******************************************************************************** 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/108/108.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10577 1.0000 500 10972 1.0000 500 11193 1.0000 500 11586 1.0000 500 12012 1.0000 500 14242 1.0000 500 17242 1.0000 500 20959 1.0000 500 21061 1.0000 500 21161 1.0000 500 21362 1.0000 500 21403 1.0000 500 21855 1.0000 500 22016 1.0000 500 22347 1.0000 500 22644 1.0000 500 23771 1.0000 500 24205 1.0000 500 24456 1.0000 500 24659 1.0000 500 24971 1.0000 500 25498 1.0000 500 25750 1.0000 500 264651 1.0000 500 264846 1.0000 500 2674 1.0000 500 31845 1.0000 500 3598 1.0000 500 3604 1.0000 500 38767 1.0000 500 6066 1.0000 500 9311 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/108/108.seqs.fa -oc motifs/108 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 32 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 16000 N= 32 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.257 C 0.231 G 0.250 T 0.262 Background letter frequencies (from dataset with add-one prior applied): A 0.257 C 0.231 G 0.250 T 0.262 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 32 llr = 317 E-value = 1.0e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 342237246264472387197 pos.-specific C 7244318238:53354128:2 probability G 11::3::21:2:2:221:1:: matrix T :34413:31121::21:1:11 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 CACTAACAACACAACCAACAA consensus ATTCCT TC ACC A sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 24971 356 1.12e-10 CAACGCTCCC CATCAACAACACAACGAACAA AGCAACCCAC 12012 141 9.65e-08 GGGAAGGTAG CACTCACGACACGAACATCAA GCCCATTCTT 21362 473 1.11e-07 CCAACAGAAC ACTAGACAACTCAACAAACAA CAGAGAA 10972 479 2.54e-07 CGGCGCAAGC CTTCATACACACCAGAAACAA T 6066 473 4.83e-07 TCTGCTTGCT CCTCGACGCAACAACCACCAA CGCCGTC 3598 263 8.86e-07 TACTTGCAAC CACTTTCCACGACACCACCAA CCCAAATGTT 24205 382 1.12e-06 AGAGGTTTAA CTTTGAACCCACCCCCATCAA AATTTGAGTT 3604 468 1.25e-06 GGAAACTGGC CTTCTCCAACAACACGAACAA TCCCCTGCCA 264846 393 1.25e-06 CAGGCAGCAA CATTAACACAACAAAGATCAA AACAATCGAA 25750 458 1.76e-06 CATTGCTCAC CGCTCTCTACTACACCAACTA TTGTACCCGT 21061 370 1.96e-06 ACAAAGAAGA AATTCTCTACGAGACTAACAA CCACAATATA 22644 160 3.01e-06 GTACGCCGAT CAACGTCGACGCTACAAACAA CAGCTTCATG 23771 132 4.10e-06 CATGTCAGTC CATAAACACCAACACCGAAAC CGAAGAGGTA 22016 76 4.10e-06 CATTGGTAGA CTTTAACTCCAAAATAGTCAA ATGTGAGAAG 24659 477 4.54e-06 TGCTACCAGT CCCACACCACAAGAGCAACAG AGA 25498 53 5.54e-06 CGGCTGCTGC CACTGACAACTCACACCAGAA CGTAAAGCAC 21161 434 6.73e-06 GGTGCACGAT CAATCACAAAGCGAGAAAAAA