCGGCACCTTCCTC GCCTTTGACA 1063 435 3.60e-08 TTCGTCATCC TCCAACAAGGCCACCAGCGGC ATGAGACGAC 37430 389 8.12e-08 TCCCCTCCTT CCAATCATCGCCCCCATCCAC ATTCCACCGA 31859 200 1.13e-07 AAACGTTCAA ACATTCCCCGCCACCACCCGC CGGCCGCTAC 37485 236 1.40e-07 GACTACAACG ACACCCGACGCCACCGACCGC GACAACAAAC 9321 329 2.36e-07 ACTCCACACC ACATCCTACAGCACCTTCGTC ATTCGCCGTC 38335 400 8.23e-07 GCTCGAAACC TCCACACCCGCCAGCATCCTC CTCTCCTATC 18991 451 8.23e-07 TCCACTGACA TCGACCACGGAGACCTTCCTC ATCTCCAAAC 31046 89 1.08e-06 CTCCGCGGTA CCAAACAACGCCGCCGTCCGT TTCGTTTGCT 34785 436 1.40e-06 GCTTCTCCTT TCTATCGAACCAACCAACCTC ACTTTTTTCT 36524 147 1.52e-06 GACGTCGAGA TGAAACATCACCACCATCGCC TTTGCTGGCG 6584 383 2.94e-06 TCAGAAAGAC ACGTCCGACCCATCCGTCGTC TCCGCTCTAC 6600 2 3.18e-06 T CCATTCAAACACCCCATCTTC CATCAATCCC 38207 444 3.72e-06 CACCACCCAT ACCATCTCTTCAACCAGCCTC CTCCGCCTTC 23584 328 5.85e-06 AAACAACGGT ACCACCACCACAACCATACAA GAACACATCA 735 456 7.81e-06 CACACACCAG ACCTCCTGGGACAACATCTTC GAACGCTCCT 36206 116 7.81e-06 GACGAGACAA ACAAACGACGACCACTGCCTT AGCACTACTG 24921 426 1.55e-05 TACTACTACT ACTACTGCACACACCGTCGCC GCGTCCGAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3486 1.2e-10 475_[+3]_4 27318 1.2e-08 103_[+3]_376 1063 3.6e-08 434_[+3]_45 37430 8.1e-08 388_[+3]_91 31859 1.1e-07 199_[+3]_280 37485 1.4e-07 235_[+3]_244 9321 2.4e-07 328_[+3]_151 38335 8.2e-07 399_[+3]_80 18991 8.2e-07 450_[+3]_29 31046 1.1e-06 88_[+3]_391 34785 1.4e-06 435_[+3]_44 36524 1.5e-06 146_[+3]_333 6584 2.9e-06 382_[+3]_97 6600 3.2e-06 1_[+3]_478 38207 3.7e-06 443_[+3]_36 23584 5.8e-06 327_[+3]_152 735 7.8e-06 455_[+3]_24 36206 7.8e-06 115_[+3]_364 24921 1.5e-05 425_[+3]_54 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=19 3486 ( 476) TCCACCACCGCCACCATCGGC 1 27318 ( 104) ACCATCATCGGCACCTTCCTC 1 1063 ( 435) TCCAACAAGGCCACCAGCGGC 1 37430 ( 389) CCAATCATCGCCCCCATCCAC 1 31859 ( 200) ACATTCCCCGCCACCACCCGC 1 37485 ( 236) ACACCCGACGCCACCGACCGC 1 9321 ( 329) ACATCCTACAGCACCTTCGTC 1 38335 ( 400) TCCACACCCGCCAGCATCCTC 1 18991 ( 451) TCGACCACGGAGACCTTCCTC 1 31046 ( 89) CCAAACAACGCCGCCGTCCGT 1 34785 ( 436) TCTATCGAACCAACCAACCTC 1 36524 ( 147) TGAAACATCACCACCATCGCC 1 6584 ( 383) ACGTCCGACCCATCCGTCGTC 1 6600 ( 2) CCATTCAAACACCCCATCTTC 1 38207 ( 444) ACCATCTCTTCAACCAGCCTC 1 23584 ( 328) ACCACCACCACAACCATACAA 1 735 ( 456) ACCTCCTGGGACAACATCTTC 1 36206 ( 116) ACAAACGACGACCACTGCCTT 1 24921 ( 426) ACTACTGCACACACCGTCGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 11520 bayes= 9.43666 E= 2.5e-005 109 -69 -1089 25 -1089 189 -214 -1089 77 53 -114 -133 147 -227 -1089 -1 -23 89 -1089 25 -223 181 -1089 -233 94 -128 18 -75 77 53 -214 -75 -65 131 -56 -233 -65 -28 132 -233 9 131 -114 -1089 -23 153 -214 -1089 157 -69 -214 -233 -123 172 -214 -1089 -1089 197 -1089 -1089 123 -1089 -14 -33 -123 -227 -56 137 -223 189 -1089 -1089 -1089 118 44 -133 -123 -128 18 99 -223 172 -1089 -133 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 19 E= 2.5e-005 0.526316 0.157895 0.000000 0.315789 0.000000 