******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.3.3 (Release date: Sun Feb 7 15:39:52 2021 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** 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 ******************************************************************************** PRIMARY SEQUENCES= ../result/final_prediction/K562/fasta/RankLinear0.6_40/SMAD2.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr22:21995757-21995837 1.0000 80 chr22:21000550-21000630 1.0000 80 chr22:21092724-21092804 1.0000 80 chr3:9835232-9835312 1.0000 80 chr1:200772180-200772260 1.0000 80 chr19:55816993-55817073 1.0000 80 chr22:22257216-22257296 1.0000 80 chr1:26560266-26560346 1.0000 80 chr6:43138545-43138625 1.0000 80 chr1:31243702-31243782 1.0000 80 chr16:14580884-14580964 1.0000 80 chr22:21305914-21305994 1.0000 80 chr22:22236399-22236479 1.0000 80 chr22:22298844-22298924 1.0000 80 chr22:23096163-23096243 1.0000 80 chr14:88237638-88237718 1.0000 80 chr1:36626825-36626905 1.0000 80 chr22:22006128-22006208 1.0000 80 chr22:23094250-23094330 1.0000 80 chr17:41401049-41401129 1.0000 80 chr17:41400135-41400215 1.0000 80 chr22:22307812-22307892 1.0000 80 chr22:21968193-21968273 1.0000 80 chr9:133778726-133778806 1.0000 80 chr21:36342782-36342862 1.0000 80 chr17:45214566-45214646 1.0000 80 chr7:150755032-150755112 1.0000 80 chr3:50397085-50397165 1.0000 80 chr20:26189981-26190061 1.0000 80 chr22:22292676-22292756 1.0000 80 chr19:48866455-48866535 1.0000 80 chr17:47492328-47492408 1.0000 80 chr22:19280040-19280120 1.0000 80 chr7:149450844-149450924 1.0000 80 chr22:19131976-19132056 1.0000 80 chr1:3827498-3827578 1.0000 80 chr22:22098200-22098280 1.0000 80 chr17:27279369-27279449 1.0000 80 chr1:16940383-16940463 1.0000 80 chr22:19166930-19167010 1.0000 80 chr19:36618752-36618832 1.0000 80 chr22:23624164-23624244 1.0000 80 chr22:21368643-21368723 1.0000 80 chr17:28431734-28431814 1.0000 80 chr13:90965011-90965091 1.0000 80 chr1:27691889-27691969 1.0000 80 chr20:26189023-26189103 1.0000 80 chr2:133034600-133034680 1.0000 80 chr22:20861796-20861876 1.0000 80 chr7:150869755-150869835 1.0000 80 chr19:13204663-13204743 1.0000 80 chr22:20793958-20794038 1.0000 80 chr16:2205674-2205754 1.0000 80 chr2:172543876-172543956 1.0000 80 chr22:19897597-19897677 1.0000 80 chr16:30103248-30103328 1.0000 80 chr1:156737217-156737297 1.0000 80 chr6:33715586-33715666 1.0000 80 chr22:23412269-23412349 1.0000 80 chr6:28912361-28912441 1.0000 80 chr1:146644145-146644225 1.0000 80 chr1:36689313-36689393 1.0000 80 chr22:21400059-21400139 1.0000 80 chr22:23412958-23413038 1.0000 80 chr22:20023093-20023173 1.0000 80 chr22:22326107-22326187 1.0000 80 chr16:87984613-87984693 1.0000 80 chr5:173043763-173043843 1.0000 80 chr22:22804941-22805021 1.0000 80 chr22:21336320-21336400 1.0000 80 chr3:14302879-14302959 1.0000 80 chr22:21104306-21104386 1.0000 80 chr22:20067432-20067512 1.0000 80 chr1:6673669-6673749 1.0000 80 chr22:19667341-19667421 1.0000 80 chr3:40626192-40626272 1.0000 80 chr12:124198558-12419863 1.0000 80 chr6:10695033-10695113 1.0000 80 chr19:49148221-49148301 1.0000 80 chr12:48357226-48357306 1.0000 80 chr22:20810489-20810569 1.0000 80 chr19:944283-944363 1.0000 80 chr7:75943731-75943811 1.0000 80 chr2:65755179-65755259 1.0000 80 chr22:22697287-22697367 1.0000 80 chr22:23421546-23421626 1.0000 80 chr22:20850869-20850949 1.0000 80 chr16:85454548-85454628 1.0000 80 chr22:23267662-23267742 1.0000 80 chr22:22326798-22326878 1.0000 80 chr4:77870633-77870713 1.0000 80 