******************************************************************************** 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/320/320.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10805 1.0000 500 1444 1.0000 500 17880 1.0000 500 19360 1.0000 500 20421 1.0000 500 20504 1.0000 500 21387 1.0000 500 21629 1.0000 500 23152 1.0000 500 23865 1.0000 500 24213 1.0000 500 2514 1.0000 500 25143 1.0000 500 25556 1.0000 500 261325 1.0000 500 262599 1.0000 500 263454 1.0000 500 269828 1.0000 500 32064 1.0000 500 33033 1.0000 500 33726 1.0000 500 33995 1.0000 500 36787 1.0000 500 37100 1.0000 500 38391 1.0000 500 39232 1.0000 500 3970 1.0000 500 6316 1.0000 500 6997 1.0000 500 7626 1.0000 500 8256 1.0000 500 8667 1.0000 500 9012 1.0000 500 9015 1.0000 500 9292 1.0000 500 9945 1.0000 500 bd1753 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/320/320.seqs.fa -oc motifs/320 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 37 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 18500 N= 37 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.261 C 0.243 G 0.233 T 0.263 Background letter frequencies (from dataset with add-one prior applied): A 0.261 C 0.243 G 0.233 T 0.263 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 18 llr = 233 E-value = 5.5e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :14:41113::3:2124:5: pos.-specific C :22:131:1:1:1:1:2:11 probability G 973a5179638296762916 matrix T 1:1::41:1726:3123143 bits 2.1 * 1.9 * * 1.7 * * * * * 1.5 * * * * * Relative 1.3 * * * * * Entropy 1.1 ** * * ** * * (18.7 bits) 0.8 ** ** ** ** * * * * 0.6 ** ** ********** * * 0.4 ** ** ********** *** 0.2 **************** *** 0.0 -------------------- Multilevel GGAGGTGGGTGTGGGGAGAG consensus G AC AG A T AT TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 9292 252 7.20e-11 ATAGGGAGAC GGAGATGGGTGTGAGGAGAG GCTGGTCGCC 25556 312 4.29e-08 CCTGGAGGAA GGAGGAAGGGGTGGGGAGTT ATTTTATGGG 33033 83 7.45e-08 CTTTTAGGGT GGAGAGGGGTTGGTGGTGTG GTTGTGTTGT 9945 98 8.28e-08 AGTATTCATG GCAGATGGGGGTCGGGCGAG GGGCTGCTAC 21387 479 8.28e-08 CGTCCACGTC GGGGGCTGGGGTGTGATGTG TG 24213 297 1.39e-07 TGATCCTTTC GGCGGTGGAGGAGGGTTGTT CATGGTCGAG 38391 357 1.70e-07 AACGTTGATG GCGGATGGGTGTGTGATGGG TGATGGCTTT 21629 306 2.06e-07 CACAAAGCCT GGAGACGGAGGAGGAAGGAG AGGGAGAAGA 20504 142 2.06e-07 GTGTTGGCGG GCGGGGTGGTGTGGGTAGAG GGCTCGGACA 23152 284 2.74e-07 GCTGGCCAAT GGAGGTGGATGTGGCGATTG GATGATGTTG 33995 290 6.71e-07 GAGGGTTTTT GAGGGCGGGGGAGGGGGGCT TCTTCGGTAG 8256 210 7.31e-07 TTCGATGTTG TGTGGTGGGTTTGGGGAGAC