******************************************************************************** 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/172/172.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10963 1.0000 500 11189 1.0000 500 13117 1.0000 500 13156 1.0000 500 14028 1.0000 500 16737 1.0000 500 20920 1.0000 500 20922 1.0000 500 21948 1.0000 500 22844 1.0000 500 25754 1.0000 500 25944 1.0000 500 261981 1.0000 500 263219 1.0000 500 264674 1.0000 500 268844 1.0000 500 268868 1.0000 500 268904 1.0000 500 270017 1.0000 500 270048 1.0000 500 32491 1.0000 500 34773 1.0000 500 34968 1.0000 500 35624 1.0000 500 37054 1.0000 500 37974 1.0000 500 38813 1.0000 500 4168 1.0000 500 5573 1.0000 500 6121 1.0000 500 6729 1.0000 500 7840 1.0000 500 8784 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/172/172.seqs.fa -oc motifs/172 -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= 33 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= 16500 N= 33 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.266 C 0.234 G 0.242 T 0.258 Background letter frequencies (from dataset with add-one prior applied): A 0.266 C 0.234 G 0.242 T 0.258 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 17 llr = 227 E-value = 1.0e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::45::::2151::2:::211 pos.-specific C 2231:4::4:15112::41:: probability G :8329:1a1131392284287 matrix T 8::2169:48246:5822512 bits 2.1 * 1.9 * 1.7 * 1.5 * ** * Relative 1.3 ** * ** * ** * Entropy 1.0 ** **** * ** * (19.3 bits) 0.8 ** **** * ** ** ** 0.6 ** **** * *** ** ** 0.4 *** **** * *** ****** 0.2 ********************* 0.0 --------------------- Multilevel TGAAGTTGCTACTGTTGGTGG consensus CC C T GTG CG sequence G A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 20920 15 2.15e-09 CTGATGACGC TGCTGCTGCTGCTGCTGCTGG CTTTGCTTCT 270048 193 4.51e-09 TTAGATGTCG TGGAGTTGTTTGTGTTGGTGG TGGCAGATGA 268904 92 1.03e-08 TGGCAGCTGC TGATGTTGTTGTTGTTGTTGT TGTTGCTGGG 34773 425 1.33e-08 GTCGAAGCAC TGAAGTGGCTACGGTGGGTGG GTGTTGTTTG 263219 84 3.50e-08 AATTCGTCTT CGCCGCTGTTGCTGCTGCTGG TCGCTAGTAT 10963 16 3.93e-08 ACTGAACATC TGAGGTTGTTTTGGGTGCGGG GAAGCTGAAA 25754 190 9.34e-08 GATGAAGAGG TCCAGTTGATACTGATGGTTG TGCAGGCCGT 25944 109 1.40e-07 TGACGGGGAG TGGAGTTGTAGATGTTGGAGG AATGAACAAT 6121 38 2.26e-07 GATGGTGTTG TCGCGTTGGTATGGTTGTTGG CTTTGGTATC 35624 211 4.60e-07 TCAACGTTGA TGGAGTTGCGATTGCGTGGGG ATGGCGATGA 38813 29 5.91e-07 GAGAAGAACA TCCATCTGCTACTCTGGGTGG TGGTATCGGT 11189 220 6.41e-07 GTTGGCAATT TGAAGCTGAGACTGTTGTCAG TTGCTTTCGT 5573 382 1.60e-06 GTTGATGTCG CGGAGTTGCTTTGGATTCGGT TGGGTTGCGC 268868 20 1.60e-06 CTGATCAACG TGATGTTGCTCCTCTTTCTGA TCAGATGGCG 22844 202 1.72e-06 GGAAGATTCA TGAGGTGGTTGCTGGTGCGAT AACCTCTAAC 16737 160 3.34e-06 ATCTTTTGGC CCAGGCTGATATCGATGGAGG TCTTATCGGA 14028 449 6.05e-06 GCTCGGCACA TGCATCTGAAACGGGTGTAGA TCGTCACCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20920 2.1e-09 14_[+1]_465 270048 4.5e-09 192_[+1]_287 268904 1e-08 91_[+1]_388 34773 1.3e-08 424_[+1]_55 263219 3.5e-08 83_[+1]_396 10963 3.9e-08 15_[+1]_464 25754 9.3e-08 189_[+1]_290 25944 1.4e-07 108_[+1]_371 6121 2.3e-07 37_[+1]_442 35624 4.6e-07 210_[+1]_269 38813 5.9e-07 28_[+1]_451 11189 6.4e-07 219_[+1]_260 5573 1.6e-06 381_[+1]_98 268868 1.6e-06 19_[+1]_460 22844 1.7e-06 201_[+1]_278 16737 3.3e-06 159_[+1]_320 14028 6e-06 448_[+1]_31 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=17 20920 ( 15) TGCTGCTGCTGCTGCTGCTGG 1 270048 ( 193) TGGAGTTGTTTGTGTTGGTGG 1 268904 ( 92) TGATGTTGTTGTTGTTGTTGT 1 34773 ( 425) TGAAGTGGCTACGGTGGGTGG 1 263219 ( 84) CGCCGCTGTTGCTGCTGCTGG 1 10963 ( 16) TGAGGTTGTTTTGGGTGCGGG 1 25754 ( 190) TCCAGTTGATACTGATGGTTG 1 25944 ( 109) TGGAGTTGTAGATGTTGGAGG 1 6121 ( 38) TCGCGTTGGTATGGTTGTTGG 1 35624 ( 211) TGGAGTTGCGATTGCGTGGGG 1 38813 ( 29) TCCATCTGCTACTCTGGGTGG 1 11189 ( 220) TGAAGCTGAGACTGTTGTCAG 1 5573 ( 382) CGGAGTTGCTTTGGATTCGGT 1 268868 ( 20) TGATGTTGCTCCTCTTTCTGA 1 22844 ( 202) TGAGGTGGTTGCTGGTGCGAT 1 16737 ( 160) CCAGGCTGATATCGATGGAGG 1 14028 ( 449) TGCATCTGAAACGGGTGTAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 15840 bayes= 10.6576 E= 1.0e-006 -1073 -41 -1073 168 -1073 0 166 -1073 63 33 28 -1073 99 -99 -46 -55 -1073 -1073 186 -113 -1073 59 -1073 133 -1073 -1073 -104 178 -1073 -1073 204 -1073 -18 59 -204 45 -117 -1073 -104 157 82 -199 28 -55 -217 117 -204 45 -1073 -199 28 133 -1073 -99 186 -1073 -59 -41 -46 87 -1073 -1073 -46 168 -1073 -1073 176 -55 -1073 59 77 -13 -59 -199 -4 104 -117 -1073 176 -213 -117 -1073 154 -55 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 17 E= 10.0e-007 0.000000 0.176471 0.000000 0.823529 0.000000 0.235294 0.764706 0.000000 0.411765 0.294118 0.294118 0.000000 0.529412 0.117647 0.176471 0.176471 0.000000 0.000000 0.882353 0.117647 0.000000 0.352941 0.000000 0.647059 0.000000 0.000000 0.117647 0.882353 0.000000 0.000000 1.000000 0.000000 0.235294 0.352941 0.058824 0.352941 0.117647 0.000000 0.117647 0.764706 0.470588 0.058824 0.294118 0.176471 0.058824 0.529412 0.058824 0.352941 0.000000 0.058824 0.294118 0.647059 0.000000 0.117647 0.882353 0.000000 0.176471 0.176471 0.176471 0.470588 0.000000 0.000000 0.176471 0.823529 0.000000 0.000000 0.823529 0.176471 0.000000 0.352941 0.411765 0.235294 0.176471 0.058824 0.235294 0.529412 0.117647 0.000000 0.823529 0.058824 0.117647 0.000000 0.705882 0.176471 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[GC][ACG]AG[TC]TG[CTA]T[AG][CT][TG]GTTG[GCT][TG]GG -------------------------------------------------------------------------------- Time 9.55 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 16 sites = 33 llr = 297 E-value = 1.1e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 264273:841281231 pos.