******************************************************************************** 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/28/28.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10228 1.0000 500 10417 1.0000 500 10892 1.0000 500 1219 1.0000 500 1385 1.0000 500 13922 1.0000 500 1506 1.0000 500 16605 1.0000 500 17707 1.0000 500 18469 1.0000 500 21170 1.0000 500 21257 1.0000 500 21360 1.0000 500 22140 1.0000 500 22150 1.0000 500 22177 1.0000 500 22418 1.0000 500 22652 1.0000 500 22863 1.0000 500 2325 1.0000 500 2462 1.0000 500 2484 1.0000 500 24887 1.0000 500 25468 1.0000 500 262510 1.0000 500 262572 1.0000 500 263062 1.0000 500 263200 1.0000 500 264495 1.0000 500 268187 1.0000 500 268911 1.0000 500 269515 1.0000 500 269968 1.0000 500 270221 1.0000 500 270261 1.0000 500 270338 1.0000 500 2950 1.0000 500 31006 1.0000 500 31021 1.0000 500 31125 1.0000 500 31829 1.0000 500 3257 1.0000 500 32723 1.0000 500 32745 1.0000 500 32874 1.0000 500 3302 1.0000 500 33389 1.0000 500 34283 1.0000 500 35464 1.0000 500 35684 1.0000 500 36078 1.0000 500 36527 1.0000 500 40788 1.0000 500 4503 1.0000 500 4722 1.0000 500 4876 1.0000 500 5389 1.0000 500 6173 1.0000 500 6431 1.0000 500 6807 1.0000 500 6896 1.0000 500 7112 1.0000 500 7191 1.0000 500 7487 1.0000 500 8410 1.0000 500 8793 1.0000 500 8872 1.0000 500 9490 1.0000 500 9513 1.0000 500 9752 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/28/28.seqs.fa -oc motifs/28 -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= 70 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= 35000 N= 70 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.258 C 0.229 G 0.250 T 0.263 Background letter frequencies (from dataset with add-one prior applied): A 0.258 C 0.229 G 0.250 T 0.263 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 66 llr = 610 E-value = 1.6e-027 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1334325:27323327655:3 pos.-specific C 555476:77:58228234493 probability G 2:1::212:11:31:11:::1 matrix T 2211::4112:1341::1112 bits 2.1 1.9 1.7 * 1.5 * Relative 1.3 * Entropy 1.1 * * * * (13.3 bits) 0.9 * ** * * * 0.6 ****** * ****** 0.4 *********** ****** 0.2 ************ ******* 0.0 --------------------- Multilevel CCCACCACCACCATCAAAACA consensus GAACA T TA GA CCCC C sequence TT T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 31006 469 4.61e-10 ACACAATCAG CCCACCACCAACAACACAACA AATAATACAA 4722 435 7.45e-09 GTGCTTCTTT GTCACCACCAACAACAACACA AAGGGAGCGT 2484 447 9.12e-09 CCCAAAGATT CCCCCCACCAACTCCAAACCG CCTCCGACGC 3257 348 6.86e-08 CAATAAGAGC TCCACGACCTCCATCACCACT AGTACCACCC 36527 480 2.45e-07 CAACAAACAA ACCACAACCAACACCAACACC 33389 196 2.84e-07 TCAACTTACC TCAACCTTCAACCTCACCACC CACTGTTGGT 22177 403 2.84e-07 TCTGCACCAA CAGCACACCACCGACCACCCC CTCCTCTCGC 6431 179 5.08e-07 TCATATCTTA CCACCCTCTAACTTCACATCC CCGGTTAGAG 5389 186 6.72e-07 CGTCACCGCA ACCACCACCTGCCTCAAAACC AGGAGGAGGA 262510 187 6.72e-07 CGTCACCGCA ACCACCACCTGCCTCAAAACC AGGAGGAGGA 36078 400 8.83e-07 AGTATCTTGT GCACCGTCAACCGTCACACCT TGCCGATGGC 270261 399 8.83e-07 AGTATCTTGT GCACCGTCAACCGTCACACCT TGCCGATGGC 262572 362 1.01e-06 GGGACTAGTT GACCCCTTCTCCGACACCCCT TCTTCGTTGG 9513 448 1.50e-06 CAAACCAAAC GCAACCTCTGCCGTCAACCCT ACACTACCAC 16605 471 1.70e-06 CGGCTCCATT CTCCCCTGCACTTCCACCCCC TCATCGCAA 6807 425 2.80e-06 GCTGCAACCT GCAACCATAACCCGCAAAACA GTTTCGTCGA 35684 480 3.56e-06 TCGCCTTCAC CCAAACACCGACACCGACACC 2325 430 4.00e-06 AACCCCGCTC CCTCACTCAACCAACCACACT TCTAACCCGC 4876 460 4.50e-06 CAGGGCAACA GCCACAACAATCGACAACACC ATCCTCTCAA 4503 444 4.50e-06 TTCTTTGGAG GCAACAGGCAACACCAACACA AACCCCTCCT 25468 479 4.50e-06 CAGCTGAACA CAAGCCTCCACCAAAAAATCA A 2462 428 4.50e-06 ACCGTGGCAA CACAACAGAACCAACCCACCT TCCCTTCGCC 1506 475 4.50e-06 CCAGCCGACG CCAACAAGCAAAGGCAACACA ACAAC 1385 98 4.50e-06 TTAGAGTTAG CAACACTGCGACTTCAAAACA TGCTGGATAT 32874 173 5.66e-06 CGAAATCCTT TTCACAACCACCGTCACCATG AACCTTTCCT 31829 418 5.66e-06 CAGGCCGCCC CAACACTCAACAAACCACCCC TCACCTTGCC 263200 480 5.66e-06 TTGAGACACC GATCCTTCCAACCTCAACACC 