******************************************************************************** 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/COPS2.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr17:36301785-36301865 1.0000 80 chr2:145440315-145440395 1.0000 80 chr7:117845791-117845871 1.0000 80 chr21:11111241-11111321 1.0000 80 chr10:74144248-74144328 1.0000 80 chr6:33037149-33037229 1.0000 80 chr7:131053866-131053946 1.0000 80 chr4:190655937-190656017 1.0000 80 chr7:117807305-117807385 1.0000 80 chr6:138257368-138257448 1.0000 80 chr13:92276568-92276648 1.0000 80 chr6:38691447-38691527 1.0000 80 chr2:91766349-91766429 1.0000 80 chr21:11073622-11073702 1.0000 80 chr2:91790989-91791069 1.0000 80 chr21:11146225-11146305 1.0000 80 chr13:91557567-91557647 1.0000 80 chr2:152252300-152252380 1.0000 80 chr6:150128989-150129069 1.0000 80 chr7:110962323-110962403 1.0000 80 chr20:29649593-29649673 1.0000 80 chr9:66484483-66484563 1.0000 80 chr21:11093201-11093281 1.0000 80 chr6:158281868-158281948 1.0000 80 chr6:6657829-6657909 1.0000 80 chr6:57535512-57535592 1.0000 80 chr21:11057701-11057781 1.0000 80 chr7:133230691-133230771 1.0000 80 chr2:69787251-69787331 1.0000 80 chr20:43485664-43485744 1.0000 80 chr9:66461460-66461540 1.0000 80 chr5:43313793-43313873 1.0000 80 chr1:228045134-228045214 1.0000 80 chr21:11042077-11042157 1.0000 80 chr21:11171847-11171927 1.0000 80 chr4:166248651-166248731 1.0000 80 chr22:42228918-42228998 1.0000 80 chr6:158739474-158739554 1.0000 80 chr7:98684344-98684424 1.0000 80 chr5:74632811-74632891 1.0000 80 chr2:91783936-91784016 1.0000 80 chr2:177319680-177319760 1.0000 80 chr12:108511298-10851137 1.0000 80 chr10:102133170-10213325 1.0000 80 chr16:70946472-70946552 1.0000 80 chr2:91786025-91786105 1.0000 80 chr10:61705906-61705986 1.0000 80 chr20:49149119-49149199 1.0000 80 chr17:36981584-36981664 1.0000 80 chr21:11057088-11057168 1.0000 80 chr17:36305093-36305173 1.0000 80 chr21:11118676-11118756 1.0000 80 chr4:120375774-120375854 1.0000 80 chr1:145104329-145104409 1.0000 80 chr21:11112650-11112730 1.0000 80 chr6:57394362-57394442 1.0000 80 chr21:11048847-11048927 1.0000 80 chr1:234290832-234290912 1.0000 80 chr5:40829488-40829568 1.0000 80 chr6:32177057-32177137 1.0000 80 chr2:203829848-203829928 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_COPS2/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/K562/fasta/RankLinear0.6_40/COPS2.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= 61 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= 4880 N= 61 sample: seed= 0 hsfrac= 0 searchsize= 4880 norand= no csites= 1000 Letter frequencies in dataset: A 0.281 C 0.208 G 0.21 T 0.301 Background letter frequencies (from file dataset with add-one prior applied): A 0.281 C 0.208 G 0.21 T 0.301 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GAKCMAAW MEME-1 width = 8 sites = 19 llr = 146 E-value = 4.9e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAKCMAAW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 3a::5aa3 pos.-specific C :::95::2 probability G 7:41:::: matrix T ::6::::5 bits 2.3 2.0 * 1.8 * * ** 1.6 * * ** Relative 1.4 * * ** Entropy 1.1 ** **** (11.1 bits) 0.9 ******* 0.7 ******* 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GATCAAAT consensus A G C A sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAKCMAAW MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:228045134-228045214 44 1.83e-05 ctcattgcaa gatccaat cagatcatgc chr20:43485664-43485744 22 1.83e-05 GTgaatgcag gatccaat cagactgtgc chr6:6657829-6657909 33 1.83e-05 ctcattgcaa gatccaat cagatcatgc