AGATTGAAGA 25143 261 7.95e-07 CTCAGTGCGT GGAGGCGGTTTAGGAGGGAG CTGGAGGCTA 32064 306 1.29e-06 AGGAAAAGTA GGTGACGAATGTGTGGCGAC GGTGGATGTT 3970 278 1.51e-06 GACGAAGATG GGGGCTGAGTGGGTGACGAG GATGACATTA 1444 271 1.90e-06 TTTACAGAGA GGCGACGGCTCGGAGGAGAG AGAGGGAGTG 6997 135 4.79e-06 CAAAAAGCAA GGCGAACGATGAGGTGAGTT GCCTCATTAC 37100 333 5.46e-06 GATTGCCAGC GAAGGTAGGTGTGATTTGTT TGTGAGAGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 9292 7.2e-11 251_[+1]_229 25556 4.3e-08 311_[+1]_169 33033 7.4e-08 82_[+1]_398 9945 8.3e-08 97_[+1]_383 21387 8.3e-08 478_[+1]_2 24213 1.4e-07 296_[+1]_184 38391 1.7e-07 356_[+1]_124 21629 2.1e-07 305_[+1]_175 20504 2.1e-07 141_[+1]_339 23152 2.7e-07 283_[+1]_197 33995 6.7e-07 289_[+1]_191 8256 7.3e-07 209_[+1]_271 25143 7.9e-07 260_[+1]_220 32064 1.3e-06 305_[+1]_175 3970 1.5e-06 277_[+1]_203 1444 1.9e-06 270_[+1]_210 6997 4.8e-06 134_[+1]_346 37100 5.5e-06 332_[+1]_148 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=18 9292 ( 252) GGAGATGGGTGTGAGGAGAG 1 25556 ( 312) GGAGGAAGGGGTGGGGAGTT 1 33033 ( 83) GGAGAGGGGTTGGTGGTGTG 1 9945 ( 98) GCAGATGGGGGTCGGGCGAG 1 21387 ( 479) GGGGGCTGGGGTGTGATGTG 1 24213 ( 297) GGCGGTGGAGGAGGGTTGTT 1 38391 ( 357) GCGGATGGGTGTGTGATGGG 1 21629 ( 306) GGAGACGGAGGAGGAAGGAG 1 20504 ( 142) GCGGGGTGGTGTGGGTAGAG 1 23152 ( 284) GGAGGTGGATGTGGCGATTG 1 33995 ( 290) GAGGGCGGGGGAGGGGGGCT 1 8256 ( 210) TGTGGTGGGTTTGGGGAGAC 1 25143 ( 261) GGAGGCGGTTTAGGAGGGAG 1 32064 ( 306) GGTGACGAATGTGTGGCGAC 1 3970 ( 278) GGGGCTGAGTGGGTGACGAG 1 1444 ( 271) GGCGACGGCTCGGAGGAGAG 1 6997 ( 135) GGCGAACGATGAGGTGAGTT 1 37100 ( 333) GAAGGTAGGTGTGATTTGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 17797 bayes= 10.7966 E= 5.5e-006 -1081 -1081 202 -224 -123 -54 163 -1081 77 -54 25 -124 -1081 -1081 210 -1081 77 -213 110 -1081 -123 46 -107 76 -123 -213 163 -124 -123 -1081 193 -1081 9 -213 139 -224 -1081 -1081 52 134 -1081 -213 174 -66 9 -1081 -48 108 -1081 -213 202 -1081 -65 -1081 125 8 -123 -213 163 -124 -23 -1081 139 -66 57 -54 -48 8 -1081 -1081 202 -224 94 -213 -207 56 -1081 -113 139 8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 18 E= 5.5e-006 0.000000 0.000000 0.944444 0.055556 0.111111 0.166667 0.722222 0.000000 0.444444 0.166667 0.277778 0.111111 0.000000 0.000000 1.000000 0.000000 0.444444 0.055556 0.500000 0.000000 0.111111 0.333333 0.111111 0.444444 0.111111 0.055556 0.722222 0.111111 0.111111 0.000000 0.888889 0.000000 0.277778 0.055556 0.611111 0.055556 0.000000 0.000000 0.333333 0.666667 0.000000 0.055556 0.777778 0.166667 0.277778 