3302 249 6.34e-06 GATACTGGCG TTACCAACCTACGACCAAACC TGGAATTGAG 31125 258 7.09e-06 CACGCAAGAT CTTCCCGCCACCTACGCAACA GGGGAGAACT 2950 443 7.09e-06 ATCTTCGACA TCCACCTCCACATTTCACTCC TCCACTTCAC 264495 371 7.93e-06 GACAAAAGTT TCCACCACTACCTTCCTCCCC TTCACCGATT 7191 242 9.86e-06 ACACCTCTGC CTCTCCACCTCATTAACAACT GAAACAATAT 32723 125 9.86e-06 GTCATCGGCT GAATCCTCCACCGTTGAACCA CTCGTGCCTT 270221 150 9.86e-06 GTCATCGGCT GAATCCTCCACCGTTGAACCA CTCGTGCCTT 18469 466 9.86e-06 TCAACTCACT CACCCCACCACTCGCAATCCG CCGCTACATC 21170 472 1.10e-05 GACACCAATA CAAACAGCCACAAAAAACACC TTCAAAAC 31021 263 1.50e-05 CCATCACAAA CCCAAATCCTCCATCAGTCCA AACGCAGAGC 24887 470 2.04e-05 TGATACACCA TCTTCCTCCACCTGACCACCA CTCCCCAACC 8793 455 2.26e-05 AGTCAGTGGA CATCAGACCAAACCCAAACCC TCCACGAAGA 10892 472 2.26e-05 AACCACCTTG GTGCCCAGCTGCGGCAACACA ACAACAAC 10417 458 2.26e-05 GTCGGTGCAC CCGAACAGCAACAGACAACCC GCTACGCTAC 7112 68 2.74e-05 GCATGGTATA TCGTCTGCCAACATCAACACT ATATTGTCGT 269968 375 2.74e-05 CATTTACACA CAGTTCACCTCCGACACACCA AAAATAACAA 8410 463 3.02e-05 CGAGCCGTCG ACCACCGGCTGCTACACACCC AGCCAACCAC 268911 89 4.02e-05 AAGCGTTGAA GACTCGTGCACCACACCACCA CGGAGGGAGA 6896 338 4.41e-05 AAAAAGCCCC CTCACCTCTTCCCTCCCTACG TCCTACTGGA 32745 477 4.83e-05 CTGCTGCTCT TCCTCCACTTCCTCCAAGCCA AGG 263062 139 5.29e-05 CGGTCAATTT TTCCCCACTAAAATAGAAACC TTTCTTTCGA 40788 464 5.79e-05 ATTTCATCAC CCCACCGCTAGCATTGCCCCA TTCCTTCAAA 9490 171 6.33e-05 TGACGCCAAG CACGCGATCATCAACACCACT ACAGCTGAGG 1219 47 6.33e-05 TCTCCGAGTG CTCCCCTCCAAACATAAAATA TTATATGAAA 7487 407 6.91e-05 TTGAGAGACA CAGAAGGTCACCCTCAACACG GAAGGGATCT 22140 314 7.54e-05 ATTGTAGTGG CACCCAACACCCAGCCAACCT CCGGTTCCAC 8872 75 1.06e-04 ATACCGACGC TAAAACATCGGCTTCAACTCT GTTCAATAGA 21360 453 1.06e-04 TCGTTGTTGC CTCCACAGAAGAGCCCAACCC GGGTGTTGTG 13922 477 1.15e-04 TCCCTCGCTC CTCCTCTGCTACTTCAACATC ATC 22863 2 1.25e-04 C CACAAGTCCACCTCCGGCTCG GAGAGGACTC 22150 439 1.86e-04 CACTTGACCC CCCTCGTCCTCCATCTCTTCT CGCCGTGTGG 22652 290 2.52e-04 CGCTAGGATC TTGACCACAAGAATCACTTCA ATGAAAAGAC 10228 246 3.14e-04 TTGTTTAGAA GAGCATACCACAGCCAAACTA CTTAACATTG 9752 447 3.37e-04 CTGTGCTTGG TACACCTCCGTCGCAAGCTCA TCATTATTGG 270338 21 3.37e-04 TGCACATTTG TCTCCGTCAACTTGAACAACA TGAGTGCGGT 269515 93 3.62e-04 GAATACCATT GCAAAGATCAATGACAACCTC TCTCGTTTGC 21257 476 7.55e-04 CCCTTCTCTC TCCGCCTCCGCCTGCTGAACG AACC 22418 20 8.04e-04 CGAAATTGTA GAACACATCTATACAAAATCT TGCCATCTCT 35464 22 8.55e-04 TCGGATTCTG TTCCAATGTAACTTCCCAATT CGGACTCTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31006 4.6e-10 468_[+1]_11 4722 7.4e-09 434_[+1]_45 2484 9.1e-09 446_[+1]_33 3257 6.9e-08 347_[+1]_132 36527 2.4e-07 479_[+1] 33389 2.8e-07 195_[+1]_284 22177 2.8e-07 402_[+1]_77 6431 5.1e-07 178_[+1]_301 5389 6.7e-07 185_[+1]_294 262510 6.7e-07 186_[+1]_293 36078 8.8e-07 399_[+1]_80 270261 8.8e-07 398_[+1]_81 262572 1e-06 361_[+1]_118 9513 1.5e-06 447_[+1]_32 16605 1.7e-06 470_[+1]_9 6807 2.8e-06 424_[+1]_55 35684 3.6e-06 479_[+1] 2325 4e-06 429_[+1]_50 4876 4.5e-06 459_[+1]_20 4503 4.5e-06 443_[+1]_36 25468 4.5e-06 478_[+1]_1 2462 4.5e-06 427_[+1]_52 1506 4.5e-06 474_[+1]_5 1385 4.5e-06 97_[+1]_382 32874 5.7e-06 172_[+1]_307 31829 5.7e-06 417_[+1]_62 263200 5.7e-06 479_[+1] 3302 6.3e-06 248_[+1]_231 31125 7.1e-06 257_[+1]_222 2950 7.1e-06 442_[+1]_37 264495 7.9e-06 370_[+1]_109 7191 9.9e-06 241_[+1]_238 32723 9.9e-06 124_[+1]_355 270221 9.9e-06 149_[+1]_330 18469 9.9e-06 465_[+1]_14 21170 1.1e-05 471_[+1]_8 31021 1.5e-05 262_[+1]_217 24887 2e-05 469_[+1]_10 8793 2.3e-05 454_[+1]_25 10892 2.3e-05 471_[+1]_8 10417 2.3e-05 457_[+1]_22 7112 2.7e-05 67_[+1]_412 269968 2.7e-05 374_[+1]_105 8410 3e-05 462_[+1]_17 268911 4e-05 88_[+1]_391 6896 4.4e-05 337_[+1]_142 32745 4.8e-05 476_[+1]_3 263062 5.3e-05 138_[+1]_341 40788 5.8e-05 463_[+1]_16 9490 6.3e-05 170_[+1]_309 1219 6.3e-05 46_[+1]_433 7487 6.9e-05 406_[+1]_73 22140 7.5e-05 313_[+1]_166 8872 0.00011 74_[+1]_405 21360 0.00011 452_[+1]_27 13922 0.00012 476_[+1]_3 22863 0.00012 1_[+1]_478 22150 0.00019 438_[+1]_41 22652 0.00025 