******************************************************************************** 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/96/96.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10128 1.0000 500 10219 1.0000 500 10371 1.0000 500 10935 1.0000 500 11048 1.0000 500 1316 1.0000 500 17673 1.0000 500 19598 1.0000 500 1979 1.0000 500 20821 1.0000 500 20868 1.0000 500 21053 1.0000 500 21308 1.0000 500 21583 1.0000 500 21606 1.0000 500 23596 1.0000 500 24597 1.0000 500 25409 1.0000 500 25814 1.0000 500 260761 1.0000 500 262193 1.0000 500 263081 1.0000 500 269866 1.0000 500 3011 1.0000 500 3108 1.0000 500 4385 1.0000 500 5161 1.0000 500 7233 1.0000 500 8130 1.0000 500 8295 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/96/96.seqs.fa -oc motifs/96 -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= 30 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= 15000 N= 30 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.261 C 0.236 G 0.232 T 0.271 Background letter frequencies (from dataset with add-one prior applied): A 0.261 C 0.236 G 0.232 T 0.271 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 19 llr = 220 E-value = 2.8e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 1161291426:15:21 pos.-specific C :2:2::::::::3137 probability G 734681568:a8:952 matrix T 2511::4::4:12::: bits 2.1 * 1.9 * * 1.7 * * 1.5 * * * * Relative 1.3 ** * ** * Entropy 1.1 ** ***** * * (16.7 bits) 0.8 * * ** ***** * * 0.6 * ********** *** 0.4 * ************** 0.2 **************** 0.0 ---------------- Multilevel GTAGGAGGGAGGAGGC consensus TGG A TA T C CG sequence T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 3011 85 2.64e-09 AGCCTGGGAC GTAGGATGGAGGAGCC CACCACAGAC 8295 158 9.53e-09 AATTAAGTTG GCAGGATGGAGGAGGC GATTTTGGGA 21606 84 4.27e-08 TCGTACGATG GTGGGATGGTGGTGGC TTCACTTGCG 20821 345 5.78e-07 GAGGAGCCTC ACAGGAGAGAGGAGCC TCTTTACGAG 21308 135 6.40e-07 CTGCTTTAGT GGGCAAGGGAGGAGCC CCCTCTATTT 8130 374 7.13e-07 TTAGAGCATC GGAGGAGAGTGGAGGA TGATTTGCCG 17673 248 8.77e-07 TTGGAGAAGA GGAGGATGGAGTTGGC TTTGTCTTGT 11048 61 9.72e-07 AAGTGTTAGG GTACGAGAGAGGCGAG GAGGGTTTGG 24597 182 1.31e-06 AATCCGTTCA GTAGAGGAGAGGCGCC TTTTTCACGT 260761 39 1.44e-06 ATGAAGAGAA ACAGGATGGTGGTGGC TACGACGCCT 21053 236 1.44e-06 CGGAGAGCGG TTGGGAGGGAGGTGAG GGAAGTGGCG 10371 231 3.51e-06 ACTGCTGAGA GGGTGATGATGGCGGC GAGGACGAGT 7233 371 4.48e-06 GGAAGGAGTT GTTGGAGGGAGACGAC GAACGGTCGC 4385 53 5.66e-06 AAGATTTTGG TTGGAAGAAAGGCGCC TTCTGTGTTT 269866 390 6.11e-06 AGTGAGACCT GGAAGGAAGAGGAGGC ACCTCTCCGC 25409 129 7.09e-06 GAGGTTTGTT GGGAGATGATGGAGGG ACGAAAAAGT 5161 249 1.08e-05 GTTGCTGCTG TTGGAATGGTGGACGC TGTTGGTGGT 25814 259 1.60e-05 CGCTCACTTT TTACGAAAGAGAAGCC