******************************************************************************** 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/206/206.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10396 1.0000 500 10731 1.0000 500 11530 1.0000 500 2060 1.0000 500 22248 1.0000 500 23931 1.0000 500 260812 1.0000 500 261126 1.0000 500 261817 1.0000 500 269777 1.0000 500 2790 1.0000 500 27986 1.0000 500 32261 1.0000 500 32507 1.0000 500 34399 1.0000 500 3621 1.0000 500 36459 1.0000 500 37264 1.0000 500 39520 1.0000 500 40826 1.0000 500 4160 1.0000 500 4981 1.0000 500 6418 1.0000 500 9065 1.0000 500 9772 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/206/206.seqs.fa -oc motifs/206 -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= 25 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= 12500 N= 25 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.257 C 0.238 G 0.236 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.257 C 0.238 G 0.236 T 0.269 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 21 llr = 265 E-value = 7.5e-013 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 3482655:83144:37:2432 pos.-specific C 76:8324a:672566287258 probability G :::::1::2::4:11::1:1: matrix T ::2::1::::1:13::1:3:: bits 2.1 1.9 * 1.7 * 1.5 * Relative 1.3 ** * * * Entropy 1.0 **** ** * * (18.2 bits) 0.8 ***** *** * *** * 0.6 ***** ***** * **** ** 0.4 ***** ************ ** 0.2 ********************* 0.0 --------------------- Multilevel CCACAAACACCACCCACCACC consensus AAT CCC A GATA TAA sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 32507 474 7.00e-12 GCTCTCGACG CCACCAACACCGCCCACCTCC GTGACC 260812 461 7.68e-10 TCCCTTCTCA CAACCCACACCACCAACCTCC TTGGTGCACC 2790 388 1.78e-09 GATCGTTTGC CCACAGACACCCATCACCTCC CAAAATCCAC 39520 453 5.47e-08 CATATTATCC ACTCAACCACTGATCACCTCC ATCCAACCCG 11530 323 1.08e-07 CAAGAACCAC CCTCAACCACCCCCGACGCCC AAACTCTCGC 4981 416 1.20e-07 CTATCAAAGT CAACAACCATTGACAACCACC TCCCCCCTCT 40826 404 1.20e-07 TCCACGTCAC ACACAACCAACGATCTCCTCC CGGACAAACG 3621 397 2.24e-07 AACAACAAAC CAACAAACGACGTGCACCAAC CAAACTTGAT 261817 106 3.66e-07 ATCCAGCGAG CAAACTCCACCACCAACCAAA CTTTTCTCCA 6418 469 5.83e-07 TGCCCCACAA CCACAACCACAACTCAACAAA GCGGCAACAC 261126 257 6.98e-07 GTCGATAGCT CCTAATACACCACCCCCATCC CCACTCAAAT 27986 445 9.08e-07 TGCTAACTAA CCACCAACGCCACAAACAAGC CGCGTCCAAC 23931 473 9.90e-07 TTCTCCAACT AATCCAACACAACCACCCCAC CATCGCC 4160 29 1.17e-06 ACTCTAGATG