289_[+1]_190 10228 0.00031 245_[+1]_234 9752 0.00034 446_[+1]_33 270338 0.00034 20_[+1]_459 269515 0.00036 92_[+1]_387 21257 0.00075 475_[+1]_4 22418 0.0008 19_[+1]_460 35464 0.00086 21_[+1]_458 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=66 31006 ( 469) CCCACCACCAACAACACAACA 1 4722 ( 435) GTCACCACCAACAACAACACA 1 2484 ( 447) CCCCCCACCAACTCCAAACCG 1 3257 ( 348) TCCACGACCTCCATCACCACT 1 36527 ( 480) ACCACAACCAACACCAACACC 1 33389 ( 196) TCAACCTTCAACCTCACCACC 1 22177 ( 403) CAGCACACCACCGACCACCCC 1 6431 ( 179) CCACCCTCTAACTTCACATCC 1 5389 ( 186) ACCACCACCTGCCTCAAAACC 1 262510 ( 187) ACCACCACCTGCCTCAAAACC 1 36078 ( 400) GCACCGTCAACCGTCACACCT 1 270261 ( 399) GCACCGTCAACCGTCACACCT 1 262572 ( 362) GACCCCTTCTCCGACACCCCT 1 9513 ( 448) GCAACCTCTGCCGTCAACCCT 1 16605 ( 471) CTCCCCTGCACTTCCACCCCC 1 6807 ( 425) GCAACCATAACCCGCAAAACA 1 35684 ( 480) CCAAACACCGACACCGACACC 1 2325 ( 430) CCTCACTCAACCAACCACACT 1 4876 ( 460) GCCACAACAATCGACAACACC 1 4503 ( 444) GCAACAGGCAACACCAACACA 1 25468 ( 479) CAAGCCTCCACCAAAAAATCA 1 2462 ( 428) CACAACAGAACCAACCCACCT 1 1506 ( 475) CCAACAAGCAAAGGCAACACA 1 1385 ( 98) CAACACTGCGACTTCAAAACA 1 32874 ( 173) TTCACAACCACCGTCACCATG 1 31829 ( 418) CAACACTCAACAAACCACCCC 1 263200 ( 480) GATCCTTCCAACCTCAACACC 1 3302 ( 249) TTACCAACCTACGACCAAACC 1 31125 ( 258) CTTCCCGCCACCTACGCAACA 1 2950 ( 443) TCCACCTCCACATTTCACTCC 1 264495 ( 371) TCCACCACTACCTTCCTCCCC 1 7191 ( 242) CTCTCCACCTCATTAACAACT 1 32723 ( 125) GAATCCTCCACCGTTGAACCA 1 270221 ( 150) GAATCCTCCACCGTTGAACCA 1 18469 ( 466) CACCCCACCACTCGCAATCCG 1 21170 ( 472) CAAACAGCCACAAAAAACACC 1 31021 ( 263) CCCAAATCCTCCATCAGTCCA 1 24887 ( 470) TCTTCCTCCACCTGACCACCA 1 8793 ( 455) CATCAGACCAAACCCAAACCC 1 10892 ( 472) GTGCCCAGCTGCGGCAACACA 1 10417 ( 458) CCGAACAGCAACAGACAACCC 1 7112 ( 68) TCGTCTGCCAACATCAACACT 1 269968 ( 375) CAGTTCACCTCCGACACACCA 1 8410 ( 463) ACCACCGGCTGCTACACACCC 1 268911 ( 89) GACTCGTGCACCACACCACCA 1 6896 ( 338) CTCACCTCTTCCCTCCCTACG 1 32745 ( 477) TCCTCCACTTCCTCCAAGCCA 1 263062 ( 139) TTCCCCACTAAAATAGAAACC 1 40788 ( 464) CCCACCGCTAGCATTGCCCCA 1 9490 ( 171) CACGCGATCATCAACACCACT 1 1219 ( 47) CTCCCCTCCAAACATAAAATA 1 7487 ( 407) CAGAAGGTCACCCTCAACACG 1 22140 ( 314) CACCCAACACCCAGCCAACCT 1 8872 ( 75) TAAAACATCGGCTTCAACTCT 1 21360 ( 453) CTCCACAGAAGAGCCCAACCC 1 13922 ( 477) CTCCTCTGCTACTTCAACATC 1 22863 ( 2) CACAAGTCCACCTCCGGCTCG 1 22150 ( 439) CCCTCGTCCTCCATCTCTTCT 1 22652 ( 290) TTGACCACAAGAATCACTTCA 1 10228 ( 246) GAGCATACCACAGCCAAACTA 1 9752 ( 447) TACACCTCCGTCGCAAGCTCA 1 270338 ( 21) TCTCCGTCAACTTGAACAACA 1 269515 ( 93) GCAAAGATCAATGACAACCTC 1 21257 ( 476) TCCGCCTCCGCCTGCTGAACG 1 22418 ( 20) GAACACATCTATACAAAATCT 1 35464 ( 22) TTCCAATGTAACTTCCCAATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 33600 bayes= 9.02442 E= 1.6e-027 -209 99 -4 -12 37 99 -1269 -31 16 113 -104 -153 77 73 -246 -95 0 164 -1269 -312 -77 147 -58 -253 91 -1269 -124 64 -1269 161 -46 -112 -63 164 -1269 -112 137 -391 -146 -21 30 117 -104 -253 -63 173 -1269 -180 37 -60 4 -3 0 -22 -87 64 -77 175 -1269 -180 134 -11 -124 -312 116 61 -204 -411 86 94 -404 -180 86 78 -1269 -95 -1269 199 -1269 -153 37 54 -124 -21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 66 E= 1.6e-027 0.060606 0.454545 0.242424 0.242424 0.333333 0.454545 0.000000 0.212121 0.287879 0.500000 0.121212 0.090909 0.439394 0.378788 0.045455 0.136364 0.257576 0.712121 0.000000 0.030303 0.151515 0.636364 0.166667 0.045455 0.484848 0.000000 0.106061 0.409091 0.000000 0.696970 0.181818 0.121212 0.166667 0.712121 0.000000 0.121212 0.666667 0.015152 0.090909 0.227273 0.318182 0.515152 0.121212 0.045455 0.166667 0.757576 0.000000 0.075758 0.333333 0.151515 0.257576 0.257576 0.257576 0.196970 0.136364 0.409091 0.151515 0.772727 0.000000 0.075758 0.651515 0.212121 0.106061 0.030303 0.575758 0.348485 0.060606 0.015152 0.469697 0.439394 0.015152 0.075758 0.469697 0.393939 0.000000 0.136364 0.000000 0.909091 0.000000 0.090909 0.333333 0.333333 0.106061 0.227273 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CGT][CAT][CA][AC][CA]C[AT]CC[AT][CA]C[AGT][TA]C[AC][AC][AC][AC]C[ACT] -------------------------------------------------------------------------------- Time 36.59 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 53 llr = 473 E-value = 6.8e-018 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::31:::::31: pos.