0.000000 0.166667 0.555556 0.000000 0.055556 0.944444 0.000000 0.166667 0.000000 0.555556 0.277778 0.111111 0.055556 0.722222 0.111111 0.222222 0.000000 0.611111 0.166667 0.388889 0.166667 0.166667 0.277778 0.000000 0.000000 0.944444 0.055556 0.500000 0.055556 0.055556 0.388889 0.000000 0.111111 0.611111 0.277778 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GG[AG]G[GA][TC]GG[GA][TG]G[TA]G[GT]G[GA][AT]G[AT][GT] -------------------------------------------------------------------------------- Time 12.04 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 32 llr = 316 E-value = 3.2e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :3135111:61262::::451 pos.-specific C 63542153a178437538447 probability G 1:11:2:1::1::211:1::: matrix T 24323735:32:132582212 bits 2.1 * 1.9 * 1.7 * 1.5 * Relative 1.3 * Entropy 1.1 * * * (14.3 bits) 0.8 * ** * ** * 0.6 * ** ***** **** ** 0.4 *** *** ***** **** ** 0.2 ************* ******* 0.0 --------------------- Multilevel CTCCATCTCACCACCCTCAAC consensus TATAT TC T CT TC CC sequence C TC A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 262599 457 2.85e-10 TTGCACTCGA CACCTTCCCACCACCCTCACC CGCATTGGAA 9292 437 7.50e-08 CATTAGTGGA CACGATCCCACCAGTTTCAAC GTTGTCTTTC 269828 149 3.62e-07 TTGCTTCAGT CTCCATCACACCAGCTCTCCC TCTACGATGC 23152 107 4.71e-07 CACTAACTGC CACATTCTCACCATTGTCACC ACTCATCATC 10805 132 6.08e-07 CATTCTCGCC CCTCTTTTCACCCTCCTGCAC CGTCGTACTA 9012 418 1.60e-06 ATAAAACTCT CCCTTTCCCCCCAACCTTCAC CGACAACGCC 3970 404 1.60e-06 TCCAGATCGA CTTCATCTCAACAAGCTCAAC ACCCCCTGCT 38391 29 2.52e-06 GTTACACACA CACACACACACCCACCTCCCC ATGTCATTCA 37100 258 2.52e-06 ACGAGCACCT CCTTCTTTCTTCATCCTCTCC AATTCGTCAG 19360 420 2.52e-06 CTCGTGTGTC TTTCCTTTCACACTTCTCAAC TGGTCTTCTC 17880 456 3.50e-06 AATCGATCAC GTGACGTTCACCAACCTCCAC CCTCGATCAC 20421 361 3.89e-06 GGACACGATC CACTTTCTCCCCTCTCTCAAC CCACCTCTTC 25143 108 6.52e-06 CCTTTCCCGC TACCATCCCTTCCCATTCCAC GAGAGGTGGG 1444 338 6.52e-06 ATGGACAAAA CTCAATATCATCCCCCTTTAT TTTGCCCTTA 33726 426 7.21e-06 CAGCACGGCC GAGCCTCTCTCCAGCCTCCCA AATAGTCCTA 2514 460 7.21e-06 CATCTCTGAA CCTCATCTCAACCCCTCCGAC AACAATACAC 25556 95 7.96e-06 CGGTGCACGA CACCTGTGCTCAATCTTCTCC CTGAAACATC 6316 322 9.67e-06 CAATCCCACT TCCCAGTCCTCCACCTCCCTC CTCTTCTTCC 9945 466 1.17e-05 GCAAAAGCCA ATCAATTGCACCTCCTTCACC ACCAAACAAC 24213 402 1.17e-05 CCCGGTACTA CCATATCCCACCACCCCATAC ACCATCGCCA 33033 388 1.55e-05 ACGCCATATT CATATGTCCAGCACCCTCACT GACGGCTCAT 9015 430 1.70e-05 AAACTCACAC TTTAATCGCTCCACCCCGACC ACGAGCTAAA 263454 311 1.70e-05 ATCAGAAGAC TTACTTCCCACCCACTTTAAA