******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 3.5.4 (Release date: ) 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= HEM3-HEM13.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ SGD_Scer_YDL205C 1.0000 860 MIT_Spar_c429_3020 1.0000 860 MIT_Smik_c193_2483 1.0000 860 MIT_Sbay_c841_3215 1.0000 860 WashU_Skud_Contig1850.5 1.0000 860 SGD_Scer_YDR044W 1.0000 1000 MIT_Spar_c130_3912 1.0000 1000 MIT_Sbay_c896_21290 1.0000 1000 WashU_Smik_Contig2283.3 1.0000 1000 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme HEM3-HEM13.fa -nostatus -dna -revcomp -nmotifs 5 -bfile yeast.nc.1.freq -maxw 20 -mod oops -dir /Volumes/DATA/Home/ajr/sw/powerpc/meme-3.5.4 model: mod= oops nmotifs= 5 evt= inf object function= E-value of product of p-values width: minw= 6 maxw= 20 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 9 maxsites= 9 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 8300 N= 9 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.301 C 0.199 G 0.199 T 0.301 Background letter frequencies (from yeast.nc.1.freq): A 0.324 C 0.176 G 0.176 T 0.324 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 20 sites = 9 llr = 197 E-value = 2.8e-022 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::::9692aa4:4::aa:a pos.-specific C :::::::::::::::3::9: probability G aa:aa1412::666:6:::: matrix T ::a:::::6:::4:a1::1: bits 2.5 ** ** 2.3 ** ** 2.0 ** ** * 1.8 ** ** * Information 1.5 ***** ** * **** content 1.3 ****** * ** * **** (31.6 bits) 1.0 ******** *********** 0.8 ******** *********** 0.5 ******************** 0.3 ******************** 0.0 -------------------- Multilevel GGTGGAAATAAGGGTGAACA consensus G A ATA C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------------------- WashU_Skud_Contig1850.5 - 716 1.22e-12 ATCCTTTGAG GGTGGAAATAAGGGTGAACA ATAAGGGGAG MIT_Sbay_c841_3215 - 735 1.22e-12 GTCGTTTGAG GGTGGAAATAAGGGTGAACA ATAAGGGGAG MIT_Spar_c429_3020 - 709 1.22e-12 ATCGTTTGAG GGTGGAAATAAGGGTGAACA ATAAGGGGAG SGD_Scer_YDL205C - 708 1.22e-12 ATCGTTTGAG GGTGGAAATAAGGGTGAACA ATAAGGGGAG MIT_Smik_c193_2483 - 709 1.22e-10 ATCGTTTGAG GGTGGAAATAAGGGTGAATA ATAAGGGGAG MIT_Spar_c130_3912 + 679 1.35e-10 CAACGATTGT GGTGGAGAGAAATATCAACA GGGCAAGGCA SGD_Scer_YDR044W + 684 3.84e-10 CAACAATTAC GGTGGGGAGAAATATCAACA AAAGGGCAAG MIT_Sbay_c896_21290 + 685 5.43e-10 CGACTAAAAC GGTGGAGGAAAATATCAACA AGGCAAGGCT WashU_Smik_Contig2283.3 + 687 5.84e-10 CAACAATTAC GGTGGAGAAAAATATTAACA AGGGAAGGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- WashU_Skud_Contig1850.5 1.2e-12 715_[-1]_125 MIT_Sbay_c841_3215 1.2e-12 734_[-1]_106 MIT_Spar_c429_3020 1.2e-12 708_[-1]_132 SGD_Scer_YDL205C 1.2e-12 707_[-1]_133 MIT_Smik_c193_2483 1.2e-10 708_[-1]_132 MIT_Spar_c130_3912 1.4e-10 678_[+1]_302 SGD_Scer_YDR044W 3.8e-10 683_[+1]_297 MIT_Sbay_c896_21290 5.4e-10 684_[+1]_296 WashU_Smik_Contig2283.3 5.8e-10 686_[+1]_294 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=20 seqs=9 WashU_Skud_Contig1850.5 ( 716) GGTGGAAATAAGGGTGAACA 