chr19:7616286-7616366 1.0000 80 chr6:31587988-31588068 1.0000 80 chr22:21239931-21240011 1.0000 80 chr1:36689928-36690008 1.0000 80 chr7:1577777-1577857 1.0000 80 chr17:46185143-46185223 1.0000 80 chr1:234664036-234664116 1.0000 80 chr22:22006607-22006687 1.0000 80 chr6:30640838-30640918 1.0000 80 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -oc ../result/final_prediction/K562/inference_raw/MEME/RankLinear0.6_40_SMAD2/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/K562/fasta/RankLinear0.6_40/SMAD2.fasta model: mod= zoops nmotifs= 5 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 8 maxw= 8 nsites: minsites= 2 maxsites= 100 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 8000 N= 100 sample: seed= 0 hsfrac= 0 searchsize= 8000 norand= no csites= 1000 Letter frequencies in dataset: A 0.198 C 0.294 G 0.302 T 0.207 Background letter frequencies (from file dataset with add-one prior applied): A 0.198 C 0.294 G 0.302 T 0.207 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTCCCAGG MEME-1 width = 8 sites = 22 llr = 179 E-value = 3.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTCCCAGG MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::8:3 pos.-specific C ::87a:2: probability G ::::::77 matrix T aa23:2:: bits 2.3 ** 2.1 ** 1.9 ** 1.6 ** ** Relative 1.4 ** ** Entropy 1.2 ****** (11.7 bits) 0.9 ****** * 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TTCCCAGG consensus T CA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCCAGG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:36689928-36690008 44 1.97e-05 AGGACTACAT TTCCCAGG AGGCAGCGGG chr19:7616286-7616366 31 1.97e-05 GCAAGGACCC TTCCCAGG TGAGAGCCGG chr1:36689313-36689393 32 1.97e-05 TTTAACAAAC TTCCCAGG ACGACAGTCA chr20:26189023-26189103 61 1.97e-05 GTGGGACGCT TTCCCAGG GCCAGGCGGC chr7:149450844-149450924 32 1.97e-05 CAGGTGAGGG TTCCCAGG GAAGGACAGG chr17:41401049-41401129 66 1.97e-05 aacgggtgcc ttcccagg cactggg chr2:172543876-172543956 45 3.26e-05 GCGACCACAA TTCCCAGA ACGCACTGCT chr17:46185143-46185223 51 4.64e-05 GCTGGTGCTG TTCTCAGG TGAGAGGGCG chr3:50397085-50397165 69 4.64e-05 GGAGTTGTAG TTCTCAGG GACC chr22:23421546-23421626 7 6.02e-05 aagagt tttccagg aggaaggaac chr22:21092724-21092804 61 8.85e-05 CTCCCCACTG TTCCCACG CTGAGATGCG chr3:14302879-14302959 55 1.09e-04 GGGCAAGACC TTCCCTGG AGACCCATGG chr22:20861796-20861876 34 1.40e-04 GAGACTCCAT TTCCCACA AGCCCTCCTT chr22:21995757-21995837 54 1.40e-04 CCAGGCATGG TTCCCACA GCCCCTTGGT chr1:156737217-156737297 51 1.82e-04 GTCCAAAGTG TTCTCTGG AAGTTGTAGT chr6:10695033-10695113 24 2.02e-04 GCTTAAAGTG TTTCCACG TTACAGGCGA chr14:88237638-88237718 1 2.02e-04 . TTTTCAGA GTAACAGTGG chr22:22307812-22307892 25 2.24e-04 agttgagcct ttctcaca ctgccacctc chr22:22257216-22257296 64 2.24e-04 cgccacatac ttcccatg actagatcc chr22:19280040-19280120 65 2.38e-04 AGGAAACACC TTTCCTGG CTCATGCG chr6:30640838-30640918 73 2.82e-04 TCTGTCCAGT TTCTCTGA chr22:21305914-21305994 37 2.82e-04 TGTCTGGAGG TTCCTAGG TTTTGAGATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCCAGG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:36689928-36690008 2e-05 43_[+1]_29 chr19:7616286-7616366 2e-05 30_[+1]_42 chr1:36689313-36689393 2e-05 31_[+1]_41 chr20:26189023-26189103 2e-05 60_[+1]_12 chr7:149450844-149450924 2e-05 31_[+1]_41 chr17:41401049-41401129 2e-05 65_[+1]_7 chr2:172543876-172543956 3.3e-05 44_[+1]_28 chr17:46185143-46185223 4.6e-05 50_[+1]_22 chr3:50397085-50397165 4.6e-05 68_[+1]_4 chr22:23421546-23421626 6e-05 6_[+1]_66 chr22:21092724-21092804 