******************************************************************************** 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/22/22.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10882 1.0000 500 11501 1.0000 500 11924 1.0000 500 12120 1.0000 500 16344 1.0000 500 20335 1.0000 500 20603 1.0000 500 20965 1.0000 500 21472 1.0000 500 21667 1.0000 500 22747 1.0000 500 2341 1.0000 500 2342 1.0000 500 2356 1.0000 500 23808 1.0000 500 24080 1.0000 500 24099 1.0000 500 24769 1.0000 500 25402 1.0000 500 2601 1.0000 500 262313 1.0000 500 262332 1.0000 500 26246 1.0000 500 2673 1.0000 500 268127 1.0000 500 268304 1.0000 500 270092 1.0000 500 270210 1.0000 500 270233 1.0000 500 270241 1.0000 500 270242 1.0000 500 2845 1.0000 500 2848 1.0000 500 29375 1.0000 500 29842 1.0000 500 30385 1.0000 500 3141 1.0000 500 31749 1.0000 500 31983 1.0000 500 33018 1.0000 500 33131 1.0000 500 33606 1.0000 500 34276 1.0000 500 3453 1.0000 500 34830 1.0000 500 35934 1.0000 500 36081 1.0000 500 38122 1.0000 500 3815 1.0000 500 3816 1.0000 500 38494 1.0000 500 38583 1.0000 500 38667 1.0000 500 38715 1.0000 500 3884 1.0000 500 39813 1.0000 500 40747 1.0000 500 42962 1.0000 500 4843 1.0000 500 4882 1.0000 500 4883 1.0000 500 4917 1.0000 500 5174 1.0000 500 6572 1.0000 500 7270 1.0000 500 7916 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/22/22.seqs.fa -oc motifs/22 -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= 66 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= 33000 N= 66 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.275 C 0.230 G 0.230 T 0.265 Background letter frequencies (from dataset with add-one prior applied): A 0.275 C 0.230 G 0.230 T 0.265 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 15 sites = 60 llr = 551 E-value = 1.9e-031 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :9727746:764642 pos.-specific C 9:372242a335347 probability G 1::1:::::::1:11 matrix T :11:1122::11:11 bits 2.1 * 1.9 * 1.7 * * 1.5 ** * Relative 1.3 ** * Entropy 1.1 ** ** (13.3 bits) 0.8 ****** ** * 0.6 ****** **** * * 0.4 ************* * 0.2 *************** 0.0 --------------- Multilevel CAACAAAACAACAAC consensus C C CT CCACC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 31749 480 3.78e-09 ACTTTGACAA CAACAACACAACAAC GCGACC 2342 481 3.78e-09 ACTTTGACAA CAACAACACAACAAC GCGAC 4843 480 2.49e-08 GAGCCTGCGG CACCAACACAACACC ACCCAA 262313 479 2.49e-08 GAGCCTGCGG CACCAACACAACACC ACCCAAC 3884 433 1.44e-07 CCCTATACAA CAACCAAACAAAAAC AACCAGGAGA 21667 466 2.00e-07 TGTCTTCCTC CAACCAAACCACAAC AAACACTAAC 3816 481 2.97e-07 CCTCCCACAA CACCAAATCAACAAC TCCAC 33131 480 2.97e-07 CCTCCCACAA CACCAAATCAACAAC TCCACC 2848 60 5.87e-07 