******************************************************************************** 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/39/39.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10081 1.0000 500 11164 1.0000 500 1734 1.0000 500 1951 1.0000 500 19526 1.0000 500 1973 1.0000 500 20843 1.0000 500 21235 1.0000 500 22114 1.0000 500 24163 1.0000 500 24613 1.0000 500 25340 1.0000 500 261684 1.0000 500 26190 1.0000 500 26191 1.0000 500 263566 1.0000 500 263788 1.0000 500 269765 1.0000 500 2714 1.0000 500 27618 1.0000 500 28865 1.0000 500 29228 1.0000 500 3073 1.0000 500 31032 1.0000 500 31265 1.0000 500 31446 1.0000 500 31451 1.0000 500 34093 1.0000 500 34170 1.0000 500 34698 1.0000 500 36774 1.0000 500 3814 1.0000 500 38800 1.0000 500 39606 1.0000 500 40597 1.0000 500 41403 1.0000 500 42000 1.0000 500 4632 1.0000 500 4900 1.0000 500 7093 1.0000 500 8094 1.0000 500 8140 1.0000 500 8153 1.0000 500 8164 1.0000 500 8799 1.0000 500 9085 1.0000 500 9323 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/39/39.seqs.fa -oc motifs/39 -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= 47 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= 23500 N= 47 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.260 C 0.245 G 0.228 T 0.266 Background letter frequencies (from dataset with add-one prior applied): A 0.260 C 0.245 G 0.228 T 0.266 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 16 sites = 47 llr = 418 E-value = 2.2e-016 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 182544253:54:64: pos.-specific C 8:7536834744721a probability G ::1:1::::11::2:: matrix T :2::11:132:23:5: bits 2.1 1.9 1.7 * 1.5 * Relative 1.3 * * * * Entropy 1.1 ** * * * * (12.8 bits) 0.9 **** * * * 0.6 **** ** ** * ** 0.4 **** *** ******* 0.2 **************** 0.0 ---------------- Multilevel CACAACCACCACCATC consensus T CCAACT CATCA sequence A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 8164 473 4.67e-09 CACAACAGCT CACCACCATCAACATC CAAAACACAG 8140 307 3.40e-08 CTTTGCTAGA CACCCACACCACCAAC CCTCCCAACC 31451 470 7.29e-08 TGCGACGCTA CACCACCACCAACCAC ACGTACACAG 4632 406 3.17e-07 TGAGGAAATC CACCACCACCACCACC CGATACCCGT 39606 322 3.17e-07 TGGCGGAATC CACCACCACCACCACC GAACCAACAG 19526 485 3.85e-07 TAGGATCAAT CACAACCTTCAACAAC 28865 462 5.63e-07 CTGCATTCCA CACACCCACCACTCTC CAAACAACAA 38800 477 9.41e-07 CAACATCCAT CACACACCACATCAAC ATCACACC 27618 484 1.10e-06 CTTAATAAAC CACACACATCATCCAC C 26191 342 1.29e-06 GAGCTGTAGG CACCAACAACGCCAAC AGGCAACCTC 29228 42 1.49e-06 GGAAGGCAAA CAACAACAACAACAAC AACAACAACA 42000 132 2.34e-06 CACATTCCTC CTCAACCCACAACCTC CTCACATCCC 