8.8e-05 60_[+1]_12 chr3:14302879-14302959 0.00011 54_[+1]_18 chr22:20861796-20861876 0.00014 33_[+1]_39 chr22:21995757-21995837 0.00014 53_[+1]_19 chr1:156737217-156737297 0.00018 50_[+1]_22 chr6:10695033-10695113 0.0002 23_[+1]_49 chr14:88237638-88237718 0.0002 [+1]_72 chr22:22307812-22307892 0.00022 24_[+1]_48 chr22:22257216-22257296 0.00022 63_[+1]_9 chr22:19280040-19280120 0.00024 64_[+1]_8 chr6:30640838-30640918 0.00028 72_[+1] chr22:21305914-21305994 0.00028 36_[+1]_36 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCCAGG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTCCCAGG width=8 seqs=22 chr1:36689928-36690008 ( 44) TTCCCAGG 1 chr19:7616286-7616366 ( 31) TTCCCAGG 1 chr1:36689313-36689393 ( 32) TTCCCAGG 1 chr20:26189023-26189103 ( 61) TTCCCAGG 1 chr7:149450844-149450924 ( 32) TTCCCAGG 1 chr17:41401049-41401129 ( 66) TTCCCAGG 1 chr2:172543876-172543956 ( 45) TTCCCAGA 1 chr17:46185143-46185223 ( 51) TTCTCAGG 1 chr3:50397085-50397165 ( 69) TTCTCAGG 1 chr22:23421546-23421626 ( 7) TTTCCAGG 1 chr22:21092724-21092804 ( 61) TTCCCACG 1 chr3:14302879-14302959 ( 55) TTCCCTGG 1 chr22:20861796-20861876 ( 34) TTCCCACA 1 chr22:21995757-21995837 ( 54) TTCCCACA 1 chr1:156737217-156737297 ( 51) TTCTCTGG 1 chr6:10695033-10695113 ( 24) TTTCCACG 1 chr14:88237638-88237718 ( 1) TTTTCAGA 1 chr22:22307812-22307892 ( 25) TTCTCACA 1 chr22:22257216-22257296 ( 64) TTCCCATG 1 chr22:19280040-19280120 ( 65) TTTCCTGG 1 chr6:30640838-30640918 ( 73) TTCTCTGA 1 chr22:21305914-21305994 ( 37) TTCCTAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCCAGG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7300 bayes= 9.39859 E= 3.5e+000 -1110 -1110 -1110 227 -1110 -1110 -1110 227 -1110 148 -1110 -19 -1110 131 -1110 40 -1110 170 -1110 -218 205 -1110 -1110 -19 -1110 -37 127 -218 47 -1110 127 -1110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCCAGG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 3.5e+000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.818182 0.000000 0.181818 0.000000 0.727273 0.000000 0.272727 0.000000 0.954545 0.000000 0.045455 0.818182 0.000000 0.000000 0.181818 0.000000 0.227273 0.727273 0.045455 0.272727 0.000000 0.727273 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCCAGG MEME-1 regular expression -------------------------------------------------------------------------------- TTC[CT]CA[GC][GA] -------------------------------------------------------------------------------- Time 1.20 secs. ******************************************************************************** ******************************************************************************** MOTIF AACTACAM MEME-2 width = 8 sites = 6 llr = 66 E-value = 4.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AACTACAM MEME-2 Description -------------------------------------------------------------------------------- Simplified A aa::a:a7 pos.-specific C ::8::a:3 probability G :::::::: matrix T ::2a:::: bits 2.3 ** ** * 2.1 ** ** * 1.9 ** **** 1.6 ** **** Relative 1.4 ** **** Entropy 1.2 ******** (15.8 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel AACTACAA consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTACAM MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr5:173043763-173043843 10 5.44e-06 GCCGAGAGA AACTACAA CTCCCGGCAG chr17:47492328-47492408 41 5.44e-06 TTAGCAGATG AACTACAA CTCCCAAAAG chr19:55816993-55817073 1 5.44e-06 . AACTACAA GTCCCAGCAG chr16:30103248-30103328 11 1.35e-05 GAACCCTCGG AACTACAC TTCCCGGCAG chr16:2205674-2205754 54 1.35e-05 