GTATCCGTTT CAACACCACACAAAC CGTTCACATC 270092 486 5.87e-07 CTCAACATCA CAACCCAACAACAAC 5174 269 1.29e-06 GAAGAGTTGG CACCAACACAAGAAC AAGATGGGGG 6572 312 1.49e-06 CGCCGTCATA CAAACAAACACCACC TCAAACCAAA 24769 36 1.73e-06 CCAACACTGC CACCATCACAACCCC CAATCTCCTC 20335 433 1.98e-06 TACGAATACA CAACAAATCACCACA ATGCAACGCA 24080 419 2.27e-06 AAGCGGAAAC CAACCAATCCACCAC GCGGCCCTCC 36081 255 3.00e-06 CACCTGAACA CAACAATACCTCAAC ATGAAGTCCG 23808 485 3.00e-06 CACCTGAACA CAACAATACCTCAAC A 33606 257 3.89e-06 TGATGTCAAT CAACAATACAAACAA TGGAAGGAAT 34830 416 5.03e-06 ATACGATTTA CAAATACACAACAAC TCACGATTTC 30385 486 5.03e-06 ATCGATAATC CTCCAACACACCACC 29842 339 5.70e-06 CAACATCAAA CAACAACTCACAACG CTTTTTATCG 38667 305 6.43e-06 AAACCTGCTT CAACCAACCAAAATC GACTGAGGTG 21472 464 6.43e-06 TCACTCGGCA CACCAATACCACACA TTCAACCTCT 11501 6 8.14e-06 ATGAC CAAGAAAACACAAGC GAAGCGAGCG 35934 444 1.03e-05 GACCAAAGAA CACCCTCTCAACACC CTCTCACAAC 7916 473 1.15e-05 TTTCCTGTGC CACACACCCAACAAC CAATCCAACA 4882 473 1.43e-05 CCTCCCCCCA CAACAAACCACACCT CTCTCTTGCA 38494 231 1.77e-05 GGAGCAAGGC GAACAAAACACAACA CGGTGATCAT 7270 446 1.97e-05 TCAGTAGCCC CATCAATACACAAGC ATCAGCAGTA 12120 475 2.18e-05 CAAGCAAACA CAACATACCAATAAC AACAAACAAC 4917 416 2.41e-05 AAAACGTCAG CAACAATACAATCCT TTGCTTGAAC 2601 486 2.41e-05 ACTCCTCTTT CTACACACCAACACC 10882 458 2.41e-05 CGACCGTTCA CAACATTACACGACC CTCTTCCTCT 3453 378 2.94e-05 AGATGCAGTA GAACACAACATCAAC TCTACAGCAT 2673 54 3.23e-05 ACCGAGGTAT CACCTACACCACCTC CAGTGGAGAT 24099 430 3.23e-05 CTTTGGCAAA CATAAATACAACAGC AGGACGAAGG 38715 153 3.56e-05 ATTTTGCTAG CAATAACACCACCTC AGTCGATTTT 3141 110 3.56e-05 CCTTTTGTTT CAAGCAAACACAACA TTCTTATCAG 270233 291 3.56e-05 ATTTTGCTAG CAATAACACCACCTC AGTCGATTTT 20603 434 3.90e-05 TTTGTCTCTG GAACACCTCCCCACC ATCATCCTAT 29375 296 5.61e-05 CGCTTTGAGA GAACCAAACACAACT TATTACAGAT 2845 347 5.61e-05 GCCCGTCTTC CACCAACACAAATCG AAACCGTATC 270241 483 5.61e-05 GCCCGTCTTC CACCAACACAAATCG AAA 268127 348 6.66e-05 TGCAAACGCG CAAATAAACACCACG TCCATTATAT 16344 476 7.25e-05 CTCAGCATCG CATCAATTCAATCAC ATTATCAACA 40747 458 8.55e-05 CCCCCGTCGC CAAGACCTCCACCGC TCTCAACAAG 3815 347 1.09e-04 CCGACCATTT CATACCCACCAAAAC GCGTGGTGAA 4883 109 1.37e-04 ATCTCCACAC CAACATCCCACGAAA TCAACTCTTG 39813 476 1.47e-04 AATAAATTTT CAACAATACCTGAAT ATTTTGCTTT 31983 14 1.58e-04 GGATCGAAAC CAACATCTCCAACGT AAGATCCGTC 26246 288 1.58e-04 CATGAAGCTT CATCTACACACACAA TGGATTGGTG 2341 13 1.58e-04 GGATCGAAAC CAACATCTCCAACGT AAGATCCGTC 42962 177 1.70e-04 TAGCGAGCGA CAAGACAACCTCAAA CTCAAATATC 38122 224 1.96e-04 TTCGTTTCGG CTAAAAACCAAACTC GGACTTTCCG 25402 235 1.96e-04 TTCGTTTCGG CTAAAAACCAAACTC GGACTTTCCG 268304 476 2.73e-04 CATCATCTAC CACAACCACCATCCA ATACGGCACC 20965 355 2.73e-04 