-specific C 13::2:::::1: probability G 5:711a11831a matrix T 56:86:99147: bits 2.1 1.9 * * 1.7 * * 1.5 * * * Relative 1.3 **** * Entropy 1.1 * **** * (12.9 bits) 0.9 *** **** * 0.6 ********* ** 0.4 ********* ** 0.2 ************ 0.0 ------------ Multilevel GTGTTGTTGTTG consensus TCA C A sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 25468 147 1.74e-07 GTGTCGTTCG TTGTTGTTGTTG TTGTTGCTGC 22177 132 5.11e-07 CGAGTGATGG GTGTTGTTGATG GGAAGGCTGA 8793 153 9.95e-07 GTTTTTGTTT TTGTCGTTGTTG CCGTAGTCAC 262572 404 1.29e-06 TGATACGTTT GCGTTGTTGGTG CTTTGTACTG 22418 226 1.29e-06 CCGAACAGTA GCGTTGTTGATG GATGCCTCAT 21360 440 2.22e-06 TTGGGAGTGG TCGTCGTTGTTG CCTCCACAGA 7487 203 3.59e-06 CTTCATTTCT TTGTGGTTGTTG TTGAGTAAGG 6173 196 4.49e-06 GTAATCGAAG GTGTTGGTGTTG GAATAGTAAG 21257 308 4.49e-06 AGTAGTGCCT GTGTTGTTGTGG TAGTGCTGTC 32723 418 5.29e-06 GAAGGATCTA GTGTTGTTGAAG AAGGATCTTG 270221 443 5.29e-06 GAAGGATCTA GTGTTGTTGAAG AAGGATCTTG 35464 293 6.38e-06 CATTATGTGA TTGATGTTGATG TGTCTATTGC 2484 168 6.38e-06 ACTGATGTGC GTGTGGTTGATG GAGCGATGAA 4722 120 7.95e-06 GCGTCTGTCA TTGTTGTTTGTG TCCATGATGA 17707 250 7.95e-06 ATCATCGTCC CTGTTGTTGGTG CTGGTAGCAT 4876 224 1.11e-05 GAGCGGGAAG TTGACGTTGTTG AAATGAACGC 34283 260 1.11e-05 GGAGGCGGTG TTGTCGTTGTCG GTCTTGGATG 269515 363 1.11e-05 TTGTCCCCCT GCGTTGTTGGAG GATATGGATG 22652 335 1.32e-05 CAACATAACT GTATTGTTGTGG CAGCGTCCAC 10417 222 1.32e-05 AGGGTGGTAG TTATTGGTGTTG CGTTTGAGGT 18469 233 1.46e-05 TCGGATGCTA CCGTTGTTGATG ATGCCGTCGT 7112 342 1.60e-05 GAGGCAGGTT GTGTCGTGGTTG TGCCGGTTTG 5389 238 1.83e-05 CTCCTCTGTT TCATTGTTGTAG TAGTAAGTGC 262510 239 1.83e-05 CTCCTCTGTT TCATTGTTGTAG TAGTAAGTGC 10892 90 2.15e-05 CGAGTAGATG GTGTCGGTGATG AGGTTAGTTG 263200 352 2.35e-05 GGGGTACAAA TCATTGTTGTGG TGGTTTGTGG 10228 81 2.35e-05 GACCACGATG TTGCTGTTGATG CGCCACGTTC 31125 52 2.47e-05 GTTGTTGCTC TCGCTGTTGTTG GCCATGGAGA 269968 457 2.47e-05 GCCACCTCTC GCAGTGTTGTTG CCTTTGCTCC 268911 258 3.16e-05 GTGAACTTCA TCGTCGTTGGGG GTTGCTTCTG 9513 95 3.41e-05 GGGGAGTGGT GCGGCGTTGATG GCTGAGTGTG 40788 283 3.41e-05 GATATGTGGT TTATCGTTGGAG GAAACGACGC 31829 94 3.77e-05 GGGATGAGAT TTATCGTTGACG AGTTTTTGAA 270338 182 3.77e-05 GGGATGAGAT TTATCGTTGACG AGTTTTTGAA 36078 324 4.10e-05 TGTGTTTGAG GCGTTGTTAGTG GCTGGGAGGT 35684 290 4.10e-05 TGGGATGTCA GCATCGTTGTCG TGTGTATCCG 270261 323 4.10e-05 TGTGTTTGAG GCGTTGTTAGTG GCTGGGAGGT 264495 133 4.10e-05 AATGGATGAT TTATAGTTGATG ATGTGTATAG 9752 219 4.42e-05 CCATTGTTTG GTGTGGTGGTTG TGTGGGCAGT 22863 301 4.77e-05 GCACTGGAAA GTGAGGTTGATG GCCTGGCAAA 4503 366 5.36e-05 TGGTATGGCT GTGATGTTGGGG GGGTTGGCTA 268187 374 5.36e-05 TGTCGAGCTG TTGATGGTGGTG GTTGGAAAGT 24887 453 5.86e-05 CCGCATCAGT TTGTTGTTGATA CACCATCTTC 13922 299 6.36e-05 CGTCGGATGT TTGGTGTTTGTG TTAAGGTTCT 1385 206 9.75e-05 CTTGGAGGTT GTATTGTGTTTG ACACTGCCAA 32745 242 1.18e-04 GACGCCATTT CTATTGTTTGTG TTGTCTCCAA 8410 21 1.44e-04 ATTACAAGGG GCATTGGGGTTG ATCTAGATAC 7191 467 1.44e-04 TATTGACCGC TCATTGTGTTTG CTGTGTTGCT 8872 123 1.91e-04 GATCAGGCAC GAGTTGTTTGTG AGCTACCACC 1506 32 1.91e-04 TGGGCTGCAA TTAGTGTTGCTG GACGTGACAC 9490 240 2.02e-04 TTGTTGTTTG GTGGGGGTGTTG GTCGGTTGAA 6807 24 2.02e-04 GGAATGAGAA TCAAAGTTGTTG ACTACGACGG 6431 315 3.57e-04 ATGAAGATTC GTGTCGATGGCG GAACAACGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25468 1.7e-07 146_[+2]_342 22177 5.1e-07 131_[+2]_357 8793 1e-06 152_[+2]_336 262572 1.3e-06 403_[+2]_85 22418 1.3e-06 225_[+2]_263 21360 2.2e-06 439_[+2]_49 7487 3.6e-06 202_[+2]_286 6173 4.5e-06 195_[+2]_293 21257 4.5e-06 307_[+2]_181 32723 5.3e-06 417_[+2]_71 270221 5.3e-06 442_[+2]_46 35464 6.4e-06 292_[+2]_196 2484 6.4e-06 167_[+2]_321 4722 8e-06 119_[+2]_369 17707 8e-06 249_[+2]_239 