AGAGGCGGGG AACTACAC GTCCCGGCGG chr13:90965011-90965091 24 1.74e-05 ggctcacagg aattacaa gcccaggaga -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTACAM MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr5:173043763-173043843 5.4e-06 9_[+2]_63 chr17:47492328-47492408 5.4e-06 40_[+2]_32 chr19:55816993-55817073 5.4e-06 [+2]_72 chr16:30103248-30103328 1.4e-05 10_[+2]_62 chr16:2205674-2205754 1.4e-05 53_[+2]_19 chr13:90965011-90965091 1.7e-05 23_[+2]_49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTACAM MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AACTACAM width=8 seqs=6 chr5:173043763-173043843 ( 10) AACTACAA 1 chr17:47492328-47492408 ( 41) AACTACAA 1 chr19:55816993-55817073 ( 1) AACTACAA 1 chr16:30103248-30103328 ( 11) AACTACAC 1 chr16:2205674-2205754 ( 54) AACTACAC 1 chr13:90965011-90965091 ( 24) AATTACAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTACAM MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7300 bayes= 10.6953 E= 4.9e+001 234 -923 -923 -923 234 -923 -923 -923 -923 150 -923 -31 -923 -923 -923 227 234 -923 -923 -923 -923 177 -923 -923 234 -923 -923 -923 175 18 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTACAM MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 4.9e+001 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTACAM MEME-2 regular expression -------------------------------------------------------------------------------- AACTACA[AC] -------------------------------------------------------------------------------- Time 2.23 secs. ******************************************************************************** ******************************************************************************** MOTIF CAGAAAAW MEME-3 width = 8 sites = 4 llr = 46 E-value = 1.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAGAAAAW MEME-3 Description -------------------------------------------------------------------------------- Simplified A :a:aaaa5 pos.-specific C a::::::: probability G ::a::::: matrix T :::::::5 bits 2.3 * **** 2.1 * **** 1.9 ** **** 1.6 ******* Relative 1.4 ******** Entropy 1.2 ******** (16.5 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CAGAAAAA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGAAAAW MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr22:22326798-22326878 59 5.35e-06 GGGGCACTCA CAGAAAAA GCTAGCAAAG chr21:36342782-36342862 53 5.35e-06 CTTCAGCCTT CAGAAAAA TCCTTCAGTG chr1:36689313-36689393 48 1.09e-05 GGACGACAGT CAGAAAAT CATAGTTACA chr1:31243702-31243782 8 1.09e-05 tttgtgc cagaaaat aaggaagaac -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGAAAAW MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr22:22326798-22326878 5.3e-06 58_[+3]_14 chr21:36342782-36342862 5.3e-06 52_[+3]_20 chr1:36689313-36689393 1.1e-05 47_[+3]_25 chr1:31243702-31243782 1.1e-05 7_[+3]_65 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGAAAAW MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CAGAAAAW width=8 seqs=4 chr22:22326798-22326878 ( 59) CAGAAAAA 1 chr21:36342782-36342862 ( 53) CAGAAAAA 1 chr1:36689313-36689393 ( 48) CAGAAAAT 1 chr1:31243702-31243782 ( 8) CAGAAAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGAAAAW MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7300 bayes= 11.5702 E= 1.1e+003 -865 176 -865 -865 234 -865 -865 -865 -865 -865 173 -865 234 -865 -865 -865 234 -865 -865 -865 234 -865 -865 -865 234 -865 -865 -865 134 -865 -865 127 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGAAAAW MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 1.1e+003 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAGAAAAW MEME-3 regular expression -------------------------------------------------------------------------------- CAGAAAA[AT] -------------------------------------------------------------------------------- Time 3.27 secs. ******************************************************************************** ******************************************************************************** MOTIF TSTKTTTT MEME-4 width = 8 sites = 8 llr = 80 E-value = 2.