1 MIT_Sbay_c841_3215 ( 735) GGTGGAAATAAGGGTGAACA 1 MIT_Spar_c429_3020 ( 709) GGTGGAAATAAGGGTGAACA 1 SGD_Scer_YDL205C ( 708) GGTGGAAATAAGGGTGAACA 1 MIT_Smik_c193_2483 ( 709) GGTGGAAATAAGGGTGAATA 1 MIT_Spar_c130_3912 ( 679) GGTGGAGAGAAATATCAACA 1 SGD_Scer_YDR044W ( 684) GGTGGGGAGAAATATCAACA 1 MIT_Sbay_c896_21290 ( 685) GGTGGAGGAAAATATCAACA 1 WashU_Smik_Contig2283.3 ( 687) GGTGGAGAAAAATATTAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 8129 bayes= 9.81734 E= 2.8e-022 -982 -982 251 -982 -982 -982 251 -982 -982 -982 -982 162 -982 -982 251 -982 -982 -982 251 -982 145 -982 -66 -982 78 -982 134 -982 145 -982 -66 -982 -55 -982 34 78 162 -982 -982 -982 162 -982 -982 -982 45 -982 166 -982 -982 -982 166 45 45 -982 166 -982 -982 -982 -982 162 -982 92 166 -154 162 -982 -982 -982 162 -982 -982 -982 -982 234 -982 -154 162 -982 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.8e-022 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.888889 0.000000 0.111111 0.000000 0.555556 0.000000 0.444444 0.000000 0.888889 0.000000 0.111111 0.000000 0.222222 0.000000 0.222222 0.555556 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.444444 0.000000 0.555556 0.000000 0.000000 0.000000 0.555556 0.444444 0.444444 0.000000 0.555556 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.555556 0.111111 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.111111 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- GGTGGA[AG]A[TAG]AA[GA][GT][GA]T[GC]AACA -------------------------------------------------------------------------------- Time 7.14 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 20 sites = 9 llr = 199 E-value = 2.7e-023 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 3::1:a:6:::a7::::1:1 pos.-specific C ::a:6:4:::a:316:a878 probability G 7a:94:::6a:::::1:::1 matrix T ::::::644::::949:13: bits 2.5 ** ** * 2.3 ** ** * 2.0 *** ** * 1.8 *** ** * Information 1.5 ***** *** * * content 1.3 ****** *** * ***** (31.9 bits) 1.0 ******* ************ 0.8 ******************** 0.5 ******************** 0.3 ******************** 0.0 -------------------- Multilevel GGCGCATAGGCAATCTCCCC consensus A G CTT C T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------------------- WashU_Skud_Contig1850.5 + 692 2.30e-13 GTGACGTTTA GGCGCATAGGCAATCTCCCC TTATTGTTCA SGD_Scer_YDL205C + 684 2.30e-13 GTGACGTTTA GGCGCATAGGCAATCTCCCC TTATTGTTCA MIT_Sbay_c841_3215 + 711 3.52e-12 GTGACGTTTT AGCGCATAGGCAATCTCCCC TTATTGTTCA MIT_Smik_c193_2483 + 685 3.52e-12 ATGACGTTTA AGCGCATAGGCAATCTCCCC TTATTATTCA MIT_Spar_c429_3020 + 685 4.30e-12 GTGACGTTTA GGCGCATAGGCAACCTCCCC TTATTGTTCA WashU_Smik_Contig2283.3 + 739 3.24e-11 ATTGAGAAGC GGCGGACTTGCACTTTCCTC GAAGAAAAAA SGD_Scer_YDR044W + 733 3.60e-10 TCTGGAAAGT GGCAGACTTGCACTTTCCTC GAAAAGAAAA MIT_Spar_c130_3912 + 730 1.03e-09 TTTTGGAAGT GGCGGACTTGCACTTTCTTG AAAAGAAAAA MIT_Sbay_c896_21290 + 731 2.40e-09 TTCGAAGAAA AGCGGACTTGCAATTGCACA ACCGTATCGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- WashU_Skud_Contig1850.5 