******************************************************************************** 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/HDAC1.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr1:167833318-167833398 1.0000 80 chr13:114919118-11491919 1.0000 80 chr7:44078860-44078940 1.0000 80 chr17:62530081-62530161 1.0000 80 chr2:111920527-111920607 1.0000 80 chr8:144025175-144025255 1.0000 80 chr16:4784636-4784716 1.0000 80 chr1:23952635-23952715 1.0000 80 chr20:37089047-37089127 1.0000 80 chr3:20083063-20083143 1.0000 80 chr22:31460131-31460211 1.0000 80 chr6:105123200-105123280 1.0000 80 chr21:33765196-33765276 1.0000 80 chr6:161827808-161827888 1.0000 80 chr2:170684849-170684929 1.0000 80 chr4:81256970-81257050 1.0000 80 chr1:228352350-228352430 1.0000 80 chr19:13002087-13002167 1.0000 80 chr10:99160965-99161045 1.0000 80 chr12:4430045-4430125 1.0000 80 chr12:125473546-12547362 1.0000 80 chr19:48673409-48673489 1.0000 80 chr16:30773284-30773364 1.0000 80 chr6:33256870-33256950 1.0000 80 chr5:175815491-175815571 1.0000 80 chr7:65580499-65580579 1.0000 80 chr7:97847741-97847821 1.0000 80 chr9:132806071-132806151 1.0000 80 chr21:46961662-46961742 1.0000 80 chr19:1864281-1864361 1.0000 80 chr10:75911075-75911155 1.0000 80 chr1:230562398-230562478 1.0000 80 chr4:110736965-110737045 1.0000 80 chr9:132020870-132020950 1.0000 80 chr11:44564053-44564133 1.0000 80 chr6:20401557-20401637 1.0000 80 chr20:20033208-20033288 1.0000 80 chr4:7044600-7044680 1.0000 80 chr14:73393260-73393340 1.0000 80 chr11:118444117-11844419 1.0000 80 chr6:136572700-136572780 1.0000 80 chr10:102747354-10274743 1.0000 80 chr11:96037308-96037388 1.0000 80 chr12:109535672-10953575 1.0000 80 chr2:120916411-120916491 1.0000 80 chr12:100594430-10059451 1.0000 80 chr7:100450069-100450149 1.0000 80 chr2:32853212-32853292 1.0000 80 chr5:138524361-138524441 1.0000 80 chr12:101673937-10167401 1.0000 80 chr5:72861593-72861673 1.0000 80 chr16:30560853-30560933 1.0000 80 chr1:156542244-156542324 1.0000 80 chr5:173043121-173043201 1.0000 80 chr15:41407809-41407889 1.0000 80 chr9:131218113-131218193 1.0000 80 chr6:142433767-142433847 1.0000 80 chr17:49336709-49336789 1.0000 80 chr1:156251136-156251216 1.0000 80 chr2:68385072-68385152 1.0000 80 chr7:45027711-45027791 1.0000 80 chr7:129595307-129595387 1.0000 80 chr16:69166553-69166633 1.0000 80 chr11:119252524-11925260 1.0000 80 chr19:41903200-41903280 1.0000 80 chr1:116963179-116963259 1.0000 80 chr22:32058098-32058178 1.0000 80 chr2:88991377-88991457 1.0000 80 chr22:19166588-19166668 1.0000 80 chr6:7312712-7312792 1.0000 80 chr4:57302568-57302648 1.0000 80 chr17:27046380-27046460 1.0000 80 chr9:33473824-33473904 1.0000 80 chr21:34100687-34100767 1.0000 80 chr4:128454711-128454791 1.0000 80 chr19:59085077-59085157 1.0000 80 chr1:154077019-154077099 1.0000 80 chr19:3185342-3185422 1.0000 80 chr15:40987419-40987499 1.0000 80 chr19:50878395-50878475 1.0000 80 chr12:31910165-31910245 1.0000 80 chr19:55691518-55691598 1.0000 80 chr16:75145090-75145170 1.0000 80 chr11:107436308-10743638 1.0000 80 chr12:49717066-49717146 1.0000 80 chr12:133712488-13371256 1.0000 80 chr16:72042714-72042794 1.0000 80 chr6:27204143-27204223 1.0000 80 chr12:64615950-64616030 1.0000 80 chr9:135545282-135545362 1.0000 80 chr17:1933424-1933504 1.0000 80 chr17:34958054-34958134 1.0000 80 chr15:41708884-41708964 1.0000 80 chr7:2354421-2354501 1.0000 80 chr22:51221991-51222071 1.0000 80 chr19:2151852-2151932 1.0000 80 chr1:26633021-26633101 1.0000 80 chr1:40840188-40840268 1.0000 80 chr3:194392783-194392863 1.0000 80 chr5:137514785-137514865 1.0000 80 chr22:40895302-40895382 1.0000 80 chr1:120930421-120930501 1.0000 80 chr1:148556802-148556882 1.0000 80 chr12:7394167-7394247 1.0000 80 chr16:21623468-21623548 1.0000 80 chr15:78730128-78730208 1.0000 80 chr16:14579259-14579339 1.0000 80 chr8:117778982-117779062 1.0000 80 chr20:47654645-47654725 1.0000 80 chr1:86173992-86174072 1.0000 80 chr16:30418664-30418744 1.0000 80 chr12:66558225-66558305 1.0000 80 chr4:113557934-113558014 1.0000 80 chr4:120987853-120987933 1.0000 80 chr19:56213861-56213941 1.0000 80 chr19:54666221-54666301 1.0000 80 chr12:105380190-10538027 1.0000 80 chr17:33469225-33469305 1.0000 80 chr21:44353021-44353101 1.0000 80 chr1:179335092-179335172 1.0000 80 chr15:85523995-85524075 1.0000 80 chr5:173315335-173315415 1.0000 80 chr12:104458403-10445848 1.0000 80 chr20:30467637-30467717 1.0000 80 chr19:10426547-10426627 1.0000 80 chr8:144416904-144416984 1.0000 80 chr8:95908042-95908122 1.0000 80 chr15:85143704-85143784 1.0000 80 chrX:117859001-117859081 1.0000 80 chr7:102715120-102715200 1.0000 80 chr11:123612275-12361235 1.0000 80 chr4:54232156-54232236 1.0000 80 chr1:8586028-8586108 1.0000 80 chr2:97001601-97001681 1.0000 80 chr1:36347618-36347698 1.0000 80 chr19:50321095-50321175 1.0000 80 chr19:8008940-8009020 1.0000 80 chr7:134278828-134278908 1.0000 80 chr16:89284112-89284192 1.0000 80 chr5:139780345-139780425 1.0000 80 chr3:49967030-49967110 1.0000 80 chr1:28851637-28851717 1.0000 80 chr19:50180731-50180811 1.0000 80 chr17:71088782-71088862 1.0000 80 chr7:102624240-102624320 1.0000 80 chr12:7080132-7080212 1.0000 80 chr16:3018960-3019040 1.0000 80 chr1:181687327-181687407 1.0000 80 chr11:73727496-73727576 1.0000 80 chr5:68530460-68530540 1.0000 80 chr8:144679227-144679307 1.0000 80 chr6:30585695-30585775 1.0000 80 chr8:27632080-27632160 1.0000 80 chr6:38764366-38764446 1.0000 80 chr16:81110683-81110763 1.0000 80 chr17:42084504-42084584 1.0000 80 chr7:150759590-150759670 1.0000 80 chr17:36831382-36831462 1.0000 80 chr19:49631593-49631673 1.0000 80 chr3:10501992-10502072 1.0000 80 chr1:210001353-210001433 1.0000 80 chr19:480463-480543 1.0000 80 chr6:10838628-10838708 1.0000 80 chr11:71640142-71640222 1.0000 80 