******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.3.0 (Release date: Sat Sep 26 01:51:56 PDT 2009) 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= pasted_sequences ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ MEME_raw_seqs.12488 1.0000 5100 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme sequences -sf pasted_sequences -dna -mod tcm -nmotifs 3 -minw 6 -maxw 50 -time 7200 -maxsize 60000 -revcomp -oc . -nostatus model: mod= tcm nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 6 maxw= 50 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 5 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= 5100 N= 1 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.225 C 0.275 G 0.275 T 0.225 Background letter frequencies (from dataset with add-one prior applied): A 0.225 C 0.275 G 0.275 T 0.225 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 45 sites = 5 llr = 181 E-value = 4.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::::::::2::846:::82:2228622::a6:2a:222:8:::26 pos.-specific C 68:662266:2::::4a22a8242286:::242::8::228a::4 probability G :::::644::42628:::4::44:2:2:a::66:8::48:2::8: matrix T 42a4424:2a4::226::2::2:::::a::2:::2:84::::a:: bits 2.2 * * * * * * 1.9 * * * * *** * ** 1.7 * * * * *** * ** 1.5 * * * * *** * * ** Relative 1.3 ** * * * ** ** * * *** **** * *** Entropy 1.1 ***** * ** **** ** * * *** **** ******* (52.2 bits) 0.9 ***** * * ** **** ** * * *** * **** ******* 0.6 ****** *** ******* ** ************** ******* 0.4 ****************** ** *********************** 0.2 ****************** ** *********************** 0.0 --------------------------------------------- Multilevel CCTCCGGCCTGAGAGTCAGCCGCAACCTGAAGGAGCTGGACCTGA consensus TT TTCTGA TGAGTC CA AAGCCAA CCA TAATCCG AC sequence TC T C T C CA G G T C A T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------------------------------------- MEME_raw_seqs.12488 + 3299 1.10e-19 CAGGACCTGG CCTCTGTGCTTAGTGCCAGCCCCAGCCTGAAGGAGCTAGACCTGC AGCAGAACAA MEME_raw_seqs.12488 + 3128 2.14e-19 AAGGACCTTG CCTTTGGGCTGAGAGCCAACCAGACCCTGACCGAGCTGGACCTGA GCTTCAATGT MEME_raw_seqs.12488 + 2957 5.80e-19 CAGATTCTCT TCTCCGTCCTCAAGGTCACCAGAAACCTGAAGGAGCTGGACCTAA GTGGAAACTC MEME_raw_seqs.12488 + 2819 1.72e-16 TTAGTGTGCA CTTTCTGCATTAAATTCAGCCGCCACGTGAAGAAGCTTCAGCTGA TTGAGGGCAG MEME_raw_seqs.12488 + 4202 1.25e-14 AACCCCAGCT TCTCCCCCTTGGGAGTCCTCCTGAAAATGATCCATAATGCCCTGC GCTTCATTCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- MEME_raw_seqs.12488 1.1e-19 2818_[+1]_93_[+1]_126_[+1]_126_ [+1]_858_[+1]_854 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=45 seqs=5 MEME_raw_seqs.12488 ( 3299) CCTCTGTGCTTAGTGCCAGCCCCAGCCTGAAGGAGCTAGACCTGC 1 MEME_raw_seqs.12488 ( 3128) CCTTTGGGCTGAGAGCCAACCAGACCCTGACCGAGCTGGACCTGA 1 MEME_raw_seqs.12488 ( 2957) TCTCCGTCCTCAAGGTCACCAGAAACCTGAAGGAGCTGGACCTAA 1 MEME_raw_seqs.12488 ( 2819) CTTTCTGCATTAAATTCAGCCGCCACGTGAAGAAGCTTCAGCTGA 1 MEME_raw_seqs.12488 ( 4202) TCTCCCCCTTGGGAGTCCTCCTGAAAATGATCCATAATGCCCTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 45 n= 5056 bayes= 10.2322 E= 4.5e-001 -897 112 -897 83 -897 154 -897 -17 -897 -897 -897 215 -897 112 -897 83 -897 112 -897 83 -897 -46 112 -17 -897 -46 54 83 -897 112 54 -897 -17 112 -897 -17 -897 -897 -897 215 -897 -46 54 83 183 -897 -46 -897 83 -897 112 -897 141 -897 -46 -17 -897 -897 154 -17 -897 54 -897 141 -897 186 -897 -897 183 -46 -897 -897 -17 -46 54 -17 -897 186 -897 -897 -17 154 -897 -897 -17 -46 54 -17 -17 54 54 -897 183 -46 -897 -897 141 -46 -46 -897 -17 154 -897 -897 -17 112 -46 -897 -897 -897 -897 215 -897 -897 186 -897 215 -897 -897 -897 141 -46 -897 -17 -897 54 112 -897 -17 -46 112 -897 215 -897 -897 -897 -897 -897 154 -17 -17 154 -897 -897 -17 -897 -897 183 -17 -897 54 83 -897 -46 154 -897 183 -46 -897 -897 -897 154 -46 -897 -897 186 -897 -897 -897 -897 -897 215 -17 -897 154 -897 141 54 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 45 nsites= 5 E= 4.5e-001 0.000000 0.600000 0.000000 0.400000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.600000 0.000000 0.400000 0.000000 0.200000 0.600000 0.200000 0.000000 0.200000 0.400000 0.400000 0.000000 0.600000 0.400000 0.000000 0.200000 0.600000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.400000 0.400000 0.800000 0.000000 0.200000 0.000000 0.400000 0.000000 0.600000 0.000000 0.600000 0.000000 0.200000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.400000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.200000 0.200000 0.400000 0.200000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.200000 0.400000 0.200000 0.200000 0.400000 0.400000 0.000000 0.800000 0.200000 0.000000 0.000000 0.600000 0.200000 0.200000 0.000000 0.200000 0.800000 0.000000 0.000000 0.200000 0.600000 0.200000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.200000 0.000000 0.200000 0.000000 0.400000 0.600000 0.000000 0.200000 0.200000 0.600000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.200000 0.800000 0.000000 0.000000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.400000 0.400000 0.000000 0.200000 0.800000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.200000 0.000000 0.800000 0.000000 0.600000 0.400000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][CT]T[CT][CT][GCT][GTC][CG][CAT]T[GTC][AG][GA][AGT][GT][TC]C[AC][GACTA]C[CA][GACTA][CGA][AC][ACG][CA][CAG]TGA[ACT][GC][GAC]A[GT][CA][TA][GTA][GC][AC][CG]CT[GA][AC] -------------------------------------------------------------------------------- Time 18.30 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 27 sites = 5 llr = 118 E-value = 6.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :4262:44:2::::26:::::2:2::: pos.-specific C 228:6::::::a:a42:6:a:622:82 probability G :2:::24:4:2::::2:2:::22:::: matrix T 82:42826688:a:4:a2a:a:66a28 bits 2.2 * * * * * 1.9 *** * *** * 1.7 *** * *** * 1.5 * *** * *** * Relative 1.3 * * * ***** * *** *** Entropy 1.1 * ** * ******* * *** *** (34.0 bits) 0.9 * ** * ******* * *** *** 0.6 * **** ******* ************ 0.4 * ************************* 0.2 *************************** 0.0 --------------------------- Multilevel TACACTATTTTCTCCATCTCTCTTTCT consensus CCATAGGAGAG TC G ACA TC sequence G T T AG T GGC T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------------------- MEME_raw_seqs.12488 - 1215 8.52e-14 GGGCCTGCCT