34093 397 2.34e-06 TGACAAAGTC CTCAACCCTCAACGTC AGCGTATCAG 4900 437 3.11e-06 GACTCTGACG CACAACCTCCCTCCTC CTTCGATACC 3814 441 4.10e-06 CCATCCTCGT AACAACCCTCATCAAC AGTGGAGACG 31446 479 4.10e-06 CCGCTTCCTC CACCTCCCTCCCCGTC AAAATC 261684 212 7.74e-06 GTCCCAATTA CAAAGCCCCCCCCCTC AGTCAGCGCC 20843 111 1.37e-05 CATCGCGCAT CTCATCCATCGACATC ATGCTACCCC 40597 456 1.90e-05 TCCTCACGTC CACCTCCATCATTGAC GGCCGTCGGC 269765 479 1.90e-05 ACCACACTTG CAGAACACACCACAAC GGCGAA 3073 259 2.34e-05 AGAGCAAATT CTGACACAACATCATC AAGACATGAA 1951 410 2.34e-05 TGTGGAGATC AAGCCCCCCCCCCAAC ACGCACACCA 41403 30 2.59e-05 CCCAAATCCT CACCGCCTCCGACGTC GGACCTCCCT 10081 208 2.59e-05 AGCTTCACCA CTCACCAAACGACAAC TCAACAAGCC 22114 391 2.86e-05 AGTCATCGTC CAAACCAATTCACATC AAAGGAAGAT 26190 443 3.16e-05 TCCTCTCACT CACAGCCACAAACGAC GACGACAGGG 34698 462 3.81e-05 TCCTTCCTTC CACAGCATCCATCGTC TCTTCGTCCA 21235 152 3.81e-05 GATCACATTT CACCGTCATCACTCAC CCGAAGCAGC 31032 210 4.58e-05 TCTTTTGACG AAACGACAACCACATC CTCACTTCTT 24613 277 4.58e-05 CGCTTCCACC CTCCACCCTTCATCTC ACATACTACT 9323 429 5.97e-05 GCCCTCGTCG CTGCCACACCCACACC GAGCGACGGT 7093 351 5.97e-05 CTGACATCTG TACCCCCCCCCCTATC TCGCCTCGAT 1734 159 5.97e-05 AAATGGTTAC CACAATCAATCATAAC AATGTTGATA 9085 478 7.70e-05 CCTTCCTTCC AAACCAACACACCATC GTCGTCA 31265 231 7.70e-05 TCACAAAGGT CACAAAAGTCACTCTC CGTCACGCCC 263566 300 1.15e-04 ACTTCTTACA CACAAACACAATCTTC CATCCAGCTC 8153 102 1.43e-04 AAAACATGCC CTCAGAAACGCCCCTC ATCCATGGCG 25340 410 1.43e-04 GTGGAACCCT CTCCTCCCTCACTTTC CCATCGGCTC 1973 329 1.43e-04 TGCCACAGAA CTCACAACAGATCAAC AACAGAATGA 2714 448 2.04e-04 TCAATCCATC ATCCAACTCTACTATC CACACCTCCT 36774 481 2.18e-04 TCGACCGCCT CACACACCTGCACATA AGTC 24163 74 2.66e-04 TAGCAATTAC AACACCACAGCATATC ATTTCCGTAT 11164 211 2.66e-04 AAAGGACAAT CAACCACGTTGCCAAC AGCGATGTGA 8799 132 2.83e-04 CAATGAAGGG CAAAACCATTCTCATG ATTGATCACA 34170 466 4.83e-04 CACGCTGACG CACCAAAAGCCCTGCC CTGTCACTCT 263788 421 6.00e-04 GTTCTTCATA AAGACAAACTACTCAC GTGCATTCAT 8094 470 7.00e-04 CCTTAGCTTC CAACTTCTCTCCCGAC AAAGAGGAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8164 4.7e-09 472_[+1]_12 8140 3.4e-08 306_[+1]_178 31451 7.3e-08 469_[+1]_15 4632 3.2e-07 405_[+1]_79 39606 3.2e-07 321_[+1]_163 19526 3.9e-07 484_[+1] 28865 5.6e-07 461_[+1]_23 38800 9.4e-07 476_[+1]_8 27618 1.1e-06 483_[+1]_1 26191 1.3e-06 341_[+1]_143 29228 1.5e-06 41_[+1]_443 42000 2.3e-06 131_[+1]_353 34093 2.3e-06 396_[+1]_88 4900 3.1e-06 436_[+1]_48 3814 4.1e-06 440_[+1]_44 31446 4.1e-06 478_[+1]_6 261684 7.7e-06 211_[+1]_273 20843 1.4e-05 110_[+1]_374 40597 1.9e-05 455_[+1]_29 269765 1.9e-05 478_[+1]_6 3073 2.3e-05 258_[+1]_226 