CCCCTCCCTT 1316 36 1.81e-05 ACCTGAAATT GAATGAGAGTGGCGAG GCAATCTATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3011 2.6e-09 84_[+1]_400 8295 9.5e-09 157_[+1]_327 21606 4.3e-08 83_[+1]_401 20821 5.8e-07 344_[+1]_140 21308 6.4e-07 134_[+1]_350 8130 7.1e-07 373_[+1]_111 17673 8.8e-07 247_[+1]_237 11048 9.7e-07 60_[+1]_424 24597 1.3e-06 181_[+1]_303 260761 1.4e-06 38_[+1]_446 21053 1.4e-06 235_[+1]_249 10371 3.5e-06 230_[+1]_254 7233 4.5e-06 370_[+1]_114 4385 5.7e-06 52_[+1]_432 269866 6.1e-06 389_[+1]_95 25409 7.1e-06 128_[+1]_356 5161 1.1e-05 248_[+1]_236 25814 1.6e-05 258_[+1]_226 1316 1.8e-05 35_[+1]_449 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=19 3011 ( 85) GTAGGATGGAGGAGCC 1 8295 ( 158) GCAGGATGGAGGAGGC 1 21606 ( 84) GTGGGATGGTGGTGGC 1 20821 ( 345) ACAGGAGAGAGGAGCC 1 21308 ( 135) GGGCAAGGGAGGAGCC 1 8130 ( 374) GGAGGAGAGTGGAGGA 1 17673 ( 248) GGAGGATGGAGTTGGC 1 11048 ( 61) GTACGAGAGAGGCGAG 1 24597 ( 182) GTAGAGGAGAGGCGCC 1 260761 ( 39) ACAGGATGGTGGTGGC 1 21053 ( 236) TTGGGAGGGAGGTGAG 1 10371 ( 231) GGGTGATGATGGCGGC 1 7233 ( 371) GTTGGAGGGAGACGAC 1 4385 ( 53) TTGGAAGAAAGGCGCC 1 269866 ( 390) GGAAGGAAGAGGAGGC 1 25409 ( 129) GGGAGATGATGGAGGG 1 5161 ( 249) TTGGAATGGTGGACGC 1 25814 ( 259) TTACGAAAGAGAAGCC 1 1316 ( 36) GAATGAGAGTGGCGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 14550 bayes= 10.4772 E= 2.8e-006 -131 -1089 156 -36 -231 -58 44 81 115 -1089 67 -236 -131 -58 144 -136 -31 -1089 176 -1089 178 -1089 -114 -1089 -131 -1089 103 64 69 -1089 132 -1089 -72 -1089 186 -1089 127 -1089 -1089 44 -1089 -1089 211 -1089 -131 -1089 186 -236 86 42 -1089 -36 -1089 -216 203 -1089 -31 42 103 -1089 -231 164 -14 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 19 E= 2.8e-006 0.105263 0.000000 0.684211 0.210526 0.052632 0.157895 0.315789 0.473684 0.578947 0.000000 0.368421 0.052632 0.105263 0.157895 0.631579 0.105263 0.210526 0.000000 0.789474 0.000000 0.894737 0.000000 0.105263 0.000000 0.105263 0.000000 0.473684 0.421053 0.421053 0.000000 0.578947 0.000000 0.157895 0.000000 0.842105 0.000000 0.631579 0.000000 0.000000 0.368421 0.000000 0.000000 1.000000 0.000000 0.105263 0.000000 0.842105 0.052632 0.473684 0.315789 0.000000 0.210526 0.000000 0.052632 0.947368 0.000000 0.210526 0.315789 0.473684 0.000000 0.052632 0.736842 0.210526 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GT][TG][AG]G[GA]A[GT][GA]G[AT]GG[ACT]G[GCA][CG] -------------------------------------------------------------------------------- Time 7.53 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 25 llr = 245 E-value = 9.0e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :::4:::1::::24:: pos.