2.3e-13 691_[+2]_149 SGD_Scer_YDL205C 2.3e-13 683_[+2]_157 MIT_Sbay_c841_3215 3.5e-12 710_[+2]_130 MIT_Smik_c193_2483 3.5e-12 684_[+2]_156 MIT_Spar_c429_3020 4.3e-12 684_[+2]_156 WashU_Smik_Contig2283.3 3.2e-11 738_[+2]_242 SGD_Scer_YDR044W 3.6e-10 732_[+2]_248 MIT_Spar_c130_3912 1e-09 729_[+2]_251 MIT_Sbay_c896_21290 2.4e-09 730_[+2]_250 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=20 seqs=9 WashU_Skud_Contig1850.5 ( 692) GGCGCATAGGCAATCTCCCC 1 SGD_Scer_YDL205C ( 684) GGCGCATAGGCAATCTCCCC 1 MIT_Sbay_c841_3215 ( 711) AGCGCATAGGCAATCTCCCC 1 MIT_Smik_c193_2483 ( 685) AGCGCATAGGCAATCTCCCC 1 MIT_Spar_c429_3020 ( 685) GGCGCATAGGCAACCTCCCC 1 WashU_Smik_Contig2283.3 ( 739) GGCGGACTTGCACTTTCCTC 1 SGD_Scer_YDR044W ( 733) GGCAGACTTGCACTTTCCTC 1 MIT_Spar_c130_3912 ( 730) GGCGGACTTGCACTTTCTTG 1 MIT_Sbay_c896_21290 ( 731) AGCGGACTTGCAATTGCACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 8129 bayes= 9.81734 E= 2.7e-023 4 -982 192 -982 -982 -982 251 -982 -982 251 -982 -982 -154 -982 234 -982 -982 166 134 -982 162 -982 -982 -982 -982 134 -982 78 78 -982 -982 45 -982 -982 166 45 -982 -982 251 -982 -982 251 -982 -982 162 -982 -982 -982 104 92 -982 -982 -982 -66 -982 145 -982 166 -982 45 -982 -982 -66 145 -982 251 -982 -982 -154 215 -982 -154 -982 192 -982 4 -154 215 -66 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 2.7e-023 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.111111 0.000000 0.888889 0.000000 0.000000 0.555556 0.444444 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.444444 0.000000 0.555556 0.555556 0.000000 0.000000 0.444444 0.000000 0.000000 0.555556 0.444444 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.111111 0.000000 0.888889 0.000000 0.555556 0.000000 0.444444 0.000000 0.000000 0.111111 0.888889 0.000000 1.000000 0.000000 0.000000 0.111111 0.777778 0.000000 0.111111 0.000000 0.666667 0.000000 0.333333 0.111111 0.777778 0.111111 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA]GCG[CG]A[TC][AT][GT]GCA[AC]T[CT]TCC[CT]C -------------------------------------------------------------------------------- Time 14.04 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 15 sites = 9 llr = 162 E-value = 1.1e-016 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 1:::::6::6:::a: pos.-specific C :79:1::a9:6a::a probability G ::189:::::4:a:: matrix T 93:2:a4:14::::: bits 2.5 * ** * 2.3 * ** * 2.0 * * ** ** * 1.8 * * ** ** * Information 1.5 **** ** ***** content 1.3 ***** ** ***** (26.0 bits) 1.0 ****** ** ***** 0.8 *************** 0.5 *************** 0.3 *************** 0.0 --------------- Multilevel TCCGGTACCACCGAC consensus T T T TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------- MIT_Smik_c193_2483 - 572 1.00e-10 TCTTGCCATA TCCGGTACCACCGAC ATACGCCGTC MIT_Spar_c429_3020 - 571 1.00e-10 CTTTGTCACA TCCGGTACCACCGAC ATTCTGTTGC MIT_Sbay_c896_21290 + 312 2.46e-09 GAAAAATGGC TTCGGTTCCTGCGAC TCGTTTAAAA SGD_Scer_YDL205C - 570 2.75e-09 GCATTATCAC