******************************************************************************** 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/120/120.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1058 1.0000 500 11867 1.0000 500 1252 1.0000 500 1487 1.0000 500 17480 1.0000 500 20813 1.0000 500 21421 1.0000 500 22583 1.0000 500 23911 1.0000 500 269487 1.0000 500 2996 1.0000 500 31928 1.0000 500 34701 1.0000 500 36108 1.0000 500 37948 1.0000 500 3956 1.0000 500 4395 1.0000 500 5657 1.0000 500 7842 1.0000 500 8828 1.0000 500 8861 1.0000 500 9047 1.0000 500 9246 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/120/120.seqs.fa -oc motifs/120 -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= 23 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= 11500 N= 23 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.259 C 0.225 G 0.248 T 0.267 Background letter frequencies (from dataset with add-one prior applied): A 0.259 C 0.225 G 0.248 T 0.267 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 18 llr = 206 E-value = 9.8e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::35:631232:82: pos.-specific C 728419:79:438:8a probability G 2513:11::61::::: matrix T 132:4:3:1225221: bits 2.1 * 1.9 * * 1.7 * * 1.5 * * * * Relative 1.3 * ** ** * Entropy 1.1 * * ** **** (16.5 bits) 0.9 * * * ** **** 0.6 *** ****** **** 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel CGCCACACCGCTCACC consensus GT AT TA AAC sequence G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 9246 129 1.33e-08 CAGCACAAGA CGCCACACCGCTCAAC GACAAGGACA 11867 114 1.33e-08 CAGCACAAGA CGCCACACCGCTCAAC GACAAGGACA 31928 485 6.76e-08 ATTCCTTCAC CTCCACACCATTCACC 7842 467 2.89e-07 TCTCCACGAA CGCGACAACGCCCTCC TCTCAAGGTG 2996 453 5.16e-07 CTTCTCTCTT CGTCTCTCCTCTCACC TCTATGTTGA 8861 391 6.40e-07 GCCTTTCCGT CTCCTCTCCGTTCTCC TAGTACTGCT 17480 446 7.11e-07 CTGTGGTAAA GTCCACTACGACCACC TCTCCATCGT 5657 430 1.19e-06 GAAGTTTACG TGCCACTCCGATCTCC AACACATTAT 23911 416 1.19e-06 TCCTCTTCTG GCCATCACCTATCACC AGACATGTAC 4395 403 2.50e-06 TCTTCTCAAA CCCATCACAGCACACC CATTACAGCA 269487 439 2.73e-06 TCAAACGAAT GTTATCACCAATCACC CCCCCGCAAA 3956 369 3.25e-06 GACCGGCGAC GTCGACGACGACCACC CTAGCTTCGG 36108 453 3.25e-06 CAGCCATCAT CTCGTCAACGCTTAAC ACCACCAACG 8828 469 4.53e-06 TCGTCCATCG CCCGCCACCGCATACC CACACCTGGT 22583 81 1.04e-05 GTTCTTTTGC TGCGTCACCTCCCATC GTCTGTGTGG 37948 91 1.56e-05 GTGCTTCTTC CGCCACACTGGATACC GACCGGGAGC 21421 157 2.02e-05 CAATTTTGCC CGTATGTCCAACCACC TCTCCTTTAG 20813 46 3.84e-05 CCGTGCCAGT CGGAACGACATACACC CGTGGCCATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9246 