TGCTGCATGC 36787 427 1.86e-05 GCGAACAACT CTACGTCTCTCAACCTTCTCT AGAACAACAA 8667 452 2.03e-05 GTAAGGTCTC GAGGATACCATCATCTTCCAC AAATCACTGT 21629 438 2.64e-05 CAACCTCTCT CTCTCTCTCTCTCTCTCTCAC ACACGGCCAA 33995 355 3.13e-05 ACATTTGTAA CACAACTTCACACTCTCCACA CAACAAATCG 6997 387 6.97e-05 AATAATGTGC TTCTATTTCTCACATGTCCAT GTTCGTCTAC 39232 199 6.97e-05 ACATCTCTCG GCATATTTCCCAAACTTCAAT TTGTAGCCCC 23865 193 7.52e-05 TACAGGACAC TTTCCACTCAGCAGTCTCTCC CATCTGGTCT 8256 431 1.01e-04 TCCGTCGTGG CCCCAGAACACCCGGTTCCTC CGAACAGTAC 32064 463 1.76e-04 TTAATCGTCT CTCGACACCATCCGCTCCTCT ATGAACAGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 262599 2.8e-10 456_[+2]_23 9292 7.5e-08 436_[+2]_43 269828 3.6e-07 148_[+2]_331 23152 4.7e-07 106_[+2]_373 10805 6.1e-07 131_[+2]_348 9012 1.6e-06 417_[+2]_62 3970 1.6e-06 403_[+2]_76 38391 2.5e-06 28_[+2]_451 37100 2.5e-06 257_[+2]_222 19360 2.5e-06 419_[+2]_60 17880 3.5e-06 455_[+2]_24 20421 3.9e-06 360_[+2]_119 25143 6.5e-06 107_[+2]_372 1444 6.5e-06 337_[+2]_142 33726 7.2e-06 425_[+2]_54 2514 7.2e-06 459_[+2]_20 25556 8e-06 94_[+2]_385 6316 9.7e-06 321_[+2]_158 9945 1.2e-05 465_[+2]_14 24213 1.2e-05 401_[+2]_78 33033 1.5e-05 387_[+2]_92 9015 1.7e-05 429_[+2]_50 263454 1.7e-05 310_[+2]_169 36787 1.9e-05 426_[+2]_53 8667 2e-05 451_[+2]_28 21629 2.6e-05 437_[+2]_42 33995 3.1e-05 354_[+2]_125 6997 7e-05 386_[+2]_93 39232 7e-05 198_[+2]_281 23865 7.5e-05 192_[+2]_287 8256 0.0001 430_[+2]_49 32064 0.00018 462_[+2]_17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=32 262599 ( 457) CACCTTCCCACCACCCTCACC 1 9292 ( 437) CACGATCCCACCAGTTTCAAC 1 269828 ( 149) CTCCATCACACCAGCTCTCCC 1 23152 ( 107) CACATTCTCACCATTGTCACC 1 10805 ( 132) CCTCTTTTCACCCTCCTGCAC 1 9012 ( 418) CCCTTTCCCCCCAACCTTCAC 1 3970 ( 404) CTTCATCTCAACAAGCTCAAC 1 38391 ( 29) CACACACACACCCACCTCCCC 1 37100 ( 258) CCTTCTTTCTTCATCCTCTCC 1 19360 ( 420) TTTCCTTTCACACTTCTCAAC 1 17880 ( 456) GTGACGTTCACCAACCTCCAC 1 20421 ( 361) CACTTTCTCCCCTCTCTCAAC 1 25143 ( 108) TACCATCCCTTCCCATTCCAC 1 1444 ( 338) CTCAATATCATCCCCCTTTAT 1 33726 ( 426) GAGCCTCTCTCCAGCCTCCCA 1 2514 ( 460) CCTCATCTCAACCCCTCCGAC 1 25556 ( 95) CACCTGTGCTCAATCTTCTCC 1 6316 ( 322) TCCCAGTCCTCCACCTCCCTC 1 9945 ( 466) ATCAATTGCACCTCCTTCACC 1 24213 ( 402) CCATATCCCACCACCCCATAC 1 33033 ( 388) CATATGTCCAGCACCCTCACT 1 9015 ( 430) TTTAATCGCTCCACCCCGACC 1 263454 ( 311) TTACTTCCCACCCACTTTAAA 1 36787 ( 427) CTACGTCTCTCAACCTTCTCT 1 8667 ( 452) GAGGATACCATCATCTTCCAC 1 21629 ( 438) CTCTCTCTCTCTCTCTCTCAC 1 33995 ( 355) CACAACTTCACACTCTCCACA 1 6997 ( 