-specific C :691296214456:35 probability G 2:::::21::2::4:: matrix T 84:5812596342265 bits 2.1 1.9 1.7 * 1.5 * * * Relative 1.3 * ** * Entropy 1.1 *** ** ** * (14.1 bits) 0.8 *** *** ** * * 0.6 ******* ** * ** 0.4 ******* ******** 0.2 **************** 0.0 ---------------- Multilevel TCCTTCCTTTCCCGTT consensus GT AC TC CTTAACC sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 11048 177 3.45e-08 GTCCACACTG TCCTTCCCTTCTCGTC CGTACGACTT 1979 303 1.27e-07 TAGGGAGGTA TTCTTCCTTTGTCGTT GCATTAACTT 21606 349 8.23e-07 CCGATCGCCC TCCATCCTTCCCTGCT CGCACGTTCA 1316 335 1.43e-06 TGCCTTACTT TCCACCCCTCTCCATT TCACAGAAGC 20821 470 2.36e-06 TTGGGAAGAT GCCTTCGTTTTTCGTC ATATCTCCTC 5161 69 2.66e-06 CTGACCTCCT TCCATCCATCCCAGCC CCTCAAATCC 20868 456 2.66e-06 TAATCTGACG TCCATCTTTTTCTATC TCCAGGATTT 24597 224 3.36e-06 TACTAAATCC TTCACCCTTTCCATTT TCACAGGTAC 21583 254 3.36e-06 ATCAAAGAGC GCCTTCCATTGTCATC TAGAGCTCTG 8130 219 4.21e-06 GTGTAGGACC TCCATCCGTTGTTGTT GTTACTGTAG 260761 129 4.21e-06 TACAACACCC GTCTTCCTCTCCCATT GGGAACAGCT 19598 372 4.21e-06 TCCGTGGTCG TCCTTCTCTTTTAGTC ACGATTTATG 21053 18 9.49e-06 CTTTGCGTCT TTCTTCTATTGCCTTT TGTTTGGTGC 8295 414 1.37e-05 CGCCAACTCA TCCCTCCTTCCCCAAC CCCCCCCTCT 25409 178 1.50e-05 GCGGAGAGGC TTCTTCGTTTCTCGGC TCTACCGCAT 23596 42 1.50e-05 CTTCTCTATC TCGATCCTTTCTCTCT TTTGATTGCC 7233 418 1.63e-05 CTCATTGGGC TTCTTTGTTCCTCATT ATTTCTTTGA 17673 367 2.11e-05 TCTCTAAAAT TTCTTCCTTTTAATTC CTCATGTAAG 25814 275 2.68e-05 AAGAGAAGCC CCCCTCCCTTTCCGTT CAAATCTCGC 4385 428 3.37e-05 TGATCCATCG TCCATTCGTCGTAATC ATCAATCCAT 269866 469 4.84e-05 TTTGGATTTC TTCACCGCTCTCATTT TTCCTCAGCA 3108 439 6.79e-05 GCATCATGCA TTCATCCTCCCCGTCT AACACCAATT 263081 269 9.30e-05 CACCAACCCT GCCTTCTGCCGCCACC TTCCGTTCAC 10371 451 1.25e-04 CGACGAGGGC TCAACCTCTTCTCACC ATCACACCAT 262193 356 1.64e-04 AAAGCTGGGT GTCTCTCTTCTCTGCT CACTCCTAAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11048 3.4e-08 176_[+2]_308 1979 1.3e-07 302_[+2]_182 21606 8.2e-07 348_[+2]_136 1316 1.4e-06 334_[+2]_150 20821 2.4e-06 469_[+2]_15 5161 2.7e-06 68_[+2]_416 20868 2.7e-06 455_[+2]_29 24597 3.4e-06 223_[+2]_261 21583 3.4e-06 253_[+2]_231 8130 4.2e-06 218_[+2]_266 260761 4.2e-06 128_[+2]_356 19598 4.2e-06 371_[+2]_113 21053 9.5e-06 17_[+2]_467 8295 1.4e-05 413_[+2]_71 25409 1.5e-05 177_[+2]_307 23596 1.5e-05 41_[+2]_443 7233 1.6e-05 417_[+2]_67 17673 2.1e-05 366_[+2]_118 25814 2.7e-05 274_[+2]_210 4385 3.4e-05 427_[+2]_57 269866 4.8e-05 468_[+2]_16 3108 6.8e-05 438_[+2]_46 263081 9.3e-05 268_[+2]_216 10371 0.00012 450_[+2]_34 262193 0.00016 355_[+2]_129 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=25 11048 ( 177) TCCTTCCCTTCTCGTC 1 1979 ( 303) TTCTTCCTTTGTCGTT 1 21606 ( 349) TCCATCCTTCCCTGCT 1 1316 ( 335) TCCACCCCTCTCCATT 1 