******************************************************************************** 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/193/193.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 14643 1.0000 500 22676 1.0000 500 24295 1.0000 500 24808 1.0000 500 25263 1.0000 500 260758 1.0000 500 260943 1.0000 500 261512 1.0000 500 26239 1.0000 500 263349 1.0000 500 263989 1.0000 500 264064 1.0000 500 269556 1.0000 500 28028 1.0000 500 3320 1.0000 500 3680 1.0000 500 37862 1.0000 500 38789 1.0000 500 4709 1.0000 500 7963 1.0000 500 7975 1.0000 500 8726 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/193/193.seqs.fa -oc motifs/193 -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= 22 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= 11000 N= 22 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.262 C 0.247 G 0.235 T 0.256 Background letter frequencies (from dataset with add-one prior applied): A 0.262 C 0.247 G 0.235 T 0.256 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 22 llr = 214 E-value = 2.7e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :122:52::31::::1 pos.-specific C 192693259:6871a6 probability G ::4:1:2112::31:1 matrix T 9:21:243:522:7:2 bits 2.1 * 1.9 * 1.7 * * * 1.5 * * * Relative 1.3 ** * * * * Entropy 1.0 ** * * ** * (14.0 bits) 0.8 ** * * ** * 0.6 ** ** ******** 0.4 ** ** ********* 0.2 ** *** ********* 0.0 ---------------- Multilevel TCGCCATCCTCCCTCC consensus AA CCT AT G T sequence C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 263349 405 8.32e-09 CGGGGGAAAC TCGCCACCCACCCTCC CAACCCAAAC 269556 430 2.29e-06 ACATACACCT TCGCCTCTCTCTCTCT CTCTCTCTGT 260758 465 2.87e-06 TATCAAAGCC CCCCCCTCCTCTCTCC TCTCCGCTGC 38789 21 3.20e-06 CGTCTCCTCA TCCACCCCGTCCCTCC TCATTCTCAT 25263 391 3.20e-06 TCGGTCAACG TCAACAGCCACCCTCG TAGTAGTAGT 28028 284 3.99e-06 CCTCCGAAAG CCACCCTTCTTCCTCC TTCGACGACC 264064 397 3.99e-06 TGCATCATCG TCACCCATCACCCTCA AAGACACGAT 3320 317 4.44e-06 CTTTTCCCAA TCTCCGTCCTCCGTCT CCGCCGCCAT 4709 404 6.05e-06 ACCACCCGTA TCCACATCCGACGTCC GCAGGCGACG 37862 10 6.69e-06 GGACAGCCA TCACCTCCCGCCGGCC GTGCCTGCCT 7975 18 7.39e-06 ACTCCATTGA TATCCCAGCTCCCTCC TCGGTATCAA 260943 442 8.16e-06 CCCACGCCCC TCGCCCGGCATCCCCC CCCCAGGCAG 14643 479 1.09e-05 ACCTTTACTC TCCCCAGCCAACCGCT ATCACG 8726 446 1.43e-05 TCTGTGAGGG TGAACATCCTCCCGCC GACTCTCCTC 7963 357 2.21e-05 TGACAACGCT TCTTCTTTCTTCCCCC CTCACTTCTA 263989 14 2.40e-05 TGGTATCGCG TCGCCTGCCTCGGCCC CCGAAGACTT 3680 450 2.61e-05 CGCCGTCAGC TAGCCATTCGCCGTCG TGGGCTCTTC 261512 61 2.61e-05 CACTATGGGA ACGCCACGCTCCGTCT CAAGTACTCT 24808 365 4.20e-05 GCAGTGGAAT TCGTGAATCGTCCTCC TGGTGCACAG 22676 