-specific C 5:68:69168217538 probability G 2:1:21::1:61:221 matrix T :4::1:12:2::222: bits 2.1 1.9 1.7 1.5 * * Relative 1.3 * * * Entropy 1.0 * * * * * (13.0 bits) 0.8 *** **** ** * 0.6 ************* * 0.4 ************* * 0.2 ************** * 0.0 ---------------- Multilevel CACCACCACCGACCAC consensus GTA A A A T C sequence A G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 270017 203 2.79e-09 TACTCTTCTC CAACACCACCGACCGC CGTCGGTCCT 6121 477 6.21e-08 ACCAACCGTA CACCAACACCAACCGC AACCAACA 34968 396 2.02e-07 CTTGCAGAGC CTCCACCTCCGACTAC ATGGAAGTGT 35624 181 8.74e-07 GTCGGTAGTG GTACACCAACGACGTC GTCATCAACG 22844 416 1.90e-06 AAGACAGACA CAACAACAACAACAAC AACACAACAA 37974 155 2.15e-06 GCCACCTCCG CTCAACCACCGGCCCC TCCTCTTGAG 14028 80 5.49e-06 CCACCATTTC ATCCAACAACGACCCA ACCGGCGAAG 37054 78 6.13e-06 GAATCTTCGA GACAACCACTAACCAC ACAGAACACC 263219 447 6.13e-06 TTGCCCACAT ATCCAGCCCCGACCCC TGGCTACACC 13117 168 6.13e-06 AGGATGCCAC CACCGCCACCGAACAA GTATGCAAAG 264674 387 6.85e-06 ACGAAGCTCT CAACACTACCGAAGCC AAGTCTACCA 25754 434 6.85e-06 CCAGCCCCTC CCCCGCCACCAACCTC GAACGTCTTC 21948 253 8.48e-06 TCAAGTCAAG GACCAACAACGACGAG GCAGAACATA 34773 76 9.42e-06 ACAAACACAA GTCCACCAACGGCAGC GAACGATTCT 261981 443 1.16e-05 AACGATAACG ATACACCTCCGATGGC TCAAGGCTTG 20920 360 1.57e-05 AGAAGGCAAC AACAAGCAACGACGTC GTACGAAGAA 268844 63 1.73e-05 ACGCCGAAGA CAGCAGCCCCGACCCC GAAGCAGAAT 8784 383 2.54e-05 GCACCCAAAC CAACTACACCGCCTGC TCCTGCCTCG 270048 8 2.54e-05 CCCAATC CTCCTCCTCCAAACTC ATCAACGCCC 268904 191 2.54e-05 AGGCACCGCC CAACGCCAATAACAGC TGTCGATACT 10963 435 3.34e-05 CCTCAGTCTT GACCAACAACAATCCA CGGCTTATCC 4168 145 4.76e-05 GTACCCGAGC CACATCCTCCCATCCC TGCGCAGTAT 32491 107 4.76e-05 CAAAGCGGAC GTACACCAGTGACAGC AGTCCTCAAG 20922 152 5.19e-05 GTTGAGGTAT CTCCACCACAGCTTCC TTTCCCCATG 13156 256 5.19e-05 TGGATATCGA CACAAGCAACAACCTG ACCATGAGCC 6729 110 6.68e-05 ATTGGACGAA AACCATCAACGAATAC ACATGCACAT 16737 16 7.87e-05 GAACCGGCCT CACCGCCACCCCCGAG ATGGCACAAG 7840 397 1.17e-04 ACTAAATCTC AAACAATTACGATCTC TTCTTTTTGG 38813 457 1.17e-04 CCACAGCGTC GACCGCTACACACCAC CCGGAGAGAA 25944 28 1.58e-04 CGTATGGAAT GTACGCCACCGTTTAC GGAGTGTCCA 268868 346 3.16e-04 CGAGACAACG CGACACCTGCCACACC TCTATTCTCT 5573 25 4.08e-04 GCAATATGCA CTGCAATACTCACTAC ATCTACCCCA 11189 135 7.40e-04 TAAGTAAGTT AAAATACAATGATATC CCTCAAGCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 270017 2.8e-09 202_[+2]_282 6121 6.2e-08 476_[+2]_8 34968 2e-07 395_[+2]_89 35624 8.7e-07 180_[+2]_304 22844 1.9e-06 415_[+2]_69 37974 2.2e-06 154_[+2]_330 14028 5.5e-06 79_[+2]_405 37054 6.1e-06 77_[+2]_407 263219 6.1e-06 446_[+2]_38 13117 6.1e-06 167_[+2]_317 264674 6.8e-06 386_[+2]_98 25754 6.8e-06 433_[+2]_51 21948 8.5e-06 252_[+2]_232 34773 9.4e-06 75_[+2]_409 261981 1.2e-05 442_[+2]_42 20920 1.6e-05 359_[+2]_125 268844 1.7e-05 62_[+2]_422 8784 2.5e-05 382_[+2]_102 270048 2.5e-05 7_[+2]_477 268904 2.5e-05 190_[+2]_294 10963 3.3e-05 