387) TTCTATTTCTCACATGTCCAT 1 39232 ( 199) GCATATTTCCCAAACTTCAAT 1 23865 ( 193) TTTCCACTCAGCAGTCTCTCC 1 8256 ( 431) CCCCAGAACACCCGGTTCCTC 1 32064 ( 463) CTCGACACCATCCGCTCCTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 17760 bayes= 9.85175 E= 3.2e-001 -306 136 -90 -27 40 4 -1164 63 -106 113 -131 -7 -6 85 -131 -27 94 -15 -290 -7 -206 -196 -58 145 -106 113 -1164 39 -148 36 -131 93 -1164 204 -1164 -1164 126 -137 -1164 10 -206 156 -190 -75 -48 168 -1164 -307 111 63 -1164 -207 -25 50 -31 -7 -306 156 -190 -49 -1164 95 -190 83 -1164 4 -1164 151 -306 163 -190 -75 52 63 -290 -27 94 85 -1164 -207 -148 156 -1164 -49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 32 E= 3.2e-001 0.031250 0.625000 0.125000 0.218750 0.343750 0.250000 0.000000 0.406250 0.125000 0.531250 0.093750 0.250000 0.250000 0.437500 0.093750 0.218750 0.500000 0.218750 0.031250 0.250000 0.062500 0.062500 0.156250 0.718750 0.125000 0.531250 0.000000 0.343750 0.093750 0.312500 0.093750 0.500000 0.000000 1.000000 0.000000 0.000000 0.625000 0.093750 0.000000 0.281250 0.062500 0.718750 0.062500 0.156250 0.187500 0.781250 0.000000 0.031250 0.562500 0.375000 0.000000 0.062500 0.218750 0.343750 0.187500 0.250000 0.031250 0.718750 0.062500 0.187500 0.000000 0.468750 0.062500 0.468750 0.000000 0.250000 0.000000 0.750000 0.031250 0.750000 0.062500 0.156250 0.375000 0.375000 0.031250 0.218750 0.500000 0.437500 0.000000 0.062500 0.093750 0.718750 0.000000 0.187500 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT][TAC][CT][CAT][ATC]T[CT][TC]C[AT]CC[AC][CTA]C[CT][TC]C[ACT][AC]C -------------------------------------------------------------------------------- Time 23.95 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 17 llr = 197 E-value = 8.8e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::21:11::1:11:22 pos.-specific C 22::2:11:2:31::2 probability G :58::8:3a2364:46 matrix T 83198186:57:5a5: bits 2.1 * 1.9 * * 1.7 * * * 1.5 * * * Relative 1.3 * *** * * Entropy 1.1 * ***** * * * (16.7 bits) 0.8 * ******* ** * 0.6 * ******* ** * * 0.4 **************** 0.2 **************** 0.0 ---------------- Multilevel TGGTTGTTGTTGTTTG consensus CT C G GGCG GA sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 32064 106 7.02e-10 GGAGCAGCGT TGGTTGTTGTTGGTTG TTTTGCAGAG 25143 185 3.84e-08 CTGGAGAATT TTGTTGTTGTTGTTGC CCAGTGCAGT 20504 227 5.17e-08 CGCTGGCTTG TTGTTGTTGTGCTTTG GAGGCCGGAG 23152 66 7.76e-08 ACCATTGCTT TGGTTGCTGTTGTTTG CATCATCAGC 24213 89 8.85e-08 TACTTTCAAC TGGTTGTGGCTCTTTG ATCTGCGGAG 1444 249 1.02e-06 GGCAAGTGAA