******************************************************************************** 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/473/473.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10057 1.0000 500 10801 1.0000 500 11072 1.0000 500 11627 1.0000 500 11897 1.0000 500 15638 1.0000 500 1706 1.0000 500 2035 1.0000 500 21538 1.0000 500 22277 1.0000 500 23334 1.0000 500 23483 1.0000 500 24562 1.0000 500 24768 1.0000 500 25237 1.0000 500 25757 1.0000 500 263899 1.0000 500 268475 1.0000 500 269496 1.0000 500 269726 1.0000 500 3136 1.0000 500 3934 1.0000 500 4672 1.0000 500 5604 1.0000 500 6292 1.0000 500 6670 1.0000 500 6705 1.0000 500 bd836 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/473/473.seqs.fa -oc motifs/473 -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= 28 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= 14000 N= 28 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.257 C 0.236 G 0.239 T 0.268 Background letter frequencies (from dataset with add-one prior applied): A 0.257 C 0.236 G 0.239 T 0.268 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 20 llr = 238 E-value = 3.6e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 151:2:15::33:::2:3121 pos.-specific C 8:282373196:2723245:9 probability G :51:6:22:224::53:1421 matrix T 1:731711a::494439417: bits 2.1 1.9 1.7 * 1.5 ** Relative 1.2 * ** * * * Entropy 1.0 ** * * ** ** * * (17.2 bits) 0.8 ** * * ** ** * * 0.6 **** ** *** *** * ** 0.4 ******* ******* * *** 0.2 *************** ***** 0.0 --------------------- Multilevel CATCGTCATCCGTCGCTCCTC consensus G TAC C AT TTT TGG sequence A G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 263899 210 2.34e-10 GAGTTCAACA CATCGTCATCCTTCGATACTC GTTCGTAGTC 1706 450 8.52e-09 TCGTTGCATT CATCGTCGTCCGTCGTCCGTC TCGTGTCGTC 5604 342 8.32e-08 CTTCTGGTCC CGTCATCTTCCTTCTCTTATC ATTTCCAGTG 11897 33 1.05e-07 GTTGATCATC CATCGCCATCGGCTGTTCGTC TCGGCCCCAG 10057 106 1.86e-07 TGATTGGGAA CACTGTTATCCATCGCTCGTC GTTGAGCCGA 24768 304 3.53e-07 TTCCAATCAT CGTTCTTATCCATTGGTTCTC CGCCACCGCT 23334 354 7.07e-07 GATATCAATA CATCATCCTGAGTTGGTTCAC GAGACACGTC 11627 199 8.54e-07 CCGGTCCAAC AGGTGTCATCCATCCCTTCTC AAAGAATGAA 15638 233 1.03e-06 CTGTGTTGCT CATTGCGACCCTTCTCTTCTC AGCATATCTC 269726 447 1.23e-06 CCACAGCAGC TGCCGCACTCCTTCTCTCCTC TCACACCTCA 268475 257 1.60e-06 CATCGGTGTT CGTTGTGCTCGGTCGGTCAGC AGCTGTCGGC 23483 402 1.60e-06 TTCCTTCATA AGCCCTCCTCATTCCTTCCTC CACCGATCCA 2035 404 1.60e-06 TTTTATTCCA CGTCGTCGTCATTTTCTAGAA AAGAAGGGAA 4672 384 2.88e-06 ACTGCAACAA CATCTTGCTGCGTCGTTAGAC ACACACGCTA 25237 238 3.12e-06 TCAACAACAA TATCATCATCAATCCACCCTC CTTAGCCAGG 3136 24 6.16e-06 TCACCGTCAC CATCGCCATCAGTTGTTGTTG CTGTTGTGTT 10801 85 6.16e-06 ACCCTCGGTG CATCTCCATCATTCTGCATGC CAAAACGTAG 25757 441 7.11e-06 TGGGCGTCCA