434_[+2]_50 4168 4.8e-05 144_[+2]_340 32491 4.8e-05 106_[+2]_378 20922 5.2e-05 151_[+2]_333 13156 5.2e-05 255_[+2]_229 6729 6.7e-05 109_[+2]_375 16737 7.9e-05 15_[+2]_469 7840 0.00012 396_[+2]_88 38813 0.00012 456_[+2]_28 25944 0.00016 27_[+2]_457 268868 0.00032 345_[+2]_139 5573 0.00041 24_[+2]_460 11189 0.00074 134_[+2]_350 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=16 seqs=33 270017 ( 203) CAACACCACCGACCGC 1 6121 ( 477) CACCAACACCAACCGC 1 34968 ( 396) CTCCACCTCCGACTAC 1 35624 ( 181) GTACACCAACGACGTC 1 22844 ( 416) CAACAACAACAACAAC 1 37974 ( 155) CTCAACCACCGGCCCC 1 14028 ( 80) ATCCAACAACGACCCA 1 37054 ( 78) GACAACCACTAACCAC 1 263219 ( 447) ATCCAGCCCCGACCCC 1 13117 ( 168) CACCGCCACCGAACAA 1 264674 ( 387) CAACACTACCGAAGCC 1 25754 ( 434) CCCCGCCACCAACCTC 1 21948 ( 253) GACCAACAACGACGAG 1 34773 ( 76) GTCCACCAACGGCAGC 1 261981 ( 443) ATACACCTCCGATGGC 1 20920 ( 360) AACAAGCAACGACGTC 1 268844 ( 63) CAGCAGCCCCGACCCC 1 8784 ( 383) CAACTACACCGCCTGC 1 270048 ( 8) CTCCTCCTCCAAACTC 1 268904 ( 191) CAACGCCAATAACAGC 1 10963 ( 435) GACCAACAACAATCCA 1 4168 ( 145) CACATCCTCCCATCCC 1 32491 ( 107) GTACACCAGTGACAGC 1 20922 ( 152) CTCCACCACAGCTTCC 1 13156 ( 256) CACAAGCAACAACCTG 1 6729 ( 110) AACCATCAACGAATAC 1 16737 ( 16) CACCGCCACCCCCGAG 1 7840 ( 397) AAACAATTACGATCTC 1 38813 ( 457) GACCGCTACACACCAC 1 25944 ( 28) GTACGCCACCGTTTAC 1 268868 ( 346) CGACACCTGCCACACC 1 5573 ( 25) CTGCAATACTCACTAC 1 11189 ( 135) AAAATACAATGATATC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 16005 bayes= 8.91886 E= 1.1e-005 -32 122 0 -1169 112 -295 -300 50 45 130 -200 -1169 -55 180 -1169 -1169 139 -1169 -41 -109 4 130 -100 -308 -1169 191 -1169 -109 151 -195 -1169 -50 45 130 -200 -1169 -213 175 -1169 -77 -13 -63 132 -1169 162 -137 -200 -308 -113 151 -1169 -28 -55 95 -41 -50 19 22 -19 -28 -155 180 -141 -1169 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 33 E= 1.1e-005 0.212121 0.545455 0.242424 0.000000 0.575758 0.030303 0.030303 0.363636 0.363636 0.575758 0.060606 0.000000 0.181818 0.818182 0.000000 0.000000 0.696970 0.000000 0.181818 0.121212 0.272727 0.575758 0.121212 0.030303 0.000000 0.878788 0.000000 0.121212 0.757576 0.060606 0.000000 0.181818 0.363636 0.575758 0.060606 0.000000 0.060606 0.787879 0.000000 0.151515 0.242424 0.151515 0.606061 0.000000 0.818182 0.090909 0.060606 0.030303 0.121212 0.666667 0.000000 0.212121 0.181818 0.454545 0.181818 0.181818 0.303030 0.272727 0.212121 0.212121 0.090909 0.818182 0.090909 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CGA][AT][CA]CA[CA]CA[CA]C[GA]A[CT]C[ACGT]C -------------------------------------------------------------------------------- Time 19.08 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 13 llr = 187 E-value = 1.4e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :3:6::3::6:::::51:2:: pos.