******************************************************************************** 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/414/414.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10409 1.0000 500 10619 1.0000 500 10929 1.0000 500 12441 1.0000 500 15545 1.0000 500 20675 1.0000 500 21122 1.0000 500 21178 1.0000 500 21410 1.0000 500 22244 1.0000 500 23279 1.0000 500 23582 1.0000 500 23754 1.0000 500 23992 1.0000 500 24604 1.0000 500 24688 1.0000 500 24852 1.0000 500 24891 1.0000 500 25023 1.0000 500 261941 1.0000 500 262352 1.0000 500 262487 1.0000 500 28004 1.0000 500 32217 1.0000 500 3375 1.0000 500 35531 1.0000 500 3704 1.0000 500 5001 1.0000 500 5869 1.0000 500 6357 1.0000 500 6720 1.0000 500 9503 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/414/414.seqs.fa -oc motifs/414 -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 0.269 C 0.227 G 0.244 T 0.261 Background letter frequencies (from dataset with add-one prior applied): A 0.269 C 0.227 G 0.244 T 0.261 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 22 llr = 253 E-value = 2.8e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :75:55:73479:532 pos.-specific C a32a41a:76219138 probability G ::::::::::1::13: matrix T ::3:13:3:::::31: bits 2.1 * * 1.9 * * * 1.7 * * * 1.5 * * * * Relative 1.3 * * * ** Entropy 1.1 * * *** ** * (16.6 bits) 0.9 ** * ******* * 0.6 ** * ******* * 0.4 ************* * 0.2 **************** 0.0 ---------------- Multilevel CAACAACACCAACACC consensus CT CT TAA TG sequence C A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 5869 460 2.32e-08 CCATCAGCAT CATCCACAACAACAGC AGCAGCAGCA 262352 24 2.74e-07 GCGGACGCAC CAACAACTCCCACTCC TCGTCGGGAC 24604 139 3.11e-07 TTCGCCACCG CCTCCACACAAACGCC ACTGGTGACA 261941 172 3.51e-07 GAAAAGCCAA CACCATCACCACCACC ATGGACATCG 24891 266 3.51e-07 TATCCGACCC CAACCGCACAAACACC GCCACCGACG 6357 456 5.00e-07 TCTCCCTACC CAACAACAACACCTGC CGAATTCTAA 23992 478 5.59e-07 CCCATACCCA CACCCACTCCCACTCC AAACACC 6720 271 6.24e-07 GCGCCCAGAG CACCACCACCAACAGA GAGAGGAGGA 10619 442 6.99e-07 AGGATTTCCC CAACCACAAAGACACC GTTCCTTCAT 23754 191 7.75e-07 AAGACGACGA CAACAACAATAACAGC AAAAACAGAA 24688 481 1.17e-06 ATCATCGCCG CCACCACAACGACAAC AACA 23279 471 1.29e-06 TCCACCGTAG CCACAACACACACCAC ACGCCCCATC 35531 451 1.72e-06 GAGAAGCTTG CATCCTCTCAAACAGA ACAAGAAGTG 21122 3 2.71e-06 AT CATCATCACCAACTAG CAACTCATCA 15545 470 3.21e-06 AAAAATCACC CATCACCACACACCAC CATCCCCTCA 32217 445 3.79e-06 GGTGACTTAT CCACAACTACAACCTC GACAACGAAC 23582 443 5.62e-06 TTTGTGATAG CTTCTACACAAACAAC ACATGAACTA 22244 265 7.04e-06 CAAAAGCCGC CCCCTTCTCCAACGGC GGCGGCCAAA 262487 463 8.12e-06 GGAGGGCATT