******************************************************************************** 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/13/13.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 1040 1.0000 500 10677 1.0000 500 14655 1.0000 500 1520 1.0000 500 16075 1.0000 500 16193 1.0000 500 18613 1.0000 500 20812 1.0000 500 21295 1.0000 500 21487 1.0000 500 21904 1.0000 500 23427 1.0000 500 23698 1.0000 500 23973 1.0000 500 25019 1.0000 500 25396 1.0000 500 25861 1.0000 500 261582 1.0000 500 263132 1.0000 500 264815 1.0000 500 2832 1.0000 500 3126 1.0000 500 31562 1.0000 500 31751 1.0000 500 33316 1.0000 500 37359 1.0000 500 37725 1.0000 500 39901 1.0000 500 4402 1.0000 500 5314 1.0000 500 5812 1.0000 500 937 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/13/13.seqs.fa -oc motifs/13 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 32 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 16000 N= 32 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.248 C 0.230 G 0.255 T 0.267 Background letter frequencies (from dataset with add-one prior applied): A 0.249 C 0.230 G 0.255 T 0.267 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 32 llr = 318 E-value = 2.1e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :35:47:32283:6:321243 pos.-specific C 821841a11813917245816 probability G :511:::21112:::112:2: matrix T 213212:46:12133432141 bits 2.1 1.9 * 1.7 * 1.5 * * Relative 1.3 * * * Entropy 1.1 * * * * * * (14.3 bits) 0.8 * * ** ** * * * * 0.6 * **** ** *** * * 0.4 * **** *** *** ** * 0.2 *********** ********* 0.0 --------------------- Multilevel CGACAACTTCAACACTCCCTC consensus AT CT AA C TTATG AA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 1040 319 2.05e-11 ACACAAAATC CGACAACATCAGCACACCCTC TCCCCTCCTC 5314 474 6.83e-08 CCATACTACC CAGCAACATCACCTCTTCCAA CATAAC 16193 468 5.68e-07 CCGTCCGAGT CGTCTACTTCGACTCTACCTC TACAATCCAA 21487 123 9.14e-07 TGAAAGTCAG CGTGCACATCAGCATACTCGC GATACTCGCG 16075 100 9.14e-07 TGAAAGTCAG CGTGCACATCAGCATACTCGC GATACTCGCG 21295 418 1.15e-06 TTCTTCACAT TGTTCCCGTCACCACACCCAC ACCCCTCCTC 4402 200 1.44e-06 GCTTCTCTCT CCTGAACAACAACACCTCCTA CGGTCGTAGC 31562 384 2.01e-06 CAACACACCG CAACACCGACACCACAACAAC GAACACCAAC 5812 277 2.49e-06 CTTTTCGGTG TATCATCGTCATCTCTTGCTC TTGCTAACCC 25396 464 2.77e-06 CTCTCGTCCT CGACAACTTCAATACACACCA AACAACAATC 39901 399 3.08e-06 TCTCCTCCTC CCACAACCACCACACGTGCAC CATGTTCGCC 3126 252 3.79e-06 TGCATTGTAC CAACAACTTGATCATTTCATA ACGTTAAATG 23427 476 3.79e-06 GACAATCGAC CGATTTCATCACCCCTCCATC AACG 37359 196 4.65e-06 AACCGCTTCG CCTCCACTTGAACTTCTGCTC CATATTTGAC 1520 457 5.67e-06 TAACACACAA CAACACCGTCAGTACCACCAC CAACACTGGC 21904 239 6.26e-06 GAGAAAGCGG CGACCACCTCAGCTGTTCAGC