ACCGGTACCACCGAC ACATTCTGCT WashU_Skud_Contig1850.5 - 575 3.32e-09 TCTTGCCACA TCCGCTACCACCGAC ACATTCCGTT MIT_Sbay_c841_3215 - 581 6.14e-09 CTTTGCCCCA TCCGGTACTACCGAC ACATTGGCCG WashU_Smik_Contig2283.3 + 309 6.34e-09 AATTTTGGTT TCGGGTTCCTGCGAC TCGTTTAAAA MIT_Spar_c130_3912 + 306 1.39e-08 GAAATTTGGA TTCTGTTCCTGCGAC TCGTTTAAAA SGD_Scer_YDR044W + 313 1.39e-08 GAAATTTGGC TTCTGTTCCTGCGAC TCGTTTAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- MIT_Smik_c193_2483 1e-10 571_[-3]_274 MIT_Spar_c429_3020 1e-10 570_[-3]_275 MIT_Sbay_c896_21290 2.5e-09 311_[+3]_674 SGD_Scer_YDL205C 2.7e-09 569_[-3]_276 WashU_Skud_Contig1850.5 3.3e-09 574_[-3]_271 MIT_Sbay_c841_3215 6.1e-09 580_[-3]_265 WashU_Smik_Contig2283.3 6.3e-09 308_[+3]_677 MIT_Spar_c130_3912 1.4e-08 305_[+3]_680 SGD_Scer_YDR044W 1.4e-08 312_[+3]_673 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=9 MIT_Smik_c193_2483 ( 572) TCCGGTACCACCGAC 1 MIT_Spar_c429_3020 ( 571) TCCGGTACCACCGAC 1 MIT_Sbay_c896_21290 ( 312) TTCGGTTCCTGCGAC 1 SGD_Scer_YDL205C ( 570) ACCGGTACCACCGAC 1 WashU_Skud_Contig1850.5 ( 575) TCCGCTACCACCGAC 1 MIT_Sbay_c841_3215 ( 581) TCCGGTACTACCGAC 1 WashU_Smik_Contig2283.3 ( 309) TCGGGTTCCTGCGAC 1 MIT_Spar_c130_3912 ( 306) TTCTGTTCCTGCGAC 1 SGD_Scer_YDR044W ( 313) TTCTGTTCCTGCGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 8174 bayes= 9.82531 E= 1.1e-016 -154 -982 -982 145 -982 192 -982 4 -982 234 -66 -982 -982 -982 215 -55 -982 -66 234 -982 -982 -982 -982 162 78 -982 -982 45 -982 251 -982 -982 -982 234 -982 -154 78 -982 -982 45 -982 166 134 -982 -982 251 -982 -982 -982 -982 251 -982 162 -982 -982 -982 -982 251 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 1.1e-016 0.111111 0.000000 0.000000 0.888889 0.000000 0.666667 0.000000 0.333333 0.000000 0.888889 0.111111 0.000000 0.000000 0.000000 0.777778 0.222222 0.000000 0.111111 0.888889 0.000000 0.000000 0.000000 0.000000 1.000000 0.555556 0.000000 0.000000 0.444444 0.000000 1.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.111111 0.555556 0.000000 0.000000 0.444444 0.000000 0.555556 0.444444 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[CT]C[GT]GT[AT]CC[AT][CG]CGAC -------------------------------------------------------------------------------- Time 20.83 secs. ******************************************************************************** ******************************************************************************** MOTIF 4 width = 20 sites = 9 llr = 178 E-value = 5.9e-016 ******************************************************************************** -------------------------------------------------------------------------------- Motif 4 Description -------------------------------------------------------------------------------- Simplified A ::2::19a91:a:99:9a2: pos.