CAACCAACAGCAACCATCAGA ACAAAGCCTC 10731 479 1.38e-06 TTAATCTTCC CAACACCCACACCGCACAAAA C 22248 409 2.23e-06 GCCGCACCTA ACAAACACACCAACAGCCGCC GACGGATCCA 37264 397 3.25e-06 GCTCGTCGCT CCACTCCCGACGACGACGACC TACGACGCTA 36459 185 4.34e-06 TAGTCCCGGT CCAACCGCCACGACCACCCCC TCGTTCGGAT 9772 211 4.65e-06 GCCAAGAAGA AATCAGCCGCCGCCGCCAAAC CGAAGAAAGA 9065 388 7.97e-06 ATTAGCATCT ACACAGAAAACCCTCATCTGC TCCCTCATAT 2060 270 2.57e-05 GTGGAGGGGA AAACAAACAATCTTCCTCCAA GCTCGGCTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 32507 7e-12 473_[+1]_6 260812 7.7e-10 460_[+1]_19 2790 1.8e-09 387_[+1]_92 39520 5.5e-08 452_[+1]_27 11530 1.1e-07 322_[+1]_157 4981 1.2e-07 415_[+1]_64 40826 1.2e-07 403_[+1]_76 3621 2.2e-07 396_[+1]_83 261817 3.7e-07 105_[+1]_374 6418 5.8e-07 468_[+1]_11 261126 7e-07 256_[+1]_223 27986 9.1e-07 444_[+1]_35 23931 9.9e-07 472_[+1]_7 4160 1.2e-06 28_[+1]_451 10731 1.4e-06 478_[+1]_1 22248 2.2e-06 408_[+1]_71 37264 3.3e-06 396_[+1]_83 36459 4.3e-06 184_[+1]_295 9772 4.7e-06 210_[+1]_269 9065 8e-06 387_[+1]_92 2060 2.6e-05 269_[+1]_210 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=21 32507 ( 474) CCACCAACACCGCCCACCTCC 1 260812 ( 461) CAACCCACACCACCAACCTCC 1 2790 ( 388) CCACAGACACCCATCACCTCC 1 39520 ( 453) ACTCAACCACTGATCACCTCC 1 11530 ( 323) CCTCAACCACCCCCGACGCCC 1 4981 ( 416) CAACAACCATTGACAACCACC 1 40826 ( 404) ACACAACCAACGATCTCCTCC 1 3621 ( 397) CAACAAACGACGTGCACCAAC 1 261817 ( 106) CAAACTCCACCACCAACCAAA 1 6418 ( 469) CCACAACCACAACTCAACAAA 1 261126 ( 257) CCTAATACACCACCCCCATCC 1 27986 ( 445) CCACCAACGCCACAAACAAGC 1 23931 ( 473) AATCCAACACAACCACCCCAC 1 4160 ( 29) CAACCAACAGCAACCATCAGA 1 10731 ( 479) CAACACCCACACCGCACAAAA 1 22248 ( 409) ACAAACACACCAACAGCCGCC 1 37264 ( 397) CCACTCCCGACGACGACGACC 1 36459 ( 185) CCAACCGCCACGACCACCCCC 1 9772 ( 211) AATCAGCCGCCGCCGCCAAAC 1 9065 ( 388) ACACAGAAAACCCTCATCTGC 1 2060 ( 270) AAACAAACAATCTTCCTCCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 12000 bayes= 10.1435 E= 7.5e-013 37 149 -1104 -1104 74 126 -1104 -1104 157 -1104 -1104 -18 -43 177 -1104 -1104 127 49 -1104 -250 103 0 -72 -150 103 85 -230 -1104 -243 200 -1104 -1104 157 -232 -31 -1104 15 138 -230 -250 -85 159 -1104 -91 57 0 69 -1104 57 114 -1104 -150 -243 126 -131 9 15 126 -72 -1104 147 -32 -230 -250 -243 177 -1104 -91 -43 159 -131 -1104 74 -32 -230 31 37 114 -72 -1104 -11 168 -1104 -1104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 21 E= 7.5e-013 0.333333 