******************************************************************************** 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/411/411.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10510 1.0000 500 1081 1.0000 500 10916 1.0000 500 10918 1.0000 500 1502 1.0000 500 1836 1.0000 500 21195 1.0000 500 2141 1.0000 500 22071 1.0000 500 22284 1.0000 500 22570 1.0000 500 23691 1.0000 500 24258 1.0000 500 24331 1.0000 500 24339 1.0000 500 24489 1.0000 500 25435 1.0000 500 25623 1.0000 500 262573 1.0000 500 262923 1.0000 500 268548 1.0000 500 270030 1.0000 500 31406 1.0000 500 35206 1.0000 500 3676 1.0000 500 3795 1.0000 500 4047 1.0000 500 4050 1.0000 24 4765 1.0000 500 5915 1.0000 500 6186 1.0000 500 7261 1.0000 500 9636 1.0000 500 bd1861 1.0000 500 bd767 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/411/411.seqs.fa -oc motifs/411 -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= 35 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= 17024 N= 35 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.267 C 0.232 G 0.238 T 0.262 Background letter frequencies (from dataset with add-one prior applied): A 0.267 C 0.232 G 0.238 T 0.262 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 20 sites = 20 llr = 242 E-value = 7.9e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 12112131:::422:11::: pos.-specific C 24415551127::6:35:38 probability G 126212::5::5::a:21:: matrix T 83:82338584292:73982 bits 2.1 * 1.9 * 1.7 * 1.5 * * Relative 1.3 * * * *** Entropy 1.1 * ** * * *** (17.4 bits) 0.8 * ** **** * ** *** 0.6 * ** **** **** *** 0.4 * ** ************** 0.2 * ****************** 0.0 -------------------- Multilevel TCGTCCCTTTCGTCGTCTTC consensus TC ATA GCTA A CT CT sequence G TGT T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 4765 62 2.12e-10 TTCGGAAGTG TCGTCGTTGTCGTCGTCTTC CTCGCGTGAA 268548 175 4.28e-09 ATCCGATTCG TCGGCCATGTTGTCGTCTTC TTCGTAGACG 35206 413 9.56e-09 GGTGTCTCAC TTGTCTCTTTCGACGTTTTC GATAGTTACA 10510 420 5.25e-08 TGATTCATCT TCGTCATCGTCATCGTCTTC AGATTCCAGC 1502 324 1.25e-07 CGCTCCGCCG TTGGAGATGTTGTCGTCTTC AATGCTTCTT 5915 403 1.76e-07 AGTTCATCAC TTGTTCATTTCATCGTTTCT GACATCATGA 24339 478 2.47e-07 TGCCTCCTCT TACTGCTTGCTGTCGTCTTC ACG 24331 197 2.75e-07 TCCGCGCCTG CAGTCCCAGTCGTCGTCTCC CTGGCTGATT 25623 28 3.78e-07 TGATTGATAA TCCTTGATGTCAATGTCTTC CATGCGTTGA 24258 112 9.18e-07 GTGTTGTGTT TTGTGCATTTCTTCGCATTC TTTCGTTACA 10918 126 1.10e-06 AAGCTGTTGT TTCTCCCACTCATTGTTTTC GTTGGCAGTG 270030 280 2.84e-06 AGCGTTGGTG TCGCCTCTTTCGTAGTGGTC AGTTTTGCTC bd767 289 3.07e-06 CTGAATCAAA