1.3e-08 128_[+1]_356 11867 1.3e-08 113_[+1]_371 31928 6.8e-08 484_[+1] 7842 2.9e-07 466_[+1]_18 2996 5.2e-07 452_[+1]_32 8861 6.4e-07 390_[+1]_94 17480 7.1e-07 445_[+1]_39 5657 1.2e-06 429_[+1]_55 23911 1.2e-06 415_[+1]_69 4395 2.5e-06 402_[+1]_82 269487 2.7e-06 438_[+1]_46 3956 3.3e-06 368_[+1]_116 36108 3.3e-06 452_[+1]_32 8828 4.5e-06 468_[+1]_16 22583 1e-05 80_[+1]_404 37948 1.6e-05 90_[+1]_394 21421 2e-05 156_[+1]_328 20813 3.8e-05 45_[+1]_439 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=18 9246 ( 129) CGCCACACCGCTCAAC 1 11867 ( 114) CGCCACACCGCTCAAC 1 31928 ( 485) CTCCACACCATTCACC 1 7842 ( 467) CGCGACAACGCCCTCC 1 2996 ( 453) CGTCTCTCCTCTCACC 1 8861 ( 391) CTCCTCTCCGTTCTCC 1 17480 ( 446) GTCCACTACGACCACC 1 5657 ( 430) TGCCACTCCGATCTCC 1 23911 ( 416) GCCATCACCTATCACC 1 4395 ( 403) CCCATCACAGCACACC 1 269487 ( 439) GTTATCACCAATCACC 1 3956 ( 369) GTCGACGACGACCACC 1 36108 ( 453) CTCGTCAACGCTTAAC 1 8828 ( 469) CCCGCCACCGCATACC 1 22583 ( 81) TGCGTCACCTCCCATC 1 37948 ( 91) CGCCACACTGGATACC 1 21421 ( 157) CGTATGTCCAACCACC 1 20813 ( 46) CGGAACGACATACACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 11155 bayes= 11.0662 E= 9.8e-007 -1081 156 -16 -127 -1081 -44 101 32 -1081 179 -216 -68 10 98 16 -1081 95 -202 -1081 73 -1081 207 -216 -1081 124 -1081 -116 5 10 168 -1081 -1081 -222 198 -1081 -226 -22 -1081 130 -68 36 98 -216 -68 -22 30 -1081 90 -1081 189 -1081 -68 169 -1081 -1081 -68 -64 179 -1081 -226 -1081 215 -1081 -1081 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 18 E= 9.8e-007 0.000000 0.666667 0.222222 0.111111 0.000000 0.166667 0.500000 0.333333 0.000000 0.777778 0.055556 0.166667 0.277778 0.444444 0.277778 0.000000 0.500000 0.055556 0.000000 0.444444 0.000000 0.944444 0.055556 0.000000 0.611111 0.000000 0.111111 0.277778 0.277778 0.722222 0.000000 0.000000 0.055556 0.888889 0.000000 0.055556 0.222222 0.000000 0.611111 0.166667 0.333333 0.444444 0.055556 0.166667 0.222222 0.277778 0.000000 0.500000 0.000000 0.833333 0.000000 0.166667 0.833333 0.000000 0.000000 0.166667 0.166667 0.777778 0.000000 0.055556 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG][GT]C[CAG][AT]C[AT][CA]C[GA][CA][TCA]CACC -------------------------------------------------------------------------------- Time 6.24 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 20 llr = 238 E-value = 7.6e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 1::12:23112::11123:83 pos.