CCTGCCGTCG 264651 235 8.15e-06 GCAAAGTCAT CAATAACAACGAACGAACCAT ACGCCGTCTC 11586 478 8.15e-06 CCGACTAAAC CCACAAATGCAAACAAAACAA CG 11193 80 1.54e-05 GAAAATGTAT CGATCTCTACAAACCCAAGAT GACAATGGGA 24456 475 1.84e-05 CGTTTAGTCC ATCTGACACCTCAACCACCTC GAGTA 14242 360 2.18e-05 TCTATCGGAC AATCGTCCGCATCAGGAACAA AAATAGAGCC 21403 475 2.57e-05 TGCTCCCTTT GCCACACAACACGCAACACAA CAACC 9311 220 3.03e-05 GGTTACAACT CACCATCTCAAAAATCGACAT ACACATACCT 21855 378 3.85e-05 CTTGGTGCAC CTCCCTCGATACCCCAAAAAC ACACGAAGAA 2674 415 6.09e-05 CACGTATCAC ATCACACTTCACGACCACGAC AACTACCTTT 17242 462 6.09e-05 AGTAACAAAA GACCGAAGGCATCAGAAACAA GTACAATGGA 20959 244 7.05e-05 CGACATGTTT GAACCAAATCACCAAGAAGAA TCGCCAGGTC 22347 291 1.00e-04 TGAAGTAGTT CCTTAACTCGGCACTCAACTA CTCGCTGGGG 31845 341 1.23e-04 TGTATGTCAC ATTCAACCATTAAATTAAAAA ATACTATTCA 10577 453 1.81e-04 TCCTCACTAA AGCTACCCTCTCACCCACCAC CTCTTCTAGC 38767 411 1.93e-04 CAGGATCAGG AGCAGAAAAAAACATTGACAA CCCCTATTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 24971 1.1e-10 355_[+1]_124 12012 9.7e-08 140_[+1]_339 21362 1.1e-07 472_[+1]_7 10972 2.5e-07 478_[+1]_1 6066 4.8e-07 472_[+1]_7 3598 8.9e-07 262_[+1]_217 24205 1.1e-06 381_[+1]_98 3604 1.3e-06 467_[+1]_12 264846 1.3e-06 392_[+1]_87 25750 1.8e-06 457_[+1]_22 21061 2e-06 369_[+1]_110 22644 3e-06 159_[+1]_320 23771 4.1e-06 131_[+1]_348 22016 4.1e-06 75_[+1]_404 24659 4.5e-06 476_[+1]_3 25498 5.5e-06 52_[+1]_427 21161 6.7e-06 433_[+1]_46 264651 8.1e-06 234_[+1]_245 11586 8.1e-06 477_[+1]_2 11193 1.5e-05 79_[+1]_400 24456 1.8e-05 474_[+1]_5 14242 2.2e-05 359_[+1]_120 21403 2.6e-05 474_[+1]_5 9311 3e-05 219_[+1]_260 21855 3.9e-05 377_[+1]_102 2674 6.1e-05 414_[+1]_65 17242 6.1e-05 461_[+1]_18 20959 7e-05 243_[+1]_236 22347 0.0001 290_[+1]_189 31845 0.00012 340_[+1]_139 10577 0.00018 452_[+1]_27 38767 0.00019 410_[+1]_69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=32 24971 ( 356) CATCAACAACACAACGAACAA 1 12012 ( 141) CACTCACGACACGAACATCAA 1 21362 ( 473) ACTAGACAACTCAACAAACAA 1 10972 ( 479) CTTCATACACACCAGAAACAA 1 6066 ( 473) CCTCGACGCAACAACCACCAA 1 3598 ( 263) CACTTTCCACGACACCACCAA 1 24205 ( 382) CTTTGAACCCACCCCCATCAA 1 3604 ( 468) CTTCTCCAACAACACGAACAA 1 264846 ( 393) CATTAACACAACAAAGATCAA 1 25750 ( 458) CGCTCTCTACTACACCAACTA 1 21061 ( 370) AATTCTCTACGAGACTAACAA 1 22644 ( 160) CAACGTCGACGCTACAAACAA 1 23771 ( 132) CATAAACACCAACACCGAAAC 1 22016 ( 76) CTTTAACTCCAAAATAGTCAA 1 24659 ( 477) CCCACACCACAAGAGCAACAG 1 25498 ( 53) CACTGACAACTCACACCAGAA 1 21161 ( 434) CAATCACAAAGCGAGAAAAAA 1 264651 ( 235) CAATAACAACGAACGAACCAT 1 11586 ( 478) CCACAAATGCAAACAAAACAA 