1951 2.3e-05 409_[+1]_75 41403 2.6e-05 29_[+1]_455 10081 2.6e-05 207_[+1]_277 22114 2.9e-05 390_[+1]_94 26190 3.2e-05 442_[+1]_42 34698 3.8e-05 461_[+1]_23 21235 3.8e-05 151_[+1]_333 31032 4.6e-05 209_[+1]_275 24613 4.6e-05 276_[+1]_208 9323 6e-05 428_[+1]_56 7093 6e-05 350_[+1]_134 1734 6e-05 158_[+1]_326 9085 7.7e-05 477_[+1]_7 31265 7.7e-05 230_[+1]_254 263566 0.00011 299_[+1]_185 8153 0.00014 101_[+1]_383 25340 0.00014 409_[+1]_75 1973 0.00014 328_[+1]_156 2714 0.0002 447_[+1]_37 36774 0.00022 480_[+1]_4 24163 0.00027 73_[+1]_411 11164 0.00027 210_[+1]_274 8799 0.00028 131_[+1]_353 34170 0.00048 465_[+1]_19 263788 0.0006 420_[+1]_64 8094 0.0007 469_[+1]_15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=16 seqs=47 8164 ( 473) CACCACCATCAACATC 1 8140 ( 307) CACCCACACCACCAAC 1 31451 ( 470) CACCACCACCAACCAC 1 4632 ( 406) CACCACCACCACCACC 1 39606 ( 322) CACCACCACCACCACC 1 19526 ( 485) CACAACCTTCAACAAC 1 28865 ( 462) CACACCCACCACTCTC 1 38800 ( 477) CACACACCACATCAAC 1 27618 ( 484) CACACACATCATCCAC 1 26191 ( 342) CACCAACAACGCCAAC 1 29228 ( 42) CAACAACAACAACAAC 1 42000 ( 132) CTCAACCCACAACCTC 1 34093 ( 397) CTCAACCCTCAACGTC 1 4900 ( 437) CACAACCTCCCTCCTC 1 3814 ( 441) AACAACCCTCATCAAC 1 31446 ( 479) CACCTCCCTCCCCGTC 1 261684 ( 212) CAAAGCCCCCCCCCTC 1 20843 ( 111) CTCATCCATCGACATC 1 40597 ( 456) CACCTCCATCATTGAC 1 269765 ( 479) CAGAACACACCACAAC 1 3073 ( 259) CTGACACAACATCATC 1 1951 ( 410) AAGCCCCCCCCCCAAC 1 41403 ( 30) CACCGCCTCCGACGTC 1 10081 ( 208) CTCACCAAACGACAAC 1 22114 ( 391) CAAACCAATTCACATC 1 26190 ( 443) CACAGCCACAAACGAC 1 34698 ( 462) CACAGCATCCATCGTC 1 21235 ( 152) CACCGTCATCACTCAC 1 31032 ( 210) AAACGACAACCACATC 1 24613 ( 277) CTCCACCCTTCATCTC 1 9323 ( 429) CTGCCACACCCACACC 1 7093 ( 351) TACCCCCCCCCCTATC 1 1734 ( 159) CACAATCAATCATAAC 1 9085 ( 478) AAACCAACACACCATC 1 31265 ( 231) CACAAAAGTCACTCTC 1 263566 ( 300) CACAAACACAATCTTC 1 8153 ( 102) CTCAGAAACGCCCCTC 1 25340 ( 410) CTCCTCCCTCACTTTC 1 1973 ( 329) CTCACAACAGATCAAC 1 2714 ( 448) ATCCAACTCTACTATC 1 36774 ( 481) CACACACCTGCACATA 1 24163 ( 74) AACACCACAGCATATC 1 11164 ( 211) CAACCACGTTGCCAAC 1 8799 ( 132) CAAAACCATTCTCATG 1 34170 ( 466) CACCAAAAGCCCTGCC 1 263788 ( 421) AAGACAAACTACTCAC 1 8094 ( 470) CAACTTCTCTCCCGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 22795 bayes= 8.91886 E= 2.2e-016 -81 176 -1220 -364 156 -1220 -1220 -19 -61 156 -110 -1220 103 93 -1220 -1220 63 47 -62 -132 56 117 -1220 -206 -15 164 -1220 -1220 97 38 -242 -106 -3 64 -342 36 -261 152 -142 -64 103 56 -110 -1220 56 72 -1220 -32 -1220 160 -1220 -6 109 -7 -42 -264 63 -153 -1220 94 -361 197 -342 -1220 