-specific C 92734873a327:85276329 probability G 111::::2:1:1912113:1: matrix T :42162:5::82123221571 bits 2.1 * 1.9 * 1.7 * * * * 1.5 * * * * Relative 1.3 * * * * * * Entropy 1.0 * *** * * ** * (20.8 bits) 0.8 * * *** ****** * ** 0.6 * ************* ** ** 0.4 * ************* ***** 0.2 ********************* 0.0 --------------------- Multilevel CTCATCCTCATCGCCACCTTC consensus ATCCTAC C T TC GCC sequence C T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 10963 75 1.16e-09 CGCAGTTTGT CACCTCCGCATCGCCACGATC ACGTCAACAG 270017 377 2.01e-09 CGCCATGACC CTCCTTATCCTCGCCACCCTC CTCCTCTCCG 37974 133 2.10e-08 TACCGACCAG CATATTCCCATTGCCACCTCC GCTCAACCAC 14028 285 2.57e-08 CACAAATAGA CGCATCCCCATCGCCACCTCT ACAACGCCTG 13156 438 2.57e-08 CCACTCCTTA CAGATCACCATCGTCACCTTC GGATGGCTCG 13117 54 2.86e-08 AACGAGACGT CTTACCCTCACTGCCACGATC ATCGGCGTTT 38813 160 6.74e-08 CTTCAAAGAC CCCACCCTCGTCGTTTCCATC CTCGCCAAAG 37054 161 8.83e-08 CCCAGCGGCA GTCACCCTCATCGCTCTCTCC CCTTCCATCG 35624 446 1.36e-07 CGCGGCTCAC CTCTTCCTCCTCGCGCTGCTC CTATATCGCT 6121 254 5.01e-07 CTATTTGCCG CTTCCCCTCCCTGCTGCGTTC CATGCTTGAA 21948 191 5.75e-07 TGCCACACTT CCCATTATCCTCGCTCCTTGC TTGTCATGCC 268844 10 9.16e-07 CGCACATCA CCCCTCCCCATGGGCTACCTC GACAACCTCT 34968 432 1.25e-06 AATCGCTGCC CACACCAGCATCTCGTGCCTC CCGTAATAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10963 1.2e-09 74_[+3]_405 270017 2e-09 376_[+3]_103 37974 2.1e-08 132_[+3]_347 14028 2.6e-08 284_[+3]_195 13156 2.6e-08 437_[+3]_42 13117 2.9e-08 53_[+3]_426 38813 6.7e-08 159_[+3]_320 37054 8.8e-08 160_[+3]_319 35624 1.4e-07 445_[+3]_34 6121 5e-07 253_[+3]_226 21948 5.8e-07 190_[+3]_289 268844 9.2e-07 9_[+3]_470 34968 1.3e-06 431_[+3]_48 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=13 10963 ( 75) CACCTCCGCATCGCCACGATC 1 270017 ( 377) CTCCTTATCCTCGCCACCCTC 1 37974 ( 133) CATATTCCCATTGCCACCTCC 1 14028 ( 285) CGCATCCCCATCGCCACCTCT 1 13156 ( 438) CAGATCACCATCGTCACCTTC 1 13117 ( 54) CTTACCCTCACTGCCACGATC 1 38813 ( 160) CCCACCCTCGTCGTTTCCATC 1 37054 ( 161) GTCACCCTCATCGCTCTCTCC 1 35624 ( 446) CTCTTCCTCCTCGCGCTGCTC 1 6121 ( 254) CTTCCCCTCCCTGCTGCGTTC 1 21948 ( 191) CCCATTATCCTCGCTCCTTGC 1 268844 ( 10) CCCCTCCCCATGGGCTACCTC 1 34968 ( 432) CACACCAGCATCTCGTGCCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 15840 bayes= 11.4147 E= 1.4e-002 -1035 198 -165 -1035 21 -2 -165 58 -1035 156 -165 -16 121 39 -1035 -174 -1035 71 -1035 126 -1035 171 -1035 -16 21 156 -1035 -1035 -1035 39 -65 106 -1035 209 -1035 -1035 121 39 -165 -1035 -1035 -61 -1035 172 -1035 156 -165 -16 -1035 -1035 193 -174 -1035 171 -165 -74 -1035 120 -65 26 80 -2 -165 -16 -179 156 -165 -74 -1035 139 34 -174 -20 39 -1035 84 -1035 -2 -165 143 -1035 198 -1035 -174 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 13 E= 1.4e-002 0.000000 0.923077 0.076923 0.000000 0.307692 0.230769 0.076923 0.384615 0.000000 0.692308 0.076923 0.230769 0.615385 0.307692 0.000000 