******************************************************************************** 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/332/332.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10037 1.0000 500 11667 1.0000 500 1645 1.0000 500 20990 1.0000 500 22032 1.0000 500 22192 1.0000 500 22640 1.0000 500 24320 1.0000 500 24396 1.0000 500 25074 1.0000 500 25172 1.0000 500 262180 1.0000 500 263473 1.0000 500 269231 1.0000 500 3839 1.0000 500 4045 1.0000 500 41636 1.0000 500 4747 1.0000 500 4958 1.0000 500 5171 1.0000 500 661 1.0000 500 6745 1.0000 500 6880 1.0000 500 8228 1.0000 500 8649 1.0000 500 8956 1.0000 500 9222 1.0000 500 954 1.0000 500 bd1851 1.0000 500 bd1888 1.0000 500 bd1954 1.0000 500 bd833 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/332/332.seqs.fa -oc motifs/332 -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= 32 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= 16000 N= 32 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.256 C 0.227 G 0.246 T 0.271 Background letter frequencies (from dataset with add-one prior applied): A 0.256 C 0.227 G 0.246 T 0.270 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 21 llr = 217 E-value = 5.5e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :3::2::21:45 pos.-specific C 9::a:18::a1: probability G :7::7::8::21 matrix T 1:a::92:9:33 bits 2.1 * 1.9 * * 1.7 ** * 1.5 * ** * ** Relative 1.3 * ** * *** Entropy 1.1 ********** (14.9 bits) 0.9 ********** 0.6 ********** 0.4 ********** 0.2 ********** * 0.0 ------------ Multilevel CGTCGTCGTCAA consensus A A TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 24396 273 5.10e-08 GCACGTTGCA CGTCGTCGTCAA TGCTGAGTAG 11667 253 5.10e-08 GCACGTTGCA CGTCGTCGTCAA TGCTGAGTAG 8956 278 1.05e-07 GTTGATGCAC CGTCGTCGTCTA GTCGTCGTCG 22032 151 4.67e-07 ACGGGATCAT CGTCGTCGTCGT GTAGATCAAT 5171 197 4.03e-06 GTGGGCGGCA CGTCGTCATCCT CCTCTTCTCC 4958 450 4.47e-06 AACATCAAGA TATCGTCGTCAA CGCCAACGCT 1645 163 4.47e-06 ATACACCGTG CGTCGTCGACGA CGACTTGATG bd1954 273 4.93e-06 GATACGGTCA CATCGTTGTCAT CTCGAAGGGA 661 175 4.93e-06 ACAAGGCCGA CGTCGTAGTCAA GAGCATTGCT 954 147 5.64e-06 ATTTCTTGCT CGTCGTCGTGAA CAGTGAACGT 6745 243 6.08e-06 AAGAGGTCGT CGTCGTTGTCTG TCGGTGAGGC 22192 244 6.08e-06 AAACACAACT CGTCATTGTCAT CGTCGGAAAT 6880 434 6.55e-06 CCGATGTTCC CGTCGCCGTCGT TTCACCTCAG 20990 452 8.88e-06 ACTAATTTAT CGTCATTGTCCA GTTTATTGAC 9222 171 9.41e-06 TCCAGACTTC CATCATCGTCTG CCCTCTCAAC 263473 18 2.08e-05 GCGAGGCGCT TGTCGTCGTCTC GGCTCTGCAT 25074 431 2.08e-05 TTGATTGCAT CATCGCCATCAA CGCCTTGACC 269231 122 2.74e-05 TGACGGCTGT CGGCATCGTCTT GGTGAGACTG bd833 312 3.59e-05 TGTTGGAGGC TGTCGTCATCGG TCGGTGGTTG 24320 265 3.82e-05 ACCTGCCAGT CATCCTCATCTA CCTACACTCC 4045 281 4.33e-05 GGCAAACAGG