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 47 E= 2.2e-016 0.148936 0.829787 0.000000 0.021277 0.765957 0.000000 0.000000 0.234043 0.170213 0.723404 0.106383 0.000000 0.531915 0.468085 0.000000 0.000000 0.404255 0.340426 0.148936 0.106383 0.382979 0.553191 0.000000 0.063830 0.234043 0.765957 0.000000 0.000000 0.510638 0.319149 0.042553 0.127660 0.255319 0.382979 0.021277 0.340426 0.042553 0.702128 0.085106 0.170213 0.531915 0.361702 0.106383 0.000000 0.382979 0.404255 0.000000 0.212766 0.000000 0.744681 0.000000 0.255319 0.553191 0.234043 0.170213 0.042553 0.404255 0.085106 0.000000 0.510638 0.021277 0.957447 0.021277 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- C[AT]C[AC][AC][CA][CA][AC][CTA]C[AC][CAT][CT][AC][TA]C -------------------------------------------------------------------------------- Time 18.05 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 19 llr = 275 E-value = 4.9e-014 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :61241231::4:44:15142 pos.-specific C 121::1:::2:::::1::::: probability G 9197:7845691a53795466 matrix T 12:161:34215:133::512 bits 2.1 * 1.9 * * 1.7 * * * 1.5 * * * * * Relative 1.3 * * * * * * Entropy 1.1 * * * * * * *** (20.9 bits) 0.9 * ***** * * *** * 0.6 * ***** ****** ****** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GAGGTGGGGGGTGGAGGGTGG consensus AA AATC A ATT AGAA sequence T T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 3814 34 1.15e-10 CGAGGTCACC GAGGTGGAGGGTGGTGGGTGT GCGTAGCAGG 2714 319 6.12e-09 AATAAGGAGA GAGGAGAGGGGAGGAGAGGGG AGGTGTGTGT 34093 241 6.92e-09 AGGTGAAAAG GTGGTGAAGGGTGGAGGATGA ACAGCGTTCT 1951 367 6.92e-09 CTGCCATGGT GTGATGGGTGGTGATGGGGAG GGGTGTGAAG 4900 133 9.80e-09 GATGGGTGGA TAGGTGGATGGTGATGGATGG AGTGACTGGG 1973 83 3.54e-08 TGTCTAGTTG GAGGTTGGGCGAGGGTGAGGG ATCGGTCTAC 9323 6 4.76e-08 TGCGG GAGGAGGTGCGGGGGGAGGGG GCGAAGGCGG 263566 169 5.24e-08 GAGCAGCTTG GAGGTGGATGGTGTATGGTTG GGTGCTTGAA 28865 77 6.33e-08 ACGTGTGAGG GAGGAGGGACGTGGTTGATGT TGCTCACTCA 34170 295 6.95e-08 GCTTGGCTTG GAGAAGGAGTGAGAAGGAAAG CGCTAGCCGT 21235 326 1.00e-07 GGTTGTTGCT GAGATGAAGGGGGGGGGGAAG GAATGCAACG 8153 478 1.19e-07 TGATGCAATA GCGATAGGTTGTGAAGGAGGG AG 7093 218 1.30e-07 CGACGACGCC GTGGACGGTGGTGTGGGGGAG CATGCTCTTG 8164 167 1.42e-07 TATGACTGAG CAGGAGGTTGGAGGTGGGTAT CTATCTTTAT 31446 7 3.47e-07 GAACTG GCGGTGGTGTTAGAATGATGG GTGGCTACTT 40597 204 5.06e-07 CGGGGATGCT GGCGTCGGGGGAGGTGGAGAG GGCGGTTAGG 31265 372 5.06e-07 CGTCGAGTAA GCGTTGGTTCGTGAATGATGA CGATGATATA 26191 143 8.92e-07 ATGGAAGGAG GAAGAAAGGGGAGAGGGGGGA TGTCCAGAGT 8094 342 1.33e-06 CTTCAAATTC GAGTTGGTATGTGGACGGTAA