0.666667 0.000000 0.000000 0.428571 0.571429 0.000000 0.000000 0.761905 0.000000 0.000000 0.238095 0.190476 0.809524 0.000000 0.000000 0.619048 0.333333 0.000000 0.047619 0.523810 0.238095 0.142857 0.095238 0.523810 0.428571 0.047619 0.000000 0.047619 0.952381 0.000000 0.000000 0.761905 0.047619 0.190476 0.000000 0.285714 0.619048 0.047619 0.047619 0.142857 0.714286 0.000000 0.142857 0.380952 0.238095 0.380952 0.000000 0.380952 0.523810 0.000000 0.095238 0.047619 0.571429 0.095238 0.285714 0.285714 0.571429 0.142857 0.000000 0.714286 0.190476 0.047619 0.047619 0.047619 0.809524 0.000000 0.142857 0.190476 0.714286 0.095238 0.000000 0.428571 0.190476 0.047619 0.333333 0.333333 0.523810 0.142857 0.000000 0.238095 0.761905 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA][CA][AT]C[AC][AC][AC]CA[CA]C[AGC][CA][CT][CA]ACC[AT][CA][CA] -------------------------------------------------------------------------------- Time 5.30 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 25 llr = 245 E-value = 2.8e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1:2:322:4:3::721 pos.-specific C ::2:1::::::::::: probability G 65:a62582734a:28 matrix T 346::6424236:362 bits 2.1 * * 1.9 * * 1.7 * * 1.5 * * * Relative 1.3 * * * Entropy 1.0 * * * * * (14.2 bits) 0.8 ** * * * *** * 0.6 ***** ** * ***** 0.4 ********** ***** 0.2 **************** 0.0 ---------------- Multilevel GGTGGTGGTGATGATG consensus TTA AGT ATGG TG sequence T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 269777 230 1.13e-08 CGCTTACCGA GGTGGTGGAGATGAGG GCGAAGAGGG 32261 291 2.55e-07 GTGGGTTGAG GGAGGAGGTGATGATG GCAGGCGATG 261126 451 1.18e-06 GTGCGTAAGT GTCGATTGTGTGGATG AATTGGAGGA 36459 350 1.36e-06 GAACATTGTT GTTGGGTGTGGTGTAG TGAGCAGCTG 22248 134 1.55e-06 CGACGTAGGA TGTGATTGATATGATG ACGATGAAGG 37264 58 2.27e-06 GTATTCATAC GGTGAGGGAGCTGATG CAAGATTTGC 32507 78 2.27e-06 ATTTGGACTG TTTGGTGGATTTGTTG ACGAGAGGTT 10731 109 5.12e-06 GCGTAAGAAA GGAGGAGGAGGGGATT AGTGTAAATA 9065 38 6.34e-06 CCGTGTAGCG TGTGGTGGTTGTGATA CTGATGATGT 6418 384 8.62e-06 GTTGAACAAC GTTGGTGTTGGTGTTT CGTAAAACGT 11530 111 8.62e-06 GCCATGCTTG GTCGATGGTGTTGATA AAGTTTTGTT 34399 25 1.05e-05 GCCTTGTTTT TCTGGTGGGGAGGATG GTTGCTCAAC 9772 428 1.15e-05 ATGATGGGAC GGAGGTTGAGTTGGGG CCTGCGGAGG 4981 106 1.39e-05 ATGCGTTGCA GTCGGTTGATGGGTGG CGATGGGTGA 260812 104 1.39e-05 GAGATACTTC AGAGGGTGAGATGAAG TTTGGAACAA 39520 286 1.67e-05 AGGCTCTCTT TGCGGTAGGGAGGAGG CTCGATTGCT 