11 4.20e-05 CTCATCCAAC TCTCCCATCAATCTCT CATCGTTGAT 26239 312 4.53e-05 AGCTGAAACT TCGACAGCCTTCCACA GCCACAACGA 24295 293 8.60e-05 GGTCGCCTAA TCCTGATCGTCTCTCC ATCTCTATAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263349 8.3e-09 404_[+1]_80 269556 2.3e-06 429_[+1]_55 260758 2.9e-06 464_[+1]_20 38789 3.2e-06 20_[+1]_464 25263 3.2e-06 390_[+1]_94 28028 4e-06 283_[+1]_201 264064 4e-06 396_[+1]_88 3320 4.4e-06 316_[+1]_168 4709 6e-06 403_[+1]_81 37862 6.7e-06 9_[+1]_475 7975 7.4e-06 17_[+1]_467 260943 8.2e-06 441_[+1]_43 14643 1.1e-05 478_[+1]_6 8726 1.4e-05 445_[+1]_39 7963 2.2e-05 356_[+1]_128 263989 2.4e-05 13_[+1]_471 3680 2.6e-05 449_[+1]_35 261512 2.6e-05 60_[+1]_424 24808 4.2e-05 364_[+1]_120 22676 4.2e-05 10_[+1]_474 26239 4.5e-05 311_[+1]_173 24295 8.6e-05 292_[+1]_192 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=22 263349 ( 405) TCGCCACCCACCCTCC 1 269556 ( 430) TCGCCTCTCTCTCTCT 1 260758 ( 465) CCCCCCTCCTCTCTCC 1 38789 ( 21) TCCACCCCGTCCCTCC 1 25263 ( 391) TCAACAGCCACCCTCG 1 28028 ( 284) CCACCCTTCTTCCTCC 1 264064 ( 397) TCACCCATCACCCTCA 1 3320 ( 317) TCTCCGTCCTCCGTCT 1 4709 ( 404) TCCACATCCGACGTCC 1 37862 ( 10) TCACCTCCCGCCGGCC 1 7975 ( 18) TATCCCAGCTCCCTCC 1 260943 ( 442) TCGCCCGGCATCCCCC 1 14643 ( 479) TCCCCAGCCAACCGCT 1 8726 ( 446) TGAACATCCTCCCGCC 1 7963 ( 357) TCTTCTTTCTTCCCCC 1 263989 ( 14) TCGCCTGCCTCGGCCC 1 3680 ( 450) TAGCCATTCGCCGTCG 1 261512 ( 61) ACGCCACGCTCCGTCT 1 24808 ( 365) TCGTGAATCGTCCTCC 1 22676 ( 11) TCTCCCATCAATCTCT 1 26239 ( 312) TCGACAGCCTTCCACA 1 24295 ( 293) TCCTGATCGTCTCTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 10670 bayes= 8.91886 E= 2.7e-004 -252 -144 -1110 175 -153 180 -237 -1110 -21 -12 63 -49 -21 136 -1110 -91 -1110 188 -137 -1110 79 36 -237 -49 -53 -12 -5 51 -1110 114 -78 31 -1110 188 -137 -1110 6 -1110 -37 109 -94 136 -1110 -17 -1110 164 -237 -49 -1110 156 22 -1110 -252 -86 -78 141 -1110 202 -1110 -1110 -153 126 -137 -17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 22 E= 2.7e-004 0.045455 0.090909 0.000000 0.863636 0.090909 0.863636 0.045455 0.000000 0.227273 0.227273 0.363636 0.181818 0.227273 0.636364 0.000000 0.136364 0.000000 0.909091 0.090909 0.000000 0.454545 0.318182 0.045455 0.181818 0.181818 0.227273 0.227273 0.363636 0.000000 0.545455 0.136364 0.318182 0.000000 0.909091 0.090909 0.000000 0.272727 0.000000 0.181818 0.545455 0.136364 0.636364 0.000000 0.227273 0.000000 0.772727 0.045455 0.181818 0.000000 0.727273 0.272727 0.000000 0.045455 0.136364 0.136364 0.681818 0.000000 1.000000 0.000000 0.000000 0.090909 0.590909 0.090909 0.227273 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- TC[GAC][CA]C[AC][TCG][CT]C[TA][CT]C[CG]TC[CT] -------------------------------------------------------------------------------- Time 4.36 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 18 llr = 215 E-value = 1.3e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 2::1::1::111142:2:131 pos.