CTTTCATTGT CAACACATCCTTCGC CTGATTGTAT 34276 9 3.10e-04 CCACCCGA CAAACAACCACACTT GCTACTCTAC 11924 5 3.10e-04 CGTT GAAGCAAACAAACAG CAGAGCCAGC 270242 46 3.50e-04 ACTGACGTAA CACACAATCACAGCC GGGTTAACTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31749 3.8e-09 479_[+1]_6 2342 3.8e-09 480_[+1]_5 4843 2.5e-08 479_[+1]_6 262313 2.5e-08 478_[+1]_7 3884 1.4e-07 432_[+1]_53 21667 2e-07 465_[+1]_20 3816 3e-07 480_[+1]_5 33131 3e-07 479_[+1]_6 2848 5.9e-07 59_[+1]_426 270092 5.9e-07 485_[+1] 5174 1.3e-06 268_[+1]_217 6572 1.5e-06 311_[+1]_174 24769 1.7e-06 35_[+1]_450 20335 2e-06 432_[+1]_53 24080 2.3e-06 418_[+1]_67 36081 3e-06 254_[+1]_231 23808 3e-06 484_[+1]_1 33606 3.9e-06 256_[+1]_229 34830 5e-06 415_[+1]_70 30385 5e-06 485_[+1] 29842 5.7e-06 338_[+1]_147 38667 6.4e-06 304_[+1]_181 21472 6.4e-06 463_[+1]_22 11501 8.1e-06 5_[+1]_480 35934 1e-05 443_[+1]_42 7916 1.1e-05 472_[+1]_13 4882 1.4e-05 472_[+1]_13 38494 1.8e-05 230_[+1]_255 7270 2e-05 445_[+1]_40 12120 2.2e-05 474_[+1]_11 4917 2.4e-05 415_[+1]_70 2601 2.4e-05 485_[+1] 10882 2.4e-05 457_[+1]_28 3453 2.9e-05 377_[+1]_108 2673 3.2e-05 53_[+1]_432 24099 3.2e-05 429_[+1]_56 38715 3.6e-05 152_[+1]_333 3141 3.6e-05 109_[+1]_376 270233 3.6e-05 290_[+1]_195 20603 3.9e-05 433_[+1]_52 29375 5.6e-05 295_[+1]_190 2845 5.6e-05 346_[+1]_139 270241 5.6e-05 482_[+1]_3 268127 6.7e-05 347_[+1]_138 16344 7.3e-05 475_[+1]_10 40747 8.6e-05 457_[+1]_28 3815 0.00011 346_[+1]_139 4883 0.00014 108_[+1]_377 39813 0.00015 475_[+1]_10 31983 0.00016 13_[+1]_472 26246 0.00016 287_[+1]_198 2341 0.00016 12_[+1]_473 42962 0.00017 176_[+1]_309 38122 0.0002 223_[+1]_262 25402 0.0002 234_[+1]_251 268304 0.00027 475_[+1]_10 20965 0.00027 354_[+1]_131 34276 0.00031 8_[+1]_477 11924 0.00031 4_[+1]_481 270242 0.00035 45_[+1]_440 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=15 seqs=60 31749 ( 480) CAACAACACAACAAC 1 2342 ( 481) CAACAACACAACAAC 1 4843 ( 480) CACCAACACAACACC 1 262313 ( 479) CACCAACACAACACC 1 3884 ( 433) CAACCAAACAAAAAC 1 21667 ( 466) CAACCAAACCACAAC 1 3816 ( 481) CACCAAATCAACAAC 1 33131 ( 480) CACCAAATCAACAAC 1 2848 ( 60) CAACACCACACAAAC 1 270092 ( 486) CAACCCAACAACAAC 1 5174 ( 269) CACCAACACAAGAAC 1 6572 ( 312) CAAACAAACACCACC 1 24769 ( 36) CACCATCACAACCCC 1 20335 ( 433) CAACAAATCACCACA 1 24080 ( 419) CAACCAATCCACCAC 1 36081 ( 255) CAACAATACCTCAAC 1 23808 ( 485) CAACAATACCTCAAC 1 33606 ( 257) CAACAATACAAACAA 1 34830 ( 416) CAAATACACAACAAC 1 30385 ( 486) CTCCAACACACCACC 1 29842 ( 339) CAACAACTCACAACG 1 38667 ( 305) CAACCAACCAAAATC 1 21472 ( 464) CACCAATACCACACA 1 11501 ( 6) CAAGAAAACACAAGC 1 35934 ( 444) CACCCTCTCAACACC 1 7916 ( 473) CACACACCCAACAAC 1 4882 ( 473) CAACAAACCACACCT 1 38494 ( 