CGGCATCTTCGGCTTGTTGTC GTCTCCTGAC 6292 278 1.07e-05 TGATGACGTT CGTCGCAGTCCATTTATACGA GAGCCGCCTC 6670 41 1.30e-05 GTGGGTTGAC CGACCTCCTGCACCTTTTGGC TTGTGAGAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 263899 2.3e-10 209_[+1]_270 1706 8.5e-09 449_[+1]_30 5604 8.3e-08 341_[+1]_138 11897 1.1e-07 32_[+1]_447 10057 1.9e-07 105_[+1]_374 24768 3.5e-07 303_[+1]_176 23334 7.1e-07 353_[+1]_126 11627 8.5e-07 198_[+1]_281 15638 1e-06 232_[+1]_247 269726 1.2e-06 446_[+1]_33 268475 1.6e-06 256_[+1]_223 23483 1.6e-06 401_[+1]_78 2035 1.6e-06 403_[+1]_76 4672 2.9e-06 383_[+1]_96 25237 3.1e-06 237_[+1]_242 3136 6.2e-06 23_[+1]_456 10801 6.2e-06 84_[+1]_395 25757 7.1e-06 440_[+1]_39 6292 1.1e-05 277_[+1]_202 6670 1.3e-05 40_[+1]_439 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=20 263899 ( 210) CATCGTCATCCTTCGATACTC 1 1706 ( 450) CATCGTCGTCCGTCGTCCGTC 1 5604 ( 342) CGTCATCTTCCTTCTCTTATC 1 11897 ( 33) CATCGCCATCGGCTGTTCGTC 1 10057 ( 106) CACTGTTATCCATCGCTCGTC 1 24768 ( 304) CGTTCTTATCCATTGGTTCTC 1 23334 ( 354) CATCATCCTGAGTTGGTTCAC 1 11627 ( 199) AGGTGTCATCCATCCCTTCTC 1 15638 ( 233) CATTGCGACCCTTCTCTTCTC 1 269726 ( 447) TGCCGCACTCCTTCTCTCCTC 1 268475 ( 257) CGTTGTGCTCGGTCGGTCAGC 1 23483 ( 402) AGCCCTCCTCATTCCTTCCTC 1 2035 ( 404) CGTCGTCGTCATTTTCTAGAA 1 4672 ( 384) CATCTTGCTGCGTCGTTAGAC 1 25237 ( 238) TATCATCATCAATCCACCCTC 1 3136 ( 24) CATCGCCATCAGTTGTTGTTG 1 10801 ( 85) CATCTCCATCATTCTGCATGC 1 25757 ( 441) CGGCATCTTCGGCTTGTTGTC 1 6292 ( 278) CGTCGCAGTCCATTTATACGA 1 6670 ( 41) CGACCTCCTGCACCTTTTGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 13440 bayes= 9.64205 E= 3.6e-004 -136 176 -1097 -142 96 -1097 106 -1097 -236 -65 -126 139 -1097 167 -1097 -10 -36 -65 120 -142 -1097 35 -1097 139 -136 146 -67 -142 81 35 -67 -142 -1097 -224 -1097 183 -1097 185 -67 -1097 22 122 -67 -1097 22 -1097 55 39 -1097 -65 -1097 167 -1097 146 -1097 39 -1097 -65 91 58 -78 35 6 16 -1097 -65 -1097 167 -4 57 -226 39 -136 93 55 -142 -78 -1097 -26 128 -136 185 -226 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 20 E= 3.6e-004 0.100000 0.800000 0.000000 0.100000 0.500000 0.000000 0.500000 0.000000 0.050000 0.150000 0.100000 0.700000 0.000000 0.750000 0.000000 0.250000 0.200000 0.150000 0.550000 0.100000 0.000000 0.300000 0.000000 0.700000 0.100000 0.650000 0.150000 0.100000 0.450000 0.300000 0.150000 0.100000 0.000000 0.050000 0.000000 0.950000 0.000000 0.850000 0.150000 0.000000 0.300000 0.550000 0.150000 0.000000 0.300000 0.000000 0.350000 0.350000 0.000000 0.150000 0.000000 0.850000 0.000000 0.650000 0.000000 0.350000 0.000000 0.150000 0.450000 0.400000 0.150000 0.300000 0.250000 0.300000 0.000000 0.150000 0.000000 0.850000 0.250000 0.350000 0.050000 0.350000 0.100000 0.450000 0.350000 0.100000 0.150000 0.000000 0.200000 0.650000 0.100000 0.850000 0.050000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AG]T[CT][GA][TC]C[AC]TC[CA][GTA]T[CT][GT][CTG]T[CTA][CG][TG]C -------------------------------------------------------------------------------- Time 6.49 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 19 sites = 18 llr = 215 E-value = 3.6e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 16a339:943523327732 pos.