GAGGTGCGTC 23698 74 7.60e-06 GTCAACGAAT CGCTAACATCGACACTGTCAC TGCTGCAAGC 31751 119 1.22e-05 ACGTTGGATT TTACCACTAAACCACTGGCGC GTTGGCCAAG 261582 119 1.22e-05 ACGTTGGATT TTACCACTAAACCACTGGCGC GTTGGCCAAG 25861 473 1.22e-05 CCATCCTCTC CTATCACCGCAACCCATCCAA ATTCACC 33316 474 1.33e-05 TTTGAGCGGC GCCCCACGACACCCCACCCTC TGCACC 2832 98 1.46e-05 GACGATGACG CATCATCAGCATCATGTCCAT CGCCAGCACG 23973 398 1.60e-05 GACGTGGACA CGCCCTCTCACACTCACCCAC CCCCGTTGCA 25019 426 1.91e-05 TCACGAAACA CTGCAACTCCATCTCACTCAT CGGTGCATCA 20812 414 2.47e-05 CCTTCACTTG CGTTTACTTCAACTTTACGTC AGAGAAGGCG 937 93 2.69e-05 CAGGCAAACT CAACCTCTGAACCATCCCTTC CAAATACGGA 14655 371 4.07e-05 GGGAAGATTC CCGCCACTTCTTGACCCCCTA ACAAAATCGG 18613 68 5.60e-05 TCGTCGCCGT CGACCACTTCTGCTTTCGTCA GCCCCAATCA 263132 446 6.05e-05 AGCTTCCCCC CACCTTCCTCCACACAAGCAA ACTCGACTCC 10677 428 6.05e-05 TCAATCAACG CGACCACTACATTCTTTACAT TGCACAGTCG 264815 360 6.54e-05 CAGCGTCGGT TGTCATGATCACCACGGTCTC ATCAGAAGAT 37725 390 2.20e-04 TAGCGAGAAA TGACAACATATTCTCGCTATT ACCATGTGAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1040 2.1e-11 318_[+1]_161 5314 6.8e-08 473_[+1]_6 16193 5.7e-07 467_[+1]_12 21487 9.1e-07 122_[+1]_357 16075 9.1e-07 99_[+1]_380 21295 1.2e-06 417_[+1]_62 4402 1.4e-06 199_[+1]_280 31562 2e-06 383_[+1]_96 5812 2.5e-06 276_[+1]_203 25396 2.8e-06 463_[+1]_16 39901 3.1e-06 398_[+1]_81 3126 3.8e-06 251_[+1]_228 23427 3.8e-06 475_[+1]_4 37359 4.6e-06 195_[+1]_284 1520 5.7e-06 456_[+1]_23 21904 6.3e-06 238_[+1]_241 23698 7.6e-06 73_[+1]_406 31751 1.2e-05 118_[+1]_361 261582 1.2e-05 118_[+1]_361 25861 1.2e-05 472_[+1]_7 33316 1.3e-05 473_[+1]_6 2832 1.5e-05 97_[+1]_382 23973 1.6e-05 397_[+1]_82 25019 1.9e-05 425_[+1]_54 20812 2.5e-05 413_[+1]_66 937 2.7e-05 92_[+1]_387 14655 4.1e-05 370_[+1]_109 18613 5.6e-05 67_[+1]_412 263132 6.1e-05 445_[+1]_34 10677 6.1e-05 427_[+1]_52 264815 6.5e-05 359_[+1]_120 37725 0.00022 389_[+1]_90 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=32 1040 ( 319) CGACAACATCAGCACACCCTC 1 5314 ( 474) CAGCAACATCACCTCTTCCAA 1 16193 ( 468) CGTCTACTTCGACTCTACCTC 1 21487 ( 123) CGTGCACATCAGCATACTCGC 1 16075 ( 100) CGTGCACATCAGCATACTCGC 1 21295 ( 418) TGTTCCCGTCACCACACCCAC 1 4402 ( 200) CCTGAACAACAACACCTCCTA 1 31562 ( 384) CAACACCGACACCACAACAAC 1 5812 ( 277) TATCATCGTCATCTCTTGCTC 1 25396 ( 464) CGACAACTTCAATACACACCA 1 39901 ( 399) CCACAACCACCACACGTGCAC 1 3126 ( 252) CAACAACTTGATCATTTCATA 1 23427 ( 476) CGATTTCATCACCCCTCCATC 1 37359 ( 196) CCTCCACTTGAACTTCTGCTC 1 1520 ( 457) CAACACCGTCAGTACCACCAC 1 21904 ( 239) CGACCACCTCAGCTGTTCAGC 1 23698 ( 74) CGCTAACATCGACACTGTCAC 1 31751 ( 119) TTACCACTAAACCACTGGCGC 1 261582 ( 119) TTACCACTAAACCACTGGCGC 1 25861 ( 473) CTATCACCGCAACCCATCCAA 