231) GAACAAAACACAACA 1 7270 ( 446) CATCAATACACAAGC 1 12120 ( 475) CAACATACCAATAAC 1 4917 ( 416) CAACAATACAATCCT 1 2601 ( 486) CTACACACCAACACC 1 10882 ( 458) CAACATTACACGACC 1 3453 ( 378) GAACACAACATCAAC 1 2673 ( 54) CACCTACACCACCTC 1 24099 ( 430) CATAAATACAACAGC 1 38715 ( 153) CAATAACACCACCTC 1 3141 ( 110) CAAGCAAACACAACA 1 270233 ( 291) CAATAACACCACCTC 1 20603 ( 434) GAACACCTCCCCACC 1 29375 ( 296) GAACCAAACACAACT 1 2845 ( 347) CACCAACACAAATCG 1 270241 ( 483) CACCAACACAAATCG 1 268127 ( 348) CAAATAAACACCACG 1 16344 ( 476) CATCAATTCAATCAC 1 40747 ( 458) CAAGACCTCCACCGC 1 3815 ( 347) CATACCCACCAAAAC 1 4883 ( 109) CAACATCCCACGAAA 1 39813 ( 476) CAACAATACCTGAAT 1 31983 ( 14) CAACATCTCCAACGT 1 26246 ( 288) CATCTACACACACAA 1 2341 ( 13) CAACATCTCCAACGT 1 42962 ( 177) CAAGACAACCTCAAA 1 38122 ( 224) CTAAAAACCAAACTC 1 25402 ( 235) CTAAAAACCAAACTC 1 268304 ( 476) CACAACCACCATCCA 1 20965 ( 355) CAACACATCCTTCGC 1 34276 ( 9) CAAACAACCACACTT 1 11924 ( 5) GAAGCAAACAAACAG 1 270242 ( 46) CACACAATCACAGCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 32076 bayes= 9.73485 E= 1.9e-031 -1255 200 -146 -1255 176 -1255 -1255 -199 128 12 -1255 -167 -58 161 -146 -299 135 2 -1255 -199 138 -46 -1255 -119 60 86 -1255 -67 121 -62 -1255 -29 -1255 212 -1255 -1255 138 30 -1255 -1255 113 38 -1255 -141 42 107 -179 -167 121 46 -378 -299 54 67 -98 -119 -87 150 -146 -119 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 60 E= 1.9e-031 0.000000 0.916667 0.083333 0.000000 0.933333 0.000000 0.000000 0.066667 0.666667 0.250000 0.000000 0.083333 0.183333 0.700000 0.083333 0.033333 0.700000 0.233333 0.000000 0.066667 0.716667 0.166667 0.000000 0.116667 0.416667 0.416667 0.000000 0.166667 0.633333 0.150000 0.000000 0.216667 0.000000 1.000000 0.000000 0.000000 0.716667 0.283333 0.000000 0.000000 0.600000 0.300000 0.000000 0.100000 0.366667 0.483333 0.066667 0.083333 0.633333 0.316667 0.016667 0.033333 0.400000 0.366667 0.116667 0.116667 0.150000 0.650000 0.083333 0.116667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- CA[AC]C[AC]A[AC][AT]C[AC][AC][CA][AC][AC]C -------------------------------------------------------------------------------- Time 32.91 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 15 llr = 268 E-value = 2.4e-022 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::11:3::::11:642::6:: pos.