chr6:150128989-150129069 8 1.83e-05 GCTAAGG GATCCAAT TGATCCCGTG chr21:11118676-11118756 15 5.57e-05 AGTCTTTGCT GATCAAAT TCAGGGGAAG chr10:102133170-10213325 51 5.57e-05 GACCACGCCG GAGCCAAT CAGCGGCCCC chr4:166248651-166248731 28 5.57e-05 TCCATCCGCG GAGCCAAT GGCTGGGACC chr20:29649593-29649673 26 5.57e-05 ggaattactg gatcaaat gatagatctg chr21:11093201-11093281 13 1.03e-04 CCATAGAAAT GATCCAAA CTCACATACT chr2:152252300-152252380 42 1.03e-04 tgggaggcat gatccaac tggatactgc chr5:43313793-43313873 43 1.63e-04 GATACGGCGA GAGCCAAC GGGAGCGGAG chr2:69787251-69787331 20 1.63e-04 TAAATCACGA GATCAAAA TCCACGCCTA chr6:57394362-57394442 47 2.89e-04 CCCCATTCAC AAGCAAAT GTGAATTTGG chr2:177319680-177319760 72 4.10e-04 GGGTTAGAGA AATCAAAA T chr17:36301785-36301865 70 4.10e-04 atggaaatag aatcaaac aat chr13:91557567-91557647 11 4.47e-04 aaaatacatg aagcaaaa actaataaaa chr21:11146225-11146305 2 4.47e-04 A AAGCAAAC TATCATCATT chr21:11073622-11073702 29 4.47e-04 ttaacaattg aagcaaaa attgttacat chr21:11048847-11048927 33 5.04e-04 ATGACCAAGA GATGAAAT ACAATAGGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAKCMAAW MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:228045134-228045214 1.8e-05 43_[+1]_29 chr20:43485664-43485744 1.8e-05 21_[+1]_51 chr6:6657829-6657909 1.8e-05 32_[+1]_40 chr6:150128989-150129069 1.8e-05 7_[+1]_65 chr21:11118676-11118756 5.6e-05 14_[+1]_58 chr10:102133170-10213325 5.6e-05 50_[+1]_22 chr4:166248651-166248731 5.6e-05 27_[+1]_45 chr20:29649593-29649673 5.6e-05 25_[+1]_47 chr21:11093201-11093281 0.0001 12_[+1]_60 chr2:152252300-152252380 0.0001 41_[+1]_31 chr5:43313793-43313873 0.00016 42_[+1]_30 chr2:69787251-69787331 0.00016 19_[+1]_53 chr6:57394362-57394442 0.00029 46_[+1]_26 chr2:177319680-177319760 0.00041 71_[+1]_1 chr17:36301785-36301865 0.00041 69_[+1]_3 chr13:91557567-91557647 0.00045 10_[+1]_62 chr21:11146225-11146305 0.00045 1_[+1]_71 chr21:11073622-11073702 0.00045 28_[+1]_44 chr21:11048847-11048927 0.0005 32_[+1]_40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAKCMAAW MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAKCMAAW width=8 seqs=19 chr1:228045134-228045214 ( 44) GATCCAAT 1 chr20:43485664-43485744 ( 22) GATCCAAT 1 chr6:6657829-6657909 ( 33) GATCCAAT 1 chr6:150128989-150129069 ( 8) GATCCAAT 1 chr21:11118676-11118756 ( 15) GATCAAAT 1 chr10:102133170-10213325 ( 51) GAGCCAAT 1 chr4:166248651-166248731 ( 28) GAGCCAAT 1 chr20:29649593-29649673 ( 26) GATCAAAT 1 chr21:11093201-11093281 ( 13) GATCCAAA 1 chr2:152252300-152252380 ( 42) GATCCAAC 1 chr5:43313793-43313873 ( 43) GAGCCAAC 1 chr2:69787251-69787331 ( 20) GATCAAAA 1 chr6:57394362-57394442 ( 47) AAGCAAAT 1 chr2:177319680-177319760 ( 72) AATCAAAA 1 chr17:36301785-36301865 ( 70) AATCAAAC 1 chr13:91557567-91557647 ( 11) AAGCAAAA 1 chr21:11146225-11146305 ( 2) AAGCAAAC 1 chr21:11073622-11073702 ( 29) AAGCAAAA 1 chr21:11048847-11048927 ( 33) GATGAAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAKCMAAW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4453 bayes= 8.76676 E= 4.9e+001 17 -1089 170 -1089 183 -1089 -1089 -1089 -1089 -1089 81 107 -1089 219 -200 -1089 91 119 -1089 -1089 183 -1089 -1089 -1089 183 -1089 -1089 -1089 -9 2 -1089 81 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAKCMAAW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 4.9e+001 0.315789 0.000000 0.684211 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.368421 0.631579 0.000000 0.947368 0.052632 0.000000 0.526316 0.473684 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.263158 0.210526 0.000000 0.526316 