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TSTKTTTT MEME-4 Description -------------------------------------------------------------------------------- Simplified A :1:::::3 pos.-specific C :5:::::: probability G :4:4:::: matrix T a:a6aaa8 bits 2.3 * * *** 2.1 * * *** 1.9 * * *** 1.6 * * *** Relative 1.4 * * **** Entropy 1.2 * ****** (14.4 bits) 0.9 * ****** 0.7 * ****** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TCTTTTTT consensus G G A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTKTTTT MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:30640838-30640918 43 4.79e-06 TCGGGGTAAT TCTTTTTT CTTCATTTCG chr19:49148221-49148301 45 4.79e-06 GAGTTGTAGT TCTTTTTT TTAATCGCTC chr21:36342782-36342862 69 9.71e-06 AATCCTTCAG TGTTTTTT CAGC chr22:20810489-20810569 41 1.67e-05 actttactga tctgtttt ctggttaaga chr6:28912361-28912441 69 1.67e-05 gggcaAGGCG TCTGTTTT GCCA chr6:43138545-43138625 64 1.99e-05 ATTTGGGCTG TATTTTTT TATTTACTG chr22:22326107-22326187 15 3.64e-05 AGGGGAGAGG TGTTTTTA AACCGGTACA chr6:33715586-33715666 9 5.77e-05 CTCAGGCT TGTGTTTA AAACTCTCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTKTTTT MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:30640838-30640918 4.8e-06 42_[+4]_30 chr19:49148221-49148301 4.8e-06 44_[+4]_28 chr21:36342782-36342862 9.7e-06 68_[+4]_4 chr22:20810489-20810569 1.7e-05 40_[+4]_32 chr6:28912361-28912441 1.7e-05 68_[+4]_4 chr6:43138545-43138625 2e-05 63_[+4]_9 chr22:22326107-22326187 3.6e-05 14_[+4]_58 chr6:33715586-33715666 5.8e-05 8_[+4]_64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTKTTTT MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TSTKTTTT width=8 seqs=8 chr6:30640838-30640918 ( 43) TCTTTTTT 1 chr19:49148221-49148301 ( 45) TCTTTTTT 1 chr21:36342782-36342862 ( 69) TGTTTTTT 1 chr22:20810489-20810569 ( 41) TCTGTTTT 1 chr6:28912361-28912441 ( 69) TCTGTTTT 1 chr6:43138545-43138625 ( 64) TATTTTTT 1 chr22:22326107-22326187 ( 15) TGTTTTTA 1 chr6:33715586-33715666 ( 9) TGTGTTTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTKTTTT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7300 bayes= 10.5697 E= 2.3e+003 -965 -965 -965 227 -66 77 31 -965 -965 -965 -965 227 -965 -965 31 159 -965 -965 -965 227 -965 -965 -965 227 -965 -965 -965 227 34 -965 -965 186 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTKTTTT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 2.3e+003 0.000000 0.000000 0.000000 1.000000 0.125000 0.500000 0.375000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.375000 0.625000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.000000 0.750000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTKTTTT MEME-4 regular expression -------------------------------------------------------------------------------- T[CG]T[TG]TTT[TA] -------------------------------------------------------------------------------- Time 4.32 secs. ******************************************************************************** ******************************************************************************** MOTIF TCCCTCCT MEME-5 width = 8 sites = 7 llr = 68 E-value = 1.