0.076923 0.000000 0.384615 0.000000 0.615385 0.000000 0.769231 0.000000 0.230769 0.307692 0.692308 0.000000 0.000000 0.000000 0.307692 0.153846 0.538462 0.000000 1.000000 0.000000 0.000000 0.615385 0.307692 0.076923 0.000000 0.000000 0.153846 0.000000 0.846154 0.000000 0.692308 0.076923 0.230769 0.000000 0.000000 0.923077 0.076923 0.000000 0.769231 0.076923 0.153846 0.000000 0.538462 0.153846 0.307692 0.461538 0.230769 0.076923 0.230769 0.076923 0.692308 0.076923 0.153846 0.000000 0.615385 0.307692 0.076923 0.230769 0.307692 0.000000 0.461538 0.000000 0.230769 0.076923 0.692308 0.000000 0.923077 0.000000 0.076923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[TAC][CT][AC][TC][CT][CA][TC]C[AC]T[CT]GC[CT][ACT]C[CG][TCA][TC]C -------------------------------------------------------------------------------- Time 27.77 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10963 7.82e-11 15_[+1(3.93e-08)]_38_[+3(1.16e-09)]_\ 339_[+2(3.34e-05)]_50 11189 2.61e-03 219_[+1(6.41e-07)]_260 13117 9.74e-07 53_[+3(2.86e-08)]_93_[+2(6.13e-06)]_\ 317 13156 7.88e-06 255_[+2(5.19e-05)]_166_\ [+3(2.57e-08)]_42 14028 2.76e-08 79_[+2(5.49e-06)]_189_\ [+3(2.57e-08)]_143_[+1(6.05e-06)]_31 16737 1.98e-03 15_[+2(7.87e-05)]_128_\ [+1(3.34e-06)]_320 20920 7.35e-07 14_[+1(2.15e-09)]_324_\ [+2(1.57e-05)]_125 20922 3.81e-02 151_[+2(5.19e-05)]_333 21948 1.10e-04 190_[+3(5.75e-07)]_41_\ [+2(8.48e-06)]_232 22844 3.94e-05 201_[+1(1.72e-06)]_193_\ [+2(1.90e-06)]_4_[+2(2.31e-05)]_49 25754 9.51e-07 189_[+1(9.34e-08)]_223_\ [+2(6.85e-06)]_51 25944 3.04e-04 108_[+1(1.40e-07)]_371 261981 1.01e-02 425_[+2(3.34e-05)]_1_[+2(1.16e-05)]_\ 42 263219 8.39e-07 83_[+1(3.50e-08)]_342_\ [+2(6.13e-06)]_38 264674 1.72e-03 59_[+3(5.64e-05)]_306_\ [+2(6.85e-06)]_98 268844 3.17e-04 9_[+3(9.16e-07)]_32_[+2(1.73e-05)]_\ 422 268868 1.03e-03 19_[+1(1.60e-06)]_460 268904 5.45e-06 8_[+1(1.72e-05)]_62_[+1(1.03e-08)]_\ 78_[+2(2.54e-05)]_294 270017 2.04e-10 202_[+2(2.79e-09)]_158_\ [+3(2.01e-09)]_103 270048 2.80e-06 7_[+2(2.54e-05)]_169_[+1(4.51e-09)]_\ 287 32491 3.73e-02 106_[+2(4.76e-05)]_378 34773 6.63e-07 75_[+2(9.42e-06)]_153_\ [+1(2.42e-06)]_159_[+1(1.33e-08)]_55 34968 3.58e-06 160_[+3(8.31e-05)]_214_\ [+2(2.02e-07)]_20_[+3(1.25e-06)]_48 35624 2.19e-09 180_[+2(8.74e-07)]_14_\ [+1(4.60e-07)]_214_[+3(1.36e-07)]_18_[+2(2.10e-05)] 37054 8.33e-06 77_[+2(6.13e-06)]_67_[+3(8.83e-08)]_\ 319 37974 1.62e-07 132_[+3(2.10e-08)]_1_[+2(2.15e-06)]_\ 330 38813 1.27e-07 28_[+1(5.91e-07)]_110_\ [+3(6.74e-08)]_320 4168 2.32e-02 144_[+2(4.76e-05)]_340 5573 6.67e-03 258_[+1(3.27e-05)]_102_\ [+1(1.60e-06)]_98 6121 3.27e-10 37_[+1(2.26e-07)]_195_\ [+3(5.01e-07)]_47_[+3(1.18e-05)]_89_[+2(8.53e-05)]_29_[+2(6.21e-08)]_8 6729 3.71e-02 109_[+2(6.68e-05)]_375 7840 3.83e-01 500 8784 3.11e-02 382_[+2(2.54e-05)]_102 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************