CACTCCATTTCATTGATTTC AGATTCGTCT 22570 205 4.87e-06 GAGCAGTCGG TGCTTCCTGTTGAAGTGTTT GTAGAGCGAG 2141 447 4.87e-06 GGTTGTTGCC TCCAATCTGTTATAGCCTCC ATCATTAACA 1081 42 4.87e-06 CTGCGATCGG GGGTCGTTTCTATCGCCTCC TTTGCGACGC 7261 386 5.64e-06 CCACCGTCCG TCCTCTCCTCCTTCGCGTTT GCGCGTCTGG 9636 251 9.82e-06 TGGAGCAATC TGAGTACTTCCATCGTTTTC AGAGTTGGTT bd1861 65 1.27e-05 GCCTACTTGT CGCTACCTTTCTTTGCTTCT GATTATATCA 10916 44 1.53e-05 CGTGGGTGCG ATGTATTTTTTGTAGCCGTC GCGGAACTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 4765 2.1e-10 61_[+1]_419 268548 4.3e-09 174_[+1]_306 35206 9.6e-09 412_[+1]_68 10510 5.3e-08 419_[+1]_61 1502 1.2e-07 323_[+1]_157 5915 1.8e-07 402_[+1]_78 24339 2.5e-07 477_[+1]_3 24331 2.7e-07 196_[+1]_284 25623 3.8e-07 27_[+1]_453 24258 9.2e-07 111_[+1]_369 10918 1.1e-06 125_[+1]_355 270030 2.8e-06 279_[+1]_201 bd767 3.1e-06 288_[+1]_192 22570 4.9e-06 204_[+1]_276 2141 4.9e-06 446_[+1]_34 1081 4.9e-06 41_[+1]_439 7261 5.6e-06 385_[+1]_95 9636 9.8e-06 250_[+1]_230 bd1861 1.3e-05 64_[+1]_416 10916 1.5e-05 43_[+1]_437 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=20 4765 ( 62) TCGTCGTTGTCGTCGTCTTC 1 268548 ( 175) TCGGCCATGTTGTCGTCTTC 1 35206 ( 413) TTGTCTCTTTCGACGTTTTC 1 10510 ( 420) TCGTCATCGTCATCGTCTTC 1 1502 ( 324) TTGGAGATGTTGTCGTCTTC 1 5915 ( 403) TTGTTCATTTCATCGTTTCT 1 24339 ( 478) TACTGCTTGCTGTCGTCTTC 1 24331 ( 197) CAGTCCCAGTCGTCGTCTCC 1 25623 ( 28) TCCTTGATGTCAATGTCTTC 1 24258 ( 112) TTGTGCATTTCTTCGCATTC 1 10918 ( 126) TTCTCCCACTCATTGTTTTC 1 270030 ( 280) TCGCCTCTTTCGTAGTGGTC 1 bd767 ( 289) CACTCCATTTCATTGATTTC 1 22570 ( 205) TGCTTCCTGTTGAAGTGTTT 1 2141 ( 447) TCCAATCTGTTATAGCCTCC 1 1081 ( 42) GGGTCGTTTCTATCGCCTCC 1 7261 ( 386) TCCTCTCCTCCTTCGCGTTT 1 9636 ( 251) TGAGTACTTCCATCGTTTTC 1 bd1861 ( 65) CGCTACCTTTCTTTGCTTCT 1 10916 ( 44) ATGTATTTTTTGTAGCCGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 16359 bayes= 11.1492 E= 7.9e-004 -241 -63 -225 152 -83 59 -25 19 -241 78 121 -1097 -241 -221 -67 152 -42 110 -125 -39 -142 95 -25 -7 17 95 -1097 -7 -142 -122 -1097 161 -1097 -221 92 93 -1097 -22 -1097 161 -1097 148 -1097 42 58 -1097 92 -81 -83 -1097 -1097 170 -42 137 -1097 -39 -1097 -1097 207 -1097 -241 37 -1097 131 -241 110 -67 19 -1097 -1097 -125 178 -1097 10 -1097 152 -1097 178 -1097 -39 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 20 E= 7.9e-004 0.050000 0.150000 0.050000 0.750000 0.150000 0.350000 0.200000 0.300000 0.050000 0.400000 0.550000 0.000000 0.050000 0.050000 0.150000 0.750000 0.200000 0.500000 0.100000 0.200000 0.100000 0.450000 0.200000 0.250000 0.300000 0.450000 0.000000 0.250000 