20821 ( 470) GCCTTCGTTTTTCGTC 1 5161 ( 69) TCCATCCATCCCAGCC 1 20868 ( 456) TCCATCTTTTTCTATC 1 24597 ( 224) TTCACCCTTTCCATTT 1 21583 ( 254) GCCTTCCATTGTCATC 1 8130 ( 219) TCCATCCGTTGTTGTT 1 260761 ( 129) GTCTTCCTCTCCCATT 1 19598 ( 372) TCCTTCTCTTTTAGTC 1 21053 ( 18) TTCTTCTATTGCCTTT 1 8295 ( 414) TCCCTCCTTCCCCAAC 1 25409 ( 178) TTCTTCGTTTCTCGGC 1 23596 ( 42) TCGATCCTTTCTCTCT 1 7233 ( 418) TTCTTTGTTCCTCATT 1 17673 ( 367) TTCTTCCTTTTAATTC 1 25814 ( 275) CCCCTCCCTTTCCGTT 1 4385 ( 428) TCCATTCGTCGTAATC 1 269866 ( 469) TTCACCGCTCTCATTT 1 3108 ( 439) TTCATCCTCCCCGTCT 1 263081 ( 269) GCCTTCTGCCGCCACC 1 10371 ( 451) TCAACCTCTTCTCACC 1 262193 ( 356) GTCTCTCTTCTCTGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 14550 bayes= 10.3166 E= 9.0e-001 -1129 -256 -22 149 -1129 134 -1129 56 -270 196 -253 -1129 75 -156 -1129 83 -1129 -24 -1129 156 -1129 190 -1129 -117 -1129 144 -54 -44 -112 2 -95 94 -1129 -98 -1129 170 -1129 76 -1129 115 -1129 90 5 24 -270 114 -1129 70 -12 125 -253 -76 46 -1129 78 -17 -270 25 -253 124 -1129 102 -1129 94 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 25 E= 9.0e-001 0.000000 0.040000 0.200000 0.760000 0.000000 0.600000 0.000000 0.400000 0.040000 0.920000 0.040000 0.000000 0.440000 0.080000 0.000000 0.480000 0.000000 0.200000 0.000000 0.800000 0.000000 0.880000 0.000000 0.120000 0.000000 0.640000 0.160000 0.200000 0.120000 0.240000 0.120000 0.520000 0.000000 0.120000 0.000000 0.880000 0.000000 0.400000 0.000000 0.600000 0.000000 0.440000 0.240000 0.320000 0.040000 0.520000 0.000000 0.440000 0.240000 0.560000 0.040000 0.160000 0.360000 0.000000 0.400000 0.240000 0.040000 0.280000 0.040000 0.640000 0.000000 0.480000 0.000000 0.520000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TG][CT]C[TA][TC]C[CT][TC]T[TC][CTG][CT][CA][GAT][TC][TC] -------------------------------------------------------------------------------- Time 15.03 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 24 llr = 220 E-value = 3.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 173235:a8:52 pos.-specific C 9:28:3a::a36 probability G :2::41::2::1 matrix T :15:3:::::3: bits 2.1 * * 1.9 ** * 1.7 ** * 1.5 * ** * Relative 1.3 * * ** * Entropy 1.1 * * **** (13.2 bits) 0.8 ** * **** 0.6 ** * **** * 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CATCGACAACAC consensus GAAAC G CA sequence C T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 25409 418 1.21e-06 AGTTGGGCTA CATCTACAACCC TTCAACACTG 25814 489 1.44e-06 AACAAGAACA CATCGACAGCAC 4385 197 3.10e-06 CCATGAACGG CATCAACAGCAC TGAATCCGTT 21583 433 4.03e-06 GCAGAGGGGT CAAAGACAACAC AAGGTCATAG 3011 462 7.03e-06 GGGCAGCACA CAAAGCCAACAC CTGCGTACTG 10219 487 7.03e-06 GGTTCATTTC