CCCCCAGAACAACTAC GTGCTGCTAC 5001 68 1.39e-05 AGAACTCTGT CAACGCCACAAACGCA TCCTCACCGT 28004 169 1.58e-05 TGATAACCAC CAACCTCACCACAATC GCATCCTACC 20675 52 2.02e-05 CCAGTACTGC CATCATCTCCAATTGA TTGGTTGGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 5869 2.3e-08 459_[+1]_25 262352 2.7e-07 23_[+1]_461 24604 3.1e-07 138_[+1]_346 261941 3.5e-07 171_[+1]_313 24891 3.5e-07 265_[+1]_219 6357 5e-07 455_[+1]_29 23992 5.6e-07 477_[+1]_7 6720 6.2e-07 270_[+1]_214 10619 7e-07 441_[+1]_43 23754 7.8e-07 190_[+1]_294 24688 1.2e-06 480_[+1]_4 23279 1.3e-06 470_[+1]_14 35531 1.7e-06 450_[+1]_34 21122 2.7e-06 2_[+1]_482 15545 3.2e-06 469_[+1]_15 32217 3.8e-06 444_[+1]_40 23582 5.6e-06 442_[+1]_42 22244 7e-06 264_[+1]_220 262487 8.1e-06 462_[+1]_22 5001 1.4e-05 67_[+1]_417 28004 1.6e-05 168_[+1]_316 20675 2e-05 51_[+1]_433 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=22 5869 ( 460) CATCCACAACAACAGC 1 262352 ( 24) CAACAACTCCCACTCC 1 24604 ( 139) CCTCCACACAAACGCC 1 261941 ( 172) CACCATCACCACCACC 1 24891 ( 266) CAACCGCACAAACACC 1 6357 ( 456) CAACAACAACACCTGC 1 23992 ( 478) CACCCACTCCCACTCC 1 6720 ( 271) CACCACCACCAACAGA 1 10619 ( 442) CAACCACAAAGACACC 1 23754 ( 191) CAACAACAATAACAGC 1 24688 ( 481) CCACCACAACGACAAC 1 23279 ( 471) CCACAACACACACCAC 1 35531 ( 451) CATCCTCTCAAACAGA 1 21122 ( 3) CATCATCACCAACTAG 1 15545 ( 470) CATCACCACACACCAC 1 32217 ( 445) CCACAACTACAACCTC 1 23582 ( 443) CTTCTACACAAACAAC 1 22244 ( 265) CCCCTTCTCCAACGGC 1 262487 ( 463) CCCCCAGAACAACTAC 1 5001 ( 68) CAACGCCACAAACGCA 1 28004 ( 169) CAACCTCACCACAATC 1 20675 ( 52) CATCATCTCCAATTGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 15520 bayes= 10.9951 E= 2.8e-012 -1110 214 -1110 -1110 134 27 -1110 -252 76 0 -1110 29 -1110 214 -1110 -1110 76 85 -242 -152 102 -73 -242 6 -1110 207 -242 -1110 144 -1110 -1110 6 24 159 -1110 -1110 44 138 -1110 -252 144 -32 -142 -1110 168 -73 -1110 -1110 -256 200 -1110 -252 76 -73 -84 6 2 49 39 -152 -56 177 -242 -1110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 22 E= 2.8e-012 0.000000 1.000000 0.000000 0.000000 0.681818 0.272727 0.000000 0.045455 0.454545 0.227273 0.000000 0.318182 0.000000 1.000000 0.000000 0.000000 0.454545 0.409091 0.045455 0.090909 0.545455 0.136364 0.045455 0.272727 0.000000 0.954545 0.045455 0.000000 0.727273 0.000000 0.000000 0.272727 0.318182 0.681818 0.000000 0.000000 0.363636 0.590909 0.000000 0.045455 0.727273 0.181818 0.090909 0.000000 0.863636 0.136364 0.000000 0.000000 0.045455 0.909091 0.000000 0.045455 0.454545 0.136364 0.136364 0.272727 0.272727 0.318182 0.318182 0.090909 0.181818 0.772727 0.045455 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AC][ATC]C[AC][AT]C[AT][CA][CA]AAC[AT][CGA]C -------------------------------------------------------------------------------- Time 8.31 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 14 llr = 209 E-value = 2.6e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 81:23:12:81:43:161621 pos.