-specific C 72:6519146373383:77 probability G 22:12::121::42::2:: matrix T ::::1:1:::2112::112 bits 2.1 1.9 * 1.7 * * 1.5 * *** Relative 1.2 * *** * Entropy 1.0 * *** ** (17.2 bits) 0.8 * ** *** * ***** 0.6 **** *** *** ***** 0.4 ************ ***** 0.2 ************* ***** 0.0 ------------------- Multilevel CAACCACAACACGCCAACC consensus GC AA CAC AAACGA sequence G CT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 23334 287 9.39e-09 ATATCACAGT CAACGACACCACGGCAAAC AGCAGCTGTT 3136 450 1.76e-08 AACTAAATGT CAACCACACCACCGCCGCC AGCCGCCATT 268475 373 3.21e-08 CTCCGAATCA CAAACACACAACGCAAAAC ACACAAGCTG 6705 99 1.21e-07 GAACATATAC CAACTACAGAACCTCAACC CTAGGACGAC 2035 158 1.54e-07 TACTCACAAT GCACAACAACTCCACAACC TGAACAGAAC 23483 434 2.19e-07 ACCGATCCAA ACAACACACACCGTCAACC TGTGCCGCCA 24562 16 3.81e-07 CAGATACAAG CAAGCACAGCCCAGCCACC GCTGTTCGCG 10057 397 4.23e-07 CTACCAACGT CAACAATACAACACCAACT CGATGGATGC 25237 460 1.63e-06 GTGTCCCCTC CGACAACAACACAACAATA TCAGAAACTG 269496 368 1.94e-06 TCAAGAACAG GCAACACAACTCCAAAAAC AGCAGTCACT 11072 477 1.94e-06 CCAGCCTCTA CGAACACAACACGCACTCC AAACA 269726 417 2.11e-06 ATACCATGGC CAAACACAGACTACCAGCA GCCACAGCAG 15638 306 4.34e-06 TCCTCTTTGC CAACCCCAACCCAAAAGCA ACTTTCACAG 22277 474 5.83e-06 TCTTTAGCAA GAACGACAAGAATTCAACC GGCAAAAC 6670 475 7.22e-06 ACTCAATATC CAACAACAGGAACACCAAT ATACATA 11627 234 8.86e-06 AATGAACCGC ACACGACACCTAGCCCGCC ACTACCAGCG bd836 432 9.48e-06 CTCCTTGACA CAACAATCAACCGTCAACT TCTCTCGTGT 6292 105 1.08e-05 AAGAAGAAGA GGAACACGCCCTGCCAAAC CGGCCAAACA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23334 9.4e-09 286_[+2]_195 3136 1.8e-08 449_[+2]_32 268475 3.2e-08 372_[+2]_109 6705 1.2e-07 98_[+2]_383 2035 1.5e-07 157_[+2]_324 23483 2.2e-07 433_[+2]_48 24562 3.8e-07 15_[+2]_466 10057 4.2e-07 396_[+2]_85 25237 1.6e-06 459_[+2]_22 269496 1.9e-06 367_[+2]_114 11072 1.9e-06 476_[+2]_5 269726 2.1e-06 416_[+2]_65 15638 4.3e-06 305_[+2]_176 22277 5.8e-06 473_[+2]_8 6670 7.2e-06 474_[+2]_7 11627 8.9e-06 233_[+2]_248 bd836 9.5e-06 431_[+2]_50 6292 1.1e-05 104_[+2]_377 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=19 seqs=18 23334 ( 287) CAACGACACCACGGCAAAC 1 3136 ( 450) CAACCACACCACCGCCGCC 1 268475 ( 373) CAAACACACAACGCAAAAC 1 6705 ( 99) CAACTACAGAACCTCAACC 1 2035 ( 158) GCACAACAACTCCACAACC 1 23483 ( 434) ACAACACACACCGTCAACC 1 24562 ( 16) CAAGCACAGCCCAGCCACC 1 10057 ( 