-specific C :15:34:132:2::213312: probability G 94:a3184:55289165:a1: matrix T :65:361373373:7314:18 bits 2.1 1.9 1.7 * * 1.5 * * * * Relative 1.3 * * * * Entropy 1.1 * ** * ** * * (17.2 bits) 0.9 * ** * * ** *** 0.6 **** ** * *** *** 0.4 **** ** * *********** 0.2 **** ** ************* 0.0 --------------------- Multilevel GTCGGTGGTGGTGGTGGTGAT consensus GT CC ACTTCT TCA A sequence T T A AC A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 1487 120 1.62e-11 GATGTCTGGT GGTGGTGGTGGTGGTGGTGAT GTTTCAGCTG 3956 228 3.90e-09 AGCATACGCA GGCGGCGGCCGTGGTGGTGAT ACATATCGTC 17480 230 1.39e-08 CTATGATATG GTCGGTGATCATGGTGGTGAA GTGCTTATCG 36108 111 5.51e-08 AGTTGCGACA GGCGGCGATTGTGGTGGAGGT CATGGTTTGG 269487 159 5.51e-08 ATTCTATTTT GGCGTTGGTGGCGGTACCGAT GTATTTTCCG 1058 127 2.81e-07 ACGAGACACC GTCGACGATTGTGGTAACGAA AGATTGATGA 9246 19 6.34e-07 TGCTGCTGCT GCTGCTGATGATGATGATGAT ACAGGTGTTG 11867 4 6.34e-07 GCT GCTGCTGATGATGATGATGAT ACAGGTGTTG 7842 6 7.67e-07 AAGAT GTTGCTGTTGTGTGTCGTGAT CCATGATACC 9047 42 1.11e-06 CTGACGCTCC GTCGGCAATGTCGGATGCGAT ACTGCGATAA 8828 397 1.58e-06 TTCTCTAGTT GTCGTCGCCCTTGGTGGAGCA GTACAAGCTA 21421 316 2.83e-06 AAGCGAAAGC GGTGACATTGATGGCTATGAT TCCAAGCAAA 8861 181 3.07e-06 GATATGTCAG GTTACTAGTGTGGGTGCAGAT AAATTTGATG 34701 221 3.32e-06 TTGGCGGTGT GTCGGTGTTGGTTGGTTTGAA GGAGAGTGAG 22583 155 4.52e-06 GGGGGGTGGT GGTGTGGTTTTGTGTGGCGCT GAGCTTATTG 5657 377 6.06e-06 TGCTAGAGCT GTCGTTTGCAGCGGGGGAGAT ATTGACGTCG 23911 174 8.03e-06 GCTTTGGAAG ATTGAGGGTTGCGGCGGCGCT GACGGCTGAC 20813 146 1.36e-05 GCTCGTTGAA GGTGTTGTAAGTTGCTCCGAT CATCGTCGCT 1252 33 1.45e-05 TATCGTTGAT ATCGACGGCTTTGGTGCACAA AGAACATTGC 4395 15 2.35e-05 AGACGCTCCT GTTGCTGCCTGTTGATCAGTT GAGATGACGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1487 1.6e-11 119_[+2]_360 3956 3.9e-09 227_[+2]_252 17480 1.4e-08 229_[+2]_250 36108 5.5e-08 110_[+2]_369 269487 5.5e-08 158_[+2]_321 1058 2.8e-07 126_[+2]_353 9246 6.3e-07 18_[+2]_461 11867 6.3e-07 3_[+2]_476 7842 7.7e-07 5_[+2]_474 9047 1.1e-06 41_[+2]_438 8828 1.6e-06 396_[+2]_83 21421 2.8e-06 315_[+2]_164 8861 3.1e-06 180_[+2]_299 34701 3.3e-06 220_[+2]_259 22583 4.5e-06 154_[+2]_325 5657 6.1e-06 376_[+2]_103 23911 8e-06 173_[+2]_306 20813 1.4e-05 145_[+2]_334 1252 1.5e-05 32_[+2]_447 4395 2.4e-05 14_[+2]_465 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=20 1487 ( 120) GGTGGTGGTGGTGGTGGTGAT 1 3956 ( 228) GGCGGCGGCCGTGGTGGTGAT 1 17480 ( 230) GTCGGTGATCATGGTGGTGAA 1 36108 ( 111) GGCGGCGATTGTGGTGGAGGT 1 269487 ( 159) GGCGTTGGTGGCGGTACCGAT 1 1058 ( 127) GTCGACGATTGTGGTAACGAA 1 9246 ( 19) GCTGCTGATGATGATGATGAT 1 11867 ( 4) GCTGCTGATGATGATGATGAT 1 7842 ( 6) GTTGCTGTTGTGTGTCGTGAT 1 9047 ( 42) GTCGGCAATGTCGGATGCGAT 1 8828 ( 397) GTCGTCGCCCTTGGTGGAGCA 