GTATTACACG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 3814 1.2e-10 33_[+2]_446 2714 6.1e-09 318_[+2]_161 34093 6.9e-09 240_[+2]_239 1951 6.9e-09 366_[+2]_113 4900 9.8e-09 132_[+2]_347 1973 3.5e-08 82_[+2]_397 9323 4.8e-08 5_[+2]_474 263566 5.2e-08 168_[+2]_311 28865 6.3e-08 76_[+2]_403 34170 6.9e-08 294_[+2]_185 21235 1e-07 325_[+2]_154 8153 1.2e-07 477_[+2]_2 7093 1.3e-07 217_[+2]_262 8164 1.4e-07 166_[+2]_313 31446 3.5e-07 6_[+2]_473 40597 5.1e-07 203_[+2]_276 31265 5.1e-07 371_[+2]_108 26191 8.9e-07 142_[+2]_337 8094 1.3e-06 341_[+2]_138 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=19 3814 ( 34) GAGGTGGAGGGTGGTGGGTGT 1 2714 ( 319) GAGGAGAGGGGAGGAGAGGGG 1 34093 ( 241) GTGGTGAAGGGTGGAGGATGA 1 1951 ( 367) GTGATGGGTGGTGATGGGGAG 1 4900 ( 133) TAGGTGGATGGTGATGGATGG 1 1973 ( 83) GAGGTTGGGCGAGGGTGAGGG 1 9323 ( 6) GAGGAGGTGCGGGGGGAGGGG 1 263566 ( 169) GAGGTGGATGGTGTATGGTTG 1 28865 ( 77) GAGGAGGGACGTGGTTGATGT 1 34170 ( 295) GAGAAGGAGTGAGAAGGAAAG 1 21235 ( 326) GAGATGAAGGGGGGGGGGAAG 1 8153 ( 478) GCGATAGGTTGTGAAGGAGGG 1 7093 ( 218) GTGGACGGTGGTGTGGGGGAG 1 8164 ( 167) CAGGAGGTTGGAGGTGGGTAT 1 31446 ( 7) GCGGTGGTGTTAGAATGATGG 1 40597 ( 204) GGCGTCGGGGGAGGTGGAGAG 1 31265 ( 372) GCGTTGGTTCGTGAATGATGA 1 26191 ( 143) GAAGAAAGGGGAGAGGGGGGA 1 8094 ( 342) GAGTTGGTATGTGGACGGTAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 22560 bayes= 11.1103 E= 4.9e-014 -1089 -222 197 -234 128 -63 -211 -75 -230 -222 197 -1089 -31 -1089 158 -134 50 -1089 -1089 125 -131 -122 169 -234 -31 -1089 179 -1089 28 -1089 88 -2 -131 -1089 121 47 -1089 -22 134 -34 -1089 -1089 205 -234 50 -1089 -112 98 -1089 -1089 213 -1089 50 -1089 121 -134 69 -1089 21 25 -1089 -222 158 -2 -131 -1089 197 -1089 86 -1089 121 -1089 -131 -1089 88 83 50 -1089 134 -234 -31 -1089 147 -75 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 19 E= 4.9e-014 0.000000 0.052632 0.894737 0.052632 0.631579 0.157895 0.052632 0.157895 0.052632 0.052632 0.894737 0.000000 0.210526 0.000000 0.684211 0.105263 0.368421 0.000000 0.000000 0.631579 0.105263 0.105263 0.736842 0.052632 0.210526 0.000000 0.789474 0.000000 0.315789 0.000000 0.421053 0.263158 0.105263 0.000000 0.526316 0.368421 0.000000 0.210526 0.578947 0.210526 0.000000 0.000000 0.947368 0.052632 0.368421 0.000000 0.105263 0.526316 0.000000 0.000000 1.000000 0.000000 0.368421 0.000000 0.526316 0.105263 0.421053 0.000000 0.263158 0.315789 0.000000 0.052632 0.684211 0.263158 0.105263 0.000000 0.894737 0.000000 0.473684 0.000000 0.526316 0.000000 0.105263 0.000000 0.421053 0.473684 0.368421 0.000000 0.578947 0.052632 0.210526 0.000000 0.631579 0.157895 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- GAG[GA][TA]G[GA][GAT][GT][GCT]G[TA]G[GA][ATG][GT]G[GA][TG][GA][GA] -------------------------------------------------------------------------------- Time 35.11 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 25 llr = 263 E-value = 8.3e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :1::2::2::324::: pos.