CAACGACAACCA CC 10128 447 7.03e-06 TCGTATCCTA CAACTACAGCAC AGCGTTCAGA 269866 258 1.00e-05 TTCGTCAGTT CATCTCCAACAG CTGATACACC 24597 140 1.29e-05 ACCATTGGAT CAACAGCAACAC GTTCAGCACG 21606 47 1.44e-05 CATAGACAGA CGACGACAACAA CTTACAATGA 1979 455 1.44e-05 TCACAACATA CACAGACAACTC TCTCCTCCAT 8295 401 1.60e-05 GGAATCCCAA CGCCGCCAACTC ATCCCTCCTT 17673 95 1.77e-05 ACGTGCTCAT CAAATACAACCC CGCCAACGGA 10371 29 1.77e-05 ATGCAGCAGC CTTCACCAACAC GGCAGGTGCA 21053 487 2.18e-05 CTCGTCGCAT CATCTCCAACTG AT 1316 436 2.89e-05 CAAACATCCC CATCAACAGCCA CTCCTACTGG 23596 107 4.87e-05 GATTGATCTC CTTCGACAGCTC AGCCATCTTG 10935 166 4.87e-05 CGATCTCACT CGTCGACAACAT TCTGATGGTC 263081 256 6.16e-05 CAATTTTTCA AACCACCAACCC TGCCTTCTGC 8130 179 6.67e-05 TTGTCACTTC CACCACCACCAC CACCACCTTC 7233 394 7.71e-05 GACGAACGGT CGCCTCCAACCA GTCTCATTGG 11048 461 9.45e-05 TCACATATAC CATCGTCAACTG TCGCCGCTGC 260761 115 1.22e-04 AGATGTGCAT AGTATACAACAC CCGTCTTCCT 20821 53 2.20e-04 GTGACGATCA AATCAGCAACTA TTCGACGTAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25409 1.2e-06 417_[+3]_71 25814 1.4e-06 488_[+3] 4385 3.1e-06 196_[+3]_292 21583 4e-06 432_[+3]_56 3011 7e-06 461_[+3]_27 10219 7e-06 486_[+3]_2 10128 7e-06 446_[+3]_42 269866 1e-05 257_[+3]_231 24597 1.3e-05 139_[+3]_349 21606 1.4e-05 46_[+3]_442 1979 1.4e-05 454_[+3]_34 8295 1.6e-05 400_[+3]_88 17673 1.8e-05 94_[+3]_394 10371 1.8e-05 28_[+3]_460 21053 2.2e-05 486_[+3]_2 1316 2.9e-05 435_[+3]_53 23596 4.9e-05 106_[+3]_382 10935 4.9e-05 165_[+3]_323 263081 6.2e-05 255_[+3]_233 8130 6.7e-05 178_[+3]_310 7233 7.7e-05 393_[+3]_95 11048 9.5e-05 460_[+3]_28 260761 0.00012 114_[+3]_374 20821 0.00022 52_[+3]_436 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=24 25409 ( 418) CATCTACAACCC 1 25814 ( 489) CATCGACAGCAC 1 4385 ( 197) CATCAACAGCAC 1 21583 ( 433) CAAAGACAACAC 1 3011 ( 462) CAAAGCCAACAC 1 10219 ( 487) CAACGACAACCA 1 10128 ( 447) CAACTACAGCAC 1 269866 ( 258) CATCTCCAACAG 1 24597 ( 140) CAACAGCAACAC 1 21606 ( 47) CGACGACAACAA 1 1979 ( 455) CACAGACAACTC 1 8295 ( 401) CGCCGCCAACTC 1 17673 ( 95) CAAATACAACCC 1 10371 ( 29) CTTCACCAACAC 1 21053 ( 487) CATCTCCAACTG 1 1316 ( 436) CATCAACAGCCA 1 23596 ( 107) CTTCGACAGCTC 1 10935 ( 166) CGTCGACAACAT 1 263081 ( 256) AACCACCAACCC 1 8130 ( 179) CACCACCACCAC 1 7233 ( 394) CGCCTCCAACCA 1 11048 ( 461) CATCGTCAACTG 1 260761 ( 115) AGTATACAACAC 1 20821 ( 53) AATCAGCAACTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 14670 bayes= 9.70135 E= 3.8e-001 -106 189 -1123 -1123 144 -1123 -16 -170 16 -18 -1123 88 -32 174 -1123 -1123 16 -1123 84 11 105 50 -148 -270 -1123 208 -1123 -1123 194 -1123 -1123 -1123 152 -250 -16 -1123 -1123 208 -1123 -1123 94 8 -1123 -11 -32 140 -89 -270 