0.100000 0.100000 0.000000 0.800000 0.000000 0.050000 0.450000 0.500000 0.000000 0.200000 0.000000 0.800000 0.000000 0.650000 0.000000 0.350000 0.400000 0.000000 0.450000 0.150000 0.150000 0.000000 0.000000 0.850000 0.200000 0.600000 0.000000 0.200000 0.000000 0.000000 1.000000 0.000000 0.050000 0.300000 0.000000 0.650000 0.050000 0.500000 0.150000 0.300000 0.000000 0.000000 0.100000 0.900000 0.000000 0.250000 0.000000 0.750000 0.000000 0.800000 0.000000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- T[CTG][GC]T[CAT][CTG][CAT]T[TG][TC][CT][GA]T[CAT]G[TC][CT]T[TC][CT] -------------------------------------------------------------------------------- Time 9.98 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 17 llr = 198 E-value = 9.2e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 2:1118:55:438:3 pos.-specific C :2::::211::2::: probability G 28:492844a652a7 matrix T 6:961:::1:1:::: bits 2.1 * * 1.9 * * 1.7 * * 1.5 * * * * * Relative 1.3 ** * * * * Entropy 1.1 ** *** * *** (16.8 bits) 0.8 ****** ** *** 0.6 ******** ** *** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel TGTTGAGAAGGGAGG consensus AC G G GG AAG A sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 7261 313 3.70e-08 AATAGAAGTT TGTTGAGAAGACAGG GTCGATCAGC 3676 77 9.73e-08 GTCTCCGTTT TGTTGAGAAGAGGGG GAGCTGAGGT 22570 8 1.17e-07 AACCCTT TGTGGAGCGGGGAGG GAAACTCGCA 268548 327 2.29e-07 GAGGCGGGAG GGTTGGGAGGGGAGG ATGTTGTCTC 23691 234 2.80e-07 TAGGTGGTAG TGTGGAGGAGGCAGA TCGCAGGCTG 1081 125 3.82e-07 CGGCCTCTCC TGTTGAGACGAGAGG GTGTGATGAG 25435 65 5.23e-07 CGGTGGATTG TGTGGACGAGGAAGG GGAGGGAGGG 10918 174 1.39e-06 GACTACCACC TGTGAAGGAGGGAGG GTATCGTGGT 9636 28 2.76e-06 GAAGAAAAAT AGTAGGGAGGGGAGG CCGTGTGTCA 21195 226 2.76e-06 GTGGTTTTGT TCTTGAGAAGAAGGA AGCTCGAGCA 22284 167 3.00e-06 GACGACGACA TGTTGAGATGTGAGG CAGAGGATTA 22071 314 4.13e-06 TTTTGAAAAG GCTTGAGGGGAAAGA AAGGAAAAAC 262573 63 5.97e-06 CATGTCCAAA ACTTGACAGGAGAGA CGCAGTACCA 4765 112 6.38e-06 AGTTCTTCAT GGAGGAGAGGGCGGG GACGGAGAGA 1502 77 7.32e-06 TAGCAGATGC ACTGGAGGAGGAGGA CTCGGATCCA 24489 378 9.45e-06 GCTCGTGAGC TGTTTGGCGGGAAGG AAGGGACCTC 35206 267 1.52e-05 GATGTGCTTC AGATGGCGAGGCAGG CGTCATGTCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 7261 3.7e-08 312_[+2]_173 3676 9.7e-08 76_[+2]_409 22570 1.2e-07 7_[+2]_478 268548 2.3e-07 326_[+2]_159 23691 2.8e-07 233_[+2]_252 1081 3.8e-07 124_[+2]_361 25435 5.2e-07 64_[+2]_421 10918 1.4e-06 173_[+2]_312 9636 2.8e-06 27_[+2]_458 21195 2.8e-06 225_[+2]_260 22284 3e-06 166_[+2]_319 22071 4.1e-06 313_[+2]_172 262573 6e-06 62_[+2]_423 