0.947368 0.052632 0.000000 0.421053 0.368421 0.105263 0.105263 0.684211 0.052632 0.000000 0.263158 0.210526 0.473684 0.000000 0.315789 0.052632 0.894737 0.000000 0.052632 0.473684 0.105263 0.263158 0.157895 0.421053 0.368421 0.052632 0.157895 0.157895 0.631579 0.157895 0.052632 0.157895 0.210526 0.578947 0.052632 0.263158 0.631579 0.105263 0.000000 0.210526 0.736842 0.052632 0.000000 0.736842 0.157895 0.052632 0.052632 0.105263 0.842105 0.052632 0.000000 0.000000 1.000000 0.000000 0.000000 0.578947 0.000000 0.210526 0.210526 0.105263 0.052632 0.157895 0.684211 0.052632 0.947368 0.000000 0.000000 0.000000 0.578947 0.315789 0.105263 0.105263 0.105263 0.263158 0.526316 0.052632 0.842105 0.000000 0.105263 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AT]C[AC][AT][CTA]C[AG][AC]C[GC][CA][CA]ACC[AGT]TC[CG][TG]C -------------------------------------------------------------------------------- Time 15.32 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1063 2.86e-09 264_[+2(3.49e-07)]_64_\ [+1(5.79e-06)]_69_[+3(3.60e-08)]_45 18991 1.09e-09 52_[+2(2.69e-06)]_38_[+2(1.33e-05)]_\ 304_[+1(3.63e-08)]_3_[+3(8.23e-07)]_29 20462 4.66e-04 147_[+2(3.61e-06)]_147_\ [+1(9.69e-06)]_169 22118 3.22e-01 310_[+2(7.28e-05)]_174 23584 1.73e-08 42_[+2(6.46e-05)]_38_[+2(3.06e-07)]_\ 215_[+1(4.73e-06)]_103_[+1(2.86e-07)]_1_[+1(1.24e-05)]_6 24068 1.07e-01 19_[+2(5.06e-05)]_465 24921 6.50e-06 55_[+2(9.14e-05)]_138_\ [+2(1.99e-06)]_200_[+3(1.55e-05)]_11_[+1(1.17e-05)]_22 27318 1.86e-11 13_[+1(4.95e-09)]_69_[+3(1.15e-08)]_\ 170_[+2(5.73e-06)]_190 31046 1.74e-04 88_[+3(1.08e-06)]_137_\ [+2(1.04e-05)]_238 31859 1.15e-11 199_[+3(1.13e-07)]_113_\ [+2(3.49e-07)]_127_[+1(4.95e-09)]_3 34785 3.54e-08 102_[+1(2.89e-08)]_274_\ [+2(2.79e-05)]_22_[+3(1.40e-06)]_44 3486 3.93e-11 75_[+2(9.14e-05)]_4_[+2(1.23e-05)]_\ 305_[+1(4.93e-07)]_38_[+3(1.20e-10)]_4 36206 8.95e-07 83_[+1(1.15e-06)]_11_[+3(7.81e-06)]_\ 229_[+2(4.36e-06)]_119 36524 4.84e-07 146_[+3(1.52e-06)]_54_\ [+2(4.18e-05)]_237_[+1(3.13e-07)]_5 37430 2.98e-09 50_[+2(5.08e-07)]_193_\ [+2(3.61e-06)]_113_[+3(8.12e-08)]_65_[+1(1.84e-06)]_5 37485 1.11e-09 37_[+2(3.96e-06)]_142_\ [+1(5.51e-05)]_19_[+3(1.40e-07)]_22_[+2(4.50e-07)]_184_[+1(4.12e-07)]_1 38207 1.27e-09 72_[+1(1.55e-09)]_58_[+2(5.23e-06)]_\ 85_[+2(9.66e-05)]_129_[+3(8.33e-05)]_25_[+3(3.72e-06)]_36 38335 4.24e-10 1_[+2(7.02e-08)]_37_[+2(8.64e-05)]_\ 279_[+1(1.60e-07)]_29_[+3(8.23e-07)]_4_[+3(8.33e-05)]_55 6376 1.91e-04 260_[+2(1.99e-06)]_192_\ [+1(1.24e-05)]_11 6584 3.16e-08 290_[+2(4.78e-06)]_76_\ [+3(2.94e-06)]_1_[+1(7.04e-08)]_75 6600 4.61e-07 1_[+3(3.18e-06)]_267_[+2(6.86e-05)]_\ 117_[+1(8.29e-05)]_11_[+1(8.71e-08)]_25 735 2.64e-08 88_[+1(3.20e-05)]_227_\ [+2(4.78e-06)]_56_[+1(1.48e-05)]_[+1(3.63e-08)]_5_[+3(7.81e-06)]_24 8937 1.57e-05 297_[+2(2.66e-07)]_128_\ [+1(4.12e-06)]_38 9321 4.29e-09 22_[+2(2.97e-06)]_268_\ [+1(1.60e-07)]_1_[+3(2.36e-07)]_151 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************