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAKCMAAW MEME-1 regular expression -------------------------------------------------------------------------------- [GA]A[TG]C[AC]AA[TAC] -------------------------------------------------------------------------------- Time 2.28 secs. ******************************************************************************** ******************************************************************************** MOTIF TCACCCCA MEME-2 width = 8 sites = 9 llr = 84 E-value = 8.2e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCACCCCA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1:a:2::a pos.-specific C :8:a79a: probability G :2:::::: matrix T 9:::11:: bits 2.3 * * 2.0 * * 1.8 ** *** 1.6 *** *** Relative 1.4 *** *** Entropy 1.1 **** *** (13.5 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TCACCCCA consensus G A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCACCCCA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr22:42228918-42228998 58 9.25e-06 TGACGCGCCA TCACCCCA CGCACCGCTT chr20:43485664-43485744 47 9.25e-06 tgctctggca tcacccca tgacaggatc chr7:110962323-110962403 53 1.86e-05 GAGGTCGAAT TGACCCCA TGACTGGTTA chr2:152252300-152252380 67 1.86e-05 tgctatgggg tgacccca gggctc chr4:190655937-190656017 52 3.11e-05 ctcttctctc tcacacca ttgcaccacc chr6:33037149-33037229 58 3.11e-05 GAGAGGGGTA TCACACCA CTGACCAGCC chr5:40829488-40829568 40 3.97e-05 TACCAACCCT ACACCCCA TCCTTCTAAC chr4:166248651-166248731 14 5.31e-05 CTCACTATCC TCACTCCA TCCGCGGAGC chr1:228045134-228045214 30 6.65e-05 cctctcaaca tcacctca ttgcaagatc -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCACCCCA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr22:42228918-42228998 9.3e-06 57_[+2]_15 chr20:43485664-43485744 9.3e-06 46_[+2]_26 chr7:110962323-110962403 1.9e-05 52_[+2]_20 chr2:152252300-152252380 1.9e-05 66_[+2]_6 chr4:190655937-190656017 3.1e-05 51_[+2]_21 chr6:33037149-33037229 3.1e-05 57_[+2]_15 chr5:40829488-40829568 4e-05 39_[+2]_33 chr4:166248651-166248731 5.3e-05 13_[+2]_59 chr1:228045134-228045214 6.7e-05 29_[+2]_43 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCACCCCA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCACCCCA width=8 seqs=9 chr22:42228918-42228998 ( 58) TCACCCCA 1 chr20:43485664-43485744 ( 47) TCACCCCA 1 chr7:110962323-110962403 ( 53) TGACCCCA 1 chr2:152252300-152252380 ( 67) TGACCCCA 1 chr4:190655937-190656017 ( 52) TCACACCA 1 chr6:33037149-33037229 ( 58) TCACACCA 1 chr5:40829488-40829568 ( 40) ACACCCCA 1 chr4:166248651-166248731 ( 14) TCACTCCA 1 chr1:228045134-228045214 ( 30) TCACCTCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCACCCCA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4453 bayes= 9.79701 E= 8.2e+001 -133 -982 -982 156 -982 190 8 -982 183 -982 -982 -982 -982 226 -982 -982 -34 168 -982 -143 -982 209 -982 -143 -982 226 -982 -982 183 -982 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCACCCCA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 8.2e+001 0.111111 0.000000 0.000000 0.888889 0.000000 0.777778 0.222222 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.222222 0.666667 0.000000 0.111111 0.000000 0.888889 0.000000 0.111111 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCACCCCA MEME-2 regular expression -------------------------------------------------------------------------------- T[CG]AC[CA]CCA -------------------------------------------------------------------------------- Time 4.01 secs. ******************************************************************************** ******************************************************************************** MOTIF CCACGCCT MEME-3 width = 8 sites = 2 llr = 24 E-value = 3.