4765 6.4e-06 111_[+2]_374 1502 7.3e-06 76_[+2]_409 24489 9.5e-06 377_[+2]_108 35206 1.5e-05 266_[+2]_219 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=17 7261 ( 313) TGTTGAGAAGACAGG 1 3676 ( 77) TGTTGAGAAGAGGGG 1 22570 ( 8) TGTGGAGCGGGGAGG 1 268548 ( 327) GGTTGGGAGGGGAGG 1 23691 ( 234) TGTGGAGGAGGCAGA 1 1081 ( 125) TGTTGAGACGAGAGG 1 25435 ( 65) TGTGGACGAGGAAGG 1 10918 ( 174) TGTGAAGGAGGGAGG 1 9636 ( 28) AGTAGGGAGGGGAGG 1 21195 ( 226) TCTTGAGAAGAAGGA 1 22284 ( 167) TGTTGAGATGTGAGG 1 22071 ( 314) GCTTGAGGGGAAAGA 1 262573 ( 63) ACTTGACAGGAGAGA 1 4765 ( 112) GGAGGAGAGGGCGGG 1 1502 ( 77) ACTGGAGGAGGAGGA 1 24489 ( 378) TGTTTGGCGGGAAGG 1 35206 ( 267) AGATGGCGAGGCAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 16534 bayes= 9.99381 E= 9.2e-003 -18 -1073 -43 116 -1073 2 168 -1073 -118 -1073 -1073 175 -218 -1073 57 116 -218 -1073 189 -215 152 -1073 -2 -1073 -1073 -40 179 -1073 99 -98 57 -1073 82 -198 79 -215 -1073 -1073 207 -1073 40 -1073 131 -215 14 2 98 -1073 152 -1073 -2 -1073 -1073 -1073 207 -1073 14 -1073 157 -1073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 17 E= 9.2e-003 0.235294 0.000000 0.176471 0.588235 0.000000 0.235294 0.764706 0.000000 0.117647 0.000000 0.000000 0.882353 0.058824 0.000000 0.352941 0.588235 0.058824 0.000000 0.882353 0.058824 0.764706 0.000000 0.235294 0.000000 0.000000 0.176471 0.823529 0.000000 0.529412 0.117647 0.352941 0.000000 0.470588 0.058824 0.411765 0.058824 0.000000 0.000000 1.000000 0.000000 0.352941 0.000000 0.588235 0.058824 0.294118 0.235294 0.470588 0.000000 0.764706 0.000000 0.235294 0.000000 0.000000 0.000000 1.000000 0.000000 0.294118 0.000000 0.705882 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TA][GC]T[TG]G[AG]G[AG][AG]G[GA][GAC][AG]G[GA] -------------------------------------------------------------------------------- Time 19.55 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 35 llr = 319 E-value = 2.9e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 5323:22673143654198:3 pos.-specific C 453:8334256233329::76 probability G :1:1133:1:213:1111:11 matrix T 1146:12::2:22113:121: 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 ACTTCGCAACCAAAAACAACC consensus CACA CGCCAGCGCCT A sequence A AT TC C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 22284 78 1.45e-09 ATATGAGGCT CCTTCGGAACCCGAATCAACA AACACTCCTC 7261 194 2.47e-09 GCATAAGTCA ACTTCTCCAACACAAACAACC GAGACGTCGA 10918 465 1.16e-07 ACTCAAACAG CACACAGAACCACCACCAACC TCTCTCTTTC 25435 464 1.60e-07 GAGCACGACG ACCTCCCAACCATCAACATCA GTTCTGAAGC 262573 154 2.54e-07 TGAATCATCA