1 33316 ( 474) GCCCCACGACACCCCACCCTC 1 2832 ( 98) CATCATCAGCATCATGTCCAT 1 23973 ( 398) CGCCCTCTCACACTCACCCAC 1 25019 ( 426) CTGCAACTCCATCTCACTCAT 1 20812 ( 414) CGTTTACTTCAACTTTACGTC 1 937 ( 93) CAACCTCTGAACCATCCCTTC 1 14655 ( 371) CCGCCACTTCTTGACCCCCTA 1 18613 ( 68) CGACCACTTCTGCTTTCGTCA 1 263132 ( 446) CACCTTCCTCCACACAAGCAA 1 10677 ( 428) CGACCACTACATTCTTTACAT 1 264815 ( 360) TGTCATGATCACCACGGTCTC 1 37725 ( 390) TGACAACATATTCTCGCTATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 15360 bayes= 8.90388 E= 2.1e-008 -1164 176 -302 -51 1 -56 88 -109 92 -88 -144 23 -1164 171 -144 -77 82 93 -1164 -109 147 -129 -1164 -29 -1164 207 -302 -1164 33 -88 -71 61 -18 -188 -144 123 -67 176 -203 -1164 159 -129 -203 -151 33 29 -44 -29 -1164 193 -302 -151 118 -88 -1164 23 -1164 158 -302 8 47 -56 -103 49 -67 82 -103 23 -199 121 -22 -51 -67 171 -302 -209 59 -188 -71 61 1 144 -1164 -109 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 32 E= 2.1e-008 0.000000 0.781250 0.031250 0.187500 0.250000 0.156250 0.468750 0.125000 0.468750 0.125000 0.093750 0.312500 0.000000 0.750000 0.093750 0.156250 0.437500 0.437500 0.000000 0.125000 0.687500 0.093750 0.000000 0.218750 0.000000 0.968750 0.031250 0.000000 0.312500 0.125000 0.156250 0.406250 0.218750 0.062500 0.093750 0.625000 0.156250 0.781250 0.062500 0.000000 0.750000 0.093750 0.062500 0.093750 0.312500 0.281250 0.187500 0.218750 0.000000 0.875000 0.031250 0.093750 0.562500 0.125000 0.000000 0.312500 0.000000 0.687500 0.031250 0.281250 0.343750 0.156250 0.125000 0.375000 0.156250 0.406250 0.125000 0.312500 0.062500 0.531250 0.218750 0.187500 0.156250 0.750000 0.031250 0.062500 0.375000 0.062500 0.156250 0.406250 0.250000 0.625000 0.000000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[GA][AT]C[AC][AT]C[TA][TA]CA[ACT]C[AT][CT][TA][CT][CG]C[TA][CA] -------------------------------------------------------------------------------- Time 9.91 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 32 llr = 290 E-value = 1.8e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 23727:341143:833 pos.-specific C :13:14::4:::212: probability G 86:81366295181:8 matrix T ::1:121:3:16:14: bits 2.1 1.9 1.7 1.5 Relative 1.3 * * * * Entropy 1.1 * * * * * * (13.1 bits) 0.8 * * ** * ** * 0.6 ***** ** ** ** * 0.4 ******** ******* 0.2 **************** 0.0 ---------------- Multilevel GGAGACGGCGGTGATG consensus AAC GAAT AAC AA sequence T G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 37725 122 1.88e-09 CTGCGAGGAG GGAGAGGGCGGTGATG AACTTCATTT 1520 97 1.61e-07 CGTGTGCGAT GAAGAGAGTGGTGATG TAATGGATAG 4402 81 3.18e-07 GAGGGCAATG GGCGACGGGGGAGAAG GTAGCACATG 31751 396 5.94e-07 CTCTCCTCAA GGAGACGATGAAGAAA