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCACGCCT MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::a::::: pos.-specific C aa:a:aa: probability G ::::a::: matrix T :::::::a bits 2.3 ** **** 2.0 ** **** 1.8 ******** 1.6 ******** Relative 1.4 ******** Entropy 1.1 ******** (17.1 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CCACGCCT consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACGCCT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr4:120375774-120375854 2 6.92e-06 C CCACGCCT CTGACGTCGC chr2:69787251-69787331 29 6.92e-06 AGATCAAAAT CCACGCCT AACAGGACTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACGCCT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr4:120375774-120375854 6.9e-06 1_[+3]_71 chr2:69787251-69787331 6.9e-06 28_[+3]_44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACGCCT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCACGCCT width=8 seqs=2 chr4:120375774-120375854 ( 2) CCACGCCT 1 chr2:69787251-69787331 ( 29) CCACGCCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACGCCT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4453 bayes= 11.1199 E= 3.1e+003 -765 226 -765 -765 -765 226 -765 -765 183 -765 -765 -765 -765 226 -765 -765 -765 -765 224 -765 -765 226 -765 -765 -765 226 -765 -765 -765 -765 -765 173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACGCCT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 3.1e+003 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 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 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACGCCT MEME-3 regular expression -------------------------------------------------------------------------------- CCACGCCT -------------------------------------------------------------------------------- Time 4.70 secs. ******************************************************************************** ******************************************************************************** MOTIF TCAWRGAA MEME-4 width = 8 sites = 11 llr = 95 E-value = 3.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCAWRGAA MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::755:aa pos.-specific C :a32:::: probability G ::::5a:: matrix T a::4:::: bits 2.3 * * 2.0 * * 1.8 ** *** 1.6 ** *** Relative 1.4 ** *** Entropy 1.1 *** **** (12.5 bits) 0.9 *** **** 0.7 *** **** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TCAAGGAA consensus CTA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCAWRGAA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr13:91557567-91557647 30 1.72e-05 ctaataaaac tcaaggaa aactgaaata chr6:32177057-32177137 28 3.57e-05 aaagttagtc tcatggaa gtagggtaga chr17:36301785-36301865 58 3.57e-05 tctagacact tcatggaa atagaatcaa chr13:92276568-92276648 30 5.87e-05 tacctacttt tcaaagaa aatatagtat chr7:117845791-117845871 35 5.87e-05 GTAATAATTA TCaaagaa aaagaagaga chr4:120375774-120375854 66 7.14e-05 CATTGTGACG TCACGGAA GGCGCGC chr10:61705906-61705986 44 8.42e-05 gaatgtgaat tccaggaa acaagtgcaa chr16:70946472-70946552 72 1.09e-04 gatgctggct tcatagaa t chr21:11111241-11111321 17 1.22e-04 CCCACCTGTG TCCTGGAA GTGCTCAGAG chr21:11048847-11048927 3 1.40e-04 AA TCACAGAA AAGACTGGAG chr21:11057701-11057781 5 1.57e-04 AATT TCCAAGAA TTTCAGAAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCAWRGAA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr13:91557567-91557647 1.7e-05 29_[+4]_43 chr6:32177057-32177137 3.6e-05 27_[+4]_45 chr17:36301785-36301865 3.6e-05 57_[+4]_15 chr13:92276568-92276648 