-specific C ::416:12:21:::1:1:::: probability G 2457196:9:8a679439348 matrix T :51::1161:::1::6::141 bits 2.1 * 1.9 * 1.7 * * * * * 1.5 * * * * * Relative 1.3 * ** * * * Entropy 1.1 * * **** ** * * (21.5 bits) 0.9 * ** * **** ** ** * 0.6 ****** ************ * 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel ATGGCGGTGAGGGGGTAGAGG consensus GGCAA A C AA GG GT sequence C A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 6357 281 1.06e-10 ATGAGGCAGC AGGGCGGTGAGGGGGGGGGGG CTTTTGTTGA 262487 284 1.27e-10 GCTGTGTTTG AGCGCGGTGCGGGGGGAGATG GCATTGTACC 3704 182 8.39e-09 TGGTTGCCTT GTGGCGGCGAGGAGGAAGAGG AATGACGTCC 10929 48 8.39e-09 TCTGCATGGC ATCACGGCGAGGAAGTGGATG GATTGAGACC 35531 138 1.16e-08 GTAGTGGTGG AAGGGGCAGAGGGGGTAGAGG AAGGTACGTT 21122 58 2.13e-08 CTTCCGATCT AGCGCGTTGAGGAGGTAGAAT GTTACCTCCG 32217 221 5.39e-08 AAGGAATCGG ATCAAGTTGAGGAGGTAGTGG GAGAGGAAAT 24852 90 5.39e-08 GCACTGCATG ATCCAGCAGAGGAGGTAGATG CACCGGCCGA 10409 136 9.00e-08 GATGGCATTG GTGAAGGTGACGGAGTGGATG GTGGTGTAGG 261941 194 1.57e-07 CACCATGGAC ATCGCGATGAAGGGGTAAAAG GACGAAGCCA 23754 310 5.25e-07 GGTCGAAGAA AAGGAGGAGCGGGAGGAGGAA GCCGACGACA 24891 113 5.60e-07 AATAAGTATC AGGGCGGTTCGGTGGTCGGTG GAATGTGGAT 3375 208 6.77e-07 TAGGGGATGT AGTGCTGTGACGGGGGAGGGA TTGGTGGAGG 5869 75 8.14e-07 TGGAACTAGA GTGGGGACGAGGGACGGGAGG TACTAAACAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 6357 1.1e-10 280_[+2]_199 262487 1.3e-10 283_[+2]_196 3704 8.4e-09 181_[+2]_298 10929 8.4e-09 47_[+2]_432 35531 1.2e-08 137_[+2]_342 21122 2.1e-08 57_[+2]_422 32217 5.4e-08 220_[+2]_259 24852 5.4e-08 89_[+2]_390 10409 9e-08 135_[+2]_344 261941 1.6e-07 193_[+2]_286 23754 5.2e-07 309_[+2]_170 24891 5.6e-07 112_[+2]_367 3375 6.8e-07 207_[+2]_272 5869 8.1e-07 74_[+2]_405 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=14 6357 ( 281) AGGGCGGTGAGGGGGGGGGGG 1 262487 ( 284) AGCGCGGTGCGGGGGGAGATG 1 3704 ( 182) GTGGCGGCGAGGAGGAAGAGG 1 10929 ( 48) ATCACGGCGAGGAAGTGGATG 1 35531 ( 138) AAGGGGCAGAGGGGGTAGAGG 1 21122 ( 58) AGCGCGTTGAGGAGGTAGAAT 1 32217 ( 221) ATCAAGTTGAGGAGGTAGTGG 1 24852 ( 90) ATCCAGCAGAGGAGGTAGATG 1 10409 ( 136) GTGAAGGTGACGGAGTGGATG 1 261941 ( 194) ATCGCGATGAAGGGGTAAAAG 1 23754 ( 310) AAGGAGGAGCGGGAGGAGGAA 1 24891 ( 113) AGGGCGGTTCGGTGGTCGGTG 1 3375 ( 208) AGTGCTGTGACGGGGGAGGGA 1 5869 ( 75) GTGGGGACGAGGGACGGGAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 