CATCATCGACCT TCCGTTTGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24396 5.1e-08 272_[+1]_216 11667 5.1e-08 252_[+1]_236 8956 1e-07 277_[+1]_211 22032 4.7e-07 150_[+1]_338 5171 4e-06 196_[+1]_292 4958 4.5e-06 449_[+1]_39 1645 4.5e-06 162_[+1]_326 bd1954 4.9e-06 272_[+1]_216 661 4.9e-06 174_[+1]_314 954 5.6e-06 146_[+1]_342 6745 6.1e-06 242_[+1]_246 22192 6.1e-06 243_[+1]_245 6880 6.6e-06 433_[+1]_55 20990 8.9e-06 451_[+1]_37 9222 9.4e-06 170_[+1]_318 263473 2.1e-05 17_[+1]_471 25074 2.1e-05 430_[+1]_58 269231 2.7e-05 121_[+1]_367 bd833 3.6e-05 311_[+1]_177 24320 3.8e-05 264_[+1]_224 4045 4.3e-05 280_[+1]_208 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=21 24396 ( 273) CGTCGTCGTCAA 1 11667 ( 253) CGTCGTCGTCAA 1 8956 ( 278) CGTCGTCGTCTA 1 22032 ( 151) CGTCGTCGTCGT 1 5171 ( 197) CGTCGTCATCCT 1 4958 ( 450) TATCGTCGTCAA 1 1645 ( 163) CGTCGTCGACGA 1 bd1954 ( 273) CATCGTTGTCAT 1 661 ( 175) CGTCGTAGTCAA 1 954 ( 147) CGTCGTCGTGAA 1 6745 ( 243) CGTCGTTGTCTG 1 22192 ( 244) CGTCATTGTCAT 1 6880 ( 434) CGTCGCCGTCGT 1 20990 ( 452) CGTCATTGTCCA 1 9222 ( 171) CATCATCGTCTG 1 263473 ( 18) TGTCGTCGTCTC 1 25074 ( 431) CATCGCCATCAA 1 269231 ( 122) CGGCATCGTCTT 1 bd833 ( 312) TGTCGTCATCGG 1 24320 ( 265) CATCCTCATCTA 1 4045 ( 281) CATCATCGACCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 15648 bayes= 10.5267 E= 5.5e-008 -1104 191 -1104 -92 16 -1104 154 -1104 -1104 -1104 -237 182 -1104 214 -1104 -1104 -11 -225 154 -1104 -1104 -125 -1104 174 -243 174 -1104 -51 -43 -1104 172 -1104 -143 -1104 -1104 174 -1104 207 -237 -1104 57 -67 -37 8 89 -225 -78 30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 21 E= 5.5e-008 0.000000 0.857143 0.000000 0.142857 0.285714 0.000000 0.714286 0.000000 0.000000 0.000000 0.047619 0.952381 0.000000 1.000000 0.000000 0.000000 0.238095 0.047619 0.714286 0.000000 0.000000 0.095238 0.000000 0.904762 0.047619 0.761905 0.000000 0.190476 0.190476 0.000000 0.809524 0.000000 0.095238 0.000000 0.000000 0.904762 0.000000 0.952381 0.047619 0.000000 0.380952 0.142857 0.190476 0.285714 0.476190 0.047619 0.142857 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[GA]TC[GA]TCGTC[AT][AT] -------------------------------------------------------------------------------- Time 8.92 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 30 llr = 279 E-value = 1.3e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 57666373:692:97 pos.