4876 1.1e-05 223_[+2]_265 34283 1.1e-05 259_[+2]_229 269515 1.1e-05 362_[+2]_126 22652 1.3e-05 334_[+2]_154 10417 1.3e-05 221_[+2]_267 18469 1.5e-05 232_[+2]_256 7112 1.6e-05 341_[+2]_147 5389 1.8e-05 237_[+2]_251 262510 1.8e-05 238_[+2]_250 10892 2.1e-05 89_[+2]_399 263200 2.4e-05 351_[+2]_137 10228 2.4e-05 80_[+2]_408 31125 2.5e-05 51_[+2]_437 269968 2.5e-05 456_[+2]_32 268911 3.2e-05 257_[+2]_231 9513 3.4e-05 94_[+2]_394 40788 3.4e-05 282_[+2]_206 31829 3.8e-05 93_[+2]_395 270338 3.8e-05 181_[+2]_307 36078 4.1e-05 323_[+2]_165 35684 4.1e-05 289_[+2]_199 270261 4.1e-05 322_[+2]_166 264495 4.1e-05 132_[+2]_356 9752 4.4e-05 218_[+2]_270 22863 4.8e-05 300_[+2]_188 4503 5.4e-05 365_[+2]_123 268187 5.4e-05 373_[+2]_115 24887 5.9e-05 452_[+2]_36 13922 6.4e-05 298_[+2]_190 1385 9.7e-05 205_[+2]_283 32745 0.00012 241_[+2]_247 8410 0.00014 20_[+2]_468 7191 0.00014 466_[+2]_22 8872 0.00019 122_[+2]_366 1506 0.00019 31_[+2]_457 9490 0.0002 239_[+2]_249 6807 0.0002 23_[+2]_465 6431 0.00036 314_[+2]_174 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=53 25468 ( 147) TTGTTGTTGTTG 1 22177 ( 132) GTGTTGTTGATG 1 8793 ( 153) TTGTCGTTGTTG 1 262572 ( 404) GCGTTGTTGGTG 1 22418 ( 226) GCGTTGTTGATG 1 21360 ( 440) TCGTCGTTGTTG 1 7487 ( 203) TTGTGGTTGTTG 1 6173 ( 196) GTGTTGGTGTTG 1 21257 ( 308) GTGTTGTTGTGG 1 32723 ( 418) GTGTTGTTGAAG 1 270221 ( 443) GTGTTGTTGAAG 1 35464 ( 293) TTGATGTTGATG 1 2484 ( 168) GTGTGGTTGATG 1 4722 ( 120) TTGTTGTTTGTG 1 17707 ( 250) CTGTTGTTGGTG 1 4876 ( 224) TTGACGTTGTTG 1 34283 ( 260) TTGTCGTTGTCG 1 269515 ( 363) GCGTTGTTGGAG 1 22652 ( 335) GTATTGTTGTGG 1 10417 ( 222) TTATTGGTGTTG 1 18469 ( 233) CCGTTGTTGATG 1 7112 ( 342) GTGTCGTGGTTG 1 5389 ( 238) TCATTGTTGTAG 1 262510 ( 239) TCATTGTTGTAG 1 10892 ( 90) GTGTCGGTGATG 1 263200 ( 352) TCATTGTTGTGG 1 10228 ( 81) TTGCTGTTGATG 1 31125 ( 52) TCGCTGTTGTTG 1 269968 ( 457) GCAGTGTTGTTG 1 268911 ( 258) TCGTCGTTGGGG 1 9513 ( 95) GCGGCGTTGATG 1 40788 ( 283) TTATCGTTGGAG 1 31829 ( 94) TTATCGTTGACG 1 270338 ( 182) TTATCGTTGACG 1 36078 ( 324) GCGTTGTTAGTG 1 35684 ( 290) GCATCGTTGTCG 1 270261 ( 323) GCGTTGTTAGTG 1 264495 ( 133) TTATAGTTGATG 1 9752 ( 219) GTGTGGTGGTTG 1 22863 ( 301) GTGAGGTTGATG 1 4503 ( 366) GTGATGTTGGGG 1 268187 ( 374) TTGATGGTGGTG 1 24887 ( 453) TTGTTGTTGATA 1 13922 ( 299) TTGGTGTTTGTG 1 1385 ( 206) GTATTGTGTTTG 1 32745 ( 242) CTATTGTTTGTG 1 8410 ( 21) GCATTGGGGTTG 1 7191 ( 467) TCATTGTGTTTG 1 8872 ( 123) GAGTTGTTTGTG 1 1506 ( 32) TTAGTGTTGCTG 1 9490 ( 240) GTGGGGGTGTTG 1 6807 ( 24) TCAAAGTTGTTG 1 6431 ( 315) GTGTCGATGGCG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 34230 bayes= 9.88353 E= 6.8e-018 -1237 -202 92 84 -377 57 -1237 129 31 -1237 144 -1237 -119 -260 -141 152 -277 10 -141 124 -1237 -1237 200 -1237 -377 -1237 -114 172 -1237 -1237 -141 178 -277 -1237 176 -122 13 -360 8 72 -119 -128 -141 141 -377 -1237 197 -1237 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 53 E= 6.8e-018 0.000000 0.056604 0.471698 0.471698 0.018868 0.339623 0.000000 0.641509 0.320755 0.000000 0.679245 0.000000 0.113208 0.037736 0.094340 0.754717 0.037736 0.245283 0.094340 0.622642 0.000000 0.000000 1.000000 0.000000 0.018868 0.000000 0.113208 0.867925 0.000000 0.000000 0.094340 0.905660 0.037736 0.000000 0.849057 0.113208 0.283019 0.018868 0.264151 0.433962 0.113208 0.094340 0.094340 0.698113 0.018868 0.000000 0.981132 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GT][TC][GA]T[TC]GTTG[TAG]TG -------------------------------------------------------------------------------- Time 72.42 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 52 llr = 507 E-value = 7.8e-015 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 163:83:53:71342:2245: pos.