-specific C 112::::1:1221:44:2211 probability G 18129:33a1162623:3724 matrix T 62871a67:772613385145 bits 2.1 * 1.9 * * 1.7 ** * 1.5 ** * Relative 1.3 ** * * Entropy 1.0 ** ** * * (17.2 bits) 0.8 ***** ** * * 0.6 ********** * *** 0.4 ************** **** * 0.2 ************** ****** 0.0 --------------------- Multilevel TGTTGTTTGTTGTGCCTTGTT consensus A G GG ATT G AG sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 7963 168 1.64e-12 GTATCCATTG TGTTGTTTGTTGTGCGTTGTT GGCAGCTCTG 8726 331 3.78e-08 TGTGGTTTGG TGTTGTGGGGTGTATGTTGGT GTCAAACGTT 7975 349 2.20e-07 TGGCACCTGA AGCGGTGTGTTTTACTTTGAT TGGTTCGTTG 4709 50 2.20e-07 ATCAAGTAAG CGTTGTTGGTTGTGGTTGTGT ATCCTCTTTC 24295 250 3.73e-07 GTGTGGATCA AGTTGTTGGTTGATTCTGGTG ATAGTGCCCG 3680 204 4.58e-07 ACGTCCGCGG TCTTGTTTGTGGCGTGTTGTG TCGAGAAGAC 14643 12 5.07e-07 TGGCTCTCAT TGTTGTGGGTTAAGCTATGAG AGAGGAGAGG 3320 155 5.60e-07 GGGTGTGTAA TGTTGTTTGTCGGAAGTGAAT GAGGAGGGAT 22676 285 9.08e-07 GTCATGGAGC TGCTGTTCGTCTTATCTTGTG GTGGAGCTGC 37862 123 9.98e-07 TGAGACTTAC CGTTGTGTGATATGCCATGAT GATACGATGT 38789 417 1.10e-06 GGCAACGAGG AGTTGTTGGCAGTAGCTGGAG AGTGGCGCTG 260943 72 3.39e-06 TTCATGTTGT TGGAGTTTGGTCTGCTTGGCT TCTTATCCTC 264064 475 3.68e-06 AGCATAAGTT TTTAGTTTGTTGTGCTTCCGA ACGGT 263349 55 3.68e-06 CTTCTCGTAT TGTGGTATGTTCGGAGTGGAC GACGACGACG 24808 335 7.38e-06 TAATCTTTGG GTTTGTTTGTTCCATCTTTTG CAGTGGAATT 28028 77 9.87e-06 AAACCATAGA TGTTGTATGCGGTGGCACCTT ACAATGAACC 269556 22 1.14e-05 TCTGTGAGAT ATTGTTGTGATGTGATTTGTG GACATCACGA 26239 239 1.30e-05 ATTAGTTCCT TGCGGTTTGTCTGACCTCCCT TTTGAGAGAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7963 1.6e-12 167_[+2]_312 8726 3.8e-08 330_[+2]_149 7975 2.2e-07 348_[+2]_131 4709 2.2e-07 49_[+2]_430 24295 3.7e-07 249_[+2]_230 3680 4.6e-07 203_[+2]_276 14643 5.1e-07 11_[+2]_468 3320 5.6e-07 154_[+2]_325 22676 9.1e-07 284_[+2]_195 37862 1e-06 122_[+2]_357 38789 1.1e-06 416_[+2]_63 260943 3.4e-06 71_[+2]_408 264064 3.7e-06 474_[+2]_5 263349 3.7e-06 54_[+2]_425 24808 7.4e-06 334_[+2]_145 28028 9.9e-06 76_[+2]_403 269556 1.1e-05 21_[+2]_458 26239 1.3e-05 238_[+2]_241 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=18 7963 ( 168) TGTTGTTTGTTGTGCGTTGTT 1 8726 ( 331) TGTTGTGGGGTGTATGTTGGT 1 7975 ( 349) AGCGGTGTGTTTTACTTTGAT 1 4709 ( 50) CGTTGTTGGTTGTGGTTGTGT 1 24295 ( 250) AGTTGTTGGTTGATTCTGGTG 