-specific C 1:214::::2:::::a:::1 probability G ::2:481:17a:a11:1:39 matrix T 9a3911::::::::::::4: bits 2.5 * * * 2.3 * * * 2.0 * * * * 1.8 * * * * Information 1.5 * * *** * * * content 1.3 ** * ************* * (28.5 bits) 1.0 ** *************** * 0.8 ** *************** * 0.5 ** ***************** 0.3 ** ***************** 0.0 -------------------- Multilevel TTTTCGAAAGGAGAACAATG consensus A G C G sequence C A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------------------- MIT_Spar_c130_3912 + 160 6.95e-11 TTATATAGCC TTTTCGAAACGAGAACAATG GACAAATCAA MIT_Sbay_c896_21290 + 166 9.05e-11 TTATATAGCT TTCTCGAAGGGAGAACAATG GATAAATCAA MIT_Smik_c193_2483 + 648 1.24e-10 CGCAAGGCGT TTATGGAAAGGAGGACAAGG TCAGAGGATG SGD_Scer_YDL205C + 647 1.24e-10 CAAGGCGTTT TTGTTGAAAGGAGAACAAGG TTAGACGGTG SGD_Scer_YDR044W + 164 4.24e-10 CTTATATAGC CTTTCGAAACGAGAACAATG GGCAAAGCAA MIT_Spar_c429_3020 + 648 6.04e-10 CAAGGCGTTT TTATGGAAAGGAGAGCGAGG TTAGAGGGTG MIT_Sbay_c841_3215 + 670 1.69e-09 CAAAGGCGCT TTGTGGGAAGGAGAACAAAC AACATTAGAG WashU_Skud_Contig1850.5 + 655 2.34e-09 ACAAGGCTTT TTCCGTAAAGGAGAACAAAG TTGGAAGGTG WashU_Smik_Contig2283.3 + 156 3.18e-09 TTATATAGCC TTTTCAAAAAGAGAACAATG GTCAAATAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- MIT_Spar_c130_3912 6.9e-11 159_[+4]_821 MIT_Sbay_c896_21290 9.1e-11 165_[+4]_815 MIT_Smik_c193_2483 1.2e-10 647_[+4]_193 SGD_Scer_YDL205C 1.2e-10 646_[+4]_194 SGD_Scer_YDR044W 4.2e-10 163_[+4]_817 MIT_Spar_c429_3020 6e-10 647_[+4]_193 MIT_Sbay_c841_3215 1.7e-09 669_[+4]_171 WashU_Skud_Contig1850.5 2.3e-09 654_[+4]_186 WashU_Smik_Contig2283.3 3.2e-09 155_[+4]_825 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 4 width=20 seqs=9 MIT_Spar_c130_3912 ( 160) TTTTCGAAACGAGAACAATG 1 MIT_Sbay_c896_21290 ( 166) TTCTCGAAGGGAGAACAATG 1 MIT_Smik_c193_2483 ( 648) TTATGGAAAGGAGGACAAGG 1 SGD_Scer_YDL205C ( 647) TTGTTGAAAGGAGAACAAGG 1 SGD_Scer_YDR044W ( 164) CTTTCGAAACGAGAACAATG 1 MIT_Spar_c429_3020 ( 648) TTATGGAAAGGAGAGCGAGG 1 MIT_Sbay_c841_3215 ( 670) TTGTGGGAAGGAGAACAAAC 1 WashU_Skud_Contig1850.5 ( 655) TTCCGTAAAGGAGAACAAAG 1 WashU_Smik_Contig2283.3 ( 156) TTTTCAAAAAGAGAACAATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 8129 bayes= 9.81734 E= 5.9e-016 -982 -66 -982 145 -982 -982 -982 162 -55 34 34 4 -982 -66 -982 145 -982 134 134 -154 -154 -982 215 -154 145 -982 -66 -982 162 -982 -982 -982 145 -982 -66 -982 -154 34 192 -982 -982 -982 251 -982 162 -982 -982 -982 -982 -982 251 -982 145 -982 -66 -982 145 -982 -66 -982 -982 251 -982 -982 145 -982 -66 -982 162 -982 -982 -982 -55 -982 92 45 -982 -66 234 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.9e-016 0.000000 0.111111 0.000000 0.888889 0.000000 0.000000 0.000000 1.000000 0.222222 0.222222 0.222222 0.333333 0.000000 0.111111 0.000000 0.888889 0.000000 0.444444 0.444444 0.111111 0.111111 0.000000 0.777778 0.111111 0.888889 0.000000 0.111111 0.000000 1.