15360 bayes= 10.7044 E= 2.6e-007 155 -1045 -18 -1045 -91 -1045 55 94 -1045 92 104 -187 -33 -166 155 -1045 9 133 -77 -1045 -1045 -1045 193 -187 -91 -67 123 -87 -33 -8 -1045 113 -1045 -1045 193 -187 155 -8 -1045 -1045 -191 -67 169 -1045 -1045 -1045 204 -1045 41 -1045 123 -187 9 -1045 155 -1045 -1045 -166 193 -1045 -191 -1045 55 113 126 -166 23 -1045 -191 -1045 193 -1045 126 -1045 23 -187 -33 -1045 81 45 -91 -1045 169 -187 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 14 E= 2.6e-007 0.785714 0.000000 0.214286 0.000000 0.142857 0.000000 0.357143 0.500000 0.000000 0.428571 0.500000 0.071429 0.214286 0.071429 0.714286 0.000000 0.285714 0.571429 0.142857 0.000000 0.000000 0.000000 0.928571 0.071429 0.142857 0.142857 0.571429 0.142857 0.214286 0.214286 0.000000 0.571429 0.000000 0.000000 0.928571 0.071429 0.785714 0.214286 0.000000 0.000000 0.071429 0.142857 0.785714 0.000000 0.000000 0.000000 1.000000 0.000000 0.357143 0.000000 0.571429 0.071429 0.285714 0.000000 0.714286 0.000000 0.000000 0.071429 0.928571 0.000000 0.071429 0.000000 0.357143 0.571429 0.642857 0.071429 0.285714 0.000000 0.071429 0.000000 0.928571 0.000000 0.642857 0.000000 0.285714 0.071429 0.214286 0.000000 0.428571 0.357143 0.142857 0.000000 0.785714 0.071429 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AG][TG][GC][GA][CA]GG[TAC]G[AC]GG[GA][GA]G[TG][AG]G[AG][GTA]G -------------------------------------------------------------------------------- Time 16.41 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 17 llr = 226 E-value = 1.9e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :31::2:1113:::2:2::41 pos.-specific C 81:81456191254:841815 probability G 141:2::21:2::6::42:1: matrix T 128274518:485:82:7244 bits 2.1 1.9 1.7 * 1.5 * * * Relative 1.3 * * * * * * Entropy 1.1 * ** * * ***** * (19.2 bits) 0.9 * *** * ** ***** ** * 0.6 * *** **** ***** ** * 0.4 * ******** ******** * 0.2 ********************* 0.0 --------------------- Multilevel CGTCTCCCTCTTTGTCCTCTC consensus A TT ACCCATG AT sequence A A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 10409 294 1.27e-11 ATTAATTTTT CGTCTTCCTCTTTCTCCTCAC TAAATCCTTG 5869 298 3.08e-10 TGCTGACCTC CGTCTACCTCTTTGACCTCTC AATCTCGCCA 15545 323 8.98e-10 TGCGAACAAC CATCTACCTCATCGTCATCAC TAAAATACAA 5001 464 1.58e-08 ATCTGTCTCT CGGCTCCCTCTTTGTTCTCTT CGTTCGTTCA 21178 68 9.63e-08 GCATCATCAT CGTCGTCGTCGTCGTCGTCGT ATTGTATTAT 20675 169 1.18e-07 ATTGGGGTGT CATCTCCCTCATCCTTGTTGT CCGATTCTGA 261941 404 1.75e-07 ACAACCTTGC CTTCGTTGTCGTCGACCTCTC ATTGGAGGGC 23279 428 1.92e-07 GGCTCCACCA CAACTCTCTCCTCCTTCTCCC CCTGATACAC 22244 186 1.92e-07 