23931 321 1.67e-05 ACGAGCTCAT TGTGATGGTGTGGTGT GGGGTCTGCT 2060 55 2.35e-05 AGATTGAGAT GGAGAGAGTTTTGTTG CAGTACCGCA 3621 32 2.56e-05 TGAAGTTGTT GGTGAATGTGGCGTTG TGGTTTGGAA 10396 129 2.56e-05 CGATGGTTCC ATTGGGAGTGTGGAAG AGTTTGCCGC 2790 95 2.77e-05 TCGAAACGGT GGTGCCGGAGGGGAAG TTGCGAAGTA 40826 1 3.51e-05 . GTTGTTGGACATGATG GAGGATAGAG 261817 456 4.09e-05 TGGTGCCATC TTTGGTATTTGGGAGG TGTTTTGGGG 27986 138 9.22e-05 TGCTACTGAG TTTGCATTGGATGATG ATTCCTTTCG 4160 204 1.55e-04 CAACTGAAAA GTAGAGTTGGTTGAAT TAAGTTTAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 269777 1.1e-08 229_[+2]_255 32261 2.5e-07 290_[+2]_194 261126 1.2e-06 450_[+2]_34 36459 1.4e-06 349_[+2]_135 22248 1.6e-06 133_[+2]_351 37264 2.3e-06 57_[+2]_427 32507 2.3e-06 77_[+2]_407 10731 5.1e-06 108_[+2]_376 9065 6.3e-06 37_[+2]_447 6418 8.6e-06 383_[+2]_101 11530 8.6e-06 110_[+2]_374 34399 1e-05 24_[+2]_460 9772 1.2e-05 427_[+2]_57 4981 1.4e-05 105_[+2]_379 260812 1.4e-05 103_[+2]_381 39520 1.7e-05 285_[+2]_199 23931 1.7e-05 320_[+2]_164 2060 2.4e-05 54_[+2]_430 3621 2.6e-05 31_[+2]_453 10396 2.6e-05 128_[+2]_356 2790 2.8e-05 94_[+2]_390 40826 3.5e-05 [+2]_484 261817 4.1e-05 455_[+2]_29 27986 9.2e-05 137_[+2]_347 4160 0.00015 203_[+2]_281 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=25 269777 ( 230) GGTGGTGGAGATGAGG 1 32261 ( 291) GGAGGAGGTGATGATG 1 261126 ( 451) GTCGATTGTGTGGATG 1 36459 ( 350) GTTGGGTGTGGTGTAG 1 22248 ( 134) TGTGATTGATATGATG 1 37264 ( 58) GGTGAGGGAGCTGATG 1 32507 ( 78) TTTGGTGGATTTGTTG 1 10731 ( 109) GGAGGAGGAGGGGATT 1 9065 ( 38) TGTGGTGGTTGTGATA 1 6418 ( 384) GTTGGTGTTGGTGTTT 1 11530 ( 111) GTCGATGGTGTTGATA 1 34399 ( 25) TCTGGTGGGGAGGATG 1 9772 ( 428) GGAGGTTGAGTTGGGG 1 4981 ( 106) GTCGGTTGATGGGTGG 1 260812 ( 104) AGAGGGTGAGATGAAG 1 39520 ( 286) TGCGGTAGGGAGGAGG 1 23931 ( 321) TGTGATGGTGTGGTGT 1 2060 ( 55) GGAGAGAGTTTTGTTG 1 3621 ( 32) GGTGAATGTGGCGTTG 1 10396 ( 129) ATTGGGAGTGTGGAAG 1 2790 ( 95) GGTGCCGGAGGGGAAG 1 40826 ( 1) GTTGTTGGACATGATG 1 261817 ( 456) TTTGGTATTTGGGAGG 1 27986 ( 138) TTTGCATTGGATGATG 1 4160 ( 204) GTAGAGTTGGTTGAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 12125 bayes= 8.91886 E= 2.8e-006 -168 -1129 135 25 -1129 -257 114 71 -10 -57 -1129 116 -1129 -1129 208 -1129 31 -157 125 -275 -68 -257 3 106 -68 -1129 103 42 -1129 -1129 183 -75 64 -1129 -56 71 -1129 -257 161 -17 31 -257 44 25 -1129 -257 61 116 -1129 -1129 208 -1129 140 -1129 -256 6 -36 -1129 3 106 -168 -1129 169 -75 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 25 E= 2.8e-006 0.080000 0.000000 0.600000 0.320000 0.000000 0.040000 0.520000 0.440000 0.240000 0.160000 0.000000 0.600000 0.000000 0.000000 1.000000 0.000000 0.320000 0.080000 0.560000 0.040000 0.160000 0.040000 0.240000 0.560000 0.160000 0.000000 0.480000 0.360000 0.000000 0.000000 0.840000 0.160000 0.400000 0.000000 0.160000 0.440000 0.000000 0.040000 0.720000 0.240000 0.320000 0.040000 0.320000 0.320000 0.000000 0.040000 0.360000 0.600000 0.000000 0.000000 1.000000 0.000000 0.680000 0.000000 0.040000 0.280000 0.200000 0.000000 0.240000 0.560000 0.080000 0.000000 0.760000 0.160000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][GT][TA]G[GA][TG][GT]G[TA][GT][AGT][TG]G[AT][TGA]G -------------------------------------------------------------------------------- Time 10.54 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 22 llr = 212 E-value = 3.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :2312::2:::4232 pos.-specific C ::::2::2:1::::: probability G 7427:48:8:a5:68 matrix T 3452562629:171: bits 2.1 1.9 * 1.7 * 1.5 * ** * Relative 1.3 * * ** * Entropy 1.0 * ** *** * (13.9 bits) 0.8 * * ** *** *** 0.6 * * ** ******* 0.4 * ** ********** 0.2 *************** 0.0 --------------- Multilevel GGTGTTGTGTGGTGG consensus TTA AG AAA sequence AG C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 23931 358 1.95e-08 CGTTCGATTT GGTGCTGTGTGATGG CGAAGGCAAG 261817 294 2.07e-06 CCTGGTAAGT GATGTTTTGTGATAG AAGAGAGGCT 9772 410 2.95e-06 ATGGGGTCAA GATGTTGTATGATGG GACGGAGGTT 269777 270 3.31e-06 GAACTTCATG GTTGGGGAGTGGTGG TCAGGTGGAG 4981 128 4.65e-06 GTGGCGATGG GTGATGGCGTGATGG GTGTCACGCA 261126 469 4.65e-06 TGTGGATGAA TTGGAGGAGTGGTGG GGGGAGATAC 11530 144 5.75e-06 GTTGGAGAAT GGATTGGTGTGATGA AATGGCAGCA 6418 80 7.85e-06 AGTACGTTGT TTTGTTGTGTGTTGA TGGTATCATC 34399 376 9.56e-06 TCTGTTTTCA GTTGATGTGTGTTTG GTATTTAATT 3621 260 1.05e-05 GAGCGATGAC GTTGTGTTTTGGTAG GTATCTTACC 2060 95 1.05e-05 TGAATAAGCA GTAGCTGTGTGAATG AGGTTACGAC 4160 96 1.27e-05 GAGGAAACGT GTTTCTGTTTGGAGG ATCTGCCAAA 36459 406 1.27e-05 CTTATGTTCG TGTGATGTGCGGTAG ATCGATCCAT 260812 189 1.27e-05 GGACAATGCC GAAGAGGTGTGGAGA ATGGAGACTA 32261 83 1.68e-05 TCATGTTGAT GGAGTTGAGTGGGAG GTTGGTGGAG 27986 379 1.68e-05 ATAATGCGTG GGAACTGCGTGAAGG ATATCTTCCT 32507 267 1.83e-05 TTTAGAGAGT TAGGTGTCGTGGTGG CCTCGAAGGG 37264 131 3.28e-05 TCGTCGCCAT GATGTTGGTTGAAGG