1 3680 ( 204) TCTTGTTTGTGGCGTGTTGTG 1 14643 ( 12) TGTTGTGGGTTAAGCTATGAG 1 3320 ( 155) TGTTGTTTGTCGGAAGTGAAT 1 22676 ( 285) TGCTGTTCGTCTTATCTTGTG 1 37862 ( 123) CGTTGTGTGATATGCCATGAT 1 38789 ( 417) AGTTGTTGGCAGTAGCTGGAG 1 260943 ( 72) TGGAGTTTGGTCTGCTTGGCT 1 264064 ( 475) TTTAGTTTGTTGTGCTTCCGA 1 263349 ( 55) TGTGGTATGTTCGGAGTGGAC 1 24808 ( 335) GTTTGTTTGTTCCATCTTTTG 1 28028 ( 77) TGTTGTATGCGGTGGCACCTT 1 269556 ( 22) ATTGTTGTGATGTGATTTGTG 1 26239 ( 239) TGCGGTTTGTCTGACCTCCCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 10560 bayes= 9.32846 E= 1.3e-002 -24 -115 -208 126 -1081 -215 173 -62 -1081 -57 -208 160 -124 -1081 -8 138 -1081 -1081 201 -220 -1081 -1081 -1081 197 -124 -1081 24 126 -1081 -215 24 138 -1081 -1081 209 -1081 -124 -115 -108 138 -223 -57 -108 138 -124 -57 124 -62 -124 -115 -49 126 57 -1081 124 -220 -65 65 -49 12 -1081 65 24 38 -65 -1081 -1081 170 -1081 -57 51 97 -223 -57 150 -120 35 -115 -49 60 -223 -215 73 97 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 18 E= 1.3e-002 0.222222 0.111111 0.055556 0.611111 0.000000 0.055556 0.777778 0.166667 0.000000 0.166667 0.055556 0.777778 0.111111 0.000000 0.222222 0.666667 0.000000 0.000000 0.944444 0.055556 0.000000 0.000000 0.000000 1.000000 0.111111 0.000000 0.277778 0.611111 0.000000 0.055556 0.277778 0.666667 0.000000 0.000000 1.000000 0.000000 0.111111 0.111111 0.111111 0.666667 0.055556 0.166667 0.111111 0.666667 0.111111 0.166667 0.555556 0.166667 0.111111 0.111111 0.166667 0.611111 0.388889 0.000000 0.555556 0.055556 0.166667 0.388889 0.166667 0.277778 0.000000 0.388889 0.277778 0.333333 0.166667 0.000000 0.000000 0.833333 0.000000 0.166667 0.333333 0.500000 0.055556 0.166667 0.666667 0.111111 0.333333 0.111111 0.166667 0.388889 0.055556 0.055556 0.388889 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TA]GT[TG]GT[TG][TG]GTTGT[GA][CT][CTG]T[TG]G[TA][TG] -------------------------------------------------------------------------------- Time 8.50 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 16 llr = 196 E-value = 6.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2588238:379:35141:671 pos.-specific C 822:531982:7726:462:9 probability G 13:12411:1::1:2:431:: matrix T :::111::::13:3161213: bits 2.1 1.9 1.7 1.5 * * * Relative 1.3 * ** * * Entropy 1.0 * ** *** ** * ** (17.6 bits) 0.8 * ** ******* * ** 0.6 * ** ******* * * ** 0.4 **** ************ ** 0.2 ********************* 0.0 --------------------- Multilevel CAAACGACCAACCACTCCAAC consensus G A A TAT AGG T sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 14643 144 1.76e-10 ACTGCCAAAG CAAACGACCAACCTCTGCTAC TGCTCTTTAC 