******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 2.2 (Release date: 1998/02/27 00:47:06) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.sdsc.edu. 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.sdsc.edu. ******************************************************************************** ******************************************************************************** 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= meme.47756.data (deleted by web version of MEME) ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ iRDN5-1 1.0000 1121 iSNR7-S 1.0000 251 itE(UUC)E2 1.0000 136 itG(GCC)E 1.0000 122 itL(CAA)A 1.0000 1269 iYAL003W 1.0000 841 iYBL003C 1.0000 701 iYBL022C 1.0000 386 iYBLWtau1 1.0000 178 iYBR297W 1.0000 703 iYCR062W 1.0000 485 iYCR063W 1.0000 519 iYDL004W 1.0000 1173 iYDL018C 1.0000 700 iYDL055C-0 1.0000 1410 iYDL101C 1.0000 265 iYDR138W 1.0000 783 iYDR189W 1.0000 213 iYDR263C 1.0000 496 iYDR296W 1.0000 660 iYDR441C 1.0000 586 iYDR507C 1.0000 668 iYEL002C 1.0000 288 iYEL074W 1.0000 767 iYER069W 1.0000 950 iYER094C 1.0000 635 iYER111C 1.0000 1357 iYER124C 1.0000 1127 iYERWdelta7 1.0000 244 iYERWomega2-0 1.0000 1066 iYGL008C 1.0000 595 iYGR107W 1.0000 521 iYGR109C 1.0000 608 iYHL049C-0 1.0000 931 iYHR142W 1.0000 1023 iYHR149C 1.0000 593 iYJL196C 1.0000 460 iYJR030C 1.0000 391 iYKL039W 1.0000 559 iYKL103C 1.0000 381 iYKL113C 1.0000 696 iYKL114C 1.0000 273 iYKL185W 1.0000 493 iYLR103C 1.0000 645 iYLR299W 1.0000 905 iYLR449W 1.0000 617 iYMR178W 1.0000 556 iYMR214W 1.0000 314 iYMR305C 1.0000 928 iYNL031C 1.0000 678 iYNL103W 1.0000 335 iYNL279W 1.0000 370 iYNL283C 1.0000 993 iYNL313C 1.0000 266 iYNR008W 1.0000 310 iYOL010W 1.0000 284 iYOR074C 1.0000 624 iYOR229W 1.0000 989 iYPR076W 1.0000 282 iYPR078C 1.0000 606 iYPR155C 1.0000 497 SNR63 1.0000 255 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 6 sites = 46.4 ******************************************************************************** Simplified A 2::::: motif letter- C 161611 probability G 417:51 matrix T 332338 bits 2.2 2.0 1.7 1.5 Information 1.3 content 1.1 (4.2 bits) 0.9 * 0.7 *** * 0.4 ***** 0.2 ***** 0.0 ------ Multilevel GCGCGT consensus TTTTT sequence A -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=6 seqs=62 iYOL010W ( 184) GCGCGT 0.710768 // ------------------------------------------------------------------- Possible examples of motif 1 in the training set ------------------------------------------------------------------- Sequence name Start Score Site ------------- ----- ----- ------ ------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 37768 bayes= 9.66564 -0.321 -0.987 0.730 0.081 -3.655 1.539 -2.042 0.050 -3.099 -1.927 1.621 -0.384 -4.243 1.443 -2.692 0.372 -3.528 -1.319 1.258 0.344 -3.259 -1.048 -1.971 1.590 letter-probability matrix: alength= 4 w= 6 n= 37768 0.225528 0.112043 0.379739 0.282690 0.022361 0.645223 0.055567 0.276849 0.032888 0.058398 0.703797 0.204917 0.014876 0.603691 0.035410 0.346023 0.024431 0.088977 0.547314 0.339278 0.029425 0.107352 0.058370 0.804853 Time 61.74 secs. ******************************************************************************** MOTIF 2 width = 6 sites = 19.2 ******************************************************************************** Simplified A 111111 motif letter- C 222323 probability G 212111 matrix T 566665 bits 2.2 2.0 1.7 1.5 Information 1.3 content 1.1 (2.3 bits) 0.9 0.7 0.4 * * 0.2 ****** 0.0 ------ Multilevel TTTTTT consensus CC CCC sequence -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=6 seqs=62 // ------------------------------------------------------------------- Possible examples of motif 2 in the training set ------------------------------------------------------------------- Sequence name Start Score Site ------------- ----- ----- ------ ------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 37768 bayes= 10.9411 -1.876 0.120 -0.551 0.976 -2.104 0.068 -1.061 1.147 -2.045 -0.327 -0.461 1.138 -2.335 0.171 -1.044 1.125 -2.013 -0.035 -0.632 1.082 -1.859 0.223 -0.801 0.992 letter-probability matrix: alength= 4 w= 6 n= 37768 0.076766 0.241351 0.156172 0.525711 0.065543 0.232782 0.109736 0.591939 0.068261 0.176971 0.166306 0.588463 0.055840 0.250019 0.111014 0.583126 0.069817 0.216661 0.147648 0.565873 0.077693 0.259216 0.131327 0.531765 Time 123.10 secs. ******************************************************************************** MOTIF 3 width = 6 sites = 15.9 ******************************************************************************** Simplified A 111111 motif letter- C 222323 probability G 212121 matrix T 565555 bits 2.2 2.0 1.7 1.5 Information 1.3 content 1.1 (1.9 bits) 0.9 0.7 0.4 0.2 ****** 0.0 ------ Multilevel TTTTTT consensus CC CCC sequence -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=6 seqs=62 // ------------------------------------------------------------------- Possible examples of motif 3 in the training set ------------------------------------------------------------------- Sequence name Start Score Site ------------- ----- ----- ------ ------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 37768 bayes= 11.2121 -1.658 0.156 -0.430 0.884 -1.865 0.158 -0.898 1.047 -1.808 -0.222 -0.330 1.033 -2.075 0.240 -0.881 1.032 -1.776 0.036 -0.494 0.981 -1.637 0.256 -0.678 0.907 letter-probability matrix: alength= 4 w= 6 n= 37768 0.089294 0.247429 0.169834 0.493443 0.077343 0.247650 0.122827 0.552181 0.080489 0.190347 0.182041 0.547124 0.066897 0.262115 0.124291 0.546697 0.082253 0.227695 0.162483 0.527569 0.090616 0.265154 0.143035 0.501194 Time 184.51 secs. ******************************************************************************** MOTIF 4 width = 6 sites = 13.8 ******************************************************************************** Simplified A 111111 motif letter- C 332323 probability G 212122 matrix T 555555 bits 2.2 2.0 1.7 1.5 Information 1.3 content 1.1 (1.6 bits) 0.9 0.7 0.4 0.2 ***** 0.0 ------ Multilevel TTTTTT consensus CC CCC sequence -------------------------------------------------------------------------------- Motif 4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 4 width=6 seqs=62 // ------------------------------------------------------------------- Possible examples of motif 4 in the training set ------------------------------------------------------------------- Sequence name Start Score Site ------------- ----- ----- ------ ------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 37768 bayes= 11.4129 -1.505 0.175 -0.356 0.818 -1.697 0.208 -0.790 0.972 -1.642 -0.157 -0.251 0.955 -1.890 0.277 -0.771 0.962 -1.612 0.078 -0.407 0.906 -1.482 0.272 -0.597 0.843 letter-probability matrix: alength= 4 w= 6 n= 37768 0.099272 0.250604 0.178886 0.471239 0.086887 0.256492 0.132330 0.524291 0.090290 0.199125 0.192302 0.518283 0.076024 0.268960 0.134137 0.520880 0.092186 0.234339 0.172590 0.500884 0.100862 0.268154 0.151320 0.479665 Time 245.92 secs. ******************************************************************************** MOTIF 5 width = 6 sites = 12.4 ******************************************************************************** Simplified A 111111 motif letter- C 332323 probability G 212122 matrix T 555555 bits 2.2 2.0 1.7 1.5 Information 1.3 content 1.1 (1.4 bits) 0.9 0.7 0.4 0.2 **** 0.0 ------ Multilevel TTTTTT consensus CCCCCC sequence -------------------------------------------------------------------------------- Motif 5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 5 width=6 seqs=62 // ------------------------------------------------------------------- Possible examples of motif 5 in the training set ------------------------------------------------------------------- Sequence name Start Score Site ------------- ----- ----- ------ ------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 37768 bayes= 11.5733 -1.388 0.185 -0.304 0.766 -1.568 0.240 -0.711 0.912 -1.515 -0.112 -0.198 0.893 -1.747 0.299 -0.689 0.906 -1.486 0.105 -0.346 0.846 -1.364 0.281 -0.538 0.793 letter-probability matrix: alength= 4 w= 6 n= 37768 0.107683 0.252382 0.185451 0.454485 0.095034 0.262202 0.139774 0.502990 0.098592 0.205452 0.199586 0.496370 0.083931 0.273149 0.141946 0.500973 0.100585 0.238750 0.180061 0.480605 0.109478 0.269748 0.157670 0.463105 Time 307.33 secs. ******************************************************************************** MOTIF 6 width = 6 sites = 11.3 ******************************************************************************** Simplified A 111111 motif letter- C 332323 probability G 212122 matrix T 455554 bits 2.2 2.0 1.7 1.5 Information 1.3 content 1.1 (1.3 bits) 0.9 0.7 0.4 0.2 * * 0.0 ------ Multilevel TTTTTT consensus CCCCCC sequence G -------------------------------------------------------------------------------- Motif 6 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 6 width=6 seqs=62 // ------------------------------------------------------------------- Possible examples of motif 6 in the training set ------------------------------------------------------------------- Sequence name Start Score Site ------------- ----- ----- ------ ------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 37768 bayes= 11.7073 -1.293 0.191 -0.265 0.723 -1.463 0.261 -0.650 0.862 -1.413 -0.078 -0.159 0.841 -1.631 0.313 -0.625 0.859 -1.385 0.123 -0.300 0.797 -1.268 0.285 -0.492 0.750 letter-probability matrix: alength= 4 w= 6 n= 37768 0.115003 0.253378 0.190480 0.441139 0.102202 0.266046 0.145868 0.485884 0.105847 0.210264 0.205030 0.478859 0.090970 0.275787 0.148392 0.484851 0.107917 0.241837 0.185859 0.464388 0.116966 0.270554 0.162775 0.449705 Time 368.73 secs. ******************************************************************************** MOTIF 7 width = 6 sites = 10.4 ******************************************************************************** Simplified A 111111 motif letter- C 332323 probability G 222222 matrix T 455554 bits 2.2 2.0 1.7 1.5 Information 1.3 content 1.1 (1.1 bits) 0.9 0.7 0.4 0.2 * * 0.0 ------ Multilevel TTTTTT consensus CCCCCC sequence G -------------------------------------------------------------------------------- Motif 7 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 7 width=6 seqs=62 // ------------------------------------------------------------------- Possible examples of motif 7 in the training set ------------------------------------------------------------------- Sequence name Start Score Site ------------- ----- ----- ------ ------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 37768 bayes= 11.8224 -1.214 0.194 -0.235 0.686 -1.375 0.275 -0.600 0.819 -1.327 -0.053 -0.129 0.797 -1.533 0.321 -0.573 0.818 -1.300 0.137 -0.265 0.754 -1.189 0.287 -0.455 0.714 letter-probability matrix: alength= 4 w= 6 n= 37768 0.121504 0.253898 0.194470 0.430128 0.108628 0.268679 0.151000 0.471693 0.112313 0.214054 0.209232 0.464401 0.097338 0.277435 0.153849 0.471378 0.114449 0.244066 0.190501 0.450985 0.123611 0.270877 0.167008 0.438504 Time 430.13 secs. ******************************************************************************** MOTIF 8 width = 6 sites = 9.7 ******************************************************************************** Simplified A 111111 motif letter- C 332323 probability G 222222 matrix T 455544 bits 2.2 2.0 1.7 1.5 Information 1.3 content 1.1 (1.0 