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.111111 0.000000 0.111111 0.222222 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.888889 0.000000 0.111111 0.000000 0.888889 0.000000 0.111111 0.000000 0.000000 1.000000 0.000000 0.000000 0.888889 0.000000 0.111111 0.000000 1.000000 0.000000 0.000000 0.000000 0.222222 0.000000 0.333333 0.444444 0.000000 0.111111 0.888889 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 4 regular expression -------------------------------------------------------------------------------- TT[TACGA]T[CG]GAAA[GC]GAGAACAA[TGA]G -------------------------------------------------------------------------------- Time 27.50 secs. ******************************************************************************** ******************************************************************************** MOTIF 5 width = 20 sites = 9 llr = 178 E-value = 5.2e-014 ******************************************************************************** -------------------------------------------------------------------------------- Motif 5 Description -------------------------------------------------------------------------------- Simplified A :::::::::::3:::a:::: pos.-specific C 84::1122:34:4a:::::: probability G :::::::::::1::::::a: matrix T 26aa9988a7666:a:aa:a bits 2.5 * * 2.3 * * 2.0 * * 1.8 * * Information 1.5 * ** * ******* content 1.3 * **** * ******* (28.6 bits) 1.0 *********** ******** 0.8 *********** ******** 0.5 *********** ******** 0.3 ******************** 0.0 -------------------- Multilevel CTTTTTTTTTTTTCTATTGT consensus TC CC CCAC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------------------- WashU_Smik_Contig2283.3 - 113 4.87e-11 CACATATTTT CCTTTTTTTCCACCTATTGT CTCACCTGTT MIT_Spar_c130_3912 - 117 1.86e-10 CACGGATTTT CCTTTTTTTCCGCCTATTGT CTTTCTTTGT WashU_Skud_Contig1850.5 + 46 2.33e-10 AGTTTTCCTG CTTTTTTTTTTTTCTATTGT TCTAGAAACT MIT_Smik_c193_2483 + 49 6.29e-10 ACTATCTGGC CTTTTTCTTTTTTCTATTGT TCTAGATACT MIT_Spar_c429_3020 + 47 7.60e-10 GATTTTCTTG CCTTTTCCTTTTTCTATTGT TCTAGATACT SGD_Scer_YDL205C + 47 1.27e-09 ATTTTCTTCG CTTTTCTTTTTTTCTATTGT TCTAGATATT MIT_Sbay_c896_21290 - 121 1.43e-09 CGCATTTTCT TTTTTTTTTTCACCTATTGT TCGCTGCCAA SGD_Scer_YDR044W - 120 1.50e-09 CGGATTTTCC TTTTTTTTTCCACCTATTGT CTTTCTTTGT MIT_Sbay_c841_3215 + 48 1.62e-09 TATTTTTTTT CCTTCTTCTTTTTCTATTGT TCTAGATGCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- WashU_Smik_Contig2283.3 4.9e-11 112_[-5]_868 MIT_Spar_c130_3912 1.9e-10 116_[-5]_864 WashU_Skud_Contig1850.5 2.3e-10 45_[+5]_795 MIT_Smik_c193_2483 6.3e-10 48_[+5]_792 MIT_Spar_c429_3020 7.6e-10 46_[+5]_794 SGD_Scer_YDL205C 1.3e-09 46_[+5]_794 MIT_Sbay_c896_21290 1.4e-09 120_[-5]_860 SGD_Scer_YDR044W 1.5e-09 119_[-5]_861 MIT_Sbay_c841_3215 1.6e-09 47_[+5]_793 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 5 width=20 seqs=9 WashU_Smik_Contig2283.3 ( 113) CCTTTTTTTCCACCTATTGT 1 MIT_Spar_c130_3912 ( 117) CCTTTTTTTCCGCCTATTGT 1 WashU_Skud_Contig1850.5 ( 46) CTTTTTTTTTTTTCTATTGT 1 MIT_Smik_c193_2483 ( 49) CTTTTTCTTTTTTCTATTGT 1 MIT_Spar_c429_3020 ( 47) CCTTTTCCTTTTTCTATTGT 1 SGD_Scer_YDL205C ( 47) CTTTTCTTTTTTTCTATTGT 1 MIT_Sbay_c896_21290 ( 121) TTTTTTTTTTCACCTATTGT 1 SGD_Scer_YDR044W ( 120) TTTTTTTTTCCACCTATTGT 1 MIT_Sbay_c841_3215 ( 48) CCTTCTTCTTTTTCTATTGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 8129 bayes= 9.81734 E= 5.2e-014 -982 215 -982 -55 -982 134 -982 78 -982 -982 -982 162 -982 -982 -982 162 -982 -66 -982 145 -982 -66 -982 145 -982 34 -982 126 -982 34 -982 126 -982 -982 -982 162 -982 92 -982 104 -982 134 -982 78 4 -982 -66 78 -982 134 -982 78 -982 251 -982 -982 -982 -982 -982 162 162 -982 -982 -982 -982 -982 -982 162 -982 -982 -982 162 -982 -982 251 -982 -982 -982 -982 162 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 5.2e-014 0.000000 0.777778 0.000000 0.222222 0.000000 0.444444 0.000000 0.555556 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.111111 0.000000 0.888889 0.000000 0.111111 0.000000 0.888889 0.000000 0.222222 0.000000 0.777778 0.000000 0.222222 0.000000 0.777778 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.444444 0.000000 0.555556 0.333333 0.000000 0.111111 0.555556 0.000000 0.444444 0.000000 0.555556 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 5 regular expression -------------------------------------------------------------------------------- [CT][TC]TTTT[TC][TC]T[TC][TC][TA][TC]CTATTGT -------------------------------------------------------------------------------- Time 34.04 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- SGD_Scer_YDL205C 3.32e-30 46_[+5(1.27e-09)]_156_[+5(7.84e-05)]_327_[-3(2.75e-09)]_62_[+4(1.24e-10)]_17_[+2(2.30e-13)]_4_[-1(1.22e-12)]_133 MIT_Spar_c429_3020 6.35e-30 46_[+5(7.60e-10)]_170_[+5(7.84e-05)]_251_[+1(3.79e-05)]_43_[-3(1.00e-10)]_62_[+4(6.04e-10)]_17_[+2(4.30e-12)]_4_[-1(1.22e-12)]_132 MIT_Smik_c193_2483 7.78e-29 48_[+5(6.29e-10)]_174_[+5(2.65e-05)]_309_[-3(1.00e-10)]_61_[+4(1.24e-10)]_17_[+2(3.52e-12)]_4_[-1(1.22e-10)]_132 MIT_Sbay_c841_3215 1.43e-27 47_[+5(1.62e-09)]_297_[-5(2.91e-05)]_196_[-3(6.14e-09)]_74_[+4(1.69e-09)]_21_[+2(3.52e-12)]_4_[-1(1.22e-12)]_106 WashU_Skud_Contig1850.5 1.30e-29 45_[+5(2.33e-10)]_131_[-4(6.41e-05)]_19_[+5(7.84e-05)]_319_[-3(3.32e-09)]_1_[-3(6.63e-05)]_49_[+4(2.34e-09)]_17_[+2(2.30e-13)]_4_[-1(1.22e-12)]_125 SGD_Scer_YDR044W 2.91e-23 119_[-5(1.50e-09)]_24_[+4(4.24e-10)]_18_[+3(7.91e-05)]_42_[+4(4.47e-05)]_34_[+3(1.39e-08)]_271_[+4(2.94e-05)]_65_[+1(3.84e-10)]_29_[+2(3.60e-10)]_248 MIT_Spar_c130_3912 7.46e-25 116_[-5(1.86e-10)]_23_[+4(6.95e-11)]_126_[+3(1.39e-08)]_358_[+1(1.35e-10)]_31_[+2(1.03e-09)]_251 MIT_Sbay_c896_21290 1.06e-23 85_[-5(1.91e-05)]_15_[-5(1.43e-09)]_25_[+4(9.05e-11)]_126_[+3(2.46e-09)]_140_[-5(3.09e-05)]_198_[+1(5.43e-10)]_26_[+2(2.40e-09)]_48_[+5(4.88e-05)]_182 WashU_Smik_Contig2283.3 5.66e-25 86_[+1(4.04e-05)]_6_[-5(4.87e-11)]_23_[+4(3.18e-09)]_133_[+3(6.34e-09)]_144_[-5(8.86e-05)]_199_[+1(5.84e-10)]_32_[+2(3.24e-11)]_27_[-1(3.56e-05)]_195 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 5 reached. ******************************************************************************** CPU: dhn02990.mrc-dunn.cam.ac.uk ********************************************************************************