22676 455 1.95e-08 TTGTCCAACC CGAACCACCAACCCGACCGAC CTCTGGCAGC 263989 132 2.88e-08 TTACCCATGT CGAACAACCAATATCAACAAC AGCAGCAGCC 3320 370 6.03e-08 GAAGAGAATA AGAAGTACCAACCACACCCAC CACACATGCC 7963 12 1.08e-07 ACTCTCAAGA CGAGAGACCAACATCACCATC CTCCAAATCA 24808 65 2.07e-07 TGTCTCAGAT CAAACTACAAACCAGTGGAAA TGACTTCGCT 269556 267 6.75e-07 GAAACACCCA AACAAGACCAACCACTGTTTC CCTCCTCCTA 37862 454 1.26e-06 CAAGGGCAGG CACACCACCCATCCAACTAAC TTGAGAGCAA 263349 454 1.26e-06 GTACGAAGCA CAAGAAGCACACCACAGCAAC AAACAACAGA 25263 122 1.26e-06 AGCAAAACAA CCAATCGCAAACAACTGCCAC GTGGATTATC 38789 67 2.83e-06 AAAGTTCGAG CAAAGGAGCAATCATTTGATC ATCGAAATGA 8726 222 3.83e-06 GCTGGGTGGG CAAACGCCCATCCCGTCGAAA GAGTAAGGCA 26239 331 5.11e-06 TTCCACAGCC ACAACGACCGACGACTACCTC CACCGAGGCT 28028 446 8.22e-06 CGAAGAGGAA GACACCACCGATCTATCCGAC CTCCTCGAAT 4709 466 8.77e-06 CATCATCACA CCATTAACACATCACACTAAC ACAACACCAT 261512 115 9.96e-06 CAGATGTCTC CGAAGAAGCATCATTTGGATC TGGAAGCAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 14643 1.8e-10 143_[+3]_336 22676 1.9e-08 454_[+3]_25 263989 2.9e-08 131_[+3]_348 3320 6e-08 369_[+3]_110 7963 1.1e-07 11_[+3]_468 24808 2.1e-07 64_[+3]_415 269556 6.8e-07 266_[+3]_213 37862 1.3e-06 453_[+3]_26 263349 1.3e-06 453_[+3]_26 25263 1.3e-06 121_[+3]_358 38789 2.8e-06 66_[+3]_413 8726 3.8e-06 221_[+3]_258 26239 5.1e-06 330_[+3]_149 28028 8.2e-06 445_[+3]_34 4709 8.8e-06 465_[+3]_14 261512 1e-05 114_[+3]_365 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=16 14643 ( 144) CAAACGACCAACCTCTGCTAC 1 22676 ( 455) CGAACCACCAACCCGACCGAC 1 263989 ( 132) CGAACAACCAATATCAACAAC 1 3320 ( 370) AGAAGTACCAACCACACCCAC 1 7963 ( 12) CGAGAGACCAACATCACCATC 1 24808 ( 65) CAAACTACAAACCAGTGGAAA 1 269556 ( 267) AACAAGACCAACCACTGTTTC 1 37862 ( 454) CACACCACCCATCCAACTAAC 1 263349 ( 454) CAAGAAGCACACCACAGCAAC 1 25263 ( 122) CCAATCGCAAACAACTGCCAC 1 38789 ( 67) CAAAGGAGCAATCATTTGATC 1 8726 ( 222) CAAACGCCCATCCCGTCGAAA 1 26239 ( 331) ACAACGACCGACGACTACCTC 1 28028 ( 446) GACACCACCGATCTATCCGAC 1 4709 ( 466) CCATTAACACATCACACTAAC 1 261512 ( 115) CGAAGAAGCATCATTTGGATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 10560 bayes= 10.102 E= 6.2e+000 -48 160 -191 -1064 93 -40 41 -1064 163 -40 -1064 -1064 163 -1064 -91 -203 -48 102 -32 -103 -7 2 67 -103 163 -198 -91 -1064 -1064 182 -91 -1064 -7 160 -1064 -1064 139 -40 -91 -1064 174 -1064 -1064 -103 -1064 147 -1064 29 -7 147 -191 -1064 93 -40 -1064 29 -107 119 -32 -103 74 -1064 -1064 114 -107 82 67 -203 -1064 119 9 -45 110 -40 -91 -103 139 -1064 -1064 29 -107 182 -1064 -1064 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 16 E= 6.2e+000 0.187500 0.750000 