TCTCTCTCTC TCTCTCTCTCTCTCACGTCTC TCCCCAGGAC 23992 228 5.17e-07 TTTCTCTTCC CTTCTTTCGCTTCGTCCGTCC GTCCCTGTTC 10619 51 5.17e-07 GATTCGGTGT CGTTCTTCTCTTCGACGGCAT TGCCACAACT 21410 202 1.44e-06 ACACACCTCC CCTCTCCTCCCCTCTCCTCTC TCCTTATTCA 24604 283 1.67e-06 GGGCTTCAGG CTTCTCTATCGCTGTTGCCAT TCCATCGTCA 6720 438 2.07e-06 TCTCTGTGCT GGACTCTCTCATTCTCATCAA CCAGAGATTC 23582 94 4.56e-06 TGACTCCGAT CATTGACGACATTGTCATCAT CGGTCAAAGC 24891 296 5.80e-06 CCGACGACGG CGTCCACCGAACCCTCGGCTC TGCTAGTGCT 21122 297 1.02e-05 GAAATAAATT TATTTTTATCTTTGTCACTTT TAAACCGGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10409 1.3e-11 293_[+3]_186 5869 3.1e-10 297_[+3]_182 15545 9e-10 322_[+3]_157 5001 1.6e-08 463_[+3]_16 21178 9.6e-08 67_[+3]_412 20675 1.2e-07 168_[+3]_311 261941 1.7e-07 403_[+3]_76 23279 1.9e-07 427_[+3]_52 22244 1.9e-07 185_[+3]_294 23992 5.2e-07 227_[+3]_252 10619 5.2e-07 50_[+3]_429 21410 1.4e-06 201_[+3]_278 24604 1.7e-06 282_[+3]_197 6720 2.1e-06 437_[+3]_42 23582 4.6e-06 93_[+3]_386 24891 5.8e-06 295_[+3]_184 21122 1e-05 296_[+3]_183 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=17 10409 ( 294) CGTCTTCCTCTTTCTCCTCAC 1 5869 ( 298) CGTCTACCTCTTTGACCTCTC 1 15545 ( 323) CATCTACCTCATCGTCATCAC 1 5001 ( 464) CGGCTCCCTCTTTGTTCTCTT 1 21178 ( 68) CGTCGTCGTCGTCGTCGTCGT 1 20675 ( 169) CATCTCCCTCATCCTTGTTGT 1 261941 ( 404) CTTCGTTGTCGTCGACCTCTC 1 23279 ( 428) CAACTCTCTCCTCCTTCTCCC 1 22244 ( 186) TCTCTCTCTCTCTCACGTCTC 1 23992 ( 228) CTTCTTTCGCTTCGTCCGTCC 1 10619 ( 51) CGTTCTTCTCTTCGACGGCAT 1 21410 ( 202) CCTCTCCTCCCCTCTCCTCTC 1 24604 ( 283) CTTCTCTATCGCTGTTGCCAT 1 6720 ( 438) GGACTCTCTCATTCTCATCAA 1 23582 ( 94) CATTGACGACATTGTCATCAT 1 24891 ( 296) CGTCCACCGAACCCTCGGCTC 1 21122 ( 297) TATTTTTATCTTTGTCACTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 15360 bayes= 11.1838 E= 1.9e-005 -1073 186 -205 -115 13 -95 76 -56 -119 -1073 -205 166 -1073 186 -1073 -56 -1073 -95 -46 144 -19 86 -1073 44 -1073 122 -1073 85 -119 151 -46 -215 -219 -194 -105 155 -219 205 -1073 -1073 13 -95 -46 66 -1073 5 -1073 155 -1073 105 -1073 102 -1073 86 127 -1073 -19 -1073 -1073 155 -1073 175 -1073 -15 -19 86 53 -1073 -1073 -95 -46 144 -1073 186 -1073 -56 39 -95 -105 66 -219 122 -1073 66 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 17 E= 1.9e-005 0.000000 0.823529 0.058824 0.117647 0.294118 0.117647 0.411765 0.176471 0.117647 0.000000 0.058824 0.823529 0.000000 0.823529 0.000000 0.176471 0.000000 0.117647 0.176471 0.705882 0.235294 0.411765 0.000000 0.352941 0.000000 0.529412 0.000000 0.470588 0.117647 0.647059 0.176471 0.058824 0.058824 0.058824 0.117647 0.764706 0.058824 0.941176 0.000000 0.000000 