1 11193 ( 80) CGATCTCTACAAACCCAAGAT 1 24456 ( 475) ATCTGACACCTCAACCACCTC 1 14242 ( 360) AATCGTCCGCATCAGGAACAA 1 21403 ( 475) GCCACACAACACGCAACACAA 1 9311 ( 220) CACCATCTCAAAAATCGACAT 1 21855 ( 378) CTCCCTCGATACCCCAAAAAC 1 2674 ( 415) ATCACACTTCACGACCACGAC 1 17242 ( 462) GACCGAAGGCATCAGAAACAA 1 20959 ( 244) GAACCAAATCACCAAGAAGAA 1 22347 ( 291) CCTTAACTCGGCACTCAACTA 1 31845 ( 341) ATTCAACCATTAAATTAAAAA 1 10577 ( 453) AGCTACCCTCTCACCCACCAC 1 38767 ( 411) AGCAGAAAAAAACATTGACAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 15360 bayes= 8.90388 E= 1.0e-007 -4 151 -141 -1164 77 -30 -100 -7 -45 81 -1164 63 -45 70 -1164 74 42 44 17 -207 135 -189 -1164 10 -45 181 -1164 -1164 55 -8 -68 -7 113 11 -141 -148 -72 170 -300 -207 128 -1164 -41 -48 66 120 -1164 -207 77 57 -41 -307 149 28 -1164 -1164 -45 102 -41 -75 28 92 -68 -148 166 -189 -100 -1164 142 -30 -1164 -107 -104 170 -100 -1164 182 -1164 -1164 -148 149 -56 -300 -148 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 32 E= 1.0e-007 0.250000 0.656250 0.093750 0.000000 0.437500 0.187500 0.125000 0.250000 0.187500 0.406250 0.000000 0.406250 0.187500 0.375000 0.000000 0.437500 0.343750 0.312500 0.281250 0.062500 0.656250 0.062500 0.000000 0.281250 0.187500 0.812500 0.000000 0.000000 0.375000 0.218750 0.156250 0.250000 0.562500 0.250000 0.093750 0.093750 0.156250 0.750000 0.031250 0.062500 0.625000 0.000000 0.187500 0.187500 0.406250 0.531250 0.000000 0.062500 0.437500 0.343750 0.187500 0.031250 0.718750 0.281250 0.000000 0.000000 0.187500 0.468750 0.187500 0.156250 0.312500 0.437500 0.156250 0.093750 0.812500 0.062500 0.125000 0.000000 0.687500 0.187500 0.000000 0.125000 0.125000 0.750000 0.125000 0.000000 0.906250 0.000000 0.000000 0.093750 0.718750 0.156250 0.031250 0.093750 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CA][AT][CT][TC][ACG][AT]C[ATC][AC]CA[CA][AC][AC]C[CA]AACAA -------------------------------------------------------------------------------- Time 10.22 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 24 llr = 267 E-value = 1.3e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 23::2313:551:51:3232: pos.-specific C ::1::1:::::2:11:61::2 probability G 7:68628485489:59:6327 matrix T 273224:32:1::43:11361 bits 2.1 1.9 1.7 1.5 * * Relative 1.3 * * * * Entropy 1.1 * * ** ** * (16.0 bits) 0.8 * * * ** ** ** * 0.6 ***** * ***** ** * 0.4 ***** ************ ** 0.2 ***** *************** 0.0 --------------------- Multilevel GTGGGTGGGGAGGAGGCGATG consensus AT AA A AG TT AATA sequence TG T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 6066 157 9.15e-11 