-specific C :::::::4:132:4:: probability G 52:a4:a2:9122236 matrix T 46a:4a:3a:344474 bits 2.1 1.9 * * * 1.7 ** ** ** 1.5 ** ** ** Relative 1.3 ** ** ** Entropy 1.1 ** ** ** (15.2 bits) 0.9 * ** ** ** ** 0.6 **** ** ** ** 0.4 ******* ** ** 0.2 ******* ** **** 0.0 ---------------- Multilevel GTTGGTGCTGTTATTG consensus TG T T AATCGT sequence A CC G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 11164 299 9.27e-08 TACGATGTCA TTTGGTGCTGGTTTTG CACCAGCAGC 40597 264 1.18e-07 TTTTGACGGG GTTGGTGTTGCTTTGG TAGTTGCTGG 31451 36 1.18e-07 GCGCCGAATC GTTGTTGGTGCTACTG CTGTTGCCGA 9323 240 2.39e-07 ATTGCTCGCT GTTGTTGTTGTTGCTG TAGCGTATGT 29228 300 3.49e-07 GTTATTTTGT GTTGGTGTTGTGTCGG ATACTTCGGC 7093 105 5.08e-07 GGCGTGGAGG GTTGTTGATGCTGCTG ATGATATGTG 28865 256 1.22e-06 GTATTTGTTC TTTGGTGGTGCATCTT GAAGAAAATG 34170 41 1.56e-06 TACTGTTGCT GTTGCTGCTGCTACTG GAGGGGGAGG 24613 427 2.16e-06 CTGTGGTTGC GTTGTTGTTGATTGGT CTCGCCTGCG 10081 166 2.62e-06 TTTGGTATTG TTTGGTGGTGAAAGTT CAAATGAAAA 26190 3 3.45e-06 GC TTTGTTGCTGGATGTT GCTCCCTTTT 27618 120 3.77e-06 GGCGTTGCGA TGTGTTGCTGTGATGT TGTGTTGTTA 4632 251 6.16e-06 TTCCATCATT GTTGTTGCTGATATCT TCTGATTTCT 34698 79 7.28e-06 GATTGACCCT TATGGTGATGACTTGG AGGACTTGAG 24163 177 8.55e-06 GTGTTTAGAT GATGATGATGAAATTG TCAATACATC 22114 10 8.55e-06 CGAAGCGCA CTTGGTGTTGACTGTG GCGACCGACC 21235 2 1.27e-05 T GTTGTTGGTGCGAAGG CTGACGATTT 3814 92 1.48e-05 TTGACATGAT GTTGTTGCTCGATGTG ATGTGTGGAG 20843 441 1.48e-05 CATGATCGTC TGTTGTGCTGTGATTG TTCACTAACA 26191 83 1.85e-05 ACCTTTGGGC GGTGGAGCTGTGGTTG AGTTCATCGT 261684 265 1.85e-05 TCCATGGTGG TGTGGTACTGATACTT TTTCACAGCT 8094 425 3.19e-05 CTTTGACATT GTTGATGATGTCTTGC TGACGTTCAG 38800 70 3.39e-05 ATGCGTATTC TGCGGTGATGTCATTT ATTGGTAGCC 4900 9 4.29e-05 CATGATGT TATGATGTTGCTCCTT GATGGCACCG 1951 1 4.81e-05 . TGTGATGTTCTCGCTG GATGAACCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11164 9.3e-08 298_[+3]_186 40597 1.2e-07 263_[+3]_221 31451 1.2e-07 35_[+3]_449 9323 2.4e-07 239_[+3]_245 29228 3.5e-07 299_[+3]_185 7093 5.1e-07 104_[+3]_380 28865 1.2e-06 255_[+3]_229 34170 1.6e-06 40_[+3]_444 24613 2.2e-06 426_[+3]_58 10081 2.6e-06 165_[+3]_319 26190 3.4e-06 2_[+3]_482 27618 3.8e-06 119_[+3]_365 4632 6.2e-06 250_[+3]_234 34698 7.3e-06 78_[+3]_406 24163 