chr19:45657990-45658070 1.0000 80 chr4:99722502-99722582 1.0000 80 chr6:33291274-33291354 1.0000 80 chr12:93571621-93571701 1.0000 80 chr1:150479052-150479132 1.0000 80 chr17:65852191-65852271 1.0000 80 chr7:100136306-100136386 1.0000 80 chr11:113185394-11318547 1.0000 80 chr1:156571172-156571252 1.0000 80 chr6:31763372-31763452 1.0000 80 chr19:45909937-45910017 1.0000 80 chr14:102771343-10277142 1.0000 80 chr19:45393638-45393718 1.0000 80 chr17:81009483-81009563 1.0000 80 chr2:73441348-73441428 1.0000 80 chr19:12807360-12807440 1.0000 80 chr12:132413792-13241387 1.0000 80 chr20:5931113-5931193 1.0000 80 chr2:43822825-43822905 1.0000 80 chr1:109757540-109757620 1.0000 80 chr17:30228571-30228651 1.0000 80 chr3:51975857-51975937 1.0000 80 chr20:33264752-33264832 1.0000 80 chr3:52720053-52720133 1.0000 80 chr2:152991150-152991230 1.0000 80 chr4:39559988-39560068 1.0000 80 chr10:103590477-10359055 1.0000 80 chr1:43148830-43148910 1.0000 80 chr2:3381469-3381549 1.0000 80 chr1:246729438-246729518 1.0000 80 chr8:67341297-67341377 1.0000 80 chr11:71159705-71159785 1.0000 80 chr12:109217692-10921777 1.0000 80 chr16:5083811-5083891 1.0000 80 chr1:100435813-100435893 1.0000 80 chr19:10812082-10812162 1.0000 80 chr8:92082637-92082717 1.0000 80 chr1:43637867-43637947 1.0000 80 chr12:114404042-11440412 1.0000 80 chr21:48055895-48055975 1.0000 80 chr8:101734802-101734882 1.0000 80 chr15:40861515-40861595 1.0000 80 chr11:66057123-66057203 1.0000 80 chr4:108913525-108913605 1.0000 80 chr6:170862885-170862965 1.0000 80 chr12:64174097-64174177 1.0000 80 chr8:37888435-37888515 1.0000 80 chr9:106856617-106856697 1.0000 80 chr19:10530562-10530642 1.0000 80 chr3:97629930-97630010 1.0000 80 chr10:104474510-10447459 1.0000 80 chr2:27440313-27440393 1.0000 80 chr9:34329060-34329140 1.0000 80 chr16:58549292-58549372 1.0000 80 chr2:85830031-85830111 1.0000 80 chr9:127963011-127963091 1.0000 80 chr21:37432403-37432483 1.0000 80 chr4:178231025-178231105 1.0000 80 chr6:43543183-43543263 1.0000 80 chr6:17820373-17820453 1.0000 80 chr1:44435698-44435778 1.0000 80 chr1:38061400-38061480 1.0000 80 chr3:158519844-158519924 1.0000 80 chr11:910592-910672 1.0000 80 chr17:58217286-58217366 1.0000 80 chr2:112641634-112641714 1.0000 80 chr16:1661944-1662024 1.0000 80 chr1:45476909-45476989 1.0000 80 chr7:50626223-50626303 1.0000 80 chr19:13096251-13096331 1.0000 80 chr19:47289528-47289608 1.0000 80 chr12:31804036-31804116 1.0000 80 chr9:130565295-130565375 1.0000 80 chr6:90529426-90529506 1.0000 80 chr20:3190263-3190343 1.0000 80 chr15:78591844-78591924 1.0000 80 chr9:135457573-135457653 1.0000 80 chr17:8152669-8152749 1.0000 80 chr7:30510010-30510090 1.0000 80 chr9:114364075-114364155 1.0000 80 chr19:55791305-55791385 1.0000 80 chr1:229762040-229762120 1.0000 80 chr16:11350343-11350423 1.0000 80 chr6:80714419-80714499 1.0000 80 chr6:106968847-106968927 1.0000 80 chr17:38444182-38444262 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_HDAC1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/K562/fasta/RankLinear0.6_40/HDAC1.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= 250 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= 20000 N= 250 sample: seed= 0 hsfrac= 0 searchsize= 20000 norand= no csites= 1000 Letter frequencies in dataset: A 0.211 C 0.289 G 0.297 T 0.204 Background letter frequencies (from file dataset with add-one prior applied): A 0.211 C 0.289 G 0.297 T 0.204 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CCACGTGS MEME-1 width = 8 sites = 40 llr = 338 E-value = 5.0e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCACGTGS MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2:a::::: pos.-specific C 7a:9:::4 probability G 1::2a:a5 matrix T :::::a:2 bits 2.3 * * 2.1 * * 1.8 ** *** 1.6 ** *** Relative 1.4 ** *** Entropy 1.1 ****** (12.2 bits) 0.9 ****** 0.7 ******* 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CCACGTGG consensus A C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACGTGS MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr9:127963011-127963091 53 2.72e-05 CCTAGAACTG CCACGTGG GGATGAGATT chr16:58549292-58549372 62 2.72e-05 AAAACAGGCA CCACGTGG TTCCGGCGCC chr2:27440313-27440393 5 2.72e-05 TTAG CCACGTGG ACCGACTCCG chr10:104474510-10447459 59 2.72e-05 CCTGCAGAAG CCACGTGG CGCGAAGTGC chr19:10812082-10812162 33 2.72e-05 GTGGTACGGC CCACGTGG TTCCGACAGT chr11:71159705-71159785 16 2.72e-05 GGCGGAGTGG CCACGTGG GCCGCGCGGA chr2:43822825-43822905 38 2.72e-05 GATTTCTGAA CCACGTGG AGTCGAGGAA chr12:132413792-13241387 7 2.72e-05 CTTCGC CCACGTGG TCCGGCTCCG chr19:50180731-50180811 67 2.72e-05 ATCCCCCCTC CCACGTGG AGGAGG chr19:2151852-2151932 38 2.72e-05 GGCGGGGCGC CCACGTGG AGCTTAGCCG chr11:119252524-11925260 8 2.72e-05 CAGAGAA CCACGTGG AGGAAAAGCA chr19:10530562-10530642 68 5.37e-05 CAGCAGCCAA CCACGTGC GCACA chr1:43637867-43637947 46 5.37e-05 CGCCGTGGCT CCACGTGC CACCGAATCG chr15:85143704-85143784 3 5.37e-05 TA CCACGTGC GAAAACAAAG chr19:41903200-41903280 44 5.37e-05 CGCGCCGAGC CCACGTGC GGCTGCAGTT chr17:49336709-49336789 21 5.37e-05 ATTTCCACCT CCACGTGC AAACCGCCTC chr15:41407809-41407889 57 5.37e-05 CCACCGGGTC CCACGTGC ACCTGGTCTA chr8:144025175-144025255 72 5.37e-05 CCTGTAATGC CCACGTGC A chr6:90529426-90529506 54 9.23e-05 GAGGGGCACC ACACGTGG GTGAGCACAC chr1:43148830-43148910 71 9.23e-05 TCAGACTCAC CCACGTGT GC chr20:5931113-5931193 56 9.23e-05 GGCACCGCCC CCACGTGT TGCACGCCGC chr17:71088782-71088862 66 9.23e-05 TCCCTCCCGC ACACGTGG CCCTCCC chr4:54232156-54232236 56 9.23e-05 TCTCCACAGT ACACGTGG TCGGCCTCTG chr1:86173992-86174072 72 9.23e-05 CTACGGCGGC CCACGTGT G chr4:57302568-57302648 56 9.23e-05 GCGCGGGCGC ACACGTGG CCCAGGCGCT chr22:19166588-19166668 50 9.23e-05 CTCCCCGAAA ACACGTGG GGCTAGCCCA chr12:109535672-10953575 72 9.23e-05 CAAATAGCCT CCACGTGT T chr1:156251136-156251216 