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCCCTCCT MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :aaa:a9: probability G :::::::3 matrix T a:::a:17 bits 2.3 * * 2.1 * * 1.9 ****** 1.6 ****** Relative 1.4 ****** Entropy 1.2 ******** (14.1 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TCCCTCCT consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCTCCT MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr22:22326107-22326187 39 1.95e-05 TACAGTTTAC TCCCTCCT TTGGCCCCAG chr22:19166930-19167010 21 1.95e-05 AACTGGCCCG TCCCTCCT ACCCATACCA chr22:22307812-22307892 47 1.95e-05 cacctctggt tccctcct ctgcttcctt chr1:36626825-36626905 67 1.95e-05 CCCCTAAGGG TCCCTCCT CTCCCG chr22:20850869-20850949 22 4.79e-05 ccttccccgc tccctccG CGGTCGGTGC chr1:31243702-31243782 66 4.79e-05 atgaagaagg tccctccg gtttctt chr22:22257216-22257296 3 6.16e-05 gt tccctctt ccagtcctct -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCTCCT MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr22:22326107-22326187 1.9e-05 38_[+5]_34 chr22:19166930-19167010 1.9e-05 20_[+5]_52 chr22:22307812-22307892 1.9e-05 46_[+5]_26 chr1:36626825-36626905 1.9e-05 66_[+5]_6 chr22:20850869-20850949 4.8e-05 21_[+5]_51 chr1:31243702-31243782 4.8e-05 65_[+5]_7 chr22:22257216-22257296 6.2e-05 2_[+5]_70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCTCCT MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCCCTCCT width=8 seqs=7 chr22:22326107-22326187 ( 39) TCCCTCCT 1 chr22:19166930-19167010 ( 21) TCCCTCCT 1 chr22:22307812-22307892 ( 47) TCCCTCCT 1 chr1:36626825-36626905 ( 67) TCCCTCCT 1 chr22:20850869-20850949 ( 22) TCCCTCCG 1 chr1:31243702-31243782 ( 66) TCCCTCCG 1 chr22:22257216-22257296 ( 3) TCCCTCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCTCCT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 7300 bayes= 10.6311 E= 1.4e+004 -945 -945 -945 227 -945 177 -945 -945 -945 177 -945 -945 -945 177 -945 -945 -945 -945 -945 227 -945 177 -945 -945 -945 154 -945 -53 -945 -945 -8 179 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCTCCT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 1.4e+004 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.000000 0.285714 0.714286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCCTCCT MEME-5 regular expression -------------------------------------------------------------------------------- TCCCTCC[TG] -------------------------------------------------------------------------------- Time 5.36 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr22:21995757-21995837 4.21e-02 80 chr22:21000550-21000630 6.26e-01 80 chr22:21092724-21092804 9.80e-02 60_[+1(8.85e-05)]_12 chr3:9835232-9835312 6.18e-01 80 chr1:200772180-200772260 1.18e-01 80 chr19:55816993-55817073 4.52e-03 [+2(5.44e-06)]_72 chr22:22257216-22257296 9.10e-04 2_[+5(6.16e-05)]_70 chr1:26560266-26560346 9.49e-01 80 chr6:43138545-43138625 3.35e-03 63_[+4(1.99e-05)]_9 chr1:31243702-31243782 3.80e-04 7_[+3(1.09e-05)]_50_[+5(4.79e-05)]_\ 7 chr16:14580884-14580964 9.98e-01 80 chr22:21305914-21305994 1.34e-01 80 chr22:22236399-22236479 2.00e-02 80 chr22:22298844-22298924 6.88e-01 80 chr22:23096163-23096243 1.08e-01 80 chr14:88237638-88237718 2.49e-01 80 chr1:36626825-36626905 4.57e-02 66_[+5(1.95e-05)]_6 chr22:22006128-22006208 9.05e-01 80 chr22:23094250-23094330 5.79e-01 80 chr17:41401049-41401129 5.14e-02 65_[+1(1.97e-05)]_7 chr17:41400135-41400215 