GCCACAGCCA 39520 336 3.56e-05 GCTGCACTTT GGAGCTGATCGGTGG AGGCCTTCGC 10731 54 5.19e-05 GAAAAAAGAT TCGTTTGTGTGATAG CAAGTGCTTG 10396 359 7.91e-05 AAGACAACGC GGTTTGTCGTGGTAA ATCTTCATTT 22248 196 9.07e-05 GCCATTGTAT TGGAATGTGTTGTGG GGACCTCGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23931 2e-08 357_[+3]_128 261817 2.1e-06 293_[+3]_192 9772 3e-06 409_[+3]_76 269777 3.3e-06 269_[+3]_216 4981 4.7e-06 127_[+3]_358 261126 4.7e-06 468_[+3]_17 11530 5.7e-06 143_[+3]_342 6418 7.8e-06 79_[+3]_406 34399 9.6e-06 375_[+3]_110 3621 1.1e-05 259_[+3]_226 2060 1.1e-05 94_[+3]_391 4160 1.3e-05 95_[+3]_390 36459 1.3e-05 405_[+3]_80 260812 1.3e-05 188_[+3]_297 32261 1.7e-05 82_[+3]_403 27986 1.7e-05 378_[+3]_107 32507 1.8e-05 266_[+3]_219 37264 3.3e-05 130_[+3]_355 39520 3.6e-05 335_[+3]_150 10731 5.2e-05 53_[+3]_432 10396 7.9e-05 358_[+3]_127 22248 9.1e-05 195_[+3]_290 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=22 23931 ( 358) GGTGCTGTGTGATGG 1 261817 ( 294) GATGTTTTGTGATAG 1 9772 ( 410) GATGTTGTATGATGG 1 269777 ( 270) GTTGGGGAGTGGTGG 1 4981 ( 128) GTGATGGCGTGATGG 1 261126 ( 469) TTGGAGGAGTGGTGG 1 11530 ( 144) GGATTGGTGTGATGA 1 6418 ( 80) TTTGTTGTGTGTTGA 1 34399 ( 376) GTTGATGTGTGTTTG 1 3621 ( 260) GTTGTGTTTTGGTAG 1 2060 ( 95) GTAGCTGTGTGAATG 1 4160 ( 96) GTTTCTGTTTGGAGG 1 36459 ( 406) TGTGATGTGCGGTAG 1 260812 ( 189) GAAGAGGTGTGGAGA 1 32261 ( 83) GGAGTTGAGTGGGAG 1 27986 ( 379) GGAACTGCGTGAAGG 1 32507 ( 267) TAGGTGTCGTGGTGG 1 37264 ( 131) GATGTTGGTTGAAGG 1 39520 ( 336) GGAGCTGATCGGTGG 1 10731 ( 54) TCGTTTGTGTGATAG 1 10396 ( 359) GGTTTGTCGTGGTAA 1 22248 ( 196) TGGAATGTGTTGTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 12150 bayes= 9.46229 E= 3.5e+000 -1110 -1110 163 2 -18 -239 63 43 8 -1110 -5 89 -92 -1110 153 -57 -18 -7 -237 89 -1110 -1110 63 124 -1110 -1110 180 -57 -50 -39 -237 113 -250 -1110 171 -57 -1110 -139 -1110 176 -1110 -1110 202 -256 67 -1110 108 -156 -18 -1110 -237 143 8 -1110 143 -156 -50 -1110 180 -1110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 22 E= 3.5e+000 0.000000 0.000000 0.727273 0.272727 0.227273 0.045455 0.363636 0.363636 0.272727 0.000000 0.227273 0.500000 0.136364 0.000000 0.681818 0.181818 0.227273 0.227273 0.045455 0.500000 0.000000 0.000000 0.363636 0.636364 0.000000 0.000000 0.818182 0.181818 0.181818 0.181818 0.045455 0.590909 0.045455 0.000000 0.772727 0.181818 0.000000 0.090909 0.000000 0.909091 0.000000 0.000000 0.954545 0.045455 