69 1.12e-04 ATGATAAGGC ACACGTGC CACC chr21:46961662-46961742 60 1.12e-04 TCCCGAAGCA ACACGTGC CTGGGCGCGA chr12:64174097-64174177 64 1.25e-04 CGCCTTTCAA ACACGTGT TAAAATCCA chr9:132020870-132020950 17 1.25e-04 GGGCTCCCAG ACACGTGT CCCCGGGAGC chr9:135457573-135457653 53 1.53e-04 ACCTCCCCGG CCAGGTGG AGAGTCATGA chr21:34100687-34100767 55 1.53e-04 GCCGAGCCAA CCAGGTGG CGCCTGAAGA chr17:8152669-8152749 26 1.80e-04 GGATCCTCCT CCAGGTGC AGCGTTTCGT chr6:33291274-33291354 72 1.80e-04 GTTTCTACTG CCAGGTGC T chr19:10426547-10426627 57 1.80e-04 GTCTGTTCCA CCAGGTGC CCCTGGCAGC chr1:154077019-154077099 38 1.80e-04 ctgcactccc ccaggtgc acagatttgg chr17:36831382-36831462 50 2.08e-04 ATGCGCCGCC GCACGTGG CCCGGTGGCG chr19:55691518-55691598 37 2.08e-04 CCCACCCCCT GCACGTGG GCGGTGGCGC chr20:47654645-47654725 9 2.75e-04 gattacag gcacgtgc caccatgccc -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACGTGS MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr9:127963011-127963091 2.7e-05 52_[+1]_20 chr16:58549292-58549372 2.7e-05 61_[+1]_11 chr2:27440313-27440393 2.7e-05 4_[+1]_68 chr10:104474510-10447459 2.7e-05 58_[+1]_14 chr19:10812082-10812162 2.7e-05 32_[+1]_40 chr11:71159705-71159785 2.7e-05 15_[+1]_57 chr2:43822825-43822905 2.7e-05 37_[+1]_35 chr12:132413792-13241387 2.7e-05 6_[+1]_66 chr19:50180731-50180811 2.7e-05 66_[+1]_6 chr19:2151852-2151932 2.7e-05 37_[+1]_35 chr11:119252524-11925260 2.7e-05 7_[+1]_65 chr19:10530562-10530642 5.4e-05 67_[+1]_5 chr1:43637867-43637947 5.4e-05 45_[+1]_27 chr15:85143704-85143784 5.4e-05 2_[+1]_70 chr19:41903200-41903280 5.4e-05 43_[+1]_29 chr17:49336709-49336789 5.4e-05 20_[+1]_52 chr15:41407809-41407889 5.4e-05 56_[+1]_16 chr8:144025175-144025255 5.4e-05 71_[+1]_1 chr6:90529426-90529506 9.2e-05 53_[+1]_19 chr1:43148830-43148910 9.2e-05 70_[+1]_2 chr20:5931113-5931193 9.2e-05 55_[+1]_17 chr17:71088782-71088862 9.2e-05 65_[+1]_7 chr4:54232156-54232236 9.2e-05 55_[+1]_17 chr1:86173992-86174072 9.2e-05 71_[+1]_1 chr4:57302568-57302648 9.2e-05 55_[+1]_17 chr22:19166588-19166668 9.2e-05 49_[+1]_23 chr12:109535672-10953575 9.2e-05 71_[+1]_1 chr1:156251136-156251216 0.00011 68_[+1]_4 chr21:46961662-46961742 0.00011 59_[+1]_13 chr12:64174097-64174177 0.00013 63_[+1]_9 chr9:132020870-132020950 0.00013 16_[+1]_56 chr9:135457573-135457653 0.00015 52_[+1]_20 chr21:34100687-34100767 0.00015 54_[+1]_18 chr17:8152669-8152749 0.00018 25_[+1]_47 chr6:33291274-33291354 0.00018 71_[+1]_1 chr19:10426547-10426627 0.00018 56_[+1]_16 chr1:154077019-154077099 0.00018 37_[+1]_35 chr17:36831382-36831462 0.00021 49_[+1]_23 chr19:55691518-55691598 0.00021 36_[+1]_36 chr20:47654645-47654725 0.00028 8_[+1]_64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACGTGS MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCACGTGS width=8 seqs=40 chr9:127963011-127963091 ( 53) CCACGTGG 1 chr16:58549292-58549372 ( 62) CCACGTGG 1 chr2:27440313-27440393 ( 5) CCACGTGG 1 chr10:104474510-10447459 ( 59) CCACGTGG 1 chr19:10812082-10812162 ( 33) CCACGTGG 1 chr11:71159705-71159785 ( 16) CCACGTGG 1 chr2:43822825-43822905 ( 38) CCACGTGG 1 chr12:132413792-13241387 ( 7) CCACGTGG 1 chr19:50180731-50180811 ( 67) CCACGTGG 1 chr19:2151852-2151932 ( 38) CCACGTGG 1 chr11:119252524-11925260 ( 8) CCACGTGG 1 chr19:10530562-10530642 ( 68) CCACGTGC 1 chr1:43637867-43637947 ( 46) CCACGTGC 1 chr15:85143704-85143784 ( 3) CCACGTGC 1 chr19:41903200-41903280 ( 44) CCACGTGC 1 chr17:49336709-49336789 ( 21) CCACGTGC 1 chr15:41407809-41407889 ( 57) CCACGTGC 1 chr8:144025175-144025255 ( 72) CCACGTGC 1 chr6:90529426-90529506 ( 54) ACACGTGG 1 chr1:43148830-43148910 ( 71) CCACGTGT 1 chr20:5931113-5931193 ( 56) CCACGTGT 1 chr17:71088782-71088862 ( 66) ACACGTGG 1 chr4:54232156-54232236 ( 56) ACACGTGG 1 chr1:86173992-86174072 ( 72) CCACGTGT 1 chr4:57302568-57302648 ( 56) ACACGTGG 1 chr22:19166588-19166668 ( 50) ACACGTGG 1 chr12:109535672-10953575 ( 72) CCACGTGT 1 chr1:156251136-156251216 ( 69) ACACGTGC 1 chr21:46961662-46961742 ( 60) ACACGTGC 1 chr12:64174097-64174177 ( 64) ACACGTGT 1 chr9:132020870-132020950 ( 17) ACACGTGT 1 chr9:135457573-135457653 ( 53) CCAGGTGG 1 chr21:34100687-34100767 ( 55) CCAGGTGG 1 chr17:8152669-8152749 ( 26) CCAGGTGC 1 chr6:33291274-33291354 ( 72) CCAGGTGC 1 chr19:10426547-10426627 ( 57) CCAGGTGC 1 chr1:154077019-154077099 ( 38) CCAGGTGC 1 chr17:36831382-36831462 ( 50) GCACGTGG 1 chr19:55691518-55691598 ( 37) GCACGTGG 1 chr20:47654645-47654725 ( 9) GCACGTGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACGTGS MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.08256 E= 5.0e-009 9 128 -198 -1197 -1197 179 -1197 -1197 225 -1197 -1197 -1197 -1197 156 -98 -1197 -1197 -1197 175 -1197 -1197 -1197 -1197 229 -1197 -1197 175 -1197 -1197 28 75 -44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACGTGS MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 40 E= 5.0e-009 0.225000 0.700000 0.075000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.850000 0.150000 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 0.350000 0.500000 0.150000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCACGTGS MEME-1 regular expression -------------------------------------------------------------------------------- [CA]CACGTG[GC] -------------------------------------------------------------------------------- Time 4.81 secs. ******************************************************************************** ******************************************************************************** MOTIF TGTSATTT MEME-2 width = 8 sites = 22 llr = 200 E-value = 3.5e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGTSATTT MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::1:9::: pos.