-specific C 2341372192167:2 probability G 2::31:1311::31: matrix T 1:::1::3:::2::2 bits 2.1 1.9 1.7 * * * 1.5 * * * Relative 1.3 * * * Entropy 1.1 * * * * ** (13.4 bits) 0.9 ** ** * * ** 0.6 *** ** * ***** 0.4 ****** ******* 0.2 ******* ******* 0.0 --------------- Multilevel AAAAACAACAACCAA consensus CCCGCACT C AG sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 24396 14 2.17e-08 CTCAGCCACT CACAACAGCAACCAA TCTAGCAATG 41636 396 1.70e-07 GTTCTACTGC TAAAACATCAACCAA ACCAATGTTT 22032 438 2.00e-07 GCGGACGCGA AAAACCAGCAACCAC AACACAACAC 9222 196 7.93e-07 TCTCAACATA GCAAAAATCAACCAA TCACACAACA 11667 479 1.21e-06 GAATCCACCG CAAAAAAACAATCAA TGCTATC 25074 134 2.46e-06 AGACTGGACG GACGCCCACAACCAA CAGAGAAGAA 24320 228 2.46e-06 ACGACCGTGC ACCACCACCAAACAA CACTGAATCT bd1954 460 4.59e-06 TAAACTTGTA TCAAACATCAACCAC TTCCTTGTCG 22192 413 4.59e-06 AAACAGCTGG AACACAAACCACCAT AAATCAGTGC 8228 460 5.17e-06 CTTTTCGTTC CACACCCTCAATCAA ATCAATCCTT 25172 28 5.17e-06 GGATGACGAA GAAGACAGCGACGAA GAGGAGGAGA bd1851 187 5.83e-06 TACTATGAAC GAAAAAATCAACGAT ATGATGGATA 661 430 6.50e-06 CCCCATTGTA AAACACATCACCCAA ACAATCAGCT 22640 459 8.97e-06 AACCAATACA TCAAAAAACAAACAA TAGCAAACCG bd833 414 1.37e-05 GACGGAAGGG GAAGCCAGCGACCAC AAAATCTGCT 8649 379 1.51e-05 TCACCTCGTT ACAAACAACCAAGAC ACATGATGCT 10037 479 1.66e-05 TCGACCATCA CACACCATCACACAA CTCAAGA 5171 62 2.20e-05 ATATATAAAA AAGCACAACAAACAA ACGCACCTGT 954 190 2.65e-05 GCATATGGGA ACCAACCGCCATGAA CCAGTTGGAG 8956 338 2.65e-05 ATGATGCGAT CAAGCCAAGCACCAA AGGTGGCTTA 6880 152 3.16e-05 GTATCGTTTG AAACACGGCCACGAA TGTTCTTTGC bd1888 157 3.44e-05 GAAAGGAGCT AAAATACTCAATCAA ACTCTCTCCT 4045 450 6.58e-05 GATACTCTCG CACGATACCAAACAA CACTTCGTTG 263473 201 7.64e-05 CAAGATGTTC ACAGACAGCAACGGT GGAAAGCCGC 1645 483 7.64e-05 CGACAACTTC CACAACGACGACGAC ACT 4958 21 1.17e-04 ATCTTTTCTG AACAGAACCCAACAT AAACACGGAA 6745 377 1.53e-04 CGACACAAGC AAAAGCAGGAACCGA GGCAGCCGCA 20990 292 2.50e-04 TCGTGCCTCC AACCAAACCGATGAT GTAGAGGGCG 3839 459 2.65e-04 CTCGTCCGAC GCCGTACACCACGAA GCCATCAGGA 269231 243 2.80e-04 ATTTGTTAGA AAAGCCCTCTACTAA CTGACTCTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24396 2.2e-08 13_[+2]_472 41636 1.7e-07 395_[+2]_90 22032 2e-07 437_[+2]_48 9222 7.9e-07 195_[+2]_290 11667 1.2e-06 478_[+2]_7 25074 2.5e-06 133_[+2]_352 24320 2.5e-06 227_[+2]_258 bd1954 4.6e-06 459_[+2]_26 22192 4.6e-06 412_[+2]_73 8228 5.2e-06 459_[+2]_26 25172 5.2e-06 27_[+2]_458 bd1851 5.8e-06 186_[+2]_299 661 6.5e-06 429_[+2]_56 22640 9e-06 458_[+2]_27 bd833 1.4e-05 413_[+2]_72 8649 1.5e-05 378_[+2]_107 10037 1.7e-05 478_[+2]_7 5171 2.2e-05 61_[+2]_424 954 2.6e-05 189_[+2]_296 8956 2.6e-05 337_[+2]_148 6880 3.2e-05 151_[+2]_334 bd1888 3.4e-05 156_[+2]_329 4045 6.6e-05 449_[+2]_36 263473 7.6e-05 200_[+2]_285 1645 7.6e-05 482_[+2]_3 4958 0.00012 20_[+2]_465 6745 0.00015 376_[+2]_109 20990 0.00025 291_[+2]_194 3839 0.00026 458_[+2]_27 269231 0.00028 242_[+2]_243 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=30 24396 ( 14) CACAACAGCAACCAA 1 41636 ( 396) TAAAACATCAACCAA 1 22032 ( 438) AAAACCAGCAACCAC 1 