GCTTGCCAAT 261582 396 5.94e-07 CTCTCCTCAA GGAGACGATGAAGAAA GCTTGCCAAT 33316 89 3.81e-06 GATCGATCCT GCAGTGGACGATGATG ATGTAGAGGA 25396 83 4.30e-06 CAGACGCGAT GGTGACGGCGATGACA CATGATTGAG 21487 220 5.41e-06 TGTTGGTTGT GGAGCCAGTGTTGATG AATGAAATGA 16075 197 5.41e-06 TGTTGGTTGT GGAGCCAGTGTTGATG AATGAAATGA 1040 174 5.41e-06 AGAGAAGGAG GGAGGGAGGGGTGAAG GTCGCAGGAG 937 199 6.05e-06 GTTTGAAATG GAAATGGGCGGTGATG TCGGCGTAGT 37359 354 6.05e-06 CATGTCGGGC GGAGCCGGCGGTGCTG CTCAACCCGA 264815 385 6.77e-06 GGTCTCATCA GAAGATGGGAGTGAAG ATTGGTTGTT 21295 103 1.16e-05 TGCCCATGGC GCAGAGGATGGACACG GCAAGGGCGA 5812 89 1.28e-05 AGTAGCAGCG GCCGAGGACGAGGAAG CGTTTTGTCG 16193 74 1.56e-05 CGGTACGCGC GACGACGACGACGACG GCCACCTTCA 21904 130 2.53e-05 GTGGAAGAGA AGAGGTGGTGGAGAAG GTGATAAACG 31562 279 2.77e-05 GATGAAGAGA AGAGAGAGAGAGGAAG GAGGGGGGGG 2832 82 3.32e-05 ACTTGTTCTC TCAGAGGACGATGACG CATCATCAGC 5314 89 3.96e-05 AGGGAATAGT AAAGATGGCGAACACA TTCAACAATT 23698 274 5.12e-05 TGCGAGTACA AGAGTTGAGGGTGACA TACTCCTTGA 25861 213 5.56e-05 TGTAAATTTG GGAGAGGGGGGGGGCA GATACAGAGT 20812 52 7.68e-05 TGATATGCAT GATGACGGCGTTGTTG GATGGTGCTC 263132 255 8.98e-05 TAGCGTTCGT AGGAACAGTGATGATG TGCAATTGCA 23427 107 8.98e-05 GGAAGAAGCA GACGACGAGGTTCGTG TTCGTGACAC 14655 32 1.13e-04 AGGCTTGCAC GGAGAGTAGAGTCAAG GCAGCGAGAA 10677 366 1.13e-04 ACATCAGCAT GGCAACAGTGGTCCAG AGTAGCTGGA 23973 109 1.21e-04 GAAGCACATA AACGACAAAAATGATG AACAGTCGTC 25019 238 1.50e-04 CTCCCTAAAT GGCAATAAAGGACATG CACTTATCCC 39901 178 1.85e-04 GTTTCGCCGT AAAGATAACGAAGTTA TGCTGTGATG 3126 183 1.85e-04 GTCTTCGCTT GACGACTGTGAAGGTA TACGAGTGAT 18613 162 3.72e-04 AGCGATCAAT GGAATTGGCTGTCAAG AGATCTCCTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37725 1.9e-09 121_[+2]_363 1520 1.6e-07 96_[+2]_388 4402 3.2e-07 80_[+2]_404 31751 5.9e-07 395_[+2]_89 261582 5.9e-07 395_[+2]_89 33316 3.8e-06 88_[+2]_396 25396 4.3e-06 82_[+2]_402 21487 5.4e-06 219_[+2]_265 16075 5.4e-06 196_[+2]_288 1040 5.4e-06 173_[+2]_311 937 6.1e-06 198_[+2]_286 37359 6.1e-06 353_[+2]_131 264815 6.8e-06 384_[+2]_100 21295 1.2e-05 102_[+2]_382 5812 1.3e-05 88_[+2]_396 16193 1.6e-05 73_[+2]_411 21904 2.5e-05 129_[+2]_355 31562 2.8e-05 278_[+2]_206 2832 3.3e-05 81_[+2]_403 5314 4e-05 88_[+2]_396 23698 5.1e-05 273_[+2]_211 25861 5.6e-05 212_[+2]_272 20812 7.7e-05 51_[+2]_433 263132 9e-05 254_[+2]_230 23427 9e-05 106_[+2]_378 14655 0.00011 31_[+2]_453 10677 0.00011 365_[+2]_119 23973 0.00012 108_[+2]_376 25019 0.00015 237_[+2]_247 39901 0.00019 177_[+2]_307 3126 0.00019 182_[+2]_302 18613 0.00037 161_[+2]_323 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=32 37725 ( 122) GGAGAGGGCGGTGATG 1 1520 ( 97) GAAGAGAGTGGTGATG 1 4402 ( 81) GGCGACGGGGGAGAAG 1 