-specific C :1:4:::3 probability G :6:6:::: matrix T a29:1aa7 bits 2.3 * ** 2.1 * ** 1.8 * * *** 1.6 * * *** Relative 1.4 * * **** Entropy 1.1 * * **** (13.1 bits) 0.9 * ****** 0.7 * ****** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TGTGATTT consensus C C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTSATTT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:109757540-109757620 63 6.58e-06 GTCAAGTACT TGTGATTT GATTTGTCTG chr1:148556802-148556882 53 6.58e-06 AAAGAGTTGC TGTGATTT CCCTGTATCT chr5:72861593-72861673 34 6.58e-06 TGAGGGTCCA TGTGATTT TTACGCCAGT chr1:228352350-228352430 11 6.58e-06 TTACCAAGGA TGTGATTT GAAGCTGTGA chr19:47289528-47289608 25 1.30e-05 TCCAGCTGTA TGTCATTT GGTTATAAGC chr1:36347618-36347698 59 1.30e-05 atagaggaac tgtcattt ctgacatgaa chr5:173315335-173315415 8 1.30e-05 AGCTGGT TGTCATTT CACTCGGCTC chr7:102624240-102624320 37 1.75e-05 agattctgca tttgattt tcaggaatct chr21:44353021-44353101 73 1.75e-05 tgattttggt tttgattt chr1:167833318-167833398 62 1.75e-05 tgattttggt tttgattt tggtttagtg chr1:44435698-44435778 30 3.12e-05 GAAGGCCGAC TGTGATTC CCCCTACCCC chr4:128454711-128454791 7 3.76e-05 CAGCTT TCTGATTT GCTTAATGGA chr6:170862885-170862965 71 4.67e-05 TAGTGTTCCT TGTCATTC TA chr15:41708884-41708964 17 4.67e-05 ccagctcagc tgtcaTTC GCACAGCCCG chr12:114404042-11440412 10 5.93e-05 CCCCGCTGT TTTGATTC CAACACGACT chr9:127963011-127963091 64 7.71e-05 CACGTGGGGA TGAGATTT GCTGGGCTG chr17:65852191-65852271 16 7.71e-05 tatcttgagc tatgattt tattgaacgt chr19:56213861-56213941 49 7.71e-05 gttgcttatc tgtgtttt acagcctgaa chr7:134278828-134278908 20 1.10e-04 GTCCCACAAT TGACATTT ACTGACCTTG chr22:40895302-40895382 8 1.10e-04 TCCTTGT TCTGATTC TCTGACTAAT chr17:1933424-1933504 8 1.10e-04 CCAGCGC TGTCTTTT TAGTACCACA chr2:112641634-112641714 6 1.28e-04 CAGCT TCTCATTC CCTCTCCCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTSATTT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:109757540-109757620 6.6e-06 62_[+2]_10 chr1:148556802-148556882 6.6e-06 52_[+2]_20 chr5:72861593-72861673 6.6e-06 33_[+2]_39 chr1:228352350-228352430 6.6e-06 10_[+2]_62 chr19:47289528-47289608 1.3e-05 24_[+2]_48 chr1:36347618-36347698 1.3e-05 58_[+2]_14 chr5:173315335-173315415 1.3e-05 7_[+2]_65 chr7:102624240-102624320 1.7e-05 36_[+2]_36 chr21:44353021-44353101 1.7e-05 72_[+2] chr1:167833318-167833398 1.7e-05 61_[+2]_11 chr1:44435698-44435778 3.1e-05 29_[+2]_43 chr4:128454711-128454791 3.8e-05 6_[+2]_66 chr6:170862885-170862965 4.7e-05 70_[+2]_2 chr15:41708884-41708964 4.7e-05 16_[+2]_56 chr12:114404042-11440412 5.9e-05 9_[+2]_63 chr9:127963011-127963091 7.7e-05 63_[+2]_9 chr17:65852191-65852271 7.7e-05 15_[+2]_57 chr19:56213861-56213941 7.7e-05 48_[+2]_24 chr7:134278828-134278908 0.00011 19_[+2]_53 chr22:40895302-40895382 0.00011 7_[+2]_65 chr17:1933424-1933504 0.00011 7_[+2]_65 chr2:112641634-112641714 0.00013 5_[+2]_67 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTSATTT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGTSATTT width=8 seqs=22 chr1:109757540-109757620 ( 63) TGTGATTT 1 chr1:148556802-148556882 ( 53) TGTGATTT 1 chr5:72861593-72861673 ( 34) TGTGATTT 1 chr1:228352350-228352430 ( 11) TGTGATTT 1 chr19:47289528-47289608 ( 25) TGTCATTT 1 chr1:36347618-36347698 ( 59) TGTCATTT 1 chr5:173315335-173315415 ( 8) TGTCATTT 1 chr7:102624240-102624320 ( 37) TTTGATTT 1 chr21:44353021-44353101 ( 73) TTTGATTT 1 chr1:167833318-167833398 ( 62) TTTGATTT 1 chr1:44435698-44435778 ( 30) TGTGATTC 1 chr4:128454711-128454791 ( 7) TCTGATTT 1 chr6:170862885-170862965 ( 71) TGTCATTC 1 chr15:41708884-41708964 ( 17) TGTCATTC 1 chr12:114404042-11440412 ( 10) TTTGATTC 1 chr9:127963011-127963091 ( 64) TGAGATTT 1 chr17:65852191-65852271 ( 16) TATGATTT 1 chr19:56213861-56213941 ( 49) TGTGTTTT 1 chr7:134278828-134278908 ( 20) TGACATTT 1 chr22:40895302-40895382 ( 8) TCTGATTC 1 chr17:1933424-1933504 ( 8) TGTCTTTT 1 chr2:112641634-112641714 ( 6) TCTCATTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTSATTT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.229 E= 3.5e-001 -1110 -1110 -1110 229 -221 -108 110 -17 -121 -1110 -1110 216 -1110 33 110 -1110 211 -1110 -1110 -117 -1110 -1110 -1110 229 -1110 -1110 -1110 229 -1110 -8 -1110 183 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTSATTT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 3.5e-001 0.000000 0.000000 0.000000 1.000000 0.045455 0.136364 0.636364 0.181818 0.090909 0.000000 0.000000 0.909091 0.000000 0.363636 0.636364 0.000000 0.909091 0.000000 0.000000 0.090909 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.272727 0.000000 0.727273 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTSATTT MEME-2 regular expression -------------------------------------------------------------------------------- TGT[GC]ATT[TC] -------------------------------------------------------------------------------- Time 8.46 secs. ******************************************************************************** ******************************************************************************** MOTIF TTATCTVY MEME-3 width = 8 sites = 15 llr = 140 E-value = 2.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTATCTVY MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::7:::2: pos.