GCGGGTGCGT GTGGGCGGGAAGGAGGCGATG CGGACTCCTC 11193 26 2.03e-08 AATCTTCATT GTTGGAGAGAAGGTGGAGTTC CGATGTCTGC 11586 247 3.12e-08 TGACGCCATG GTGGGTGTGGAGGCTGCATTG GTATTGGTCT 21403 242 3.03e-07 GAGGGAGGTT GTTGTTGGGAGGGAGGCAGCG CATGCTTTTT 20959 94 4.72e-07 GGTTGGTTTG TTTGGTGTGAAGGAGGCCGTC GTCGGCGGGA 3604 129 6.51e-07 AGATTGTCCC TTGTATGAGAACGTGGCGGTG AATGAGTCAG 24456 249 8.90e-07 TGGTGGAGTA GTTGGAGGTGAGGATACGTTG GTTGAGATGA 21855 231 1.09e-06 TTTTGTGTTG TTGTGTAGTAGGGAGGCGTTG AGTAGGAAAA 21061 60 1.46e-06 AAGGGAATCA GTGGAGGAGGGCGTGGATAGG AGAACCTACG 10577 102 1.61e-06 AGCATCGTTT GTGGTCGGGGGGGATCCGTAG ATACCAATAC 21161 80 1.95e-06 GACGAGGGCA GAGGGTGAGAGAGAGGTTATG TTTGGTTGGT 17242 336 2.14e-06 AGCCATGAGT GGTGGTGGGGTGGTTGAAATG TTGATGATTC 21362 380 2.83e-06 GTGATGCGTG ATGGGGGGGGGGGTAGCAAAT AACAGTGACA 10972 235 3.69e-06 CGAAAGTAGA GTTGATGGGGGGAAAGAAATG AAGTACTTTA 264846 105 5.68e-06 TGGATGAGAT TTTGTAGAGGACGATGAGATT TTGTAGAGGA 24205 44 6.71e-06 ACTGTGGATA GAGGTGATGGTGGTTGCGAAG AGGATGGCAG 23771 6 6.71e-06 TTTTG GTGGTGGTGAAGGACGCCTGC CTCACCAGAG 22644 297 7.90e-06 TGAAAATGAA GAGGAACTGGACGAGGCGGAG GAAAACGGAC 24659 403 8.56e-06 GCGACTTGGT GTGTGGGGTGGGGCGGAGGGC GGAGGGAGGC 3598 171 1.09e-05 CGACAACGAG AACGGAGGGGGGGGGGCGTTT TTTCGGTTTC 38767 191 1.17e-05 ATGTTGTTGT ATTGGTGAGAGGGTCGCTCGG TTGGGCAACA 12012 30 1.37e-05 TAGGATTGCA AAGGGCGTCATGGTGGAGGTG TACATCGTGA 22347 112 2.45e-05 TGCTGCCAGT GTGTGTAAGAAGCAAGAGGAG TCAGACGCGG 31845 94 4.21e-05 ATACAGCCCC GACGAAGATGAAGTGGTGTTG TAGTCGCTAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6066 9.2e-11 156_[+2]_323 11193 2e-08 25_[+2]_454 11586 3.1e-08 246_[+2]_233 21403 3e-07 241_[+2]_238 20959 4.7e-07 93_[+2]_386 3604 6.5e-07 128_[+2]_351 24456 8.9e-07 248_[+2]_231 21855 1.1e-06 230_[+2]_249 21061 1.5e-06 59_[+2]_420 10577 1.6e-06 101_[+2]_378 21161 2e-06 79_[+2]_400 17242 2.1e-06 335_[+2]_144 21362 2.8e-06 379_[+2]_100 10972 3.7e-06 234_[+2]_245 264846 5.7e-06 104_[+2]_375 24205 6.7e-06 43_[+2]_436 23771 6.7e-06 5_[+2]_474 22644 7.9e-06 296_[+2]_183 24659 8.6e-06 402_[+2]_77 3598 1.1e-05 170_[+2]_309 38767 1.2e-05 190_[+2]_289 12012 1.4e-05 29_[+2]_450 22347 2.5e-05 111_[+2]_368 31845 4.2e-05 93_[+2]_386 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=24 6066 ( 157) GTGGGCGGGAAGGAGGCGATG 1 11193 ( 26) GTTGGAGAGAAGGTGGAGTTC 1 11586 ( 247) GTGGGTGTGGAGGCTGCATTG 1 21403 ( 242) GTTGTTGGGAGGGAGGCAGCG 1 20959 ( 94) TTTGGTGTGAAGGAGGCCGTC 1 3604 ( 129) TTGTATGAGAACGTGGCGGTG 1 24456 ( 249) GTTGGAGGTGAGGATACGTTG 1 21855 ( 231) TTGTGTAGTAGGGAGGCGTTG 1 21061 ( 60) GTGGAGGAGGGCGTGGATAGG 1 10577 ( 102) GTGGTCGGGGGGGATCCGTAG 