1.02e-01 80 chr22:22307812-22307892 3.98e-03 46_[+5(1.95e-05)]_26 chr22:21968193-21968273 8.06e-02 80 chr9:133778726-133778806 9.76e-01 80 chr21:36342782-36342862 2.79e-05 52_[+3(5.35e-06)]_8_[+4(9.71e-06)]_\ 4 chr17:45214566-45214646 4.29e-01 80 chr7:150755032-150755112 5.53e-01 80 chr3:50397085-50397165 2.12e-01 68_[+1(4.64e-05)]_4 chr20:26189981-26190061 3.43e-01 80 chr22:22292676-22292756 6.87e-01 80 chr19:48866455-48866535 3.80e-01 80 chr17:47492328-47492408 2.03e-02 40_[+2(5.44e-06)]_32 chr22:19280040-19280120 1.34e-01 80 chr7:149450844-149450924 2.38e-02 31_[+1(1.97e-05)]_41 chr22:19131976-19132056 6.35e-01 80 chr1:3827498-3827578 1.00e+00 80 chr22:22098200-22098280 3.63e-01 80 chr17:27279369-27279449 5.40e-01 80 chr1:16940383-16940463 6.64e-01 80 chr22:19166930-19167010 2.50e-02 20_[+5(1.95e-05)]_52 chr19:36618752-36618832 9.91e-01 80 chr22:23624164-23624244 6.12e-01 80 chr22:21368643-21368723 8.87e-01 80 chr17:28431734-28431814 7.76e-01 80 chr13:90965011-90965091 6.03e-02 23_[+2(1.74e-05)]_49 chr1:27691889-27691969 7.90e-01 80 chr20:26189023-26189103 2.48e-02 60_[+1(1.97e-05)]_12 chr2:133034600-133034680 1.12e-01 80 chr22:20861796-20861876 6.06e-02 80 chr7:150869755-150869835 8.41e-01 80 chr19:13204663-13204743 5.23e-01 80 chr22:20793958-20794038 1.06e-01 80 chr16:2205674-2205754 1.19e-01 53_[+2(1.35e-05)]_19 chr2:172543876-172543956 3.32e-02 44_[+1(3.26e-05)]_28 chr22:19897597-19897677 6.65e-01 80 chr16:30103248-30103328 7.74e-02 10_[+2(1.35e-05)]_62 chr1:156737217-156737297 3.28e-02 80 chr6:33715586-33715666 4.33e-02 8_[+4(5.77e-05)]_64 chr22:23412269-23412349 9.48e-01 80 chr6:28912361-28912441 6.80e-02 68_[+4(1.67e-05)]_4 chr1:146644145-146644225 4.56e-01 80 chr1:36689313-36689393 4.12e-04 31_[+1(1.97e-05)]_8_[+3(1.09e-05)]_\ 25 chr22:21400059-21400139 1.38e-01 80 chr22:23412958-23413038 1.00e+00 80 chr22:20023093-20023173 9.72e-01 80 chr22:22326107-22326187 3.01e-03 14_[+4(3.64e-05)]_16_[+5(1.95e-05)]_\ 34 chr16:87984613-87984693 4.20e-01 80 chr5:173043763-173043843 1.47e-02 9_[+2(5.44e-06)]_63 chr22:22804941-22805021 4.02e-01 80 chr22:21336320-21336400 6.91e-01 80 chr3:14302879-14302959 1.35e-01 80 chr22:21104306-21104386 3.85e-01 80 chr22:20067432-20067512 4.43e-01 80 chr1:6673669-6673749 5.16e-01 80 chr22:19667341-19667421 7.78e-01 80 chr3:40626192-40626272 9.88e-01 80 chr12:124198558-12419863 6.29e-01 80 chr6:10695033-10695113 1.68e-01 80 chr19:49148221-49148301 2.87e-03 44_[+4(4.79e-06)]_28 chr12:48357226-48357306 9.48e-01 80 chr22:20810489-20810569 1.94e-03 40_[+4(1.67e-05)]_32 chr19:944283-944363 9.80e-01 80 chr7:75943731-75943811 3.50e-01 80 chr2:65755179-65755259 7.40e-01 80 chr22:22697287-22697367 8.40e-01 80 chr22:23421546-23421626 1.78e-01 6_[+1(6.02e-05)]_66 chr22:20850869-20850949 2.17e-01 21_[+5(4.79e-05)]_51 chr16:85454548-85454628 9.03e-01 80 chr22:23267662-23267742 2.67e-01 80 chr22:22326798-22326878 2.65e-03 58_[+3(5.35e-06)]_14 chr4:77870633-77870713 9.86e-01 80 chr19:7616286-7616366 5.61e-02 30_[+1(1.97e-05)]_42 chr6:31587988-31588068 1.96e-01 80 chr22:21239931-21240011 9.98e-01 80 chr1:36689928-36690008 3.08e-02 43_[+1(1.97e-05)]_29 chr7:1577777-1577857 1.45e-01 80 chr17:46185143-46185223 1.60e-01 50_[+1(4.64e-05)]_22 chr1:234664036-234664116 1.57e-01 80 chr22:22006607-22006687 8.93e-01 80 chr6:30640838-30640918 1.86e-04 42_[+4(4.79e-06)]_30 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n07.farnam.hpc.yale.internal ********************************************************************************