397) CAACAATACAACACCAACT 1 25237 ( 460) CGACAACAACACAACAATA 1 269496 ( 368) GCAACACAACTCCAAAAAC 1 11072 ( 477) CGAACACAACACGCACTCC 1 269726 ( 417) CAAACACAGACTACCAGCA 1 15638 ( 306) CAACCCCAACCCAAAAGCA 1 22277 ( 474) GAACGACAAGAATTCAACC 1 6670 ( 475) CAACAACAGGAACACCAAT 1 11627 ( 234) ACACGACACCTAGCCCGCC 1 bd836 ( 432) CAACAATCAACCGTCAACT 1 6292 ( 105) GGAACACGCCCTGCCAAAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 13496 bayes= 10.954 E= 3.6e-003 -121 150 -11 -1081 125 -9 -52 -1081 196 -1081 -1081 -1081 38 137 -210 -1081 11 108 -52 -226 188 -209 -1081 -1081 -1081 191 -1081 -127 179 -209 -210 -1081 60 72 -11 -1081 38 123 -111 -1081 96 50 -1081 -68 -62 161 -1081 -127 11 23 70 -226 11 50 -52 -27 -21 172 -1081 -1081 149 23 -1081 -1081 149 -1081 -11 -226 11 150 -1081 -226 -62 150 -1081 -68 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 18 E= 3.6e-003 0.111111 0.666667 0.222222 0.000000 0.611111 0.222222 0.166667 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.611111 0.055556 0.000000 0.277778 0.500000 0.166667 0.055556 0.944444 0.055556 0.000000 0.000000 0.000000 0.888889 0.000000 0.111111 0.888889 0.055556 0.055556 0.000000 0.388889 0.388889 0.222222 0.000000 0.333333 0.555556 0.111111 0.000000 0.500000 0.333333 0.000000 0.166667 0.166667 0.722222 0.000000 0.111111 0.277778 0.277778 0.388889 0.055556 0.277778 0.333333 0.166667 0.222222 0.222222 0.777778 0.000000 0.000000 0.722222 0.277778 0.000000 0.000000 0.722222 0.000000 0.222222 0.055556 0.277778 0.666667 0.000000 0.055556 0.166667 0.666667 0.000000 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CG][AC]A[CA][CA]ACA[ACG][CA][AC]C[GAC][CAT][CA][AC][AG][CA]C -------------------------------------------------------------------------------- Time 12.63 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 19 sites = 21 llr = 230 E-value = 6.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:12413222:2:5:13:: pos.-specific C 1::3:11:3::11::::1: probability G :58:45:82:9672a9:77 matrix T 8414236:281:12::712 bits 2.1 1.9 * 1.7 * * 1.5 * * Relative 1.2 * * ** Entropy 1.0 * * ** ** * (15.8 bits) 0.8 * * * ** * ***** 0.6 *** ** **** ***** 0.4 *** * ** ********** 0.2 ******** ********** 0.0 ------------------- Multilevel TGGTAGTGCTGGGAGGTGG consensus T CGTA A A G A T sequence G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------------- 1706 241 2.06e-08 CGGAAGGAAT TGGAGGAGAAGGGAGGTGG ACAGAGTCTG 11072 115 2.38e-08 TTGAAAAGAG TTGCAGCGGTGGGTGGTGG AGCCGCTCCG 24562 196 4.19e-08 TGGATGCGCT GGGTGTTGTTGGGAGGTGG GCGCTCTCTC 5604 68 1.19e-07 GAGAGTCCAT TTGTGGTGGAGGGGGGTTG GTGTCGAGCT 25757 167 1.34e-07 TGCTACTTGA TGGCAGTATTGGGGGGTTG TTTCCCCTCC 2035 349 8.12e-07 TCATCGAAAG AGGCACTGCTGCGAGGAGG CAATGCTAAC 3136 281 1.10e-06 CAGACGCCAC AGATGGTGATGGGTGGAGG