1 21161 ( 80) GAGGGTGAGAGAGAGGTTATG 1 17242 ( 336) GGTGGTGGGGTGGTTGAAATG 1 21362 ( 380) ATGGGGGGGGGGGTAGCAAAT 1 10972 ( 235) GTTGATGGGGGGAAAGAAATG 1 264846 ( 105) TTTGTAGAGGACGATGAGATT 1 24205 ( 44) GAGGTGATGGTGGTTGCGAAG 1 23771 ( 6) GTGGTGGTGAAGGACGCCTGC 1 22644 ( 297) GAGGAACTGGACGAGGCGGAG 1 24659 ( 403) GTGTGGGGTGGGGCGGAGGGC 1 3598 ( 171) AACGGAGGGGGGGGGGCGTTT 1 38767 ( 191) ATTGGTGAGAGGGTCGCTCGG 1 12012 ( 30) AAGGGCGTCATGGTGGAGGTG 1 22347 ( 112) GTGTGTAAGAAGCAAGAGGAG 1 31845 ( 94) GACGAAGATGAAGTGGTGTTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 15360 bayes= 9.76773 E= 1.3e-002 -62 -1123 142 -65 -4 -1123 -258 143 -1123 -147 122 35 -1123 -1123 174 -65 -30 -1123 122 -33 -4 -89 -26 67 -104 -247 174 -1123 38 -1123 74 -7 -1123 -247 166 -65 84 -1123 112 -1123 84 -1123 74 -107 -162 -47 158 -1123 -262 -247 187 -1123 96 -147 -258 52 -104 -147 112 -7 -262 -247 187 -1123 38 134 -1123 -165 -30 -147 122 -107 38 -247 22 35 -30 -247 -58 115 -1123 -47 150 -107 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 24 E= 1.3e-002 0.166667 0.000000 0.666667 0.166667 0.250000 0.000000 0.041667 0.708333 0.000000 0.083333 0.583333 0.333333 0.000000 0.000000 0.833333 0.166667 0.208333 0.000000 0.583333 0.208333 0.250000 0.125000 0.208333 0.416667 0.125000 0.041667 0.833333 0.000000 0.333333 0.000000 0.416667 0.250000 0.000000 0.041667 0.791667 0.166667 0.458333 0.000000 0.541667 0.000000 0.458333 0.000000 0.416667 0.125000 0.083333 0.166667 0.750000 0.000000 0.041667 0.041667 0.916667 0.000000 0.500000 0.083333 0.041667 0.375000 0.125000 0.083333 0.541667 0.250000 0.041667 0.041667 0.916667 0.000000 0.333333 0.583333 0.000000 0.083333 0.208333 0.083333 0.583333 0.125000 0.333333 0.041667 0.291667 0.333333 0.208333 0.041667 0.166667 0.583333 0.000000 0.166667 0.708333 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- G[TA][GT]G[GAT][TAG]G[GAT]G[GA][AG]GG[AT][GT]G[CA][GA][ATG][TA]G -------------------------------------------------------------------------------- Time 20.81 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 12 llr = 171 E-value = 4.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :34:2:21::31:22:3231: pos.-specific C 34:a6243798188:934493 probability G :13::13::1::31:1:11:8 matrix T 733:38163::8::8:333:: bits 2.1 * 1.9 * 1.7 * * * * 1.5 * * * * Relative 1.3 * ** * ** ** Entropy 1.1 * * ******** ** (20.6 bits) 0.8 * * * ******** ** 0.6 * *** ********* ** 0.4 * **** ********** ** 0.2 ********************* 0.0 --------------------- Multilevel TCACCTCTCCCTCCTCACCCG consensus CAT T GCT A G CTA C sequence TG