5.9e-05 29_[+4]_43 chr7:117845791-117845871 5.9e-05 34_[+4]_38 chr4:120375774-120375854 7.1e-05 65_[+4]_7 chr10:61705906-61705986 8.4e-05 43_[+4]_29 chr16:70946472-70946552 0.00011 71_[+4]_1 chr21:11111241-11111321 0.00012 16_[+4]_56 chr21:11048847-11048927 0.00014 2_[+4]_70 chr21:11057701-11057781 0.00016 4_[+4]_68 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCAWRGAA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCAWRGAA width=8 seqs=11 chr13:91557567-91557647 ( 30) TCAAGGAA 1 chr6:32177057-32177137 ( 28) TCATGGAA 1 chr17:36301785-36301865 ( 58) TCATGGAA 1 chr13:92276568-92276648 ( 30) TCAAAGAA 1 chr7:117845791-117845871 ( 35) TCAAAGAA 1 chr4:120375774-120375854 ( 66) TCACGGAA 1 chr10:61705906-61705986 ( 44) TCCAGGAA 1 chr16:70946472-70946552 ( 72) TCATAGAA 1 chr21:11111241-11111321 ( 17) TCCTGGAA 1 chr21:11048847-11048927 ( 3) TCACAGAA 1 chr21:11057701-11057781 ( 5) TCCAAGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCAWRGAA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4453 bayes= 8.2088 E= 3.7e+003 -1010 -1010 -1010 173 -1010 226 -1010 -1010 137 39 -1010 -1010 69 -19 -1010 27 69 -1010 137 -1010 -1010 -1010 225 -1010 183 -1010 -1010 -1010 183 -1010 -1010 -1010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCAWRGAA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 11 E= 3.7e+003 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.727273 0.272727 0.000000 0.000000 0.454545 0.181818 0.000000 0.363636 0.454545 0.000000 0.545455 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCAWRGAA MEME-4 regular expression -------------------------------------------------------------------------------- TC[AC][AT][GA]GAA -------------------------------------------------------------------------------- Time 5.30 secs. ******************************************************************************** ******************************************************************************** MOTIF GCWGCTCT MEME-5 width = 8 sites = 4 llr = 43 E-value = 5.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCWGCTCT MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::5::::: pos.-specific C :a::a:a: probability G a::a:::: matrix T ::5::a:a bits 2.3 ** ** * 2.0 ** ** * 1.8 ** ***** 1.6 ** ***** Relative 1.4 ** ***** Entropy 1.1 ** ***** (15.5 bits) 0.9 ** ***** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GCAGCTCT consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWGCTCT MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr20:43485664-43485744 1 1.01e-05 . GCAGCTCT GAGGTgaatg chr6:33037149-33037229 32 1.01e-05 AGATTTTATG GCAGCTCT GAATCACAGA chr5:40829488-40829568 5 2.09e-05 GATC GCTGCTCT TCCCTGAATT chr21:11042077-11042157 16 2.09e-05 gaataaatgt gctgctct acaacccaga -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWGCTCT MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr20:43485664-43485744 1e-05 [+5]_72 chr6:33037149-33037229 1e-05 31_[+5]_41 chr5:40829488-40829568 2.1e-05 4_[+5]_68 chr21:11042077-11042157 2.1e-05 15_[+5]_57 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWGCTCT MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GCWGCTCT width=8 seqs=4 chr20:43485664-43485744 ( 1) GCAGCTCT 1 chr6:33037149-33037229 ( 32) GCAGCTCT 1 chr5:40829488-40829568 ( 5) GCTGCTCT 1 chr21:11042077-11042157 ( 16) GCTGCTCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWGCTCT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 4453 bayes= 10.1193 E= 5.6e+003 -865 -865 225 -865 -865 226 -865 -865 83 -865 -865 73 -865 -865 225 -865 -865 226 -865 -865 -865 -865 -865 173 -865 