9222 ( 196) GCAAAAATCAACCAA 1 11667 ( 479) CAAAAAAACAATCAA 1 25074 ( 134) GACGCCCACAACCAA 1 24320 ( 228) ACCACCACCAAACAA 1 bd1954 ( 460) TCAAACATCAACCAC 1 22192 ( 413) AACACAAACCACCAT 1 8228 ( 460) CACACCCTCAATCAA 1 25172 ( 28) GAAGACAGCGACGAA 1 bd1851 ( 187) GAAAAAATCAACGAT 1 661 ( 430) AAACACATCACCCAA 1 22640 ( 459) TCAAAAAACAAACAA 1 bd833 ( 414) GAAGCCAGCGACCAC 1 8649 ( 379) ACAAACAACCAAGAC 1 10037 ( 479) CACACCATCACACAA 1 5171 ( 62) AAGCACAACAAACAA 1 954 ( 190) ACCAACCGCCATGAA 1 8956 ( 338) CAAGCCAAGCACCAA 1 6880 ( 152) AAACACGGCCACGAA 1 bd1888 ( 157) AAAATACTCAATCAA 1 4045 ( 450) CACGATACCAAACAA 1 263473 ( 201) ACAGACAGCAACGGT 1 1645 ( 483) CACAACGACGACGAC 1 4958 ( 21) AACAGAACCCAACAT 1 6745 ( 377) AAAAGCAGGAACCGA 1 20990 ( 292) AACCAAACCGATGAT 1 3839 ( 459) GCCGTACACCACGAA 1 269231 ( 243) AAAGCCCTCTACTAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 15552 bayes= 8.94003 E= 1.3e-006 86 4 -30 -143 152 23 -1155 -1155 114 82 -288 -1155 123 -77 12 -1155 114 40 -188 -202 23 155 -1155 -302 152 -18 -188 -1155 23 -77 12 15 -1155 204 -188 -1155 123 4 -88 -302 186 -177 -1155 -1155 -14 140 -1155 -70 -1155 155 29 -302 186 -1155 -188 -1155 138 -45 -1155 -70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 30 E= 1.3e-006 0.466667 0.233333 0.200000 0.100000 0.733333 0.266667 0.000000 0.000000 0.566667 0.400000 0.033333 0.000000 0.600000 0.133333 0.266667 0.000000 0.566667 0.300000 0.066667 0.066667 0.300000 0.666667 0.000000 0.033333 0.733333 0.200000 0.066667 0.000000 0.300000 0.133333 0.266667 0.300000 0.000000 0.933333 0.066667 0.000000 0.600000 0.233333 0.133333 0.033333 0.933333 0.066667 0.000000 0.000000 0.233333 0.600000 0.000000 0.166667 0.000000 0.666667 0.300000 0.033333 0.933333 0.000000 0.066667 0.000000 0.666667 0.166667 0.000000 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [ACG][AC][AC][AG][AC][CA][AC][ATG]C[AC]A[CA][CG]AA -------------------------------------------------------------------------------- Time 17.71 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 20 llr = 222 E-value = 3.7e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::::1122:::8212: pos.-specific C 31::::1:::1::51: probability G 744299:18572813a matrix T 16681188253:1451 bits 2.1 1.9 1.7 * 1.5 * Relative 1.3 *** * * * Entropy 1.1 ***** * ** * (16.0 bits) 0.9 * *********** * 0.6 ************* * 0.4 ************** * 0.2 **************** 0.0 ---------------- Multilevel GTTTGGTTGGGAGCTG consensus CGGG TTTG TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 4045 44 3.26e-08 CGAGTGATTT GTTTGGTTGTGAGATG GTGCAGTGCG 24320 332 3.94e-08 CACGCAATAC GGTTGGTTGGTAGCGG CGTTTTTGCC 661 130 7.28e-08 AAGTTGATGT GTGTGGTTTTGAGTTG GAACGCTTTT bd1954 325 2.04e-07 CTCGTCGGGA