31751 ( 396) GGAGACGATGAAGAAA 1 261582 ( 396) GGAGACGATGAAGAAA 1 33316 ( 89) GCAGTGGACGATGATG 1 25396 ( 83) GGTGACGGCGATGACA 1 21487 ( 220) GGAGCCAGTGTTGATG 1 16075 ( 197) GGAGCCAGTGTTGATG 1 1040 ( 174) GGAGGGAGGGGTGAAG 1 937 ( 199) GAAATGGGCGGTGATG 1 37359 ( 354) GGAGCCGGCGGTGCTG 1 264815 ( 385) GAAGATGGGAGTGAAG 1 21295 ( 103) GCAGAGGATGGACACG 1 5812 ( 89) GCCGAGGACGAGGAAG 1 16193 ( 74) GACGACGACGACGACG 1 21904 ( 130) AGAGGTGGTGGAGAAG 1 31562 ( 279) AGAGAGAGAGAGGAAG 1 2832 ( 82) TCAGAGGACGATGACG 1 5314 ( 89) AAAGATGGCGAACACA 1 23698 ( 274) AGAGTTGAGGGTGACA 1 25861 ( 213) GGAGAGGGGGGGGGCA 1 20812 ( 52) GATGACGGCGTTGTTG 1 263132 ( 255) AGGAACAGTGATGATG 1 23427 ( 107) GACGACGAGGTTCGTG 1 14655 ( 32) GGAGAGTAGAGTCAAG 1 10677 ( 366) GGCAACAGTGGTCCAG 1 23973 ( 109) AACGACAAAAATGATG 1 25019 ( 238) GGCAATAAAGGACATG 1 39901 ( 178) AAAGATAACGAAGTTA 1 3126 ( 183) GACGACTGTGAAGGTA 1 18613 ( 162) GGAATTGGCTGTCAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 15520 bayes= 8.91886 E= 1.8e-004 -18 -1164 156 -309 33 -88 114 -1164 140 12 -302 -209 -67 -1164 173 -1164 153 -129 -203 -109 -1164 93 43 -29 33 -1164 129 -209 71 -1164 122 -1164 -141 71 -22 23 -141 -1164 178 -309 71 -1164 88 -109 18 -288 -144 115 -1164 -7 162 -1164 165 -188 -144 -209 47 -7 -1164 71 1 -1164 156 -1164 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 32 E= 1.8e-004 0.218750 0.000000 0.750000 0.031250 0.312500 0.125000 0.562500 0.000000 0.656250 0.250000 0.031250 0.062500 0.156250 0.000000 0.843750 0.000000 0.718750 0.093750 0.062500 0.125000 0.000000 0.437500 0.343750 0.218750 0.312500 0.000000 0.625000 0.062500 0.406250 0.000000 0.593750 0.000000 0.093750 0.375000 0.218750 0.312500 0.093750 0.000000 0.875000 0.031250 0.406250 0.000000 0.468750 0.125000 0.281250 0.031250 0.093750 0.593750 0.000000 0.218750 0.781250 0.000000 0.781250 0.062500 0.093750 0.062500 0.343750 0.218750 0.000000 0.437500 0.250000 0.000000 0.750000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA][GA][AC]GA[CGT][GA][GA][CTG]G[GA][TA][GC]A[TAC][GA] -------------------------------------------------------------------------------- Time 19.17 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 32 llr = 307 E-value = 2.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:22:26::3:333:1322:: pos.