AGAAGGACAT 24768 229 3.14e-06 GTTGGCTCGG TTGATGTGATGCGTGGCGG TGAAACGAGA 4672 89 4.11e-06 CCGCGGTTGA TTATGATGCTGATTGGTGG CATTTGAACC 23483 49 4.48e-06 TCGTGTTGGT CTGCAAAGTTGGGAGGTAG CGTAGCCTTG 21538 137 5.33e-06 GCTGAAGTTG TGGTAGAAGTGGCAGGAGA GGTTGCTACC 10801 218 5.33e-06 TGCCGCAGTA TTGTAGTGCCGGTAGGTTT AGAGAGAGAT 3934 187 5.80e-06 GAGCCGCCGA TGTCATCGCTGGGAGAAGG AGTGCTGCTA 6670 75 6.32e-06 TGAGAGATCG TCGATTTGATGGGAGTTGG AAGAGCCGAG 6292 222 6.32e-06 CCTTCATCTG TGGATGTGGAGATGGGTGT TGCGAAGACG 269726 205 6.32e-06 TCGTAGTGAA TAGCGTTGGTGGGGCGAGG GGTGTGCAAT 11627 352 8.10e-06 CGGATGTGAG TTGGAGAACTGCGAGGTCG TCTGTCTGTC 10057 32 1.41e-05 TTGTCGGTTT TGTTGTTACAGAGGGGTGT AGCTGTCCGA bd836 138 1.77e-05 GAAGAACGAA TGGTTCAGATTGCTGGAGG GAGTATCATT 11897 243 1.77e-05 CCTGGTGTTC CGGTGTTGTTGACAGATGT GGATACTACT 25237 301 2.37e-05 GACAGGACCT TTGCAAAGTTTAGAGGTCT GATGTTGTGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1706 2.1e-08 240_[+3]_241 11072 2.4e-08 114_[+3]_367 24562 4.2e-08 195_[+3]_286 5604 1.2e-07 67_[+3]_414 25757 1.3e-07 166_[+3]_315 2035 8.1e-07 348_[+3]_133 3136 1.1e-06 280_[+3]_201 24768 3.1e-06 228_[+3]_253 4672 4.1e-06 88_[+3]_393 23483 4.5e-06 48_[+3]_433 21538 5.3e-06 136_[+3]_345 10801 5.3e-06 217_[+3]_264 3934 5.8e-06 186_[+3]_295 6670 6.3e-06 74_[+3]_407 6292 6.3e-06 221_[+3]_260 269726 6.3e-06 204_[+3]_277 11627 8.1e-06 351_[+3]_130 10057 1.4e-05 31_[+3]_450 bd836 1.8e-05 137_[+3]_344 11897 1.8e-05 242_[+3]_239 25237 2.4e-05 300_[+3]_181 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=19 seqs=21 1706 ( 241) TGGAGGAGAAGGGAGGTGG 1 11072 ( 115) TTGCAGCGGTGGGTGGTGG 1 24562 ( 196) GGGTGTTGTTGGGAGGTGG 1 5604 ( 68) TTGTGGTGGAGGGGGGTTG 1 25757 ( 167) TGGCAGTATTGGGGGGTTG 1 2035 ( 349) AGGCACTGCTGCGAGGAGG 1 3136 ( 281) AGATGGTGATGGGTGGAGG 1 24768 ( 229) TTGATGTGATGCGTGGCGG 1 4672 ( 89) TTATGATGCTGATTGGTGG 1 23483 ( 49) CTGCAAAGTTGGGAGGTAG 1 21538 ( 137) TGGTAGAAGTGGCAGGAGA 1 10801 ( 218) TTGTAGTGCCGGTAGGTTT 1 3934 ( 187) TGTCATCGCTGGGAGAAGG 1 6670 ( 75) TCGATTTGATGGGAGTTGG 1 6292 ( 222) TGGATGTGGAGATGGGTGT 1 269726 ( 205) TAGCGTTGGTGGGGCGAGG 1 11627 ( 352) TTGGAGAACTGCGAGGTCG 1 10057 ( 32) TGTTGTTACAGAGGGGTGT 1 bd836 ( 138) TGGTTCAGATTGCTGGAGG 1 11897 ( 243) CGGTGTTGTTGACAGATGT 1 25237 ( 301) TTGCAAAGTTTAGAGGTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 19 n= 13496 bayes= 9.63096 E= 6.8e-001 -143 -131 -233 151 -243 -231 113 51 -143 -1104 176 -149 -43 50 -233 68 74 -1104 67 -49 -85 -131 99 9 15 -131 -1104 121 -43 -1104 176 -1104 -11 27 -1 -17 -43 -231 -1104 151 -1104 -1104 192 -149 -11 -72 137 -1104 -1104 -72 158 -90 103 -1104 -1 -17 -1104 -231 199 -1104 -143 -1104 184 -249 15 -231 -1104 132 -243 -131 158 -90 -243 -1104 158 -17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 19 nsites= 