-specific C 311:31:::3::6:::::1:: probability G 5588:1:a9:9:34569a:9a matrix T 141175a:17:91:121:31: bits 2.1 * * * 1.9 ** * * 1.7 ** * * * 1.5 *** ** ** ** Relative 1.3 * *** ** ** ** Entropy 1.1 *** ****** * ** ** (25.8 bits) 0.8 *** ******** ** ** 0.6 ***** *************** 0.4 ***** *************** 0.2 ********************* 0.0 --------------------- Multilevel GGGGTTTGGTGTCAGGGGAGG consensus CT CA C GGAA T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 31983 116 8.96e-11 CACATACGGT CGGGCATGGCGTCAAGGGAGG TCTTGACGGC 31749 119 8.96e-11 CACATACGGT CGGGCATGGCGTCAAGGGAGG TCTTGACGGC 2342 120 8.96e-11 CACATACGGT CGGGCATGGCGTCAAGGGAGG TCTTGACGGC 2341 115 8.96e-11 CACATACGGT CGGGCATGGCGTCAAGGGAGG TCTTGACGGC 270092 303 1.36e-10 AAGTTGCGTT GGGGTTTGGTGTGATGGGTGG GAGGGGCAGG 4883 228 1.99e-10 AGAGAGAGGT GTGGTTTGTTGTGGGGGGAGG CCGAACCTTG 262332 28 1.99e-10 AGAGAGAGGT GTGGTTTGTTGTGGGGGGAGG CCGAACCTTG 42962 217 3.34e-09 GCTGTGATAG GTGGTTTGGTATCAAAGGTGG TGTGGCGGCA 20965 186 3.34e-09 GACCATGGCG GCCGTTTGGTGTCGAAGGAGG GAGTGATTCA 7270 155 1.13e-08 GGTCGTCGGC GGTGTCTGGTGTCGGTGGTGG AACGATTGCC 270233 50 2.13e-08 TTGAGGGCGG TGGTCTTGGCGACGGGGGAGG CAGATTGGAA 3884 359 3.78e-08 TCTGGCTTTC CCATTTTGGTGTCAGAGGTGG CCGACGTGGC 3815 205 4.02e-08 GGTGGAGTTG TTGATTTGGTGTTGTGGGAGG GCGATGGCTA 2845 181 4.80e-08 AAGCCTCTGC GTGGTGTGGTGTGAGTTGCTG AGACAAACGG 270241 317 4.80e-08 AAGCCTCTGC GTGGTGTGGTGTGAGTTGCTG AGACAAACGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31983 9e-11 115_[+2]_364 31749 9e-11 118_[+2]_361 2342 9e-11 119_[+2]_360 2341 9e-11 114_[+2]_365 270092 1.4e-10 302_[+2]_177 4883 2e-10 227_[+2]_252 262332 2e-10 27_[+2]_452 42962 3.3e-09 216_[+2]_263 20965 3.3e-09 185_[+2]_294 7270 1.1e-08 154_[+2]_325 270233 2.1e-08 49_[+2]_430 3884 3.8e-08 358_[+2]_121 3815 4e-08 204_[+2]_275 2845 4.8e-08 180_[+2]_299 270241 4.8e-08 316_[+2]_163 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=15 31983 ( 116) CGGGCATGGCGTCAAGGGAGG 1 31749 ( 119) CGGGCATGGCGTCAAGGGAGG 1 2342 ( 120) CGGGCATGGCGTCAAGGGAGG 1 2341 ( 115) CGGGCATGGCGTCAAGGGAGG 1 270092 ( 303) GGGGTTTGGTGTGATGGGTGG 1 4883 ( 228) GTGGTTTGTTGTGGGGGGAGG 1 262332 ( 28) GTGGTTTGTTGTGGGGGGAGG 1 42962 ( 217) GTGGTTTGGTATCAAAGGTGG 1 20965 ( 186) GCCGTTTGGTGTCGAAGGAGG 1 7270 ( 155) GGTGTCTGGTGTCGGTGGTGG 1 270233 ( 50) TGGTCTTGGCGACGGGGGAGG 1 3884 ( 359) CCATTTTGGTGTCAGAGGTGG 1 3815 ( 205) TTGATTTGGTGTTGTGGGAGG 1 2845 ( 181) GTGGTGTGGTGTGAGTTGCTG 1 270241 ( 317) GTGGTGTGGTGTGAGTTGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 31680 bayes= 10.112 E= 2.4e-022 -1055 54 121 -99 -1055 -79 102 59 -204 -178 180 -199 -204 -1055 180 -99 -1055 54 -1055 133 -4 -178 -79 101 -1055 -1055 -1055 191 -1055 -1055 212 -1055 -1055 -1055 191 -99 -1055 54 -1055 133 -204 -1055 202 -1055 -204 -1055 -1055 181 -1055 138 54 -199 113 -1055 80 -1055 54 -1055 102 -99 -46 -1055 138 -41 -1055 -1055 191 -99 -1055 -1055 212 -1055 113 -79 -1055 1 -1055 -1055 191 -99 -1055 -1055 212 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 15 E= 2.4e-022 0.000000 0.333333 