0.409091 0.000000 0.500000 0.090909 0.227273 0.000000 0.045455 0.727273 0.272727 0.000000 0.636364 0.090909 0.181818 0.000000 0.818182 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GT][GTA][TAG]G[TAC][TG]GTGTG[GA][TA][GA]G -------------------------------------------------------------------------------- Time 15.22 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10396 1.17e-02 128_[+2(2.56e-05)]_214_\ [+3(7.91e-05)]_127 10731 6.67e-06 53_[+3(5.19e-05)]_40_[+2(5.12e-06)]_\ 354_[+1(1.38e-06)]_1 11530 1.49e-07 110_[+2(8.62e-06)]_17_\ [+3(5.75e-06)]_164_[+1(1.08e-07)]_157 2060 8.18e-05 54_[+2(2.35e-05)]_24_[+3(1.05e-05)]_\ 160_[+1(2.57e-05)]_210 22248 5.76e-06 133_[+2(1.55e-06)]_46_\ [+3(9.07e-05)]_198_[+1(2.23e-06)]_24_[+1(2.07e-05)]_26 23931 1.14e-08 320_[+2(1.67e-05)]_21_\ [+3(1.95e-08)]_100_[+1(9.90e-07)]_7 260812 5.13e-09 103_[+2(1.39e-05)]_69_\ [+3(1.27e-05)]_257_[+1(7.68e-10)]_19 261126 1.11e-07 256_[+1(6.98e-07)]_173_\ [+2(1.18e-06)]_2_[+3(4.65e-06)]_17 261817 7.29e-07 105_[+1(3.66e-07)]_167_\ [+3(2.07e-06)]_147_[+2(4.09e-05)]_29 269777 1.69e-06 145_[+2(7.63e-05)]_68_\ [+2(1.13e-08)]_24_[+3(3.31e-06)]_216 2790 1.27e-06 94_[+2(2.77e-05)]_277_\ [+1(1.78e-09)]_92 27986 2.16e-05 137_[+2(9.22e-05)]_225_\ [+3(1.68e-05)]_51_[+1(9.08e-07)]_35 32261 1.09e-04 76_[+2(2.27e-06)]_180_\ [+2(4.73e-05)]_2_[+2(2.55e-07)]_194 32507 1.68e-11 77_[+2(2.27e-06)]_173_\ [+3(1.83e-05)]_192_[+1(7.00e-12)]_6 34399 7.08e-04 24_[+2(1.05e-05)]_335_\ [+3(9.56e-06)]_110 3621 1.33e-06 [+2(5.08e-05)]_15_[+2(2.56e-05)]_\ 126_[+3(9.69e-05)]_71_[+3(1.05e-05)]_97_[+1(2.44e-05)]_4_[+1(2.24e-07)]_83 36459 1.62e-06 184_[+1(4.34e-06)]_20_\ [+2(2.77e-05)]_108_[+2(1.36e-06)]_40_[+3(1.27e-05)]_80 37264 4.63e-06 57_[+2(2.27e-06)]_57_[+3(3.28e-05)]_\ 251_[+1(3.25e-06)]_83 39520 7.59e-07 285_[+2(1.67e-05)]_34_\ [+3(3.56e-05)]_20_[+3(8.47e-05)]_67_[+1(5.47e-08)]_27 40826 9.89e-05 [+2(3.51e-05)]_387_[+1(1.20e-07)]_\ 76 4160 3.29e-05 28_[+1(1.17e-06)]_46_[+3(1.27e-05)]_\ 263_[+1(7.93e-05)]_106 4981 2.09e-07 105_[+2(1.39e-05)]_6_[+3(4.65e-06)]_\ 112_[+3(1.99e-05)]_146_[+1(1.20e-07)]_64 6418 9.12e-07 79_[+3(7.85e-06)]_254_\ [+1(4.67e-05)]_14_[+2(8.62e-06)]_69_[+1(5.83e-07)]_11 9065 5.37e-04 37_[+2(6.34e-06)]_334_\ [+1(7.97e-06)]_92 9772 3.18e-06 210_[+1(4.65e-06)]_14_\ [+1(9.73e-05)]_143_[+3(2.95e-06)]_3_[+2(1.15e-05)]_26_[+3(6.02e-05)]_16 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************