8.6e-06 176_[+3]_308 22114 8.6e-06 9_[+3]_475 21235 1.3e-05 1_[+3]_483 3814 1.5e-05 91_[+3]_393 20843 1.5e-05 440_[+3]_44 26191 1.9e-05 82_[+3]_402 261684 1.9e-05 264_[+3]_220 8094 3.2e-05 424_[+3]_60 38800 3.4e-05 69_[+3]_415 4900 4.3e-05 8_[+3]_476 1951 4.8e-05 [+3]_484 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=25 11164 ( 299) TTTGGTGCTGGTTTTG 1 40597 ( 264) GTTGGTGTTGCTTTGG 1 31451 ( 36) GTTGTTGGTGCTACTG 1 9323 ( 240) GTTGTTGTTGTTGCTG 1 29228 ( 300) GTTGGTGTTGTGTCGG 1 7093 ( 105) GTTGTTGATGCTGCTG 1 28865 ( 256) TTTGGTGGTGCATCTT 1 34170 ( 41) GTTGCTGCTGCTACTG 1 24613 ( 427) GTTGTTGTTGATTGGT 1 10081 ( 166) TTTGGTGGTGAAAGTT 1 26190 ( 3) TTTGTTGCTGGATGTT 1 27618 ( 120) TGTGTTGCTGTGATGT 1 4632 ( 251) GTTGTTGCTGATATCT 1 34698 ( 79) TATGGTGATGACTTGG 1 24163 ( 177) GATGATGATGAAATTG 1 22114 ( 10) CTTGGTGTTGACTGTG 1 21235 ( 2) GTTGTTGGTGCGAAGG 1 3814 ( 92) GTTGTTGCTCGATGTG 1 20843 ( 441) TGTTGTGCTGTGATTG 1 26191 ( 83) GGTGGAGCTGTGGTTG 1 261684 ( 265) TGTGGTACTGATACTT 1 8094 ( 425) GTTGATGATGTCTTGC 1 38800 ( 70) TGCGGTGATGTCATTT 1 4900 ( 9) TATGATGTTGCTCCTT 1 1951 ( 1) TGTGATGTTCTCGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 22795 bayes= 10.3215 E= 8.3e-004 -1129 -261 119 73 -112 -1129 7 127 -1129 -261 -1129 185 -1129 -1129 207 -273 -70 -261 95 44 -270 -1129 -1129 185 -270 -1129 207 -1129 -38 55 -51 7 -1129 -1129 -1129 191 -1129 -161 201 -1129 10 19 -93 27 -38 -29 -19 59 62 -261 -51 59 -270 55 -19 59 -1129 -261 29 135 -1129 -261 139 44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 25 E= 8.3e-004 0.000000 0.040000 0.520000 0.440000 0.120000 0.000000 0.240000 0.640000 0.000000 0.040000 0.000000 0.960000 0.000000 0.000000 0.960000 0.040000 0.160000 0.040000 0.440000 0.360000 0.040000 0.000000 0.000000 0.960000 0.040000 0.000000 0.960000 0.000000 0.200000 0.360000 0.160000 0.280000 0.000000 0.000000 0.000000 1.000000 0.000000 0.080000 0.920000 0.000000 0.280000 0.280000 0.120000 0.320000 0.200000 0.200000 0.200000 0.400000 0.400000 0.040000 0.160000 0.400000 0.040000 0.360000 0.200000 0.400000 0.000000 0.040000 0.280000 0.680000 0.000000 0.040000 0.600000 0.360000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GT][TG]TG[GT]TG[CTA]TG[TAC][TACG][AT][TCG][TG][GT] -------------------------------------------------------------------------------- Time 52.20 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10081 2.03e-04 165_[+3(2.62e-06)]_26_\ [+1(2.59e-05)]_277 11164 4.10e-04 298_[+3(9.27e-08)]_148_\ [+3(7.39e-05)]_22 1734 5.80e-02 158_[+1(5.97e-05)]_326 1951 2.08e-07 [+3(4.81e-05)]_350_[+2(6.92e-09)]_\ 22_[+1(2.34e-05)]_75 19526 