0.294118 0.117647 0.176471 0.411765 0.000000 0.235294 0.000000 0.764706 0.000000 0.470588 0.000000 0.529412 0.000000 0.411765 0.588235 0.000000 0.235294 0.000000 0.000000 0.764706 0.000000 0.764706 0.000000 0.235294 0.235294 0.411765 0.352941 0.000000 0.000000 0.117647 0.176471 0.705882 0.000000 0.823529 0.000000 0.176471 0.352941 0.117647 0.117647 0.411765 0.058824 0.529412 0.000000 0.411765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- C[GA]TCT[CTA][CT]CTC[TA][TC][TC][GC][TA][CT][CGA]TC[TA][CT] -------------------------------------------------------------------------------- Time 24.53 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10409 5.01e-11 135_[+2(9.00e-08)]_137_\ [+3(1.27e-11)]_186 10619 6.05e-06 50_[+3(5.17e-07)]_370_\ [+1(6.99e-07)]_4_[+1(1.00e-05)]_23 10929 2.48e-04 47_[+2(8.39e-09)]_432 12441 3.50e-01 500 15545 1.48e-07 322_[+3(8.98e-10)]_126_\ [+1(3.21e-06)]_15 20675 6.22e-06 51_[+1(2.02e-05)]_101_\ [+3(1.18e-07)]_311 21122 1.95e-08 2_[+1(2.71e-06)]_39_[+2(2.13e-08)]_\ 218_[+3(1.02e-05)]_183 21178 3.06e-04 67_[+3(9.63e-08)]_412 21410 1.50e-03 201_[+3(1.44e-06)]_278 22244 1.46e-05 185_[+3(1.92e-07)]_58_\ [+1(7.04e-06)]_220 23279 7.16e-06 427_[+3(1.92e-07)]_22_\ [+1(1.29e-06)]_14 23582 4.86e-04 34_[+3(9.72e-05)]_38_[+3(4.56e-06)]_\ 328_[+1(5.62e-06)]_42 23754 5.04e-07 190_[+1(7.75e-07)]_103_\ [+2(5.25e-07)]_23_[+3(5.13e-05)]_126 23992 7.57e-06 196_[+1(1.07e-05)]_15_\ [+3(5.17e-07)]_229_[+1(5.59e-07)]_7 24604 7.74e-06 138_[+1(3.11e-07)]_128_\ [+3(1.67e-06)]_197 24688 5.42e-03 267_[+1(3.34e-05)]_197_\ [+1(1.17e-06)]_4 24852 7.72e-05 89_[+2(5.39e-08)]_390 24891 3.61e-08 112_[+2(5.60e-07)]_13_\ [+2(8.81e-05)]_98_[+1(3.51e-07)]_14_[+3(5.80e-06)]_184 25023 4.00e-01 500 261941 4.41e-10 171_[+1(3.51e-07)]_6_[+2(1.57e-07)]_\ 160_[+1(1.31e-05)]_13_[+3(1.75e-07)]_19_[+1(2.07e-06)]_41 262352 3.10e-04 23_[+1(2.74e-07)]_461 262487 1.26e-08 283_[+2(1.27e-10)]_158_\ [+1(8.12e-06)]_22 28004 4.57e-02 168_[+1(1.58e-05)]_21_\ [+1(7.46e-05)]_279 32217 2.88e-06 180_[+2(2.90e-05)]_19_\ [+2(5.39e-08)]_203_[+1(3.79e-06)]_17_[+1(1.49e-05)]_7 3375 5.78e-03 207_[+2(6.77e-07)]_272 35531 4.90e-07 116_[+2(8.01e-05)]_[+2(1.16e-08)]_\ 95_[+2(1.07e-05)]_88_[+1(3.00e-05)]_72_[+1(1.72e-06)]_34 3704 1.57e-04 181_[+2(8.39e-09)]_298 5001 7.90e-06 67_[+1(1.39e-05)]_351_\ [+3(7.75e-05)]_8_[+3(1.58e-08)]_16 5869 4.22e-13 74_[+2(8.14e-07)]_202_\ [+3(3.08e-10)]_141_[+1(2.32e-08)]_25 6357 6.97e-10 280_[+2(1.06e-10)]_154_\ [+1(5.00e-07)]_29 6720 2.57e-06 114_[+1(2.27e-05)]_140_\ [+1(6.24e-07)]_151_[+3(2.07e-06)]_42 9503 2.50e-01 500 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************