TTCTCTGATTTCTCTCTCTCTCTTTCT CTGATTTCTG MEME_raw_seqs.12488 + 5017 3.49e-12 TGATTTTGCC TACACTGTTTTCTCAATTTCTAGTTTT CTACAAAGAT MEME_raw_seqs.12488 - 4902 1.49e-11 TCTGCCTTCT TCCTTTTTTTTCTCTGTCTCTCCATCT GCATCTGTAT MEME_raw_seqs.12488 - 2790 5.12e-11 GCAGAAAGTG CACACTAAGAGCTCCATGTCTGTTTCT ACACACATGC MEME_raw_seqs.12488 - 2601 6.54e-11 CAGCCGGCAG TGAAAGATGTTCTCCATCTCTCTCTCC CCCTCATCAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- MEME_raw_seqs.12488 8.5e-14 1214_[-2]_1359_[-2]_162_[-2]_2085_ [-2]_88_[+2]_57 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=27 seqs=5 MEME_raw_seqs.12488 ( 1215) TTCTCTGATTTCTCTCTCTCTCTTTCT 1 MEME_raw_seqs.12488 ( 5017) TACACTGTTTTCTCAATTTCTAGTTTT 1 MEME_raw_seqs.12488 ( 4902) TCCTTTTTTTTCTCTGTCTCTCCATCT 1 MEME_raw_seqs.12488 ( 2790) CACACTAAGAGCTCCATGTCTGTTTCT 1 MEME_raw_seqs.12488 ( 2601) TGAAAGATGTTCTCCATCTCTCTCTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 27 n= 5074 bayes= 10.2373 E= 6.7e+002 -897 -46 -897 183 83 -46 -46 -17 -17 154 -897 -897 141 -897 -897 83 -17 112 -897 -17 -897 -897 -46 183 83 -897 54 -17 83 -897 -897 141 -897 -897 54 141 -17 -897 -897 183 -897 -897 -46 183 -897 186 -897 -897 -897 -897 -897 215 -897 186 -897 -897 -17 54 -897 83 141 -46 -46 -897 -897 -897 -897 215 -897 112 -46 -17 -897 -897 -897 215 -897 186 -897 -897 -897 -897 -897 215 -17 112 -46 -897 -897 -46 -46 141 -17 -46 -897 141 -897 -897 -897 215 -897 154 -897 -17 -897 -46 -897 183 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 27 nsites= 5 E= 6.7e+002 0.000000 0.200000 0.000000 0.800000 0.400000 0.200000 0.200000 0.200000 0.200000 0.800000 0.000000 0.000000 0.600000 0.000000 0.000000 0.400000 0.200000 0.600000 0.000000 0.200000 0.000000 0.000000 0.200000 0.800000 0.400000 0.000000 0.400000 0.200000 0.400000 0.000000 0.000000 0.600000 0.000000 0.000000 0.400000 0.600000 0.200000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.400000 0.000000 0.400000 0.600000 0.200000 0.200000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.200000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.200000 0.600000 0.200000 0.000000 0.000000 0.200000 0.200000 0.600000 0.200000 0.200000 0.000000 0.600000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.200000 0.000000 0.800000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [TC][ACGTC][CA][AT][CAT][TG][AGT][TA][TG][TA][TG]CTC[CTA][ACG]T[CGT]TCT[CAG][TCG][TAC]T[CT][TC] -------------------------------------------------------------------------------- Time 35.94 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 width = 27 sites = 5 llr = 118 E-value = 9.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::4:::8:::2422:6:66628a6a:8 pos.-specific C 8:28::::::62:4::244:::::::: probability G ::2::a:aa6:4:2646::282:4:a2 matrix T 2a22a:2::42:824:2::2::::::: bits 2.2 * * * * 1.9 * ** ** * ** 1.7 * ** ** * ** 1.5 * ***** * * ** Relative 1.3 ** ****** * *** *** Entropy 1.1 ** ******* * ** ** ******* (34.0 bits) 0.9 ** ******* * ** ** ******* 0.6 ** ******** * ************* 0.4 ** ********** ************* 0.2 ************* ************* 0.0 --------------------------- Multilevel CTACTGAGGGCATCGAGAAAGAAAAGA