CCGTTGTGGGTGTTTA CAGAGAGGCG 23865 77 1.13e-06 ACGATGTTTC TGATTGTTGTGCGTAG GATTTGAGGG 17880 318 1.37e-06 GTCACCGTCT TCGTCTTTGGTGTTTG AGTCTGTTTC 7626 216 2.15e-06 TTGCGTTGTT TCTTTGTTGGTGTTAG CTTTATGAGA 6997 217 4.18e-06 TGCGGGTGTA TTATTGTTGATGTTGC GCGAAGGAGT 9292 76 5.24e-06 TCTGTTGACG TTGACGTTGCTGGTGG ACTCTGCTGA 9015 9 5.24e-06 TGATTCAG TGGTCAATGTTGGTTG GCTCTCCTCT 9945 72 6.54e-06 ATGGTGATGC CGGTCGTGGTGCGTGC AGTATTCATG 8256 273 9.30e-06 TTGAAGTATT TGGTTTTGGTTAGTGA GAAAAGGGGG 261325 44 1.06e-05 ATTGCAAACT TGGTTGAGGCTGCTGA GAACATGCAG 6316 46 1.46e-05 CTGGAAGAAT CCATTGTCGTGCTTTG ATGTGTTGAT 20421 226 1.56e-05 AAAGCCAGTT CTGTTGTTGGGGATAA CTTCACTAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 32064 7e-10 105_[+3]_379 25143 3.8e-08 184_[+3]_300 20504 5.2e-08 226_[+3]_258 23152 7.8e-08 65_[+3]_419 24213 8.9e-08 88_[+3]_396 1444 1e-06 248_[+3]_236 23865 1.1e-06 76_[+3]_408 17880 1.4e-06 317_[+3]_167 7626 2.1e-06 215_[+3]_269 6997 4.2e-06 216_[+3]_268 9292 5.2e-06 75_[+3]_409 9015 5.2e-06 8_[+3]_476 9945 6.5e-06 71_[+3]_413 8256 9.3e-06 272_[+3]_212 261325 1.1e-05 43_[+3]_441 6316 1.5e-05 45_[+3]_439 20421 1.6e-05 225_[+3]_259 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=17 32064 ( 106) TGGTTGTTGTTGGTTG 1 25143 ( 185) TTGTTGTTGTTGTTGC 1 20504 ( 227) TTGTTGTTGTGCTTTG 1 23152 ( 66) TGGTTGCTGTTGTTTG 1 24213 ( 89) TGGTTGTGGCTCTTTG 1 1444 ( 249) CCGTTGTGGGTGTTTA 1 23865 ( 77) TGATTGTTGTGCGTAG 1 17880 ( 318) TCGTCTTTGGTGTTTG 1 7626 ( 216) TCTTTGTTGGTGTTAG 1 6997 ( 217) TTATTGTTGATGTTGC 1 9292 ( 76) TTGACGTTGCTGGTGG 1 9015 ( 9) TGGTCAATGTTGGTTG 1 9945 ( 72) CGGTCGTGGTGCGTGC 1 8256 ( 273) TGGTTTTGGTTAGTGA 1 261325 ( 44) TGGTTGAGGCTGCTGA 1 6316 ( 46) CCATTGTCGTGCTTTG 1 20421 ( 226) CTGTTGTTGGGGATAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 17945 bayes= 10.8377 E= 8.8e+000 -1073 -5 -1073 154 -1073 -5 101 16 -56 -1073 171 -216 -215 -1073 -1073 184 -1073 -5 -1073 154 -215 -1073 182 -116 -115 -204 -1073 165 -1073 -204 34 130 -1073 -1073 210 -1073 -215 -46 1 101 -1073 -1073 34 142 -215 28 147 -1073 -215 -204 60 101 -1073 -1073 -1073 193 -56 -1073 60 84 -15 -46 134 -1073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 17 E= 8.8e+000 0.000000 0.235294 0.000000 0.764706 0.000000 0.235294 0.470588 0.294118 0.176471 0.000000 0.764706 0.058824 0.058824 0.000000 0.000000 0.941176 0.000000 0.235294 0.000000 0.764706 0.058824 0.000000 0.823529 0.117647 0.117647 0.058824 0.000000 0.823529 0.000000 0.058824 0.294118 0.647059 0.000000 0.000000 1.000000 0.000000 0.058824 0.176471 0.235294 