-specific C ::::a:43 probability G ::3:::3: matrix T aa:a:a17 bits 2.3 ** * * 2.1 ** * * 1.8 ** *** 1.6 ** *** Relative 1.4 ****** Entropy 1.1 ****** * (13.5 bits) 0.9 ****** * 0.7 ****** * 0.5 ****** * 0.2 ****** * 0.0 -------- Multilevel TTATCTCT consensus G GC sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTATCTVY MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr17:30228571-30228651 63 6.23e-06 CGTTCCTGAA TTATCTCT GCCATGAGGT chr20:47654645-47654725 54 6.23e-06 GGTTAACCTC TTATCTCT TGTCCCTCCC chr16:30560853-30560933 69 6.23e-06 tgacatgcct ttatctct ctct chr6:38764366-38764446 3 1.08e-05 tg ttatctat agattccaga chr12:31910165-31910245 13 1.08e-05 agtagtggtg ttatctat aggagcaatt chr2:152991150-152991230 55 1.72e-05 ctcagtgtcc ttatctgt aagacagggc chr12:133712488-13371256 25 2.16e-05 TAACCTCAGC TTATCTTT TGTCAGCAGC chr4:128454711-128454791 65 3.04e-05 AGCTGAGTTG TTATCTCC CTGCACCT chr1:246729438-246729518 7 4.56e-05 ATGTCC TTGTCTCT CAGGCCCGCT chr4:108913525-108913605 35 5.47e-05 GTGGTTTAGC TTATCTGC TTTTGCACCC chr11:73727496-73727576 47 5.47e-05 CTAGGGGGCC TTATCTGC AAGGCCCAGG chr12:4430045-4430125 56 5.47e-05 GCCGGCTTCC TTATCTGC CCCGAACGCA chr19:8008940-8009020 42 6.11e-05 TCCAGAGTAA TTGTCTAT GGCTGCCCCT chr6:33256870-33256950 28 8.25e-05 GGTCTGAAGT TTGTCTTT CTTGGGCGGG chr19:12807360-12807440 68 9.49e-05 GCCTCGCGTC TTGTCTCC TAGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTATCTVY MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:30228571-30228651 6.2e-06 62_[+3]_10 chr20:47654645-47654725 6.2e-06 53_[+3]_19 chr16:30560853-30560933 6.2e-06 68_[+3]_4 chr6:38764366-38764446 1.1e-05 2_[+3]_70 chr12:31910165-31910245 1.1e-05 12_[+3]_60 chr2:152991150-152991230 1.7e-05 54_[+3]_18 chr12:133712488-13371256 2.2e-05 24_[+3]_48 chr4:128454711-128454791 3e-05 64_[+3]_8 chr1:246729438-246729518 4.6e-05 6_[+3]_66 chr4:108913525-108913605 5.5e-05 34_[+3]_38 chr11:73727496-73727576 5.5e-05 46_[+3]_26 chr12:4430045-4430125 5.5e-05 55_[+3]_17 chr19:8008940-8009020 6.1e-05 41_[+3]_31 chr6:33256870-33256950 8.2e-05 27_[+3]_45 chr19:12807360-12807440 9.5e-05 67_[+3]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTATCTVY MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTATCTVY width=8 seqs=15 chr17:30228571-30228651 ( 63) TTATCTCT 1 chr20:47654645-47654725 ( 54) TTATCTCT 1 chr16:30560853-30560933 ( 69) TTATCTCT 1 chr6:38764366-38764446 ( 3) TTATCTAT 1 chr12:31910165-31910245 ( 13) TTATCTAT 1 chr2:152991150-152991230 ( 55) TTATCTGT 1 chr12:133712488-13371256 ( 25) TTATCTTT 1 chr4:128454711-128454791 ( 65) TTATCTCC 1 chr1:246729438-246729518 ( 7) TTGTCTCT 1 chr4:108913525-108913605 ( 35) TTATCTGC 1 chr11:73727496-73727576 ( 47) TTATCTGC 1 chr12:4430045-4430125 ( 56) TTATCTGC 1 chr19:8008940-8009020 ( 42) TTGTCTAT 1 chr6:33256870-33256950 ( 28) TTGTCTTT 1 chr19:12807360-12807440 ( 68) TTGTCTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTATCTVY MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.9222 E= 2.8e+003 -1055 -1055 -1055 229 -1055 -1055 -1055 229 180 -1055 -15 -1055 -1055 -1055 -1055 229 -1055 179 -1055 -1055 -1055 -1055 -1055 229 -8 47 -15 -61 -1055 21 -1055 171 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTATCTVY MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 15 E= 2.8e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.733333 0.000000 0.266667 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 0.200000 0.400000 0.266667 0.133333 0.000000 0.333333 0.000000 0.666667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTATCTVY MEME-3 regular expression -------------------------------------------------------------------------------- TT[AG]TCT[CGA][TC] -------------------------------------------------------------------------------- Time 12.07 secs. ******************************************************************************** ******************************************************************************** MOTIF ARAAATCA MEME-4 width = 8 sites = 30 llr = 248 E-value = 3.8e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif ARAAATCA MEME-4 Description -------------------------------------------------------------------------------- Simplified A 749a93:9 pos.-specific C :2::1:a: probability G 141::::: matrix T 1::::7:1 bits 2.3 2.1 * 1.8 ** ** 1.6 *** ** Relative 1.4 ****** Entropy 1.1 * ****** (11.9 bits) 0.9 * ****** 0.7 * ****** 0.5 * ****** 0.2 ******** 0.0 -------- Multilevel AAAAATCA consensus G A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAAATCA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr4:39559988-39560068 23 5.20e-06 tgcttgcctg aaaaatca cagctgctgc chr12:7394167-7394247 45 5.20e-06 TGTTGACCAC AAAAATCA CAGGAGTGTT chr6:142433767-142433847 55 5.20e-06 AATCTCAGTT AAAAATCA CTGGCTGAAA chr6:105123200-105123280 65 5.20e-06 atcaatgtcc aaaaatca caagcatt chr7:50626223-50626303 16 2.50e-05 AAGAAACCAA ACAAATCA GCAgtgctca chr5:138524361-138524441 3 2.50e-05 AT ACAAATCA GAGGAAAGCA chr12:4430045-4430125 34 2.50e-05 CGCAACAACC ACAAATCA GTGCGCCGGC chr5:68530460-68530540 69 3.76e-05 CTGGTAATGT AGAAAACA CCCA chr6:7312712-7312792 68 3.76e-05 TTAGATGTGT AGAAAACA AGGGT chr17:42084504-42084584 27 4.50e-05 CTCCTTGAAT GAAAATCA CAGACAAATC chr5:173043121-173043201 11 4.50e-05 CTCGGCTTTC GAAAATCA AAGCTGCCAC chr1:246729438-246729518 27 5.94e-05 GGCCCGCTCC AAGAATCA CCTAGTGCAG chr1:181687327-181687407 69 5.94e-05 CATGAGGCAC TGAAATCA GAAT chr9:132806071-132806151 29 5.94e-05 CTCTCAGGCG TGAAATCA CGTTACCGCC chr16:58549292-58549372 50 6.67e-05 AGCGTGGACG ACAAAACA GGCACCACGT chr19:3185342-3185422 45 6.67e-05 catcatatgc acaaaaca gacaaaagtt chr12:93571621-93571701 15 8.92e-05 ggcatttcaa ggaaatca cttctcttct chr6:136572700-136572780 14 8.92e-05 GCCCTTGTGA ATAAATCA CGACTTTATA chr11:118444117-11844419 37 8.92e-05 TGAGGATGGA GGAAATCA GAACTGCTGA chr16:21623468-21623548 68 9.94e-05 TTTTCTTGTC TAAAAACA AGGAT chr6:20401557-20401637 39 9.94e-05 ACGTATCTGG AAAAATCT CCTGCGCTGT chr17:62530081-62530161 44 9.94e-05 GGAGAGATTT AAAAATCT TTGCCTGAGT chr11:73727496-73727576 68 1.10e-04 GCCCAGGCCC AGGAATCA GAACA chr16:1661944-1662024 52 1.34e-04 CACACTTCTC AGAACTCA GGTTCGCGCC chr3:51975857-51975937 57 1.34e-04 CAGCGGCCGC AGAACTCA CGTGGCAGCT chr4:54232156-54232236 1 1.34e-04 . AGAACTCA CCGCTTCCGG chr3:97629930-97630010 62 1.56e-04 TGAGATAACC AAGAAACA ATTCTAAGTA chr7:134278828-134278908 41 1.56e-04 GACCTTGTGG AAGAAACA AATTGCCTGA chr15:78730128-78730208 6 1.56e-04 CCACT TGAAAACA CGCGTGTGGG chr19:56213861-56213941 65 2.12e-04 ttacagcctg