1 21421 ( 316) GGTGACATTGATGGCTATGAT 1 8861 ( 181) GTTACTAGTGTGGGTGCAGAT 1 34701 ( 221) GTCGGTGTTGGTTGGTTTGAA 1 22583 ( 155) GGTGTGGTTTTGTGTGGCGCT 1 5657 ( 377) GTCGTTTGCAGCGGGGGAGAT 1 23911 ( 174) ATTGAGGGTTGCGGCGGCGCT 1 20813 ( 146) GGTGTTGTAAGTTGCTCCGAT 1 1252 ( 33) ATCGACGGCTTTGGTGCACAA 1 4395 ( 15) GTTGCTGCCTGTTGATCAGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 11040 bayes= 10.0506 E= 7.6e-008 -137 -1097 186 -1097 -1097 -117 50 104 -1097 115 -1097 90 -237 -1097 194 -1097 -37 15 27 -10 -1097 63 -131 104 -79 -1097 169 -242 21 -117 50 -10 -237 15 -1097 139 -137 -59 86 17 -37 -1097 101 17 -1097 -17 -72 128 -1097 -1097 160 -10 -137 -1097 186 -1097 -137 -59 -131 128 -137 -217 127 -10 -37 15 101 -242 21 41 -1097 58 -1097 -217 194 -1097 153 -59 -231 -242 -5 -1097 -1097 149 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 20 E= 7.6e-008 0.100000 0.000000 0.900000 0.000000 0.000000 0.100000 0.350000 0.550000 0.000000 0.500000 0.000000 0.500000 0.050000 0.000000 0.950000 0.000000 0.200000 0.250000 0.300000 0.250000 0.000000 0.350000 0.100000 0.550000 0.150000 0.000000 0.800000 0.050000 0.300000 0.100000 0.350000 0.250000 0.050000 0.250000 0.000000 0.700000 0.100000 0.150000 0.450000 0.300000 0.200000 0.000000 0.500000 0.300000 0.000000 0.200000 0.150000 0.650000 0.000000 0.000000 0.750000 0.250000 0.100000 0.000000 0.900000 0.000000 0.100000 0.150000 0.100000 0.650000 0.100000 0.050000 0.600000 0.250000 0.200000 0.250000 0.500000 0.050000 0.300000 0.300000 0.000000 0.400000 0.000000 0.050000 0.950000 0.000000 0.750000 0.150000 0.050000 0.050000 0.250000 0.000000 0.000000 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[TG][CT]G[GCTA][TC]G[GAT][TC][GT][GTA][TC][GT]GT[GT][GCA][TAC]GA[TA] -------------------------------------------------------------------------------- Time 12.15 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 16 llr = 206 E-value = 1.0e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2:142312::312:1::41:6 pos.-specific C 11::::1:11:1::11:1::: probability G 169463:83:641138928a1 matrix T 64:3359169148951141:3 bits 2.1 1.9 * 1.7 * * 1.5 * * * * Relative 1.3 * * * * * * Entropy 1.1 * ** * * ** * (18.5 bits) 0.9 * ** ** ** ** ** 0.6 ** * ***** ** ** *** 0.4 *********** ** ** *** 0.2 ********************* 0.0 --------------------- Multilevel TGGAGTTGTTGGTTTGGAGGA consensus T GTA G AT G T T sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 17480 272 1.65e-09 TGCTTTTCGG TGGAGGTGTTGTATGGGTGGA TAGAAGGTTG 37948 289 3.00e-09 ATCTGACATG TTGAGATGTTAGTTGGGGGGA GCGTTGGAAA 9246 202 2.74e-08 