-specific C :12:21::1::3:12:1111: probability G 714a:59269256237355:6 matrix T 231::1:31111133343:34 bits 2.1 1.9 * 1.7 * 1.5 * * * Relative 1.3 ** * * Entropy 1.1 ** * * * * (14.1 bits) 0.9 * ** * * * * 0.6 * ** * ** * * * 0.4 ** ** ******* * *** 0.2 ************** ****** 0.0 --------------------- Multilevel GAGGAGGAGGAGGATGTGGAG consensus TA A TA GCATGTGTATT sequence GA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 262572 216 5.93e-13 GTGAGGGGAA GAGGAGGAGGAGGAGGTGGAG GAGGAGACCA 4722 48 1.17e-09 GTGCTCGCGT GAAGAAGAGGAGGTGGTGGTG CCCATCGTTC 7487 239 1.54e-08 AGGTGCCCAG GACGAGGAGGACGACGGTGAG GAACTGAGGA 32723 83 1.89e-08 GTTTGTAGTA GTGGAGGTGGAGGTTGGTGAT GTACTGTTGA 270221 108 1.89e-08 GTTTGTAGTA GTGGAGGTGGAGGTTGGTGAT GTACTGTTGA 8793 83 9.85e-08 TGGATTCTTG GAGGCAGAGGAGGGTGGGGTT GGAGTGGTGG 22140 17 2.20e-07 AGAGGGGGGC GTGGAAGGGGACGAGGAAAAG TTTCTTCTCC 9513 121 6.11e-07 AGTGTGAGAG GAGGAGGATGGCGAGTAGGAG GAGGGTTTTC 18469 280 7.01e-07 AGTTGAGTCG GAGGAAGAAGGGGATGAAATT GGAAGGAGGA 1385 16 8.01e-07 TTTGGTGCTG GATGAGGAAGGCGAAGTTATT ACAAACAAAT 3302 64 1.19e-06 CAAAACTCAG GAGGAGGTGGATGCTGTAAAT AGGCAGTAGA 6807 362 1.53e-06 TCTTCGACAC GTCGAGGAGGTGAAAGTAGTG GGAACGTGTG 21170 372 2.78e-06 GAGACTTCGG GGGGAGGGGGGGAGCGTGAAT CAAAACTCCG 10892 2 2.78e-06 A GTAGATGAGGAGTGTTTGGTG ATTGCGTCTG 35684 252 3.49e-06 ATGCCAACGC GACGAGCAAGAGAGGGTTGAG CCGGTGATGG 22418 281 3.91e-06 ATCTGAAACG GCGGAAGAAGGCAAGGTGCAG ATAGTGTCCC 268187 47 4.87e-06 GGGTATTGTC AAAGATGTGGAGGATGAGACG TGAGTATGGG 25468 273 4.87e-06 CGCCGATACA GAGGAGGGCGAGTGTGATGAT GATTAGCCAC 4876 11 6.03e-06 ATGTTATTTT CACGAGGAGGACAATGTGCTG GGATTGGACG 10417 174 8.22e-06 GCGCAACACT TAGGAAGATGTGATGGTGATG GCAGGTTATC 2462 131 1.01e-05 GTACTGAGAT GATGAAGAGGAAAGATTGCAT AACAGCAAAT 35464 244 1.35e-05 AGCGAAGGAG TTTGCGGTAGAGATGGAGGAG CTCCCTTGAT 269515 465 1.35e-05 TCGTGCCATT GAAGCTGGGGAAGATGTTCAG GGAAGTGGTG 16605 273 1.35e-05 TTGCAACTGT GAAGAAATGGACGATTTCGAG AGGAGAAGCG 36078 453 1.48e-05 GGCGTGTGGG TTGGCGGGGGACGAATGTATG CGCATTCACT 270261 452 1.48e-05 GGCGTGTGGG TTGGCGGGGGACGAATGTATG CGCATTCACT 24887 99 1.48e-05 CAATGAAAGA GTTGACGTGGACGGATCGATG ATGCTGACAT 7191 10 1.78e-05 GGGGAGCGA GAAGATGAGTGCATAGTTGAG TTGGCACACA 6896 21 1.95e-05 AACGCCCCTG GCTGAGGTGGAGGTGGCGCCG GGGCGAATGA 6431 476 2.14e-05 GAGAAGTGCC GAGGCCGTGGAAGGGGACAAG TATC 31125 67 2.14e-05 GTTGTTGGCC ATGGAGAGGGAGGTGGCGGAG CGAGCATTGG 40788 48 2.34e-05 TACCCTAAGT TAAGAAGGCGTGAAAGTGAAT TGCATTCCAT 6173 86 2.56e-05 CCTCGGCGTC GTAGAAGTAGGAGACGCGGCG GGAGGTGCCC 31021 354 3.04e-05 CGTCGGTGCC GTGGCCGTGGGAAGTGGGGTG TATGCTGTGA 263200 98 3.04e-05 AGCATCCAGC TCCGAAGTAGACGTCTTGGAG AGAGTCTTCC 22177 15 3.04e-05 AACTCCGAGG GAAGAAGTCGTTGTTGGGATT TCCAAGTGTC 33389 82 3.61e-05 AGATCACTTC GAGGAGGAATGCACAGATAAG CAGAGGCGTT 268911 112 3.61e-05 CACCACCACG GAGGGAGAGGACGCCGTCGAT GCACGACGTG 22863 408 3.61e-05 GGTTAGTTCT GTGGAGGACGGTGTAGCAAAT TCGCTCCTGA 9490 271 3.92e-05 AGATTGATGG AAAGAGGACGAGTACGTTGCT CACAGAGGAC 7112 294 3.92e-05 TTGGCGTTGT GTAGAGGTGGACGTCTGCGGT TGCGATTGTT 22652 24 3.92e-05 GGGGGTTGCA GAAGAGCATGAGGTCGTTACT ATTAATACGG 269968 149 4.26e-05 TGAGACCTTC ATTGCAGAAGAGAATTTGATT ACTTTGGACG 2484 314 4.26e-05 GACACAACCC GAAGAGGGGGAAACGTGGAGG TGAAGCTTCA 22150 310 4.62e-05 TAGCGGTGGC AACGAGGGAGTGAAGGGGGCT TCTGTCTGCT 4503 418 6.87e-05 TCAGACGGCC GACGACGATGGCGATTTTCTT TGGAGGCAAC 264495 6 7.41e-05 ATAGT GATGACGAAAACAGCGTGAAT TCTTTTGGAA 36527 8 9.28e-05 GTAGATT GTCGAGGAGGATATTTAGTTT GGTGAGGAGG 34283 239 9.28e-05 TCAACAAAGG GAGAAGGAATGGGAGGCGGTG TTGTCGTTGT 21360 77 9.98e-05 ACACCTGTTT GGGGATGAAGAGTTATGAATG TCCATGTGAG 2325 123 1.15e-04 GTCTAGTTGT TTAGATGTAGTGAAGTGAAAG GAAAAGTACA 9752 233 1.52e-04 GGTGGTTGTG TGGGCAGTGGAGTGTGAAGAG AGCAGGTGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 262572 5.9e-13 215_[+3]_264 4722 1.2e-09 47_[+3]_432 7487 1.5e-08 238_[+3]_241 32723 1.9e-08 82_[+3]_397 270221 1.9e-08 107_[+3]_372 8793 9.8e-08 82_[+3]_397 22140 2.2e-07 16_[+3]_463 9513 6.1e-07 120_[+3]_359 18469 7e-07 279_[+3]_200 1385 8e-07 15_[+3]_464 3302 1.2e-06 63_[+3]_416 6807 1.5e-06 361_[+3]_118 21170 2.8e-06 371_[+3]_108 10892 2.8e-06 1_[+3]_478 35684 3.5e-06 251_[+3]_228 22418 3.9e-06 280_[+3]_199 268187 4.9e-06 46_[+3]_433 25468 4.9e-06 272_[+3]_207 4876 6e-06 10_[+3]_469 10417 8.2e-06 173_[+3]_306 2462 1e-05 130_[+3]_349 35464 1.3e-05 