CCCTCAGACCCGTACACAACC GTATGAGAAC 24339 116 6.01e-07 GGAGCCGATG CCTACGCCATCTGACGCAACC GAATTCCAAA 22570 480 6.89e-07 ATCCACTACT CCCTCGGAACGACCCTCAATC 21195 478 1.17e-06 GCTGGTGGCT ACTTGCACAAGAAAAACAACA AT 4765 396 1.50e-06 CTTCACTACA ACAACCGAAAGAAAAACAAGA CCGCCGTCGA 3795 418 2.17e-06 CACAAAAGAG AAAACGGCAACCGCATCATCC CAACACAACA 2141 474 2.17e-06 TCCATCATTA ACATCGTCATCCACATCAAGC AATCGC 6186 266 2.75e-06 CCCTCCCGTC ACAACCTCACAACAGACAACC CGTCGTCGAC 25623 470 4.33e-06 TCTCCGAGAC CACTCACAACCTGAACAAACA CAAGATAAAG 23691 477 5.40e-06 CCACCGACGG CAAACGCAACGATACGCAACA ACA 268548 462 6.70e-06 TTCGAAGCCG CGTTCTCCACCTCTCCCAACC TCCGCTATCC 1502 247 7.44e-06 CCCTTTCGCA TCTGCTTAACCCTACTCAACC GCTGCCGGTG 10916 472 9.16e-06 TCATTGGCTA ATCTCCCACTCATATCCAACC AAAGCATA bd767 471 1.66e-05 ACACACACAC ACCACACAAATCGATTCAACC TCTACCAAC 3676 32 2.65e-05 GTCAAAGTCC AGCTCGTCATCAAAATCATCG GTATCATCCC 270030 351 2.91e-05 TCCCGTGGAC AACACGACAACAATCCCATCA TTCACAGCCA 1081 95 3.47e-05 CTCCACTGCC ACTTCTCCTCCGGCCTCATCC GGCCTCTCCT bd1861 198 4.13e-05 AAGATGGAAG AATTGATACAGAGAAACAAGC TGCTTGAAAG 5915 456 4.50e-05 ACGCAGATGA ACCAGGAAGCAACAAACAACA ATTGAACACA 4047 211 4.90e-05 TACCCTCTTC ATTTCTCCAAATGCATCAAGC CCTACGACTG 1836 150 8.02e-05 AAGCCATTCC TCCTCCTAAACCGCCTCGTCC GTTCACCTTA 24489 8 1.01e-04 CGCAGCA TTATCAGCAACGATATCAACA ACATTCTGTC 22071 402 1.01e-04 ATTCGGATAG CATTTAAAAACGGAAACAATC TACAAGGTGA 35206 107 1.47e-04 GAATGGATCA AGAACGACATGATAAACTACA AATTGGAAGT 10510 92 1.47e-04 CAAAGCTAGT CCAACGGAACCTAGTCCTACC GGAGAGGGAG 24258 386 2.26e-04 CGCGAGCACT CCCGCCCAGCCCAACACGACG AAAACTAGTT 31406 457 2.59e-04 GGTAGTACTT ACTTCCGACCGGAAACGAAAA TTGTCGAAAA 24331 440 2.95e-04 CCGAATAATC ATTTCCACCCCCCATCAAATC GGCGAAATAC 4050 4 5.21e-04 GTT CATGCCGACTCTCCGGCAATC 262923 303 6.98e-04 GCTGGTAAAC CATGGGGCACGACAGAAAAGA CTGGTAAGAG 9636 420 8.73e-04 TCGTCCGTCC CGTTGCTACAATACCAGAACC CATCATGGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 22284 1.5e-09 77_[+3]_402 7261 2.5e-09 193_[+3]_286 10918 1.2e-07 464_[+3]_15 25435 1.6e-07 463_[+3]_16 262573 2.5e-07 153_[+3]_326 24339 6e-07 115_[+3]_364 22570 6.9e-07 479_[+3] 21195 1.2e-06 477_[+3]_2 4765 1.5e-06 395_[+3]_84 3795 2.2e-06 417_[+3]_62 2141 2.2e-06 473_[+3]_6 6186 2.7e-06 265_[+3]_214 25623 4.3e-06 469_[+3]_10 23691 5.4e-06 476_[+3]_3 268548 6.7e-06 461_[+3]_18 1502 7.4e-06 246_[+3]_233 10916 9.2e-06 471_[+3]_8 bd767 1.7e-05 470_[+3]_9 3676 2.7e-05 31_[+3]_448 270030 2.9e-05 350_[+3]_129 1081 3.5e-05 94_[+3]_385 bd1861 4.1e-05 197_[+3]_282 5915 4.5e-05 455_[+3]_24 4047 4.9e-05 210_[+3]_269 1836 8e-05 149_[+3]_330 24489 0.0001 