CATCGTGAGC AGAGTTTGTTGGTTGGGTGGA ATGGTGCCAT 11867 187 2.74e-08 CATCGTGAGC AGAGTTTGTTGGTTGGGTGGA ATGGTGCCAT 34701 198 1.38e-07 AGATTCATGA TTGTGTTATTATTTTGGCGGT GTGTCGGTGT 1252 211 1.38e-07 AGAATCATCA GTGTTTTATTGCTTTGGAGGA ACCAGAAAGC 5657 66 2.24e-07 CCATGTGCAA TTGTAGTGGTAGTTTTGAGGA CTAACACTAA 1487 291 2.24e-07 CAGGAGGGTA TGGAGTTGGTGGTGTCGAGGT GTGGCATTTT 36108 179 9.82e-07 GATTGGGATT CGGAGGCGGTGGTTTGGAGGG CGAGGGGGAG 23911 125 1.15e-06 TGTAGTCTTG TTGAGTTGCTGAATTGGATGG TATTCCAATT 9047 240 1.24e-06 ACAAGAAAGA TGGGGATGCCATATCGGAGGA TCAGTGGATG 4395 107 1.34e-06 CATCGAAGTT TCGGGATTTTGTTTTGGTTGT TGCTCTCGAT 3956 59 1.57e-06 ATAGTGTCGG TGGTGTAGTTTCTTTGGTAGA CCAATGGCGA 269487 354 1.96e-06 GGCGAGAGAT ATGATATATTGTTGAGGGGGA TTGGTCTCGG 20813 104 4.22e-06 AAGATGGATG TGGGATTGGTAAGTCTGTGGA GACTTTGATC 22583 105 1.01e-05 TCGTCTGTGT GGGGAGTGTTGTTTAGTGAGT AGTGTAGTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17480 1.6e-09 271_[+3]_208 37948 3e-09 288_[+3]_191 9246 2.7e-08 201_[+3]_278 11867 2.7e-08 186_[+3]_293 34701 1.4e-07 197_[+3]_282 1252 1.4e-07 210_[+3]_269 5657 2.2e-07 65_[+3]_414 1487 2.2e-07 290_[+3]_189 36108 9.8e-07 178_[+3]_301 23911 1.2e-06 124_[+3]_355 9047 1.2e-06 239_[+3]_240 4395 1.3e-06 106_[+3]_373 3956 1.6e-06 58_[+3]_421 269487 2e-06 353_[+3]_126 20813 4.2e-06 103_[+3]_376 22583 1e-05 104_[+3]_375 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=16 17480 ( 272) TGGAGGTGTTGTATGGGTGGA 1 37948 ( 289) TTGAGATGTTAGTTGGGGGGA 1 9246 ( 202) AGAGTTTGTTGGTTGGGTGGA 1 11867 ( 187) AGAGTTTGTTGGTTGGGTGGA 1 34701 ( 198) TTGTGTTATTATTTTGGCGGT 1 1252 ( 211) GTGTTTTATTGCTTTGGAGGA 1 5657 ( 66) TTGTAGTGGTAGTTTTGAGGA 1 1487 ( 291) TGGAGTTGGTGGTGTCGAGGT 1 36108 ( 179) CGGAGGCGGTGGTTTGGAGGG 1 23911 ( 125) TTGAGTTGCTGAATTGGATGG 1 9047 ( 240) TGGGGATGCCATATCGGAGGA 1 4395 ( 107) TCGGGATTTTGTTTTGGTTGT 1 3956 ( 59) TGGTGTAGTTTCTTTGGTAGA 1 269487 ( 354) ATGATATATTGTTGAGGGGGA 1 20813 ( 104) TGGGATTGGTAAGTCTGTGGA 1 22583 ( 105) GGGGAGTGTTGTTTAGTGAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 11040 bayes= 9.42836 E= 1.0e-003 -47 -185 -99 122 -1064 -185 118 49 -105 -1064 182 -1064 53 -1064 60 -10 -47 -1064 118 -10 -5 -1064 1 90 -205 -185 -1064 171 -47 -1064 160 -209 -1064 -85 1 122 -1064 -185 -1064 181 27 -1064 133 -209 -105 -85 60 49 -47 -1064 -199 149 -1064 -1064 -99 171 -105 -85 1 90 -1064 -185 171 -110 -1064 -1064 192 -209 53 -185 -40 49 -105 -1064 160 -110 -1064 -1064 201 -1064 127 -1064 -99 -10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 16 E= 1.0e-003 0.187500 0.062500 0.125000 0.625000 0.000000 0.062500 0.562500 