0.533333 0.133333 0.000000 0.133333 0.466667 0.400000 0.066667 0.066667 0.800000 0.066667 0.066667 0.000000 0.800000 0.133333 0.000000 0.333333 0.000000 0.666667 0.266667 0.066667 0.133333 0.533333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.866667 0.133333 0.000000 0.333333 0.000000 0.666667 0.066667 0.000000 0.933333 0.000000 0.066667 0.000000 0.000000 0.933333 0.000000 0.600000 0.333333 0.066667 0.600000 0.000000 0.400000 0.000000 0.400000 0.000000 0.466667 0.133333 0.200000 0.000000 0.600000 0.200000 0.000000 0.000000 0.866667 0.133333 0.000000 0.000000 1.000000 0.000000 0.600000 0.133333 0.000000 0.266667 0.000000 0.000000 0.866667 0.133333 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GC][GT]GG[TC][TA]TGG[TC]GT[CG][AG][GA][GAT]GG[AT]GG -------------------------------------------------------------------------------- Time 64.82 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 16 llr = 267 E-value = 6.4e-020 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 26231:41:6:193::13:2 pos.-specific C 218:3a::a:79:33:2::: probability G 63:77:69:13::2:9::a7 matrix T 1::::::::3::138178:1 bits 2.1 * * * 1.9 * * * 1.7 * * * 1.5 * ** ** * * Relative 1.3 * * ** *** * * Entropy 1.1 ******* *** ** ** (24.0 bits) 0.8 ******** *** ****** 0.6 ************ ****** 0.4 ************* ****** 0.2 ************* ****** 0.0 -------------------- Multilevel GACGGCGGCACCACTGTTGG consensus G AC A TG AC A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 31983 141 3.91e-12 GGGAGGTCTT GACGGCAGCACCATTGTTGG CAGGTGCAAA 2341 140 3.91e-12 GGGAGGTCTT GACGGCAGCACCATTGTTGG CAGGTGCAAA 31749 144 2.27e-11 GGGAGGTCTT GACGGCAGCTCCATTGTTGG ATGGAGCGAA 2342 145 2.27e-11 GGGAGGTCTT GACGGCAGCTCCATTGTTGG ATGGAGCGAA 38122 177 1.40e-09 TTCGTCGGCG GACGGCGGCAGCAGCGTTGA GACTGTTTGG 25402 188 1.40e-09 TTCGTCGGCG GACGGCGGCAGCAGCGTTGA GACTGTTTGG 4882 159 6.93e-09 ACGCCGGAGC GAAGGCAGCAGCACTGCAGG CAAGGGATGC 33018 117 1.71e-08 GGGCAGGAGC AAAGGCGGCAGCACTGCAGG CAAGGGTAGC 4843 284 3.26e-08 AGGTAGTGGT GACACCGACACCAACGTAGG TGACGTTCGC 262313 283 3.26e-08 AGGTAGTGGT GACACCGACACCAACGTAGG TGACGTTCGC 42962 90 5.45e-08 ACGTGTAGTG TGCACCAGCACCAATGATGG CAGGGGGTGG 21472 208 1.12e-07 TGTCGGCAAC AGCAACAGCACCTCTGTTGG TTGTGTGAGT 38715 302 1.19e-07 CGTTTAGGAA CGCGGCGGCTCAACTTTTGT TCCTCTTTGT 270233 440 1.19e-07 CGTTTAGGAA CGCGGCGGCTCAACTTTTGT TCCTCTTTGT 39813 192 1.50e-07 GGGCAAAGGC CGAAGCGGCGGCAATGCTGG AGGCGATGAG 24769 178 1.59e-07 GGCCGAAGTT ACCGCCGGCTCCAGTGATGA TGATTGTCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31983 3.9e-12 140_[+3]_340 2341 3.9e-12 139_[+3]_341 31749 2.3e-11 143_[+3]_337 2342 2.3e-11 144_[+3]_336 38122 1.4e-09 176_[+3]_304 25402 1.4e-09 187_[+3]_293 