CGTTGGTAGTGAGTTG ATACTAGACG 24396 58 5.86e-07 AGAAATCGCT GTGTGGTTTTCAGCTG GAGAGGACGT 11667 38 5.86e-07 AGAAATCGCT GTGTGGTTTTCAGCTG GAGAGGACGT 5171 466 8.03e-07 CAAACGCCCA CGTTGTTTGGGAGTGG GCCACCTTCA bd1888 44 1.96e-06 GCACTGACCT CTTTGTTTGTGAACTG AGTTCATCGC bd833 325 2.15e-06 CGTCATCGGT CGGTGGTTGTGAGGAG GTCGTCTCTG 8649 141 3.09e-06 GGAACGGAGA GTTGAGTTTGGAGTTG GAGTGCTAGA 6880 226 4.35e-06 GAACATCGTT GTTTGGAAGGGAGTCG TCATCCCGTC 41636 123 4.35e-06 CGAGAGGTTG TTGTGGTTGTTGGCTG TGGGTGCCGG 8956 109 6.04e-06 ACGATGATGG GTTGAGTTGGTGGCTG CGACGAGGGA 4747 59 7.09e-06 TCGGTTTGCT GTTTGGTGGGGAGCAT GGAGAGAGAG 22032 67 7.09e-06 ACGAACGATG GTTGGATTGGGAATTG AAGGAGGTGT 20990 184 7.09e-06 ACCTTGGTTT CGTTGGATGGGGACGG TAGAAGATGA 263473 83 7.66e-06 TAGTATCAGA GGTGGGTTGGTATTGG CACGGATGCT 9222 267 8.95e-06 ACTTATCGGT GCGTTGTTGTGAGTGG GTGCTGTAAT 3839 333 1.84e-05 CGGAGGGACC GGGTGGCGGTGAGAGG ATTTGATCCC 1645 344 3.30e-05 CTGGACGCGA CGGTGGAAGGTGGCAG AGGAGGGTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4045 3.3e-08 43_[+3]_441 24320 3.9e-08 331_[+3]_153 661 7.3e-08 129_[+3]_355 bd1954 2e-07 324_[+3]_160 24396 5.9e-07 57_[+3]_427 11667 5.9e-07 37_[+3]_447 5171 8e-07 465_[+3]_19 bd1888 2e-06 43_[+3]_441 bd833 2.2e-06 324_[+3]_160 8649 3.1e-06 140_[+3]_344 6880 4.3e-06 225_[+3]_259 41636 4.3e-06 122_[+3]_362 8956 6e-06 108_[+3]_376 4747 7.1e-06 58_[+3]_426 22032 7.1e-06 66_[+3]_418 20990 7.1e-06 183_[+3]_301 263473 7.7e-06 82_[+3]_402 9222 8.9e-06 266_[+3]_218 3839 1.8e-05 332_[+3]_152 1645 3.3e-05 343_[+3]_141 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=20 4045 ( 44) GTTTGGTTGTGAGATG 1 24320 ( 332) GGTTGGTTGGTAGCGG 1 661 ( 130) GTGTGGTTTTGAGTTG 1 bd1954 ( 325) CGTTGGTAGTGAGTTG 1 24396 ( 58) GTGTGGTTTTCAGCTG 1 11667 ( 38) GTGTGGTTTTCAGCTG 1 5171 ( 466) CGTTGTTTGGGAGTGG 1 bd1888 ( 44) CTTTGTTTGTGAACTG 1 bd833 ( 325) CGGTGGTTGTGAGGAG 1 8649 ( 141) GTTGAGTTTGGAGTTG 1 6880 ( 226) GTTTGGAAGGGAGTCG 1 41636 ( 123) TTGTGGTTGTTGGCTG 1 8956 ( 109) GTTGAGTTGGTGGCTG 1 4747 ( 59) GTTTGGTGGGGAGCAT 1 22032 ( 67) GTTGGATTGGGAATTG 1 20990 ( 184) CGTTGGATGGGGACGG 1 263473 ( 83) GGTGGGTTGGTATTGG 1 9222 ( 267) GCGTTGTTGTGAGTGG 1 3839 ( 333) GGGTGGCGGTGAGAGG 1 1645 ( 344) CGGTGGAAGGTGGCAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 15520 bayes= 9.84989 E= 3.7e-003 -1097 40 140 -243 -1097 -218 70 102 -1097 -1097 70 115 -1097 -1097 -30 156 -136 -1097 179 -243 -235 -1097 179 -143 -77 -218 -1097 156 -77 -1097 -130 147 -1097 -1097 170 -44 -1097 -1097 102 89 -1097 -118 140 -11 164 -1097 -30 -1097 -77 -1097 170 -243 -136 98 -230 56 -77 -218 29 89 -1097 -1097 195 -243 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 20 E= 3.7e-003 0.000000 0.300000 0.650000 0.050000 0.000000 0.050000 0.400000 