-specific C 11:14121::::1::3221:2 probability G :57:27:68:86516543383 matrix T 84184:2327221541:4525 bits 2.1 1.9 1.7 1.5 Relative 1.3 * * Entropy 1.1 * * * (13.9 bits) 0.8 * * *** * * 0.6 **** ******* * * 0.4 ***************** ** 0.2 ***************** *** 0.0 --------------------- Multilevel TGGTTGAGGTGGGTGGGTTGT consensus TA C T A AAATCAGG G sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 25019 139 3.21e-10 CAGTCGCTCG TTGTTGAGGTGAGTGGATTGT TCGTGTACTA 1520 247 1.28e-07 TTCGGTTCTT TCGTCGATGTGGGTGAGTGGG ATTAGGGCCG 21487 192 3.47e-07 CCCCTCGATC TGTTGGAGGAGGATGGCATGT TGGTTGTGGA 16075 169 3.47e-07 CCCCTCGATC TGTTGGAGGAGGATGGCATGT TGGTTGTGGA 263132 303 6.68e-07 ATGACTTGGA TTGTTACGGTTGGTTCGTTGT TCGTTGATTT 33316 201 7.58e-07 TGCAAATGTG TGGTTGATGTGATGGCATGGT GATGAGTAGT 21904 191 1.24e-06 CGAATGCTTT TGATGGCTGTGGGAGCGGAGG CGAGAGGAGG 937 151 1.39e-06 TTCTAGATAT TTGTCGAGGATGGATCGTAGC CTTGACAGTG 5812 343 2.76e-06 CGAGCGTCGT TGGTCGAGGAGGAAGGTGGTT GTCAGGAGAC 264815 51 3.82e-06 GGTCTCCCGT TGGATGAGGACGAAGGAGGGT CTTGGCGGCC 20812 125 3.82e-06 GGCGCTGTTG TTGACGATGAGACTGGCTGGG CTCTTCCTCT 31562 201 5.22e-06 GAGCTCAGTA TTAATGCGGTGGAAGCGGAGC TGAGTACTTT 4402 329 5.78e-06 ACATAGCCAG AGATCAAGGTTGGTTGATGGT GTTGGTGTAC 3126 442 5.78e-06 ATTTTCATTT TCGTCGAGGCGAAAGCCTTGG TGCTGAAAAG 21295 307 5.78e-06 GTGTAGTGAG TTGTCGAGTTGTTGTGGTTGT CTTTCTCACA 23698 241 6.40e-06 TTCAAGATAG TGAACGACGTGAGAGAATTGT TCTGCGAGTA 37725 79 7.81e-06 GGGGTGGATT TGGTGAAGGAGGAGGGGGTGA AGGCAGAGGC 5314 166 1.51e-05 GGAACTCGTG TCGTCTCGGAGGATTCCTTGT CGTGGATGTA 25396 279 1.51e-05 ACGTTGCAAG AGGTTGAGGAGAGAGAGCCGG GGAGAAAAGG 23427 204 1.51e-05 TTGTACTTAG CGTTGGATGTGTATGGGATGT TTAATTGATA 14655 5 1.66e-05 CGAA TTGTTGAGTTGAGGGAAAGGC TTGCACGGAG 2832 384 2.16e-05 TGCTGTGCTT TGTTCGATGTGTGATCGCCGC CGCAAGTTAT 37359 1 2.57e-05 . TGGTGGTGGTGGGCCGGGGGG GGGGGGGCTC 10677 222 2.80e-05 CTGGCCCGTG TGGTTACCGTGAGTTGAGTTG GGCCTTAGGG 18613 128 4.58e-05 CTTGATACCA ATGTGAATGTGAGAGGGAGTG AGAAGCGATC 23973 130 1.05e-04 TGATGAACAG TCGTCAAGTATGGTGGACTTG ATCGTTTCAC 31751 299 1.12e-04 ATCCTTGGGG TTACTCTTGTGGCTTCAGTGT TATTACCAGC 261582 299 1.12e-04 ATCCTTGGGG TTACTCTTGTGGCTTCAGTGT TATTACCAGC 16193 40 1.12e-04 GTCGTTTGAG CGGTTGCTGTTGGTTTCGTGC TCACGGTACG 25861 11 1.48e-04 CATTGGCAGA GTGTCGTGTTGTGTGCCCAGT GGAGACTGCC 1040 48 1.58e-04 CGTTGGCTGC TGAATCTGTTGTATTGGCGGT ATTGGTGCTG 39901 113 5.23e-04 TTTGGTGAAC ATGATGTTGTGGTATTGTATT CTATTCTGCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 25019 3.2e-10 138_[+3]_341 1520 1.3e-07 246_[+3]_233 21487 3.5e-07 191_[+3]_288 16075 3.5e-07 168_[+3]_311 263132 6.7e-07 302_[+3]_177 33316 7.6e-07 200_[+3]_279 21904 1.2e-06 190_[+3]_289 937 1.4e-06 150_[+3]_329 5812 2.8e-06 342_[+3]_137 264815 3.8e-06 50_[+3]_429 20812 3.8e-06 124_[+3]_355 31562 5.2e-06 200_[+3]_279 4402 5.8e-06 328_[+3]_151 3126 5.8e-06 441_[+3]_38 21295 5.8e-06 306_[+3]_173 23698 6.4e-06 240_[+3]_239 37725 7.8e-06 78_[+3]_401 5314 1.5e-05 165_[+3]_314 25396 1.5e-05 278_[+3]_201 23427 1.5e-05 203_[+3]_276 14655 1.7e-05 4_[+3]_475 2832 2.2e-05 383_[+3]_96 37359 2.6e-05 [+3]_479 10677 2.8e-05 221_[+3]_258 