4882 6.9e-09 158_[+3]_322 33018 1.7e-08 116_[+3]_364 4843 3.3e-08 283_[+3]_197 262313 3.3e-08 282_[+3]_198 42962 5.5e-08 89_[+3]_391 21472 1.1e-07 207_[+3]_273 38715 1.2e-07 301_[+3]_179 270233 1.2e-07 439_[+3]_41 39813 1.5e-07 191_[+3]_289 24769 1.6e-07 177_[+3]_303 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=16 31983 ( 141) GACGGCAGCACCATTGTTGG 1 2341 ( 140) GACGGCAGCACCATTGTTGG 1 31749 ( 144) GACGGCAGCTCCATTGTTGG 1 2342 ( 145) GACGGCAGCTCCATTGTTGG 1 38122 ( 177) GACGGCGGCAGCAGCGTTGA 1 25402 ( 188) GACGGCGGCAGCAGCGTTGA 1 4882 ( 159) GAAGGCAGCAGCACTGCAGG 1 33018 ( 117) AAAGGCGGCAGCACTGCAGG 1 4843 ( 284) GACACCGACACCAACGTAGG 1 262313 ( 283) GACACCGACACCAACGTAGG 1 42962 ( 90) TGCACCAGCACCAATGATGG 1 21472 ( 208) AGCAACAGCACCTCTGTTGG 1 38715 ( 302) CGCGGCGGCTCAACTTTTGT 1 270233 ( 440) CGCGGCGGCTCAACTTTTGT 1 39813 ( 192) CGAAGCGGCGGCAATGCTGG 1 24769 ( 178) ACCGCCGGCTCCAGTGATGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 31746 bayes= 10.9536 E= 6.4e-020 -55 -29 129 -208 119 -188 44 -1064 -55 182 -1064 -1064 19 -1064 158 -1064 -213 12 158 -1064 -1064 212 -1064 -1064 67 -1064 129 -1064 -113 -1064 193 -1064 -1064 212 -1064 -1064 119 -1064 -188 24 -1064 158 44 -1064 -113 193 -1064 -1064 177 -1064 -1064 -208 -14 44 -29 -9 -1064 12 -1064 150 -1064 -1064 193 -109 -113 -29 -1064 137 -14 -1064 -1064 150 -1064 -1064 212 -1064 -55 -1064 158 -109 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 16 E= 6.4e-020 0.187500 0.187500 0.562500 0.062500 0.625000 0.062500 0.312500 0.000000 0.187500 0.812500 0.000000 0.000000 0.312500 0.000000 0.687500 0.000000 0.062500 0.250000 0.687500 0.000000 0.000000 1.000000 0.000000 0.000000 0.437500 0.000000 0.562500 0.000000 0.125000 0.000000 0.875000 0.000000 0.000000 1.000000 0.000000 0.000000 0.625000 0.000000 0.062500 0.312500 0.000000 0.687500 0.312500 0.000000 0.125000 0.875000 0.000000 0.000000 0.937500 0.000000 0.000000 0.062500 0.250000 0.312500 0.187500 0.250000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.875000 0.125000 0.125000 0.187500 0.000000 0.687500 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.187500 0.000000 0.687500 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[AG]C[GA][GC]C[GA]GC[AT][CG]CA[CAT][TC]GT[TA]GG -------------------------------------------------------------------------------- Time 97.08 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10882 4.36e-02 457_[+1(2.41e-05)]_28 11501 1.35e-02 5_[+1(8.14e-06)]_480 11924 4.49e-02 500 12120 3.25e-02 474_[+1(2.18e-05)]_11 16344 1.66e-01 475_[+1(7.25e-05)]_10 20335 3.16e-03 432_[+1(1.98e-06)]_53 20603 6.92e-02 433_[+1(3.90e-05)]_52 20965 2.26e-06 185_[+2(3.34e-09)]_294 21472 8.94e-06 