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 24 E= 3.8e-001 0.125000 0.875000 0.000000 0.000000 0.708333 0.000000 0.208333 0.083333 0.291667 0.208333 0.000000 0.500000 0.208333 0.791667 0.000000 0.000000 0.291667 0.000000 0.416667 0.291667 0.541667 0.333333 0.083333 0.041667 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.041667 0.208333 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.250000 0.000000 0.250000 0.208333 0.625000 0.125000 0.041667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[AG][TAC][CA][GAT][AC]CA[AG]C[ACT][CA] -------------------------------------------------------------------------------- Time 22.07 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10128 1.77e-02 446_[+3(7.03e-06)]_42 10219 4.02e-02 465_[+3(2.39e-05)]_9_[+3(7.03e-06)]_\ 2 10371 9.65e-05 28_[+3(1.77e-05)]_190_\ [+1(3.51e-06)]_254 10935 2.88e-02 165_[+3(4.87e-05)]_323 11048 9.24e-08 60_[+1(9.72e-07)]_100_\ [+2(3.45e-08)]_268_[+3(9.45e-05)]_28 1316 1.27e-05 35_[+1(1.81e-05)]_283_\ [+2(1.43e-06)]_85_[+3(2.89e-05)]_53 17673 6.11e-06 94_[+3(1.77e-05)]_141_\ [+1(8.77e-07)]_103_[+2(2.11e-05)]_118 19598 2.97e-03 371_[+2(4.21e-06)]_22_\ [+1(8.46e-05)]_75 1979 4.21e-05 302_[+2(1.27e-07)]_136_\ [+3(1.44e-05)]_5_[+2(4.52e-05)]_13 20821 5.46e-06 326_[+1(3.56e-05)]_2_[+1(5.78e-07)]_\ 109_[+2(2.36e-06)]_15 20868 8.74e-03 455_[+2(2.66e-06)]_29 21053 5.64e-06 17_[+2(9.49e-06)]_202_\ [+1(1.44e-06)]_235_[+3(2.18e-05)]_2 21308 2.93e-03 134_[+1(6.40e-07)]_350 21583 2.05e-04 253_[+2(3.36e-06)]_163_\ [+3(4.03e-06)]_37_[+3(3.16e-05)]_7 21606 1.75e-08 46_[+3(1.44e-05)]_25_[+1(4.27e-08)]_\ 118_[+1(9.15e-05)]_115_[+2(8.23e-07)]_136 23596 2.88e-03 41_[+2(1.50e-05)]_49_[+3(4.87e-05)]_\ 382 24597 1.28e-06 139_[+3(1.29e-05)]_30_\ [+1(1.31e-06)]_26_[+2(3.36e-06)]_261 25409 2.66e-06 128_[+1(7.09e-06)]_33_\ [+2(1.50e-05)]_224_[+3(1.21e-06)]_71 25814 1.08e-05 258_[+1(1.60e-05)]_[+2(2.68e-05)]_\ 198_[+3(1.44e-06)] 260761 1.24e-05 38_[+1(1.44e-06)]_74_[+2(4.21e-06)]_\ 356 262193 1.70e-01 500 263081 3.41e-02 255_[+3(6.16e-05)]_1_[+2(9.30e-05)]_\ 216 269866 4.26e-05 257_[+3(1.00e-05)]_120_\ [+1(6.11e-06)]_63_[+2(4.84e-05)]_16 3011 8.62e-07 84_[+1(2.64e-09)]_361_\ [+3(7.03e-06)]_27 3108 1.88e-01 438_[+2(6.79e-05)]_46 4385 1.04e-05 52_[+1(5.66e-06)]_128_\ [+3(3.10e-06)]_219_[+2(3.37e-05)]_57 5161 4.79e-04 68_[+2(2.66e-06)]_164_\ [+1(1.08e-05)]_236 7233 7.42e-05 346_[+1(5.77e-05)]_8_[+1(4.48e-06)]_\ 7_[+3(7.71e-05)]_12_[+2(1.63e-05)]_67 8130 3.93e-06 178_[+3(6.67e-05)]_28_\ [+2(4.21e-06)]_139_[+1(7.13e-07)]_111 8295 6.40e-08 157_[+1(9.53e-09)]_80_\ [+1(8.46e-05)]_131_[+3(1.60e-05)]_1_[+2(1.37e-05)]_71 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************