7_[+3]_472 22071 0.0001 401_[+3]_78 35206 0.00015 106_[+3]_373 10510 0.00015 91_[+3]_388 24258 0.00023 385_[+3]_94 31406 0.00026 456_[+3]_23 24331 0.0003 439_[+3]_40 4050 0.00052 3_[+3] 262923 0.0007 302_[+3]_177 9636 0.00087 419_[+3]_60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=35 22284 ( 78) CCTTCGGAACCCGAATCAACA 1 7261 ( 194) ACTTCTCCAACACAAACAACC 1 10918 ( 465) CACACAGAACCACCACCAACC 1 25435 ( 464) ACCTCCCAACCATCAACATCA 1 262573 ( 154) CCCTCAGACCCGTACACAACC 1 24339 ( 116) CCTACGCCATCTGACGCAACC 1 22570 ( 480) CCCTCGGAACGACCCTCAATC 1 21195 ( 478) ACTTGCACAAGAAAAACAACA 1 4765 ( 396) ACAACCGAAAGAAAAACAAGA 1 3795 ( 418) AAAACGGCAACCGCATCATCC 1 2141 ( 474) ACATCGTCATCCACATCAAGC 1 6186 ( 266) ACAACCTCACAACAGACAACC 1 25623 ( 470) CACTCACAACCTGAACAAACA 1 23691 ( 477) CAAACGCAACGATACGCAACA 1 268548 ( 462) CGTTCTCCACCTCTCCCAACC 1 1502 ( 247) TCTGCTTAACCCTACTCAACC 1 10916 ( 472) ATCTCCCACTCATATCCAACC 1 bd767 ( 471) ACCACACAAATCGATTCAACC 1 3676 ( 32) AGCTCGTCATCAAAATCATCG 1 270030 ( 351) AACACGACAACAATCCCATCA 1 1081 ( 95) ACTTCTCCTCCGGCCTCATCC 1 bd1861 ( 198) AATTGATACAGAGAAACAAGC 1 5915 ( 456) ACCAGGAAGCAACAAACAACA 1 4047 ( 211) ATTTCTCCAAATGCATCAAGC 1 1836 ( 150) TCCTCCTAAACCGCCTCGTCC 1 24489 ( 8) TTATCAGCAACGATATCAACA 1 22071 ( 402) CATTTAAAAACGGAAACAATC 1 35206 ( 107) AGAACGACATGATAAACTACA 1 10510 ( 92) CCAACGGAACCTAGTCCTACC 1 24258 ( 386) CCCGCCCAGCCCAACACGACG 1 31406 ( 457) ACTTCCGACCGGAAACGAAAA 1 24331 ( 440) ATTTCCACCCCCCATCAAATC 1 4050 ( 4) CATGCCGACTCTCCGGCAATC 1 262923 ( 303) CATGGGGCACGACAGAAAAGA 1 9636 ( 420) CGTTGCTACAATACCAGAACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 16324 bayes= 8.96502 E= 2.9e-002 94 78 -1177 -161 -6 115 -106 -120 -23 56 -1177 71 23 -1177 -106 112 -1177 183 -74 -320 -42 43 53 -88 -64 43 40 -39 110 88 -1177 -1177 142 -22 -206 -320 36 106 -1177 -61 -122 143 -6 -320 68 -2 -74 -39 10 15 26 -61 117 30 -306 -161 86 43 -147 -120 48 -2 -147 26 -164 188 -206 -1177 173 -1177 -206 -220 163 -1177 -1177 -61 -322 162 -74 -120 36 137 -206 -1177 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 35 E= 2.9e-002 0.514286 0.400000 0.000000 0.085714 0.257143 0.514286 0.114286 0.114286 0.228571 0.342857 0.000000 0.428571 0.314286 0.000000 0.114286 0.571429 0.000000 0.828571 0.142857 0.028571 0.200000 0.314286 0.342857 0.142857 0.171429 0.314286 0.314286 0.200000 0.571429 0.428571 0.000000 0.000000 0.714286 0.200000 0.057143 0.028571 0.342857 0.485714 0.000000 0.171429 0.114286 0.628571 0.228571 0.028571 0.428571 0.228571 0.142857 0.200000 0.285714 0.257143 0.285714 0.171429 