aaagatca ggctgctc -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAAATCA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr4:39559988-39560068 5.2e-06 22_[+4]_50 chr12:7394167-7394247 5.2e-06 44_[+4]_28 chr6:142433767-142433847 5.2e-06 54_[+4]_18 chr6:105123200-105123280 5.2e-06 64_[+4]_8 chr7:50626223-50626303 2.5e-05 15_[+4]_57 chr5:138524361-138524441 2.5e-05 2_[+4]_70 chr12:4430045-4430125 2.5e-05 33_[+4]_39 chr5:68530460-68530540 3.8e-05 68_[+4]_4 chr6:7312712-7312792 3.8e-05 67_[+4]_5 chr17:42084504-42084584 4.5e-05 26_[+4]_46 chr5:173043121-173043201 4.5e-05 10_[+4]_62 chr1:246729438-246729518 5.9e-05 26_[+4]_46 chr1:181687327-181687407 5.9e-05 68_[+4]_4 chr9:132806071-132806151 5.9e-05 28_[+4]_44 chr16:58549292-58549372 6.7e-05 49_[+4]_23 chr19:3185342-3185422 6.7e-05 44_[+4]_28 chr12:93571621-93571701 8.9e-05 14_[+4]_58 chr6:136572700-136572780 8.9e-05 13_[+4]_59 chr11:118444117-11844419 8.9e-05 36_[+4]_36 chr16:21623468-21623548 9.9e-05 67_[+4]_5 chr6:20401557-20401637 9.9e-05 38_[+4]_34 chr17:62530081-62530161 9.9e-05 43_[+4]_29 chr11:73727496-73727576 0.00011 67_[+4]_5 chr16:1661944-1662024 0.00013 51_[+4]_21 chr3:51975857-51975937 0.00013 56_[+4]_16 chr4:54232156-54232236 0.00013 [+4]_72 chr3:97629930-97630010 0.00016 61_[+4]_11 chr7:134278828-134278908 0.00016 40_[+4]_32 chr15:78730128-78730208 0.00016 5_[+4]_67 chr19:56213861-56213941 0.00021 64_[+4]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAAATCA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ARAAATCA width=8 seqs=30 chr4:39559988-39560068 ( 23) AAAAATCA 1 chr12:7394167-7394247 ( 45) AAAAATCA 1 chr6:142433767-142433847 ( 55) AAAAATCA 1 chr6:105123200-105123280 ( 65) AAAAATCA 1 chr7:50626223-50626303 ( 16) ACAAATCA 1 chr5:138524361-138524441 ( 3) ACAAATCA 1 chr12:4430045-4430125 ( 34) ACAAATCA 1 chr5:68530460-68530540 ( 69) AGAAAACA 1 chr6:7312712-7312792 ( 68) AGAAAACA 1 chr17:42084504-42084584 ( 27) GAAAATCA 1 chr5:173043121-173043201 ( 11) GAAAATCA 1 chr1:246729438-246729518 ( 27) AAGAATCA 1 chr1:181687327-181687407 ( 69) TGAAATCA 1 chr9:132806071-132806151 ( 29) TGAAATCA 1 chr16:58549292-58549372 ( 50) ACAAAACA 1 chr19:3185342-3185422 ( 45) ACAAAACA 1 chr12:93571621-93571701 ( 15) GGAAATCA 1 chr6:136572700-136572780 ( 14) ATAAATCA 1 chr11:118444117-11844419 ( 37) GGAAATCA 1 chr16:21623468-21623548 ( 68) TAAAAACA 1 chr6:20401557-20401637 ( 39) AAAAATCT 1 chr17:62530081-62530161 ( 44) AAAAATCT 1 chr11:73727496-73727576 ( 68) AGGAATCA 1 chr16:1661944-1662024 ( 52) AGAACTCA 1 chr3:51975857-51975937 ( 57) AGAACTCA 1 chr4:54232156-54232236 ( 1) AGAACTCA 1 chr3:97629930-97630010 ( 62) AAGAAACA 1 chr7:134278828-134278908 ( 41) AAGAAACA 1 chr15:78730128-78730208 ( 6) TGAAAACA 1 chr19:56213861-56213941 ( 65) AAAGATCA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAAATCA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.5224 E= 3.8e+002 180 -1155 -115 -61 104 -79 31 -261 204 -1155 -115 -1155 220 -1155 -315 -1155 209 -153 -1155 -1155 34 -1155 -1155 185 -1155 179 -1155 -1155 215 -1155 -1155 -161 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAAATCA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 30 E= 3.8e+002 0.733333 0.000000 0.133333 0.133333 0.433333 0.166667 0.366667 0.033333 0.866667 0.000000 0.133333 0.000000 0.966667 0.000000 0.033333 0.000000 0.900000 0.100000 0.000000 0.000000 0.266667 0.000000 0.000000 0.733333 0.000000 1.000000 0.000000 0.000000 0.933333 0.000000 0.000000 0.066667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAAATCA MEME-4 regular expression -------------------------------------------------------------------------------- A[AG]AAA[TA]CA -------------------------------------------------------------------------------- Time 15.65 secs. ******************************************************************************** ******************************************************************************** MOTIF TGATTTTG MEME-5 width = 8 sites = 7 llr = 76 E-value = 6.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGATTTTG MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::a::::: pos.-specific C 3::::::: probability G :a:::::9 matrix T 7::aaaa1 bits 2.3 ***** 2.1 ***** 1.8 ****** 1.6 ****** Relative 1.4 ******* Entropy 1.1 ******** (15.7 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TGATTTTG consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGATTTTG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3:97629930-97630010 4 6.58e-06 CCC TGATTTTG ACTGATCTTT chr21:44353021-44353101 63 6.58e-06 ctggatactc tgattttg gttttgattt chr16:21623468-21623548 24 6.58e-06 GTTTGTTTGG TGATTTTG AGTTAAGGCA chr1:167833318-167833398 52 6.58e-06 ctgaatactc tgattttg gttttgattt chr16:11350343-11350423 9 1.59e-05 GGCGACCC CGATTTTG CCCCGCTACC chr1:44435698-44435778 55 1.59e-05 CCCCACAAGG CGATTTTG ACCCCCTGAG chr2:170684849-170684929 18 2.04e-05 TGAGGGGAAA TGATTTTT GGGGAAGCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGATTTTG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3:97629930-97630010 6.6e-06 3_[+5]_69 chr21:44353021-44353101 6.6e-06 62_[+5]_10 chr16:21623468-21623548 6.6e-06 23_[+5]_49 chr1:167833318-167833398 6.6e-06 51_[+5]_21 chr16:11350343-11350423 1.6e-05 8_[+5]_64 chr1:44435698-44435778 1.6e-05 54_[+5]_18 chr2:170684849-170684929 2e-05 17_[+5]_55 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGATTTTG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGATTTTG width=8 seqs=7 chr3:97629930-97630010 ( 4) TGATTTTG 1 chr21:44353021-44353101 ( 63) TGATTTTG 1 chr16:21623468-21623548 ( 24) TGATTTTG 1 chr1:167833318-167833398 ( 52) TGATTTTG 1 chr16:11350343-11350423 ( 9) CGATTTTG 1 chr1:44435698-44435778 ( 55) CGATTTTG 1 chr2:170684849-170684929 ( 18) TGATTTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGATTTTG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.9536 E= 6.6e+003 -945 -1 -945 181 -945 -945 175 -945 224 -945 -945 -945 -945 -945 -945 229 -945 -945 -945 229 -945 -945 -945 229 -945 -945 -945 229 -945 -945 153 -51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGATTTTG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 6.6e+003 0.000000 0.285714 0.000000 0.714286 0.000000 0.000000 1.000000 0.