consensus T CT T TAGAATGCCCGAG G G sequence G TC G T T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- --------------------------- MEME_raw_seqs.12488 + 3827 3.31e-13 GGGCCTGTGG CTACTGAGGTAGTTGACAAAGAAAAGA ACTTGTACCG MEME_raw_seqs.12488 + 2279 7.88e-13 TGCTCTCTGG CTGCTGAGGGCATCTGGCAAAAAAAGA CCCTTTTCAG MEME_raw_seqs.12488 - 2307 2.96e-11 TAACCCATGC TTCCTGAGGTCATCTGGACTGAAAAGG GTCTTTTTTT MEME_raw_seqs.12488 + 3536 3.16e-11 GTGATGACCC CTACTGAGGGCCTGGATACGGGAGAGA TGAGTAATAG MEME_raw_seqs.12488 + 4850 7.47e-11 TGGATGCCTG CTTTTGTGGGTGAAGAGCAAGAAGAGA AAACAGGTTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- MEME_raw_seqs.12488 3.3e-13 2278_[+3]_1_[-3]_1202_[+3]_264_ [+3]_996_[+3]_224 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=27 seqs=5 MEME_raw_seqs.12488 ( 3827) CTACTGAGGTAGTTGACAAAGAAAAGA 1 MEME_raw_seqs.12488 ( 2279) CTGCTGAGGGCATCTGGCAAAAAAAGA 1 MEME_raw_seqs.12488 ( 2307) TTCCTGAGGTCATCTGGACTGAAAAGG 1 MEME_raw_seqs.12488 ( 3536) CTACTGAGGGCCTGGATACGGGAGAGA 1 MEME_raw_seqs.12488 ( 4850) CTTTTGTGGGTGAAGAGCAAGAAGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 27 n= 5074 bayes= 9.98556 E= 9.7e+002 -897 154 -897 -17 -897 -897 -897 215 83 -46 -46 -17 -897 154 -897 -17 -897 -897 -897 215 -897 -897 186 -897 183 -897 -897 -17 -897 -897 186 -897 -897 -897 186 -897 -897 -897 112 83 -17 112 -897 -17 83 -46 54 -897 -17 -897 -897 183 -17 54 -46 -17 -897 -897 112 83 141 -897 54 -897 -897 -46 112 -17 141 54 -897 -897 141 54 -897 -897 141 -897 -46 -17 -17 -897 154 -897 183 -897 -46 -897 215 -897 -897 -897 141 -897 54 -897 215 -897 -897 -897 -897 -897 186 -897 183 -897 -46 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 27 nsites= 5 E= 9.7e+002 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 0.400000 0.200000 0.200000 0.200000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.400000 0.200000 0.600000 0.000000 0.200000 0.400000 0.200000 0.400000 0.000000 0.200000 0.000000 0.000000 0.800000 0.200000 0.400000 0.200000 0.200000 0.000000 0.000000 0.600000 0.400000 0.600000 0.000000 0.400000 0.000000 0.000000 0.200000 0.600000 0.200000 0.600000 0.400000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 0.600000 0.000000 0.200000 0.200000 0.200000 0.000000 0.800000 0.000000 0.800000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [CT]T[ACGTC][CT]TG[AT]GG[GT][CAT][AGC][TA][CAGTA][GT][AG][GCT][AC][AC][AGT][GA][AG]A[AG]AG[AG] -------------------------------------------------------------------------------- Time 52.45 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- MEME_raw_seqs.12488 9.31e-30 169_[+3(3.49e-05)]_172_[-3(4.74e-05)]_91_[-3(4.03e-06)]_70_[+1(4.40e-05)]_586_[-2(8.52e-14)]_452_[+3(3.34e-05)]_558_[+3(7.88e-13)]_1_[-3(2.96e-11)]_267_[-2(6.54e-11)]_162_[-2(5.12e-11)]_2_[+1(1.72e-16)]_93_[+1(5.80e-19)]_8_[+3(7.96e-05)]_91_[+1(2.14e-19)]_126_[+1(1.10e-19)]_192_[+3(3.16e-11)]_24_[-2(2.80e-05)]_213_[+3(3.31e-13)]_348_[+1(1.25e-14)]_603_[+3(7.47e-11)]_25_[-2(1.49e-11)]_3_[-2(1.29e-05)]_58_[+2(3.49e-12)]_57 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: compute-0-13.local ********************************************************************************