18613 4.6e-05 127_[+3]_352 23973 0.0001 129_[+3]_350 31751 0.00011 298_[+3]_181 261582 0.00011 298_[+3]_181 16193 0.00011 39_[+3]_440 25861 0.00015 10_[+3]_469 1040 0.00016 47_[+3]_432 39901 0.00052 112_[+3]_367 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=32 25019 ( 139) TTGTTGAGGTGAGTGGATTGT 1 1520 ( 247) TCGTCGATGTGGGTGAGTGGG 1 21487 ( 192) TGTTGGAGGAGGATGGCATGT 1 16075 ( 169) TGTTGGAGGAGGATGGCATGT 1 263132 ( 303) TTGTTACGGTTGGTTCGTTGT 1 33316 ( 201) TGGTTGATGTGATGGCATGGT 1 21904 ( 191) TGATGGCTGTGGGAGCGGAGG 1 937 ( 151) TTGTCGAGGATGGATCGTAGC 1 5812 ( 343) TGGTCGAGGAGGAAGGTGGTT 1 264815 ( 51) TGGATGAGGACGAAGGAGGGT 1 20812 ( 125) TTGACGATGAGACTGGCTGGG 1 31562 ( 201) TTAATGCGGTGGAAGCGGAGC 1 4402 ( 329) AGATCAAGGTTGGTTGATGGT 1 3126 ( 442) TCGTCGAGGCGAAAGCCTTGG 1 21295 ( 307) TTGTCGAGTTGTTGTGGTTGT 1 23698 ( 241) TGAACGACGTGAGAGAATTGT 1 37725 ( 79) TGGTGAAGGAGGAGGGGGTGA 1 5314 ( 166) TCGTCTCGGAGGATTCCTTGT 1 25396 ( 279) AGGTTGAGGAGAGAGAGCCGG 1 23427 ( 204) CGTTGGATGTGTATGGGATGT 1 14655 ( 5) TTGTTGAGTTGAGGGAAAGGC 1 2832 ( 384) TGTTCGATGTGTGATCGCCGC 1 37359 ( 1) TGGTGGTGGTGGGCCGGGGGG 1 10677 ( 222) TGGTTACCGTGAGTTGAGTTG 1 18613 ( 128) ATGTGAATGTGAGAGGGAGTG 1 23973 ( 130) TCGTCAAGTATGGTGGACTTG 1 31751 ( 299) TTACTCTTGTGGCTTCAGTGT 1 261582 ( 299) TTACTCTTGTGGCTTCAGTGT 1 16193 ( 40) CGGTTGCTGTTGGTTTCGTGC 1 25861 ( 11) GTGTCGTGTTGTGTGCCCAGT 1 1040 ( 48) TGAATCTGTTGTATTGGCGGT 1 39901 ( 113) ATGATGTTGTGGTATTGTATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 15360 bayes= 8.90388 E= 2.5e-002 -99 -188 -302 155 -1164 -88 97 49 -18 -1164 136 -109 -41 -188 -1164 149 -1164 71 -22 61 -41 -129 143 -309 133 -29 -1164 -51 -1164 -188 122 37 -1164 -1164 173 -77 33 -288 -1164 130 -1164 -288 167 -77 18 -1164 114 -77 33 -129 97 -151 47 -288 -103 91 -1164 -288 122 49 -99 58 88 -209 33 -7 78 -309 -67 -56 29 49 -67 -188 29 81 -1164 -1164 173 -77 -299 -56 14 99 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 32 E= 2.5e-002 0.125000 0.062500 0.031250 0.781250 0.000000 0.125000 0.500000 0.375000 0.218750 0.000000 0.656250 0.125000 0.187500 0.062500 0.000000 0.750000 0.000000 0.375000 0.218750 0.406250 0.187500 0.093750 0.687500 0.031250 0.625000 0.187500 0.000000 0.187500 0.000000 0.062500 0.593750 0.343750 0.000000 0.000000 0.843750 0.156250 0.312500 0.031250 0.000000 0.656250 0.000000 0.031250 0.812500 0.156250 0.281250 0.000000 0.562500 0.156250 0.312500 0.093750 0.500000 0.093750 0.343750 0.031250 0.125000 0.500000 0.000000 0.031250 0.593750 0.375000 0.125000 0.343750 0.468750 0.062500 0.312500 0.218750 0.437500 0.031250 0.156250 0.156250 0.312500 0.375000 0.156250 0.062500 0.312500 0.468750 0.000000 0.000000 0.843750 0.156250 