1.51e-03 484_[+1(3.85e-07)] 1973 1.01e-04 82_[+2(3.54e-08)]_349_\ [+2(1.20e-05)]_27 20843 1.60e-03 110_[+1(1.37e-05)]_314_\ [+3(1.48e-05)]_44 21235 1.09e-06 1_[+3(1.27e-05)]_134_[+1(3.81e-05)]_\ 158_[+2(1.00e-07)]_154 22114 4.88e-04 9_[+3(8.55e-06)]_365_[+1(2.86e-05)]_\ 94 24163 3.59e-03 176_[+3(8.55e-06)]_83_\ [+3(1.48e-05)]_34_[+3(3.39e-05)]_159 24613 6.88e-04 276_[+1(4.58e-05)]_117_\ [+3(6.65e-05)]_1_[+3(2.16e-06)]_58 25340 9.74e-02 500 261684 9.44e-04 211_[+1(7.74e-06)]_37_\ [+3(1.85e-05)]_220 26190 4.82e-04 2_[+3(3.45e-06)]_424_[+1(3.16e-05)]_\ 42 26191 5.21e-07 82_[+3(1.85e-05)]_44_[+2(8.92e-07)]_\ 178_[+1(1.29e-06)]_143 263566 2.16e-05 168_[+2(5.24e-08)]_311 263788 1.01e-01 358_[+2(7.72e-05)]_121 269765 1.33e-01 478_[+1(1.90e-05)]_6 2714 2.51e-05 318_[+2(6.12e-09)]_161 27618 2.57e-06 119_[+3(3.77e-06)]_46_\ [+2(3.04e-05)]_281_[+1(1.10e-06)]_1 28865 1.79e-09 76_[+2(6.33e-08)]_158_\ [+3(1.22e-06)]_190_[+1(5.63e-07)]_23 29228 8.20e-06 41_[+1(1.49e-06)]_2_[+1(1.49e-06)]_\ 224_[+3(3.49e-07)]_185 3073 1.75e-01 258_[+1(2.34e-05)]_226 31032 2.63e-02 209_[+1(4.58e-05)]_275 31265 6.73e-04 230_[+1(7.70e-05)]_125_\ [+2(5.06e-07)]_108 31446 2.48e-05 6_[+2(3.47e-07)]_451_[+1(4.10e-06)]_\ 6 31451 3.00e-08 35_[+3(1.18e-07)]_418_\ [+1(7.29e-08)]_15 34093 6.03e-07 240_[+2(6.92e-09)]_135_\ [+1(2.34e-06)]_46_[+1(3.47e-05)]_26 34170 1.06e-06 40_[+3(1.56e-06)]_47_[+2(7.47e-05)]_\ 170_[+2(6.95e-08)]_185 34698 1.84e-03 78_[+3(7.28e-06)]_301_\ [+1(9.81e-05)]_50_[+1(3.81e-05)]_23 36774 4.07e-01 500 3814 3.28e-10 33_[+2(1.15e-10)]_37_[+3(1.48e-05)]_\ 333_[+1(4.10e-06)]_44 38800 5.05e-05 69_[+3(3.39e-05)]_391_\ [+1(9.41e-07)]_8 39606 7.39e-03 321_[+1(3.17e-07)]_26_\ [+1(4.10e-06)]_121 40597 3.62e-08 75_[+2(1.31e-05)]_47_[+2(7.17e-06)]_\ 39_[+2(5.06e-07)]_39_[+3(1.18e-07)]_176_[+1(1.90e-05)]_29 41403 2.28e-02 29_[+1(2.59e-05)]_455 42000 2.16e-02 131_[+1(2.34e-06)]_208_\ [+1(2.34e-05)]_82_[+1(5.33e-06)]_31 4632 5.59e-05 250_[+3(6.16e-06)]_139_\ [+1(3.17e-07)]_79 4900 4.10e-08 8_[+3(4.29e-05)]_86_[+2(4.51e-05)]_\ 1_[+2(9.80e-09)]_283_[+1(3.11e-06)]_48 7093 1.12e-07 104_[+3(5.08e-07)]_97_\ [+2(1.30e-07)]_112_[+1(5.97e-05)]_134 8094 2.69e-04 341_[+2(1.33e-06)]_62_\ [+3(3.19e-05)]_60 8140 1.60e-05 205_[+2(3.65e-05)]_80_\ [+1(3.40e-08)]_159_[+1(1.71e-05)]_3 8153 2.10e-04 477_[+2(1.19e-07)]_2 8164 6.88e-09 166_[+2(1.42e-07)]_46_\ [+2(6.77e-05)]_218_[+1(4.67e-09)]_12 8799 1.37e-01 500 9085 2.87e-01 477_[+1(7.70e-05)]_7 9323 2.24e-08 5_[+2(4.76e-08)]_8_[+2(6.34e-05)]_\ 184_[+3(2.39e-07)]_173_[+1(5.97e-05)]_56 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************