243_[+3]_236 269515 1.3e-05 464_[+3]_15 16605 1.3e-05 272_[+3]_207 36078 1.5e-05 452_[+3]_27 270261 1.5e-05 451_[+3]_28 24887 1.5e-05 98_[+3]_381 7191 1.8e-05 9_[+3]_470 6896 2e-05 20_[+3]_459 6431 2.1e-05 475_[+3]_4 31125 2.1e-05 66_[+3]_413 40788 2.3e-05 47_[+3]_432 6173 2.6e-05 85_[+3]_394 31021 3e-05 353_[+3]_126 263200 3e-05 97_[+3]_382 22177 3e-05 14_[+3]_465 33389 3.6e-05 81_[+3]_398 268911 3.6e-05 111_[+3]_368 22863 3.6e-05 407_[+3]_72 9490 3.9e-05 270_[+3]_209 7112 3.9e-05 293_[+3]_186 22652 3.9e-05 23_[+3]_456 269968 4.3e-05 148_[+3]_331 2484 4.3e-05 313_[+3]_166 22150 4.6e-05 309_[+3]_170 4503 6.9e-05 417_[+3]_62 264495 7.4e-05 5_[+3]_474 36527 9.3e-05 7_[+3]_472 34283 9.3e-05 238_[+3]_241 21360 0.0001 76_[+3]_403 2325 0.00012 122_[+3]_357 9752 0.00015 232_[+3]_247 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=52 262572 ( 216) GAGGAGGAGGAGGAGGTGGAG 1 4722 ( 48) GAAGAAGAGGAGGTGGTGGTG 1 7487 ( 239) GACGAGGAGGACGACGGTGAG 1 32723 ( 83) GTGGAGGTGGAGGTTGGTGAT 1 270221 ( 108) GTGGAGGTGGAGGTTGGTGAT 1 8793 ( 83) GAGGCAGAGGAGGGTGGGGTT 1 22140 ( 17) GTGGAAGGGGACGAGGAAAAG 1 9513 ( 121) GAGGAGGATGGCGAGTAGGAG 1 18469 ( 280) GAGGAAGAAGGGGATGAAATT 1 1385 ( 16) GATGAGGAAGGCGAAGTTATT 1 3302 ( 64) GAGGAGGTGGATGCTGTAAAT 1 6807 ( 362) GTCGAGGAGGTGAAAGTAGTG 1 21170 ( 372) GGGGAGGGGGGGAGCGTGAAT 1 10892 ( 2) GTAGATGAGGAGTGTTTGGTG 1 35684 ( 252) GACGAGCAAGAGAGGGTTGAG 1 22418 ( 281) GCGGAAGAAGGCAAGGTGCAG 1 268187 ( 47) AAAGATGTGGAGGATGAGACG 1 25468 ( 273) GAGGAGGGCGAGTGTGATGAT 1 4876 ( 11) CACGAGGAGGACAATGTGCTG 1 10417 ( 174) TAGGAAGATGTGATGGTGATG 1 2462 ( 131) GATGAAGAGGAAAGATTGCAT 1 35464 ( 244) TTTGCGGTAGAGATGGAGGAG 1 269515 ( 465) GAAGCTGGGGAAGATGTTCAG 1 16605 ( 273) GAAGAAATGGACGATTTCGAG 1 36078 ( 453) TTGGCGGGGGACGAATGTATG 1 270261 ( 452) TTGGCGGGGGACGAATGTATG 1 24887 ( 99) GTTGACGTGGACGGATCGATG 1 7191 ( 10) GAAGATGAGTGCATAGTTGAG 1 6896 ( 21) GCTGAGGTGGAGGTGGCGCCG 1 6431 ( 476) GAGGCCGTGGAAGGGGACAAG 1 31125 ( 67) ATGGAGAGGGAGGTGGCGGAG 1 40788 ( 48) TAAGAAGGCGTGAAAGTGAAT 1 6173 ( 86) GTAGAAGTAGGAGACGCGGCG 1 31021 ( 354) GTGGCCGTGGGAAGTGGGGTG 1 263200 ( 98) TCCGAAGTAGACGTCTTGGAG 1 22177 ( 15) GAAGAAGTCGTTGTTGGGATT 1 33389 ( 82) GAGGAGGAATGCACAGATAAG 1 268911 ( 112) GAGGGAGAGGACGCCGTCGAT 1 22863 ( 408) GTGGAGGACGGTGTAGCAAAT 1 9490 ( 271) AAAGAGGACGAGTACGTTGCT 1 7112 ( 294) GTAGAGGTGGACGTCTGCGGT 1 22652 ( 24) GAAGAGCATGAGGTCGTTACT 1 269968 ( 149) ATTGCAGAAGAGAATTTGATT 1 2484 ( 314) GAAGAGGGGGAAACGTGGAGG 1 22150 ( 310) AACGAGGGAGTGAAGGGGGCT 1 4503 ( 418) GACGACGATGGCGATTTTCTT 1 264495 ( 6) GATGACGAAAACAGCGTGAAT 1 36527 ( 8) GTCGAGGAGGATATTTAGTTT 1 34283 ( 239) GAGAAGGAATGGGAGGCGGTG 1 21360 ( 77) GGGGATGAAGAGTTATGAATG 1 2325 ( 123) TTAGATGTAGTGAAGTGAAAG 1 9752 ( 233) TGGGCAGTGGAGTGTGAAGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 33600 bayes= 9.8647 E= 7.8e-015 -142 -357 155 -77 111 -199 -211 31 6 -57 82 -97 -374 -1234 197 -1234 165 -40 -370 -1234 16 -125 100 -119 -274 -257 188 -1234 96 -1234 -38 23 6 -125 116 -177 -374 -1234 188 -219 134 -1234 -12 -119 -116 51 94 -177 42 -1234 116 -145 71 -157 -24 13 -29 -40 21 31 -1234 -1234 151 13 -42 -99 0 75 -75 -157 100 3 65 -99 88 -377 96 -99 -270 40 -1234 -1234 125 62 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 52 E= 7.8e-015 0.096154 0.019231 0.730769 0.153846 0.557692 0.057692 0.057692 0.326923 0.269231 0.153846 0.442308 0.134615 0.019231 0.000000 0.980769 0.000000 0.807692 0.173077 0.019231 0.000000 0.288462 0.096154 0.500000 0.115385 0.038462 0.038462 0.923077 0.000000 0.500000 0.000000 0.192308 0.307692 0.269231 0.096154 0.557692 0.076923 0.019231 0.000000 0.923077 0.057692 0.653846 0.000000 0.230769 0.115385 0.115385 0.326923 0.480769 0.076923 0.346154 0.000000 0.557692 0.096154 0.423077 0.076923 0.211538 0.288462 0.211538 0.173077 0.288462 0.326923 0.000000 0.000000 0.711538 0.288462 0.192308 0.115385 0.250000 0.442308 0.153846 0.076923 0.500000 0.269231 0.403846 0.115385 0.461538 0.019231 0.500000 0.115385 0.038462 0.346154 0.000000 0.000000 