0.375000 0.125000 0.000000 0.875000 0.000000 0.375000 0.000000 0.375000 0.250000 0.187500 0.000000 0.562500 0.250000 0.250000 0.000000 0.250000 0.500000 0.062500 0.062500 0.000000 0.875000 0.187500 0.000000 0.750000 0.062500 0.000000 0.125000 0.250000 0.625000 0.000000 0.062500 0.000000 0.937500 0.312500 0.000000 0.625000 0.062500 0.125000 0.125000 0.375000 0.375000 0.187500 0.000000 0.062500 0.750000 0.000000 0.000000 0.125000 0.875000 0.125000 0.125000 0.250000 0.500000 0.000000 0.062500 0.812500 0.125000 0.000000 0.000000 0.937500 0.062500 0.375000 0.062500 0.187500 0.375000 0.125000 0.000000 0.750000 0.125000 0.000000 0.000000 1.000000 0.000000 0.625000 0.000000 0.125000 0.250000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[GT]G[AGT][GT][TAG]TG[TG]T[GA][GT]TT[TG]GG[AT]GG[AT] -------------------------------------------------------------------------------- Time 17.85 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1058 4.16e-03 126_[+2(2.81e-07)]_353 11867 1.35e-11 3_[+2(6.34e-07)]_2_[+3(9.20e-05)]_\ 66_[+1(1.33e-08)]_57_[+3(2.74e-08)]_256_[+1(4.28e-05)]_21 1252 4.76e-05 32_[+2(1.45e-05)]_157_\ [+3(1.38e-07)]_269 1487 7.00e-11 73_[+3(7.28e-05)]_25_[+2(1.62e-11)]_\ 150_[+3(2.24e-07)]_189 17480 1.11e-12 229_[+2(1.39e-08)]_21_\ [+3(1.65e-09)]_153_[+1(7.11e-07)]_39 20813 3.22e-05 45_[+1(3.84e-05)]_42_[+3(4.22e-06)]_\ 21_[+2(1.36e-05)]_334 21421 1.91e-04 156_[+1(2.02e-05)]_143_\ [+2(2.83e-06)]_164 22583 8.30e-06 80_[+1(1.04e-05)]_8_[+3(1.01e-05)]_\ 29_[+2(4.52e-06)]_325 23911 2.84e-07 124_[+3(1.15e-06)]_28_\ [+2(8.03e-06)]_221_[+1(1.19e-06)]_69 269487 1.04e-08 158_[+2(5.51e-08)]_174_\ [+3(1.96e-06)]_64_[+1(2.73e-06)]_46 2996 1.56e-03 452_[+1(5.16e-07)]_32 31928 1.68e-03 484_[+1(6.76e-08)] 34701 7.66e-06 197_[+3(1.38e-07)]_2_[+2(3.32e-06)]_\ 259 36108 6.47e-09 110_[+2(5.51e-08)]_47_\ [+3(9.82e-07)]_253_[+1(3.25e-06)]_32 37948 1.24e-06 90_[+1(1.56e-05)]_182_\ [+3(3.00e-09)]_191 3956 8.59e-10 58_[+3(1.57e-06)]_148_\ [+2(3.90e-09)]_120_[+1(3.25e-06)]_116 4395 1.68e-06 14_[+2(2.35e-05)]_71_[+3(1.34e-06)]_\ 238_[+1(5.54e-05)]_21_[+1(2.50e-06)]_82 5657 4.94e-08 65_[+3(2.24e-07)]_290_\ [+2(6.06e-06)]_32_[+1(1.19e-06)]_55 7842 2.19e-06 5_[+2(7.67e-07)]_207_[+2(1.28e-05)]_\ 212_[+1(2.89e-07)]_18 8828 5.78e-05 396_[+2(1.58e-06)]_51_\ [+1(4.53e-06)]_16 8861 1.86e-05 180_[+2(3.07e-06)]_189_\ [+1(6.40e-07)]_94 9047 2.19e-05 41_[+2(1.11e-06)]_177_\ [+3(1.24e-06)]_240 9246 1.35e-11 18_[+2(6.34e-07)]_2_[+3(9.20e-05)]_\ 66_[+1(1.33e-08)]_57_[+3(2.74e-08)]_278 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************