21 E= 6.8e-001 0.095238 0.095238 0.047619 0.761905 0.047619 0.047619 0.523810 0.380952 0.095238 0.000000 0.809524 0.095238 0.190476 0.333333 0.047619 0.428571 0.428571 0.000000 0.380952 0.190476 0.142857 0.095238 0.476190 0.285714 0.285714 0.095238 0.000000 0.619048 0.190476 0.000000 0.809524 0.000000 0.238095 0.285714 0.238095 0.238095 0.190476 0.047619 0.000000 0.761905 0.000000 0.000000 0.904762 0.095238 0.238095 0.142857 0.619048 0.000000 0.000000 0.142857 0.714286 0.142857 0.523810 0.000000 0.238095 0.238095 0.000000 0.047619 0.952381 0.000000 0.095238 0.000000 0.857143 0.047619 0.285714 0.047619 0.000000 0.666667 0.047619 0.095238 0.714286 0.142857 0.047619 0.000000 0.714286 0.238095 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[GT]G[TC][AG][GT][TA]G[CAGT]TG[GA]G[AGT]GG[TA]G[GT] -------------------------------------------------------------------------------- Time 18.56 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10057 3.51e-08 31_[+3(1.41e-05)]_55_[+1(1.86e-07)]_\ 270_[+2(4.23e-07)]_85 10801 2.17e-04 84_[+1(6.16e-06)]_112_\ [+3(5.33e-06)]_264 11072 1.15e-06 114_[+3(2.38e-08)]_343_\ [+2(1.94e-06)]_5 11627 1.34e-06 198_[+1(8.54e-07)]_14_\ [+2(8.86e-06)]_99_[+3(8.10e-06)]_130 11897 5.21e-05 32_[+1(1.05e-07)]_70_[+1(5.52e-05)]_\ 98_[+3(1.77e-05)]_239 15638 6.25e-05 232_[+1(1.03e-06)]_52_\ [+2(4.34e-06)]_176 1706 1.01e-08 240_[+3(2.06e-08)]_190_\ [+1(8.52e-09)]_30 2035 7.31e-09 157_[+2(1.54e-07)]_172_\ [+3(8.12e-07)]_36_[+1(1.60e-06)]_76 21538 2.08e-02 136_[+3(5.33e-06)]_345 22277 3.57e-02 473_[+2(5.83e-06)]_8 23334 2.36e-07 286_[+2(9.39e-09)]_48_\ [+1(7.07e-07)]_126 23483 4.84e-08 48_[+3(4.48e-06)]_241_\ [+2(7.55e-05)]_74_[+1(1.60e-06)]_11_[+2(2.19e-07)]_48 24562 5.36e-07 15_[+2(3.81e-07)]_161_\ [+3(4.19e-08)]_286 24768 2.02e-06 228_[+3(3.14e-06)]_56_\ [+1(3.53e-07)]_106_[+2(8.90e-05)]_51 25237 2.45e-06 237_[+1(3.12e-06)]_42_\ [+3(2.37e-05)]_140_[+2(1.63e-06)]_22 25757 2.86e-05 166_[+3(1.34e-07)]_255_\ [+1(7.11e-06)]_39 263899 9.96e-06 209_[+1(2.34e-10)]_270 268475 2.09e-06 256_[+1(1.60e-06)]_95_\ [+2(3.21e-08)]_109 269496 2.45e-02 367_[+2(1.94e-06)]_114 269726 4.08e-07 204_[+3(6.32e-06)]_193_\ [+2(2.11e-06)]_11_[+1(1.23e-06)]_33 3136 4.53e-09 23_[+1(6.16e-06)]_236_\ [+3(1.10e-06)]_150_[+2(1.76e-08)]_32 3934 1.44e-02 186_[+3(5.80e-06)]_295 4672 6.76e-05 88_[+3(4.11e-06)]_276_\ [+1(2.88e-06)]_96 5604 1.39e-07 67_[+3(1.19e-07)]_255_\ [+1(8.32e-08)]_44_[+1(4.77e-05)]_73 6292 1.22e-05 104_[+2(1.08e-05)]_98_\ [+3(6.32e-06)]_37_[+1(1.07e-05)]_202 6670 1.01e-05 19_[+3(5.74e-05)]_2_[+1(1.30e-05)]_\ 13_[+3(6.32e-06)]_381_[+2(7.22e-06)]_7 6705 4.40e-04 98_[+2(1.21e-07)]_383 bd836 1.13e-03 137_[+3(1.77e-05)]_275_\ [+2(9.48e-06)]_50 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************