0.596154 0.403846 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- G[AT][GA]GA[GA]G[AT][GA]G[AG][GC][GA][ATG][TGA][GT][TG][GT][GA][AT][GT] -------------------------------------------------------------------------------- Time 107.51 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10228 2.60e-02 80_[+2(2.35e-05)]_408 10417 3.55e-05 74_[+3(9.98e-05)]_78_[+3(8.22e-06)]_\ 27_[+2(1.32e-05)]_57_[+1(7.54e-05)]_146_[+1(2.26e-05)]_22 10892 2.10e-05 1_[+3(2.78e-06)]_67_[+2(2.15e-05)]_\ 370_[+1(2.26e-05)]_8 1219 2.77e-01 46_[+1(6.33e-05)]_433 1385 6.33e-06 15_[+3(8.01e-07)]_61_[+1(4.50e-06)]_\ 87_[+2(9.75e-05)]_283 13922 3.46e-02 298_[+2(6.36e-05)]_190 1506 4.04e-03 474_[+1(4.50e-06)]_5 16605 3.43e-04 272_[+3(1.35e-05)]_111_\ [+1(5.79e-05)]_45_[+1(1.70e-06)]_9 17707 6.76e-02 249_[+2(7.95e-06)]_239 18469 2.11e-06 141_[+2(2.35e-05)]_79_\ [+2(1.46e-05)]_35_[+3(7.01e-07)]_165_[+1(9.86e-06)]_14 21170 5.51e-04 371_[+3(2.78e-06)]_38_\ [+1(5.79e-05)]_20_[+1(1.10e-05)]_8 21257 1.97e-02 307_[+2(4.49e-06)]_181 21360 2.44e-04 76_[+3(9.98e-05)]_342_\ [+2(2.22e-06)]_49 22140 3.22e-04 16_[+3(2.20e-07)]_276_\ [+1(7.54e-05)]_166 22150 1.67e-02 309_[+3(4.62e-05)]_170 22177 1.25e-07 14_[+3(3.04e-05)]_96_[+2(5.11e-07)]_\ 16_[+2(4.77e-05)]_231_[+1(2.84e-07)]_77 22418 4.73e-05 225_[+2(1.29e-06)]_43_\ [+3(3.91e-06)]_199 22652 1.02e-03 23_[+3(3.92e-05)]_290_\ [+2(1.32e-05)]_154 22863 1.58e-03 300_[+2(4.77e-05)]_95_\ [+3(3.61e-05)]_72 2325 4.43e-03 201_[+1(4.83e-05)]_207_\ [+1(4.00e-06)]_50 2462 6.20e-04 130_[+3(1.01e-05)]_276_\ [+1(4.50e-06)]_52 2484 7.32e-08 167_[+2(6.38e-06)]_134_\ [+3(4.26e-05)]_112_[+1(9.12e-09)]_33 24887 1.96e-04 98_[+3(1.48e-05)]_333_\ [+2(5.86e-05)]_5_[+1(2.04e-05)]_10 25468 1.10e-07 146_[+2(1.74e-07)]_114_\ [+3(4.87e-06)]_185_[+1(4.50e-06)]_1 262510 1.22e-04 138_[+1(5.29e-05)]_27_\ [+1(6.72e-07)]_31_[+2(1.83e-05)]_250 262572 6.27e-14 215_[+3(5.93e-13)]_125_\ [+1(1.01e-06)]_21_[+2(1.29e-06)]_85 263062 2.63e-01 138_[+1(5.29e-05)]_222_\ [+1(5.29e-05)]_98 263200 5.51e-05 97_[+3(3.04e-05)]_233_\ [+2(2.35e-05)]_116_[+1(5.66e-06)] 264495 2.54e-04 5_[+3(7.41e-05)]_106_[+2(4.10e-05)]_\ 226_[+1(7.93e-06)]_109 268187 3.43e-03 46_[+3(4.87e-06)]_306_\ [+2(5.36e-05)]_115 268911 4.40e-04 88_[+1(4.02e-05)]_2_[+3(3.61e-05)]_\ 125_[+2(3.16e-05)]_231 269515 4.79e-04 362_[+2(1.11e-05)]_90_\ [+3(1.35e-05)]_15 269968 2.98e-04 148_[+3(4.26e-05)]_205_\ [+1(2.74e-05)]_61_[+2(2.47e-05)]_32 270221 3.18e-08 107_[+3(1.89e-08)]_21_\ [+1(9.86e-06)]_272_[+2(5.29e-06)]_46 270261 9.30e-06 233_[+1(8.95e-05)]_68_\ [+2(4.10e-05)]_64_[+1(8.83e-07)]_32_[+3(1.48e-05)]_28 270338 3.43e-02 181_[+2(3.77e-05)]_307 2950 2.26e-02 442_[+1(7.09e-06)]_37 31006 1.19e-05 400_[+1(9.86e-06)]_47_\ [+1(4.61e-10)]_11 31021 2.32e-03 262_[+1(1.50e-05)]_70_\ [+3(3.04e-05)]_126 31125 5.15e-05 36_[+2(3.16e-05)]_3_[+2(2.47e-05)]_\ 3_[+3(2.14e-05)]_62_[+3(5.01e-05)]_87_[+1(7.09e-06)]_222 31829 1.41e-03 93_[+2(3.77e-05)]_312_\ [+1(5.66e-06)]_62 3257 8.02e-04 347_[+1(6.86e-08)]_132 32723 3.18e-08 82_[+3(1.89e-08)]_21_[+1(9.86e-06)]_\ 272_[+2(5.29e-06)]_71 32745 3.13e-02 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85_[+3(2.56e-05)]_89_[+2(4.49e-06)]_\ 293 6431 4.96e-05 178_[+1(5.08e-07)]_276_\ [+3(2.14e-05)]_4 6807 1.37e-05 361_[+3(1.53e-06)]_42_\ [+1(2.80e-06)]_13_[+1(8.84e-06)]_21 6896 4.60e-03 20_[+3(1.95e-05)]_296_\ [+1(4.41e-05)]_142 7112 1.92e-04 67_[+1(2.74e-05)]_205_\ [+3(3.92e-05)]_27_[+2(1.60e-05)]_147 7191 2.63e-04 9_[+3(1.78e-05)]_211_[+1(9.86e-06)]_\ 238 7487 1.08e-07 202_[+2(3.59e-06)]_24_\ [+3(1.54e-08)]_9_[+3(6.87e-05)]_117_[+1(6.91e-05)]_43_[+2(2.86e-05)]_18 8410 1.06e-02 462_[+1(3.02e-05)]_17 8793 6.63e-08 82_[+3(9.85e-08)]_49_[+2(9.95e-07)]_\ 290_[+1(2.26e-05)]_25 8872 3.48e-02 500 9490 3.12e-03 170_[+1(6.33e-05)]_79_\ [+3(3.92e-05)]_209 9513 7.32e-07 1_[+3(2.34e-05)]_72_[+2(3.41e-05)]_\ 14_[+3(6.11e-07)]_306_[+1(1.50e-06)]_32 9752 1.01e-02 218_[+2(4.42e-05)]_270 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************