T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 17242 3 1.02e-10 CG TAGCCTCTCCCTCCTCCCTCG GCGGTGAGTG 21061 24 3.16e-09 CTGTTAGCCA TCACATTCCCCTCCTCTCCCG TGCAAAAGGG 25750 399 6.07e-09 ATCATCATCA TCGCCTCTCCATCATCTCACG TGAGCGTCTC 2674 239 3.33e-08 ACAATTTCAA CCTCTTCTCCCTCCTCCGGCG CCAAGTGCAG 22644 11 1.36e-07 GGCACAGAGA CCACCTATCCCCGCTCCAACG ACAGCAATAT 21403 45 1.61e-07 TCCAGCACCT TCACCGGATCCTCCACACCCG CACCCTCGCA 14242 475 1.90e-07 AAATCGTACT CTTCATCTTCATCATCATCCG ACGCA 11586 27 2.06e-07 TAAGCTCGTT TTACCCGCCCCTGCACTTCCC AATATTATAC 21161 311 3.29e-07 TATGTTTTTG TTGCTTGCCCAACCTCATTCG TCACCGCCAC 6066 411 3.81e-07 TTCCCGGCAT TGTCCCGTCCCTCGTCACACC TGAAACTGAC 12012 361 7.16e-07 AATGTCTCCG TATCTTCTTGCTGCTCTTTCC TTCCTCTGTT 10577 173 1.42e-06 GGATAGACCC CAACCTACTCCTCCTGCACAG CATTCTCCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 17242 1e-10 2_[+3]_477 21061 3.2e-09 23_[+3]_456 25750 6.1e-09 398_[+3]_81 2674 3.3e-08 238_[+3]_241 22644 1.4e-07 10_[+3]_469 21403 1.6e-07 44_[+3]_435 14242 1.9e-07 474_[+3]_5 11586 2.1e-07 26_[+3]_453 21161 3.3e-07 310_[+3]_169 6066 3.8e-07 410_[+3]_69 12012 7.2e-07 360_[+3]_119 10577 1.4e-06 172_[+3]_307 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=12 17242 ( 3) TAGCCTCTCCCTCCTCCCTCG 1 21061 ( 24) TCACATTCCCCTCCTCTCCCG 1 25750 ( 399) TCGCCTCTCCATCATCTCACG 1 2674 ( 239) CCTCTTCTCCCTCCTCCGGCG 1 22644 ( 11) CCACCTATCCCCGCTCCAACG 1 21403 ( 45) TCACCGGATCCTCCACACCCG 1 14242 ( 475) CTTCATCTTCATCATCATCCG 1 11586 ( 27) TTACCCGCCCCTGCACTTCCC 1 21161 ( 311) TTGCTTGCCCAACCTCATTCG 1 6066 ( 411) TGTCCCGTCCCTCGTCACACC 1 12012 ( 361) TATCTTCTTGCTGCTCTTTCC 1 10577 ( 173) CAACCTACTCCTCCTGCACAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 15360 bayes= 11.4209 E= 4.0e+000 -1023 53 -1023 134 -4 85 -158 -7 70 -1023 0 35 -1023 211 -1023 -1023 -62 133 -1023 -7 -1023 -47 -158 151 -62 85 42 -165 -162 53 -1023 115 -1023 153 -1023 35 -1023 199 -158 -1023 -4 170 -1023 -1023 -162 -147 -1023 167 -1023 170 0 -1023 -62 170 -158 -1023 -62 -1023 -1023 167 -1023 199 -158 -1023 38 53 -1023 35 -62 85 -158 35 -4 85 -158 -7 -162 199 -1023 -1023 -1023 11 158 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 12 E= 4.0e+000 0.000000 0.333333 0.000000 0.666667 0.250000 0.416667 0.083333 0.250000 0.416667 0.000000 0.250000 0.333333 0.000000 1.000000 0.000000 0.000000 0.166667 0.583333 0.000000 0.250000 0.000000 0.166667 0.083333 0.750000 0.166667 0.416667 0.333333 0.083333 0.083333 0.333333 0.000000 0.583333 0.000000 0.666667 0.000000 0.333333 0.000000 0.916667 0.083333 0.000000 0.250000 0.750000 0.000000 0.000000 0.083333 