226 -865 -865 -865 -865 -865 173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWGCTCT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 4 E= 5.6e+003 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 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 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCWGCTCT MEME-5 regular expression -------------------------------------------------------------------------------- GC[AT]GCTCT -------------------------------------------------------------------------------- Time 5.90 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:36301785-36301865 2.69e-03 57_[+4(3.57e-05)]_15 chr2:145440315-145440395 7.06e-01 80 chr7:117845791-117845871 1.84e-01 34_[+4(5.87e-05)]_38 chr21:11111241-11111321 3.44e-03 80 chr10:74144248-74144328 4.99e-01 80 chr6:33037149-33037229 3.48e-04 31_[+5(1.01e-05)]_18_[+2(3.11e-05)]_\ 15 chr7:131053866-131053946 8.50e-01 80 chr4:190655937-190656017 1.00e-02 51_[+2(3.11e-05)]_21 chr7:117807305-117807385 8.00e-01 80 chr6:138257368-138257448 7.57e-01 80 chr13:92276568-92276648 6.07e-02 29_[+4(5.87e-05)]_43 chr6:38691447-38691527 7.70e-01 80 chr2:91766349-91766429 9.72e-01 80 chr21:11073622-11073702 6.00e-01 80 chr2:91790989-91791069 9.78e-01 80 chr21:11146225-11146305 1.90e-01 80 chr13:91557567-91557647 2.44e-02 29_[+4(1.72e-05)]_43 chr2:152252300-152252380 7.65e-04 66_[+2(1.86e-05)]_6 chr6:150128989-150129069 1.13e-01 7_[+1(1.83e-05)]_65 chr7:110962323-110962403 2.41e-02 52_[+2(1.86e-05)]_20 chr20:29649593-29649673 1.13e-01 25_[+1(5.57e-05)]_47 chr9:66484483-66484563 1.76e-01 80 chr21:11093201-11093281 8.99e-02 80 chr6:158281868-158281948 7.95e-01 80 chr6:6657829-6657909 4.50e-04 18_[+2(6.65e-05)]_6_[+1(1.83e-05)]_\ 19_[+2(6.65e-05)]_13 chr6:57535512-57535592 9.90e-01 80 chr21:11057701-11057781 1.95e-01 80 chr7:133230691-133230771 8.21e-01 80 chr2:69787251-69787331 3.64e-03 28_[+3(6.92e-06)]_44 chr20:43485664-43485744 2.46e-06 [+5(1.01e-05)]_13_[+1(1.83e-05)]_17_\ [+2(9.25e-06)]_26 chr9:66461460-66461540 6.29e-01 80 chr5:43313793-43313873 1.29e-01 80 chr1:228045134-228045214 6.34e-05 2_[+1(1.83e-05)]_19_[+2(6.65e-05)]_\ 6_[+1(1.83e-05)]_29 chr21:11042077-11042157 1.34e-03 15_[+5(2.09e-05)]_57 chr21:11171847-11171927 8.63e-01 80 chr4:166248651-166248731 1.24e-03 13_[+2(5.31e-05)]_6_[+1(5.57e-05)]_\ 45 chr22:42228918-42228998 2.17e-03 57_[+2(9.25e-06)]_15 chr6:158739474-158739554 2.45e-01 80 chr7:98684344-98684424 4.99e-01 80 chr5:74632811-74632891 7.89e-01 80 chr2:91783936-91784016 5.86e-01 80 chr2:177319680-177319760 1.51e-01 80 chr12:108511298-10851137 5.84e-01 80 chr10:102133170-10213325 5.53e-04 42_[+3(2.30e-05)]_[+1(5.57e-05)]_22 chr16:70946472-70946552 9.86e-02 80 chr2:91786025-91786105 4.07e-01 80 chr10:61705906-61705986 2.80e-01 43_[+4(8.42e-05)]_29 chr20:49149119-49149199 4.59e-01 80 chr17:36981584-36981664 1.44e-01 80 chr21:11057088-11057168 9.91e-01 80 chr17:36305093-36305173 6.80e-01 80 chr21:11118676-11118756 4.62e-02 14_[+1(5.57e-05)]_58 chr4:120375774-120375854 3.08e-04 1_[+3(6.92e-06)]_56_[+4(7.14e-05)]_\ 7 chr1:145104329-145104409 1.84e-02 12_[+5(8.29e-05)]_60 chr21:11112650-11112730 5.34e-01 80 chr6:57394362-57394442 1.92e-01 80 chr21:11048847-11048927 5.54e-02 80 chr1:234290832-234290912 7.97e-01 80 chr5:40829488-40829568 3.70e-04 4_[+5(2.09e-05)]_27_[+2(3.97e-05)]_\ 33 chr6:32177057-32177137 8.49e-02 27_[+4(3.57e-05)]_45 chr2:203829848-203829928 9.01e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c17n09.farnam.hpc.yale.internal ********************************************************************************