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.857143 0.142857 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGATTTTG MEME-5 regular expression -------------------------------------------------------------------------------- [TC]GATTTTG -------------------------------------------------------------------------------- Time 19.16 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:167833318-167833398 7.24e-04 51_[+5(6.58e-06)]_4_[+5(6.58e-06)]_\ 9 chr13:114919118-11491919 5.87e-01 80 chr7:44078860-44078940 9.86e-01 80 chr17:62530081-62530161 4.01e-02 43_[+4(9.94e-05)]_29 chr2:111920527-111920607 1.64e-01 80 chr8:144025175-144025255 5.10e-02 71_[+1(5.37e-05)]_1 chr16:4784636-4784716 9.64e-01 80 chr1:23952635-23952715 9.49e-01 80 chr20:37089047-37089127 4.54e-03 80 chr3:20083063-20083143 6.66e-01 80 chr22:31460131-31460211 7.45e-01 80 chr6:105123200-105123280 8.22e-02 64_[+4(5.20e-06)]_8 chr21:33765196-33765276 6.05e-01 80 chr6:161827808-161827888 1.82e-01 80 chr2:170684849-170684929 9.18e-03 17_[+5(2.04e-05)]_55 chr4:81256970-81257050 3.80e-01 80 chr1:228352350-228352430 9.30e-04 10_[+2(6.58e-06)]_62 chr19:13002087-13002167 9.70e-01 80 chr10:99160965-99161045 4.51e-01 80 chr12:4430045-4430125 1.95e-03 33_[+4(2.50e-05)]_14_[+3(5.47e-05)]_\ 17 chr12:125473546-12547362 9.95e-01 80 chr19:48673409-48673489 8.81e-01 80 chr16:30773284-30773364 5.95e-01 80 chr6:33256870-33256950 2.12e-02 27_[+3(8.25e-05)]_45 chr5:175815491-175815571 5.02e-01 80 chr7:65580499-65580579 2.24e-02 80 chr7:97847741-97847821 1.76e-01 80 chr9:132806071-132806151 1.80e-01 28_[+4(5.94e-05)]_44 chr21:46961662-46961742 3.14e-01 80 chr19:1864281-1864361 7.69e-01 80 chr10:75911075-75911155 9.99e-01 80 chr1:230562398-230562478 6.91e-01 80 chr4:110736965-110737045 7.81e-01 80 chr9:132020870-132020950 1.37e-01 80 chr11:44564053-44564133 7.27e-01 80 chr6:20401557-20401637 2.20e-02 38_[+4(9.94e-05)]_34 chr20:20033208-20033288 9.97e-01 80 chr4:7044600-7044680 9.56e-01 80 chr14:73393260-73393340 9.14e-01 80 chr11:118444117-11844419 2.61e-02 36_[+4(8.92e-05)]_36 chr6:136572700-136572780 4.16e-02 13_[+4(8.92e-05)]_59 chr10:102747354-10274743 9.80e-01 80 chr11:96037308-96037388 4.30e-02 80 chr12:109535672-10953575 1.43e-01 71_[+1(9.23e-05)]_1 chr2:120916411-120916491 5.38e-01 80 chr12:100594430-10059451 5.49e-02 80 chr7:100450069-100450149 3.08e-01 80 chr2:32853212-32853292 5.36e-02 80 chr5:138524361-138524441 5.93e-02 2_[+4(2.50e-05)]_70 chr12:101673937-10167401 9.17e-01 80 chr5:72861593-72861673 3.34e-04 33_[+2(6.58e-06)]_39 chr16:30560853-30560933 7.49e-03 68_[+3(6.23e-06)]_4 chr1:156542244-156542324 9.41e-01 80 chr5:173043121-173043201 3.09e-02 10_[+4(4.50e-05)]_62 chr15:41407809-41407889 2.07e-01 56_[+1(5.37e-05)]_16 chr9:131218113-131218193 6.27e-01 80 chr6:142433767-142433847 3.21e-04 54_[+4(5.20e-06)]_18 chr17:49336709-49336789 7.96e-02 20_[+1(5.37e-05)]_52 chr1:156251136-156251216 5.05e-02 80 chr2:68385072-68385152 9.86e-01 80 chr7:45027711-45027791 6.47e-01 80 chr7:129595307-129595387 1.81e-01 80 chr16:69166553-69166633 8.75e-01 80 chr11:119252524-11925260 1.14e-02 7_[+1(2.72e-05)]_65 chr19:41903200-41903280 1.08e-02 43_[+1(5.37e-05)]_29 chr1:116963179-116963259 2.96e-01 80 chr22:32058098-32058178 4.42e-01 80 chr2:88991377-88991457 4.83e-01 80 chr22:19166588-19166668 2.28e-01 49_[+1(9.23e-05)]_23 chr6:7312712-7312792 4.75e-02 67_[+4(3.76e-05)]_5 chr4:57302568-57302648 1.27e-01 55_[+1(9.23e-05)]_17 chr17:27046380-27046460 2.04e-01 80 chr9:33473824-33473904 3.27e-01 80 chr21:34100687-34100767 4.95e-01 80 chr4:128454711-128454791 5.42e-05 6_[+2(3.76e-05)]_50_[+3(3.04e-05)]_\ 8 chr19:59085077-59085157 4.50e-01 80 chr1:154077019-154077099 1.83e-02 80 chr19:3185342-3185422 1.05e-02 44_[+4(6.67e-05)]_28 chr15:40987419-40987499 2.70e-01 80 chr19:50878395-50878475 9.24e-01 80 chr12:31910165-31910245 2.22e-02 12_[+3(1.08e-05)]_60 chr19:55691518-55691598 5.06e-01 80 chr16:75145090-75145170 9.01e-01 80 chr11:107436308-10743638 5.82e-01 80 chr12:49717066-49717146 9.61e-01 80 chr12:133712488-13371256 2.89e-03 24_[+3(2.16e-05)]_48 chr16:72042714-72042794 9.86e-01 80 chr6:27204143-27204223 5.47e-02 80 chr12:64615950-64616030 9.90e-01 80 chr9:135545282-135545362 6.29e-01 80 chr17:1933424-1933504 1.71e-02 80 chr17:34958054-34958134 5.16e-01 80 chr15:41708884-41708964 4.35e-02 16_[+2(4.67e-05)]_56 chr7:2354421-2354501 4.43e-01 80 chr22:51221991-51222071 7.63e-01 80 chr19:2151852-2151932 1.55e-01 37_[+1(2.72e-05)]_35 chr1:26633021-26633101 9.26e-01 80 chr1:40840188-40840268 4.95e-01 80 chr3:194392783-194392863 3.19e-01 80 chr5:137514785-137514865 5.63e-01 80 chr22:40895302-40895382 3.99e-03 80 chr1:120930421-120930501 1.47e-01 80 chr1:148556802-148556882 2.32e-03 52_[+2(6.58e-06)]_20 chr12:7394167-7394247 3.23e-02 44_[+4(5.20e-06)]_28 chr16:21623468-21623548 5.61e-05 23_[+5(6.58e-06)]_36_[+4(9.94e-05)]_\ 5 chr15:78730128-78730208 9.99e-02 80 chr16:14579259-14579339 2.55e-01 80 chr8:117778982-117779062 7.83e-01 80 chr20:47654645-47654725 6.20e-04 53_[+3(6.23e-06)]_19 chr1:86173992-86174072 5.62e-02 71_[+1(9.23e-05)]_1 chr16:30418664-30418744 9.56e-01 80 chr12:66558225-66558305 1.03e-01 80 chr4:113557934-113558014 1.60e-01 80 chr4:120987853-120987933 1.74e-01 80 chr19:56213861-56213941 1.20e-04 43_[+3(1.72e-05)]_29 chr19:54666221-54666301 8.36e-01 80 chr12:105380190-10538027 1.00e+00 80 chr17:33469225-33469305 1.00e+00 80 