0.083333 0.000000 0.833333 0.000000 0.750000 0.250000 0.000000 0.166667 0.750000 0.083333 0.000000 0.166667 0.000000 0.000000 0.833333 0.000000 0.916667 0.083333 0.000000 0.333333 0.333333 0.000000 0.333333 0.166667 0.416667 0.083333 0.333333 0.250000 0.416667 0.083333 0.250000 0.083333 0.916667 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [TC][CAT][ATG]C[CT]T[CG][TC][CT]C[CA]T[CG]CTC[ACT][CT][CAT]C[GC] -------------------------------------------------------------------------------- Time 30.54 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10577 7.12e-06 101_[+2(1.61e-06)]_50_\ [+3(1.42e-06)]_307 10972 2.85e-06 234_[+2(3.69e-06)]_223_\ [+1(2.54e-07)]_1 11193 9.84e-06 25_[+2(2.03e-08)]_33_[+1(1.54e-05)]_\ 400 11586 2.09e-09 26_[+3(2.06e-07)]_199_\ [+2(3.12e-08)]_210_[+1(8.15e-06)]_2 12012 3.00e-08 29_[+2(1.37e-05)]_90_[+1(9.65e-08)]_\ 199_[+3(7.16e-07)]_119 14242 4.63e-05 359_[+1(2.18e-05)]_94_\ [+3(1.90e-07)]_5 17242 5.81e-10 2_[+3(1.02e-10)]_312_[+2(2.14e-06)]_\ 105_[+1(6.09e-05)]_18 20959 7.45e-05 93_[+2(4.72e-07)]_129_\ [+1(7.05e-05)]_236 21061 4.13e-10 23_[+3(3.16e-09)]_15_[+2(1.46e-06)]_\ 289_[+1(1.96e-06)]_110 21161 1.21e-07 79_[+2(1.95e-06)]_210_\ [+3(3.29e-07)]_102_[+1(6.73e-06)]_46 21362 8.06e-06 379_[+2(2.83e-06)]_72_\ [+1(1.11e-07)]_7 21403 3.88e-08 44_[+3(1.61e-07)]_85_[+2(2.13e-05)]_\ 18_[+2(1.84e-05)]_31_[+2(3.03e-07)]_42_[+2(2.82e-05)]_149_[+1(2.57e-05)]_5 21855 2.17e-04 230_[+2(1.09e-06)]_126_\ [+1(3.85e-05)]_102 22016 3.59e-02 75_[+1(4.10e-06)]_404 22347 9.81e-03 111_[+2(2.45e-05)]_368 22644 9.24e-08 10_[+3(1.36e-07)]_128_\ [+1(3.01e-06)]_92_[+2(3.69e-05)]_3_[+2(7.90e-06)]_183 23771 4.68e-04 5_[+2(6.71e-06)]_105_[+1(4.10e-06)]_\ 348 24205 1.29e-04 43_[+2(6.71e-06)]_317_\ [+1(1.12e-06)]_98 24456 1.58e-04 248_[+2(8.90e-07)]_205_\ [+1(1.84e-05)]_5 24659 2.44e-04 380_[+2(6.56e-05)]_1_[+2(8.56e-06)]_\ 53_[+1(4.54e-06)]_3 24971 1.80e-06 355_[+1(1.12e-10)]_124 25498 1.27e-02 52_[+1(5.54e-06)]_427 25750 3.95e-07 239_[+3(7.63e-05)]_138_\ [+3(6.07e-09)]_38_[+1(1.76e-06)]_22 264651 6.06e-02 234_[+1(8.15e-06)]_245 264846 7.12e-05 104_[+2(5.68e-06)]_267_\ [+1(1.25e-06)]_87 2674 5.48e-05 238_[+3(3.33e-08)]_155_\ [+1(6.09e-05)]_65 31845 1.40e-02 93_[+2(4.21e-05)]_386 3598 7.68e-05 170_[+2(1.09e-05)]_71_\ [+1(8.86e-07)]_217 3604 2.04e-05 128_[+2(6.51e-07)]_22_\ [+2(2.45e-05)]_275_[+1(1.25e-06)]_12 38767 5.19e-03 190_[+2(1.17e-05)]_289 6066 1.14e-12 156_[+2(9.15e-11)]_233_\ [+3(3.81e-07)]_41_[+1(4.83e-07)]_7 9311 5.23e-02 219_[+1(3.03e-05)]_260 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************