207_[+3(1.12e-07)]_236_\ [+1(6.43e-06)]_22 21667 9.92e-04 465_[+1(2.00e-07)]_20 22747 1.06e-01 500 2341 4.95e-15 114_[+2(8.96e-11)]_4_[+3(3.91e-12)]_\ 341 2342 1.06e-18 119_[+2(8.96e-11)]_4_[+3(2.27e-11)]_\ 40_[+3(2.67e-05)]_256_[+1(3.78e-09)]_5 2356 1.07e-01 251_[+3(8.98e-05)]_229 23808 1.98e-02 484_[+1(3.00e-06)]_1 24080 1.64e-02 14_[+1(7.88e-05)]_389_\ [+1(2.27e-06)]_67 24099 5.03e-02 429_[+1(3.23e-05)]_56 24769 2.43e-06 35_[+1(1.73e-06)]_13_[+1(2.94e-05)]_\ 99_[+3(1.59e-07)]_303 25402 7.97e-06 187_[+3(1.40e-09)]_293 2601 7.21e-03 63_[+2(6.24e-05)]_401_\ [+1(2.41e-05)] 262313 1.84e-09 49_[+2(5.59e-05)]_212_\ [+3(3.26e-08)]_69_[+2(7.34e-05)]_86_[+1(2.49e-08)]_7 262332 7.46e-06 27_[+2(1.99e-10)]_452 26246 9.47e-02 500 2673 1.37e-02 53_[+1(3.23e-05)]_432 268127 2.23e-02 347_[+1(6.66e-05)]_138 268304 2.79e-01 500 270092 4.41e-10 302_[+2(1.36e-10)]_162_\ [+1(5.87e-07)] 270210 1.81e-01 500 270233 3.47e-09 49_[+2(2.13e-08)]_220_\ [+1(3.56e-05)]_134_[+3(1.19e-07)]_41 270241 3.50e-05 316_[+2(4.80e-08)]_145_\ [+1(5.61e-05)]_3 270242 1.95e-01 500 2845 3.50e-05 180_[+2(4.80e-08)]_145_\ [+1(5.61e-05)]_139 2848 2.53e-03 59_[+1(5.87e-07)]_426 29375 1.76e-01 295_[+1(5.61e-05)]_190 29842 1.25e-03 338_[+1(5.70e-06)]_147 30385 8.06e-03 218_[+1(2.66e-05)]_252_\ [+1(5.03e-06)] 3141 2.92e-02 109_[+1(3.56e-05)]_376 31749 1.06e-18 118_[+2(8.96e-11)]_4_[+3(2.27e-11)]_\ 40_[+3(2.67e-05)]_256_[+1(3.78e-09)]_6 31983 4.95e-15 115_[+2(8.96e-11)]_4_[+3(3.91e-12)]_\ 340 33018 2.07e-04 116_[+3(1.71e-08)]_364 33131 4.55e-03 479_[+1(2.97e-07)]_6 33606 4.40e-03 256_[+1(3.89e-06)]_229 34276 4.43e-01 500 3453 9.18e-02 377_[+1(2.94e-05)]_108 34830 4.36e-02 415_[+1(5.03e-06)]_70 35934 1.00e-02 443_[+1(1.03e-05)]_42 36081 1.61e-02 254_[+1(3.00e-06)]_231 38122 7.97e-06 176_[+3(1.40e-09)]_304 3815 4.83e-06 204_[+2(4.02e-08)]_250_\ [+3(6.07e-05)]_5 3816 4.55e-03 480_[+1(2.97e-07)]_5 38494 9.65e-02 230_[+1(1.77e-05)]_255 38583 2.98e-01 500 38667 1.04e-02 304_[+1(6.43e-06)]_181 38715 2.47e-05 152_[+1(3.56e-05)]_134_\ [+3(1.19e-07)]_179 3884 1.23e-07 358_[+2(3.78e-08)]_53_\ [+1(1.44e-07)]_53 39813 6.76e-05 191_[+3(1.50e-07)]_289 40747 1.37e-01 457_[+1(8.55e-05)]_28 42962 1.25e-09 89_[+3(5.45e-08)]_107_\ [+2(3.34e-09)]_263 4843 1.84e-09 50_[+2(5.59e-05)]_212_\ [+3(3.26e-08)]_69_[+2(7.34e-05)]_86_[+1(2.49e-08)]_6 4882 1.62e-06 158_[+3(6.93e-09)]_294_\ [+1(1.43e-05)]_13 4883 4.28e-07 227_[+2(1.99e-10)]_252 4917 9.96e-02 415_[+1(2.41e-05)]_70 5174 1.77e-03 268_[+1(1.29e-06)]_217 6572 1.55e-03 311_[+1(1.49e-06)]_174 7270 5.30e-06 154_[+2(1.13e-08)]_270_\ [+1(1.97e-05)]_40 7916 7.24e-02 472_[+1(1.15e-05)]_13 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************