0.529412 0.000000 0.000000 0.294118 0.705882 0.058824 0.294118 0.647059 0.000000 0.058824 0.058824 0.352941 0.529412 0.000000 0.000000 0.000000 1.000000 0.176471 0.000000 0.352941 0.470588 0.235294 0.176471 0.588235 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TC][GTC]GT[TC]GT[TG]G[TG][TG][GC][TG]T[TG][GA] -------------------------------------------------------------------------------- Time 35.56 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10805 1.98e-03 131_[+2(6.08e-07)]_348 1444 3.24e-07 248_[+3(1.02e-06)]_6_[+1(1.90e-06)]_\ 47_[+2(6.52e-06)]_142 17880 9.74e-06 317_[+3(1.37e-06)]_122_\ [+2(3.50e-06)]_24 19360 9.19e-03 419_[+2(2.52e-06)]_60 20421 9.08e-04 225_[+3(1.56e-05)]_119_\ [+2(3.89e-06)]_119 20504 3.36e-07 141_[+1(2.06e-07)]_65_\ [+3(5.17e-08)]_258 21387 8.53e-04 478_[+1(8.28e-08)]_2 21629 9.99e-05 305_[+1(2.06e-07)]_112_\ [+2(2.64e-05)]_42 23152 4.57e-10 65_[+3(7.76e-08)]_25_[+2(4.71e-07)]_\ 156_[+1(2.74e-07)]_197 23865 5.34e-04 76_[+3(1.13e-06)]_100_\ [+2(7.52e-05)]_287 24213 5.38e-09 88_[+3(8.85e-08)]_192_\ [+1(1.39e-07)]_85_[+2(1.17e-05)]_78 2514 5.15e-02 459_[+2(7.21e-06)]_20 25143 7.27e-09 107_[+2(6.52e-06)]_56_\ [+3(3.84e-08)]_20_[+3(6.42e-05)]_24_[+1(7.95e-07)]_220 25556 1.15e-05 94_[+2(7.96e-06)]_196_\ [+1(4.29e-08)]_169 261325 4.16e-02 43_[+3(1.06e-05)]_441 262599 3.43e-06 456_[+2(2.85e-10)]_23 263454 2.48e-02 310_[+2(1.70e-05)]_169 269828 1.29e-03 148_[+2(3.62e-07)]_331 32064 5.71e-09 105_[+3(7.02e-10)]_184_\ [+1(1.29e-06)]_175 33033 2.59e-05 82_[+1(7.45e-08)]_285_\ [+2(1.55e-05)]_92 33726 3.82e-02 425_[+2(7.21e-06)]_54 33995 3.78e-04 289_[+1(6.71e-07)]_45_\ [+2(3.13e-05)]_125 36787 6.71e-03 242_[+2(3.69e-05)]_105_\ [+3(8.17e-05)]_42_[+2(1.86e-05)]_53 37100 1.24e-04 257_[+2(2.52e-06)]_54_\ [+1(5.46e-06)]_148 38391 8.70e-06 28_[+2(2.52e-06)]_307_\ [+1(1.70e-07)]_124 39232 1.54e-01 198_[+2(6.97e-05)]_281 3970 4.02e-05 277_[+1(1.51e-06)]_106_\ [+2(1.60e-06)]_76 6316 2.05e-04 45_[+3(1.46e-05)]_260_\ [+2(9.67e-06)]_158 6997 2.14e-05 134_[+1(4.79e-06)]_62_\ [+3(4.18e-06)]_154_[+2(6.97e-05)]_93 7626 7.07e-03 215_[+3(2.15e-06)]_269 8256 1.14e-05 209_[+1(7.31e-07)]_43_\ [+3(9.30e-06)]_212 8667 6.35e-02 451_[+2(2.03e-05)]_28 9012 2.35e-02 417_[+2(1.60e-06)]_62 9015 7.08e-04 8_[+3(5.24e-06)]_372_[+2(6.97e-05)]_\ 12_[+2(1.70e-05)]_50 9292 1.87e-12 75_[+3(5.24e-06)]_160_\ [+1(7.20e-11)]_165_[+2(7.50e-08)]_43 9945 1.73e-07 71_[+3(6.54e-06)]_10_[+1(8.28e-08)]_\ 348_[+2(1.17e-05)]_14 bd1753 7.11e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************