0.600000 0.285714 0.028571 0.085714 0.485714 0.314286 0.085714 0.114286 0.371429 0.228571 0.085714 0.314286 0.085714 0.857143 0.057143 0.000000 0.885714 0.000000 0.057143 0.057143 0.828571 0.000000 0.000000 0.171429 0.028571 0.714286 0.142857 0.114286 0.342857 0.600000 0.057143 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [AC][CA][TCA][TA]C[GCA][CGT][AC][AC][CA][CG][ACT][AGC][AC][AC][ATC]CAAC[CA] -------------------------------------------------------------------------------- Time 29.49 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10510 7.58e-05 419_[+1(5.25e-08)]_61 1081 1.41e-06 41_[+1(4.87e-06)]_33_[+3(3.47e-05)]_\ 9_[+2(3.82e-07)]_361 10916 1.64e-03 43_[+1(1.53e-05)]_408_\ [+3(9.16e-06)]_8 10918 6.57e-09 125_[+1(1.10e-06)]_28_\ [+2(1.39e-06)]_276_[+3(1.16e-07)]_15 1502 1.84e-07 76_[+2(7.32e-06)]_155_\ [+3(7.44e-06)]_12_[+3(4.90e-05)]_23_[+1(1.25e-07)]_157 1836 1.52e-01 149_[+3(8.02e-05)]_330 21195 1.40e-05 225_[+2(2.76e-06)]_237_\ [+3(1.17e-06)]_2 2141 8.16e-05 446_[+1(4.87e-06)]_7_[+3(2.17e-06)]_\ 6 22071 4.62e-03 115_[+2(3.43e-05)]_183_\ [+2(4.13e-06)]_172 22284 2.25e-07 77_[+3(1.45e-09)]_68_[+2(3.00e-06)]_\ 17_[+2(4.81e-05)]_287 22570 1.36e-08 7_[+2(1.17e-07)]_182_[+1(4.87e-06)]_\ 255_[+3(6.89e-07)] 23691 2.77e-05 233_[+2(2.80e-07)]_228_\ [+3(5.40e-06)]_3 24258 2.30e-03 111_[+1(9.18e-07)]_369 24331 1.11e-03 196_[+1(2.75e-07)]_284 24339 3.77e-06 115_[+3(6.01e-07)]_341_\ [+1(2.47e-07)]_3 24489 8.41e-03 377_[+2(9.45e-06)]_108 25435 1.76e-06 64_[+2(5.23e-07)]_294_\ [+2(3.00e-05)]_75_[+3(1.60e-07)]_16 25623 1.97e-05 27_[+1(3.78e-07)]_422_\ [+3(4.33e-06)]_10 262573 4.04e-05 62_[+2(5.97e-06)]_76_[+3(2.54e-07)]_\ 326 262923 3.31e-01 500 268548 3.09e-10 174_[+1(4.28e-09)]_132_\ [+2(2.29e-07)]_120_[+3(6.70e-06)]_18 270030 2.09e-04 279_[+1(2.84e-06)]_51_\ [+3(2.91e-05)]_129 31406 1.21e-02 207_[+2(3.70e-05)]_53_\ [+2(7.52e-05)]_210 35206 5.05e-07 266_[+2(1.52e-05)]_131_\ [+1(9.56e-09)]_68 3676 2.40e-05 31_[+3(2.65e-05)]_24_[+2(9.73e-08)]_\ 409 3795 1.27e-02 417_[+3(2.17e-06)]_62 4047 1.04e-01 210_[+3(4.90e-05)]_269 4050 3.91e-02 24 4765 1.03e-10 61_[+1(2.12e-10)]_30_[+2(6.38e-06)]_\ 269_[+3(1.50e-06)]_84 5915 1.48e-04 402_[+1(1.76e-07)]_33_\ [+3(4.50e-05)]_24 6186 1.81e-02 265_[+3(2.75e-06)]_214 7261 2.86e-11 193_[+3(2.47e-09)]_98_\ [+2(3.70e-08)]_58_[+1(5.64e-06)]_95 9636 2.15e-04 27_[+2(2.76e-06)]_208_\ [+1(9.82e-06)]_230 bd1861 1.37e-03 64_[+1(1.27e-05)]_113_\ [+3(4.13e-05)]_282 bd767 8.43e-04 288_[+1(3.07e-06)]_162_\ [+3(1.66e-05)]_9 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************