bits) 0.9 0.7 0.4 0.2 * 0.0 ------ Multilevel TTTTTT consensus CCCCCC sequence G -------------------------------------------------------------------------------- Motif 8 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 8 width=6 seqs=62 // ------------------------------------------------------------------- Possible examples of motif 8 in the training set ------------------------------------------------------------------- Sequence name Start Score Site ------------- ----- ----- ------ ------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 37768 bayes= 11.9232 -1.146 0.195 -0.211 0.655 -1.300 0.285 -0.558 0.782 -1.254 -0.032 -0.107 0.758 -1.450 0.327 -0.530 0.783 -1.227 0.146 -0.236 0.718 -1.121 0.287 -0.424 0.682 letter-probability matrix: alength= 4 w= 6 n= 37768 0.127358 0.254110 0.197715 0.420817 0.114464 0.270481 0.155412 0.459643 0.118157 0.217114 0.212549 0.452179 0.103168 0.278415 0.158557 0.459860 0.120350 0.245705 0.194304 0.439641 0.129593 0.270887 0.170596 0.428924 Time 491.54 secs. ******************************************************************************** MOTIF 9 width = 6 sites = 9.1 ******************************************************************************** Simplified A 111111 motif letter- C 332323 probability G 222222 matrix T 444444 bits 2.2 2.0 1.7 1.5 Information 1.3 content 1.1 (0.9 bits) 0.9 0.7 0.4 0.2 0.0 ------ Multilevel TTTTTT consensus CCCCCC sequence G G -------------------------------------------------------------------------------- Motif 9 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 9 width=6 seqs=62 // ------------------------------------------------------------------- Possible examples of motif 9 in the training set ------------------------------------------------------------------- Sequence name Start Score Site ------------- ----- ----- ------ ------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 37768 bayes= 12.013 -1.086 0.195 -0.192 0.627 -1.234 0.291 -0.523 0.749 -1.190 -0.016 -0.089 0.724 -1.376 0.329 -0.493 0.751 -1.164 0.153 -0.213 0.685 -1.061 0.286 -0.398 0.654 letter-probability matrix: alength= 4 w= 6 n= 37768 0.132691 0.254118 0.200410 0.412780 0.119821 0.271698 0.159268 0.449212 0.123498 0.219634 0.215223 0.441644 0.108555 0.278933 0.162680 0.449831 0.125741 0.246927 0.197479 0.429853 0.135043 0.270687 0.173695 0.420575 Time 552.94 secs. ******************************************************************************** MOTIF 10 width = 6 sites = 8.6 ******************************************************************************** Simplified A 111111 motif letter- C 332323 probability G 222222 matrix T 444444 bits 2.2 2.0 1.7 1.5 Information 1.3 content 1.1 (0.9 bits) 0.9 0.7 0.4 0.2 0.0 ------ Multilevel TTTTTT consensus CCCCCC sequence G G G -------------------------------------------------------------------------------- Motif 10 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 10 width=6 seqs=62 // ------------------------------------------------------------------- Possible examples of motif 10 in the training set ------------------------------------------------------------------- Sequence name Start Score Site ------------- ----- ----- ------ ------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 37768 bayes= 12.0939 -1.034 0.194 -0.175 0.602 -1.175 0.296 -0.493 0.719 -1.134 -0.002 -0.074 0.694 -1.311 0.330 -0.461 0.722 -1.108 0.159 -0.193 0.656 -1.009 0.284 -0.376 0.628 letter-probability matrix: alength= 4 w= 6 n= 37768 0.137588 0.253985 0.202684 0.405743 0.124773 0.272490 0.162680 0.440058 0.128418 0.221740 0.217406 0.432436 0.113564 0.279120 0.166331 0.440985 0.130704 0.247839 0.200169 0.421288 0.140046 0.270346 0.176405 0.413204 Time 614.34 secs. Stopped because nmotifs = 10 reached. CPU: golden