0.062500 0.000000 0.500000 0.187500 0.312500 0.000000 0.812500 0.187500 0.000000 0.000000 0.812500 0.000000 0.125000 0.062500 0.187500 0.500000 0.187500 0.125000 0.250000 0.250000 0.375000 0.125000 0.812500 0.062500 0.125000 0.000000 0.000000 0.875000 0.125000 0.000000 0.250000 0.750000 0.000000 0.000000 0.687500 0.187500 0.125000 0.000000 0.875000 0.000000 0.000000 0.125000 0.000000 0.687500 0.000000 0.312500 0.250000 0.687500 0.062500 0.000000 0.500000 0.187500 0.000000 0.312500 0.125000 0.562500 0.187500 0.125000 0.437500 0.000000 0.000000 0.562500 0.125000 0.437500 0.375000 0.062500 0.000000 0.562500 0.250000 0.187500 0.562500 0.187500 0.125000 0.125000 0.687500 0.000000 0.000000 0.312500 0.125000 0.875000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[AG]AAC[GAC]AC[CA]AA[CT][CA][AT]C[TA][CG][CG]A[AT]C -------------------------------------------------------------------------------- Time 12.47 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 14643 5.13e-11 11_[+2(5.07e-07)]_111_\ [+3(1.76e-10)]_314_[+1(1.09e-05)]_6 22676 2.41e-08 10_[+1(4.20e-05)]_258_\ [+2(9.08e-07)]_149_[+3(1.95e-08)]_25 24295 4.68e-04 249_[+2(3.73e-07)]_22_\ [+1(8.60e-05)]_192 24808 1.39e-06 64_[+3(2.07e-07)]_249_\ [+2(7.38e-06)]_9_[+1(4.20e-05)]_120 25263 9.13e-05 121_[+3(1.26e-06)]_76_\ [+3(5.63e-05)]_6_[+3(8.43e-05)]_124_[+1(3.20e-06)]_94 260758 1.32e-02 464_[+1(2.87e-06)]_20 260943 1.79e-04 71_[+2(3.39e-06)]_349_\ [+1(8.16e-06)]_43 261512 3.44e-03 60_[+1(2.61e-05)]_38_[+3(9.96e-06)]_\ 365 26239 4.23e-05 238_[+2(1.30e-05)]_52_\ [+1(4.53e-05)]_3_[+3(5.11e-06)]_149 263349 1.59e-09 54_[+2(3.68e-06)]_329_\ [+1(8.32e-09)]_33_[+3(1.26e-06)]_26 263989 1.76e-05 13_[+1(2.40e-05)]_102_\ [+3(2.88e-08)]_348 264064 1.48e-04 396_[+1(3.99e-06)]_62_\ [+2(3.68e-06)]_5 269556 4.34e-07 21_[+2(1.14e-05)]_97_[+1(1.31e-05)]_\ 111_[+3(6.75e-07)]_142_[+1(2.29e-06)]_55 28028 5.93e-06 76_[+2(9.87e-06)]_186_\ [+1(3.99e-06)]_146_[+3(8.22e-06)]_34 3320 5.58e-09 154_[+2(5.60e-07)]_141_\ [+1(4.44e-06)]_37_[+3(6.03e-08)]_110 3680 2.64e-04 203_[+2(4.58e-07)]_37_\ [+2(1.14e-05)]_167_[+1(2.61e-05)]_35 37862 2.23e-07 9_[+1(6.69e-06)]_97_[+2(9.98e-07)]_\ 310_[+3(1.26e-06)]_26 38789 2.60e-07 20_[+1(3.20e-06)]_30_[+3(2.83e-06)]_\ 329_[+2(1.10e-06)]_63 4709 3.00e-07 49_[+2(2.20e-07)]_333_\ [+1(6.05e-06)]_46_[+3(8.77e-06)]_14 7963 2.87e-13 11_[+3(1.08e-07)]_135_\ [+2(1.64e-12)]_168_[+1(2.21e-05)]_128 7975 4.03e-05 17_[+1(7.39e-06)]_260_\ [+2(2.82e-05)]_34_[+2(2.20e-07)]_131 8726 6.22e-08 221_[+3(3.83e-06)]_88_\ [+2(3.78e-08)]_94_[+1(1.43e-05)]_39 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************