0.031250 0.156250 0.281250 0.531250 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[GT][GA]T[TCG]GA[GT]G[TA]G[GA][GA][TA][GT][GC][GAC][TG][TG]G[TG] -------------------------------------------------------------------------------- Time 27.25 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 1040 7.39e-10 173_[+2(5.41e-06)]_129_\ [+1(2.05e-11)]_161 10677 1.43e-03 221_[+3(2.80e-05)]_185_\ [+1(6.05e-05)]_52 14655 6.64e-04 4_[+3(1.66e-05)]_345_[+1(4.07e-05)]_\ 109 1520 4.44e-09 96_[+2(1.61e-07)]_134_\ [+3(1.28e-07)]_189_[+1(5.67e-06)]_23 16075 5.24e-08 99_[+1(9.14e-07)]_48_[+3(3.47e-07)]_\ 7_[+2(5.41e-06)]_225_[+1(5.18e-05)]_42 16193 1.57e-05 73_[+2(1.56e-05)]_378_\ [+1(5.68e-07)]_12 18613 5.06e-03 67_[+1(5.60e-05)]_39_[+3(4.58e-05)]_\ 352 20812 8.99e-05 51_[+2(7.68e-05)]_57_[+3(3.82e-06)]_\ 268_[+1(2.47e-05)]_66 21295 1.65e-06 12_[+1(7.61e-05)]_69_[+2(1.16e-05)]_\ 188_[+3(5.78e-06)]_90_[+1(1.15e-06)]_62 21487 5.24e-08 122_[+1(9.14e-07)]_48_\ [+3(3.47e-07)]_7_[+2(5.41e-06)]_225_[+1(5.18e-05)]_19 21904 3.78e-06 129_[+2(2.53e-05)]_45_\ [+3(1.24e-06)]_27_[+1(6.26e-06)]_86_[+3(5.79e-05)]_134 23427 6.68e-05 106_[+2(8.98e-05)]_81_\ [+3(1.51e-05)]_251_[+1(3.79e-06)]_4 23698 3.57e-05 73_[+1(7.60e-06)]_146_\ [+3(6.40e-06)]_12_[+2(5.12e-05)]_211 23973 1.48e-03 397_[+1(1.60e-05)]_82 25019 2.86e-08 138_[+3(3.21e-10)]_266_\ [+1(1.91e-05)]_54 25396 3.53e-06 82_[+2(4.30e-06)]_6_[+2(3.03e-05)]_\ 158_[+3(1.51e-05)]_164_[+1(2.77e-06)]_16 25861 8.28e-04 212_[+2(5.56e-05)]_244_\ [+1(1.22e-05)]_7 261582 1.31e-05 118_[+1(1.22e-05)]_256_\ [+2(5.94e-07)]_89 263132 4.88e-05 176_[+3(6.25e-05)]_57_\ [+2(8.98e-05)]_32_[+3(6.68e-07)]_122_[+1(6.05e-05)]_34 264815 2.53e-05 50_[+3(3.82e-06)]_288_\ [+1(6.54e-05)]_4_[+2(6.77e-06)]_100 2832 1.25e-04 81_[+2(3.32e-05)]_[+1(1.46e-05)]_\ 265_[+3(2.16e-05)]_96 3126 5.32e-05 251_[+1(3.79e-06)]_169_\ [+3(5.78e-06)]_38 31562 5.39e-06 200_[+3(5.22e-06)]_57_\ [+2(2.77e-05)]_89_[+1(2.01e-06)]_96 31751 1.31e-05 118_[+1(1.22e-05)]_256_\ [+2(5.94e-07)]_89 33316 8.83e-07 88_[+2(3.81e-06)]_96_[+3(7.58e-07)]_\ 252_[+1(1.33e-05)]_6 37359 1.21e-05 [+3(2.57e-05)]_174_[+1(4.65e-06)]_\ 137_[+2(6.05e-06)]_131 37725 8.86e-08 78_[+3(7.81e-06)]_22_[+2(1.88e-09)]_\ 363 39901 1.87e-03 398_[+1(3.08e-06)]_50_\ [+1(4.78e-05)]_10 4402 7.82e-08 61_[+2(7.10e-05)]_3_[+2(3.18e-07)]_\ 103_[+1(1.44e-06)]_108_[+3(5.78e-06)]_151 5314 9.25e-07 88_[+2(3.96e-05)]_61_[+3(1.51e-05)]_\ 287_[+1(6.83e-08)]_6 5812 1.86e-06 88_[+2(1.28e-05)]_172_\ [+1(2.49e-06)]_45_[+3(2.76e-06)]_68_[+2(8.98e-05)]_53 937 4.32e-06 92_[+1(2.69e-05)]_37_[+3(1.39e-06)]_\ 27_[+2(6.05e-06)]_142_[+2(6.04e-05)]_128 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************