0.550000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 0.200000 0.800000 0.100000 0.000000 0.850000 0.050000 0.050000 0.000000 0.850000 0.100000 0.150000 0.050000 0.000000 0.800000 0.150000 0.000000 0.100000 0.750000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.500000 0.500000 0.000000 0.100000 0.650000 0.250000 0.800000 0.000000 0.200000 0.000000 0.150000 0.000000 0.800000 0.050000 0.100000 0.450000 0.050000 0.400000 0.150000 0.050000 0.300000 0.500000 0.000000 0.000000 0.950000 0.050000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC][TG][TG][TG]GGTT[GT][GT][GT][AG]G[CT][TG]G -------------------------------------------------------------------------------- Time 25.86 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10037 2.28e-02 478_[+2(1.66e-05)]_7 11667 1.55e-09 37_[+3(5.86e-07)]_199_\ [+1(5.10e-08)]_214_[+2(1.21e-06)]_7 1645 1.35e-04 162_[+1(4.47e-06)]_169_\ [+3(3.30e-05)]_123_[+2(7.64e-05)]_3 20990 1.74e-04 183_[+3(7.09e-06)]_252_\ [+1(8.88e-06)]_37 22032 2.25e-08 66_[+3(7.09e-06)]_68_[+1(4.67e-07)]_\ 126_[+3(7.37e-05)]_133_[+2(2.00e-07)]_5_[+2(7.64e-05)]_28 22192 1.41e-04 243_[+1(6.08e-06)]_157_\ [+2(4.59e-06)]_73 22640 1.53e-02 458_[+2(8.97e-06)]_27 24320 1.08e-07 227_[+2(2.46e-06)]_22_\ [+1(3.82e-05)]_55_[+3(3.94e-08)]_153 24396 3.65e-11 13_[+2(2.17e-08)]_29_[+3(5.86e-07)]_\ 199_[+1(5.10e-08)]_216 25074 9.27e-04 133_[+2(2.46e-06)]_282_\ [+1(2.08e-05)]_58 25172 3.88e-02 27_[+2(5.17e-06)]_458 262180 6.25e-01 500 263473 1.45e-04 17_[+1(2.08e-05)]_53_[+3(7.66e-06)]_\ 102_[+2(7.64e-05)]_285 269231 2.85e-02 121_[+1(2.74e-05)]_367 3839 1.64e-02 332_[+3(1.84e-05)]_152 4045 1.96e-06 43_[+3(3.26e-08)]_221_\ [+1(4.33e-05)]_157_[+2(6.58e-05)]_36 41636 1.78e-05 122_[+3(4.35e-06)]_257_\ [+2(1.70e-07)]_90 4747 8.98e-03 58_[+3(7.09e-06)]_426 4958 3.01e-03 449_[+1(4.47e-06)]_39 5171 1.57e-06 61_[+2(2.20e-05)]_120_\ [+1(4.03e-06)]_257_[+3(8.03e-07)]_19 661 7.13e-08 129_[+3(7.28e-08)]_29_\ [+1(4.93e-06)]_243_[+2(6.50e-06)]_56 6745 3.12e-03 242_[+1(6.08e-06)]_246 6880 1.50e-05 151_[+2(3.16e-05)]_59_\ [+3(4.35e-06)]_192_[+1(6.55e-06)]_55 8228 3.40e-02 459_[+2(5.17e-06)]_26 8649 5.63e-04 121_[+3(6.98e-05)]_3_[+3(3.09e-06)]_\ 222_[+2(1.51e-05)]_107 8956 4.26e-07 108_[+3(6.04e-06)]_153_\ [+1(1.05e-07)]_48_[+2(2.65e-05)]_148 9222 1.49e-06 170_[+1(9.41e-06)]_13_\ [+2(7.93e-07)]_56_[+3(8.95e-06)]_218 954 1.33e-03 146_[+1(5.64e-06)]_31_\ [+2(2.65e-05)]_296 bd1851 1.49e-02 186_[+2(5.83e-06)]_299 bd1888 8.04e-04 43_[+3(1.96e-06)]_97_[+2(3.44e-05)]_\ 329 bd1954 1.33e-07 272_[+1(4.93e-06)]_40_\ [+3(2.04e-07)]_119_[+2(4.59e-06)]_26 bd833 1.73e-05 311_[+1(3.59e-05)]_1_[+3(2.15e-06)]_\ 73_[+2(1.37e-05)]_72 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************