chr21:44353021-44353101 8.79e-04 62_[+5(6.58e-06)]_2_[+2(1.75e-05)] chr1:179335092-179335172 8.44e-01 80 chr15:85523995-85524075 5.29e-01 80 chr5:173315335-173315415 3.03e-03 7_[+2(1.30e-05)]_65 chr12:104458403-10445848 2.84e-01 80 chr20:30467637-30467717 5.11e-01 80 chr19:10426547-10426627 1.40e-01 80 chr8:144416904-144416984 9.46e-01 80 chr8:95908042-95908122 4.58e-01 80 chr15:85143704-85143784 1.30e-01 2_[+1(5.37e-05)]_70 chrX:117859001-117859081 7.04e-02 80 chr7:102715120-102715200 5.65e-01 80 chr11:123612275-12361235 5.50e-01 80 chr4:54232156-54232236 2.58e-03 55_[+1(9.23e-05)]_17 chr1:8586028-8586108 2.70e-01 80 chr2:97001601-97001681 1.00e+00 80 chr1:36347618-36347698 5.63e-04 58_[+2(1.30e-05)]_14 chr19:50321095-50321175 9.98e-01 80 chr19:8008940-8009020 1.59e-02 41_[+3(6.11e-05)]_31 chr7:134278828-134278908 3.94e-03 80 chr16:89284112-89284192 8.64e-01 80 chr5:139780345-139780425 7.53e-01 80 chr3:49967030-49967110 1.94e-01 80 chr1:28851637-28851717 1.07e-01 80 chr19:50180731-50180811 4.20e-02 66_[+1(2.72e-05)]_6 chr17:71088782-71088862 1.82e-01 65_[+1(9.23e-05)]_7 chr7:102624240-102624320 2.18e-04 36_[+2(1.75e-05)]_36 chr12:7080132-7080212 2.98e-01 80 chr16:3018960-3019040 8.64e-01 80 chr1:181687327-181687407 3.77e-02 68_[+4(5.94e-05)]_4 chr11:73727496-73727576 1.55e-02 46_[+3(5.47e-05)]_26 chr5:68530460-68530540 1.81e-01 68_[+4(3.76e-05)]_4 chr8:144679227-144679307 9.99e-01 80 chr6:30585695-30585775 9.51e-02 80 chr8:27632080-27632160 9.63e-01 80 chr6:38764366-38764446 3.41e-03 2_[+3(1.08e-05)]_70 chr16:81110683-81110763 9.24e-01 80 chr17:42084504-42084584 4.21e-02 26_[+4(4.50e-05)]_22_[+4(5.94e-05)]_\ 16 chr7:150759590-150759670 4.51e-01 80 chr17:36831382-36831462 3.05e-02 80 chr19:49631593-49631673 2.64e-01 80 chr3:10501992-10502072 4.09e-01 80 chr1:210001353-210001433 1.28e-01 80 chr19:480463-480543 9.95e-01 80 chr6:10838628-10838708 9.88e-01 80 chr11:71640142-71640222 7.22e-01 80 chr19:45657990-45658070 1.63e-01 80 chr4:99722502-99722582 6.55e-01 80 chr6:33291274-33291354 1.99e-01 80 chr12:93571621-93571701 6.16e-02 14_[+4(8.92e-05)]_58 chr1:150479052-150479132 8.71e-03 57_[+3(8.25e-05)]_15 chr17:65852191-65852271 1.03e-03 17_[+5(3.79e-05)]_55 chr7:100136306-100136386 5.00e-01 80 chr11:113185394-11318547 5.76e-01 80 chr1:156571172-156571252 3.54e-01 80 chr6:31763372-31763452 8.65e-01 80 chr19:45909937-45910017 9.97e-01 80 chr14:102771343-10277142 3.82e-01 80 chr19:45393638-45393718 8.34e-01 80 chr17:81009483-81009563 9.99e-01 80 chr2:73441348-73441428 2.85e-01 80 chr19:12807360-12807440 2.30e-02 67_[+3(9.49e-05)]_5 chr12:132413792-13241387 2.02e-01 6_[+1(2.72e-05)]_66 chr20:5931113-5931193 2.80e-01 55_[+1(9.23e-05)]_17 chr2:43822825-43822905 4.17e-03 37_[+1(2.72e-05)]_35 chr1:109757540-109757620 6.36e-04 62_[+2(6.58e-06)]_10 chr17:30228571-30228651 1.25e-02 62_[+3(6.23e-06)]_10 chr3:51975857-51975937 3.94e-02 80 chr20:33264752-33264832 3.18e-01 80 chr3:52720053-52720133 2.07e-01 80 chr2:152991150-152991230 2.73e-02 54_[+3(1.72e-05)]_18 chr4:39559988-39560068 3.60e-02 22_[+4(5.20e-06)]_50 chr10:103590477-10359055 9.02e-01 80 chr1:43148830-43148910 1.74e-01 70_[+1(9.23e-05)]_2 chr2:3381469-3381549 9.88e-01 80 chr1:246729438-246729518 2.91e-03 6_[+3(4.56e-05)]_12_[+4(5.94e-05)]_\ 46 chr8:67341297-67341377 9.93e-01 80 chr11:71159705-71159785 1.09e-02 15_[+1(2.72e-05)]_57 chr12:109217692-10921777 1.92e-02 80 chr16:5083811-5083891 9.97e-01 80 chr1:100435813-100435893 8.32e-01 80 chr19:10812082-10812162 1.63e-01 32_[+1(2.72e-05)]_40 chr8:92082637-92082717 9.57e-01 80 chr1:43637867-43637947 2.99e-01 45_[+1(5.37e-05)]_27 chr12:114404042-11440412 8.67e-02 9_[+2(5.93e-05)]_63 chr21:48055895-48055975 8.56e-01 80 chr8:101734802-101734882 9.77e-01 80 chr15:40861515-40861595 3.62e-01 80 chr11:66057123-66057203 8.81e-01 80 chr4:108913525-108913605 4.75e-03 34_[+3(5.47e-05)]_38 chr6:170862885-170862965 1.13e-03 70_[+2(4.67e-05)]_2 chr12:64174097-64174177 2.10e-01 80 chr8:37888435-37888515 5.64e-02 80 chr9:106856617-106856697 2.64e-01 80 chr19:10530562-10530642 1.23e-01 67_[+1(5.37e-05)]_5 chr3:97629930-97630010 1.10e-04 3_[+5(6.58e-06)]_69 chr10:104474510-10447459 2.17e-01 58_[+1(2.72e-05)]_14 chr2:27440313-27440393 2.85e-02 4_[+1(2.72e-05)]_68 chr9:34329060-34329140 9.37e-01 80 chr16:58549292-58549372 3.84e-03 49_[+4(6.67e-05)]_4_[+1(2.72e-05)]_\ 11 chr2:85830031-85830111 2.09e-01 80 chr9:127963011-127963091 1.23e-03 52_[+1(2.72e-05)]_3_[+2(7.71e-05)]_\ 9 chr21:37432403-37432483 7.03e-01 80 chr4:178231025-178231105 8.57e-01 80 chr6:43543183-43543263 7.09e-01 80 chr6:17820373-17820453 6.05e-01 80 chr1:44435698-44435778 1.34e-03 29_[+2(3.12e-05)]_17_[+5(1.59e-05)]_\ 18 chr1:38061400-38061480 3.58e-01 80 chr3:158519844-158519924 1.70e-01 80 chr11:910592-910672 5.07e-01 80 chr17:58217286-58217366 7.75e-01 80 chr2:112641634-112641714 9.08e-02 80 chr16:1661944-1662024 2.27e-02 80 chr1:45476909-45476989 7.89e-01 80 chr7:50626223-50626303 4.90e-03 15_[+4(2.50e-05)]_57 chr19:13096251-13096331 3.76e-01 80 chr19:47289528-47289608 5.74e-03 24_[+2(1.30e-05)]_48 chr12:31804036-31804116 3.05e-01 80 chr9:130565295-130565375 8.74e-01 80 chr6:90529426-90529506 1.09e-01 53_[+1(9.23e-05)]_19 chr20:3190263-3190343 9.90e-01 80 chr15:78591844-78591924 9.84e-01 80 chr9:135457573-135457653 3.74e-01 80 chr17:8152669-8152749 1.58e-01 80 chr7:30510010-30510090 7.81e-02 80 chr9:114364075-114364155 5.55e-02 80 chr19:55791305-55791385 6.69e-01 80 chr1:229762040-229762120 4.25e-01 80 chr16:11350343-11350423 5.15e-02 8_[+5(1.59e-05)]_64 chr6:80714419-80714499 1.23e-01 80 chr6:106968847-106968927 1.32e-01 80 chr17:38444182-38444262 9.16e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c17n10.farnam.hpc.yale.internal ********************************************************************************