******************************************************************************** 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/GM12878/fasta/RankLinear0.6_10/BCLAF1.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr5:42756891-42756911 1.0000 20 chr6:6584260-6584280 1.0000 20 chr7:2178166-2178186 1.0000 20 chr6:27356745-27356765 1.0000 20 chr13:114103657-11410367 1.0000 20 chr13:50510493-50510513 1.0000 20 chr16:2771154-2771174 1.0000 20 chr2:171786960-171786980 1.0000 20 chrX:130845177-130845197 1.0000 20 chr18:3297562-3297582 1.0000 20 chr20:62259809-62259829 1.0000 20 chr11:43333473-43333493 1.0000 20 chr18:43355282-43355302 1.0000 20 chr6:28220058-28220078 1.0000 20 chr1:241715478-241715498 1.0000 20 chr12:50478886-50478906 1.0000 20 chr9:130218072-130218092 1.0000 20 chrX:130897932-130897952 1.0000 20 chr2:232646340-232646360 1.0000 20 chr7:133977893-133977913 1.0000 20 chr1:155113027-155113047 1.0000 20 chr2:157192221-157192241 1.0000 20 chr8:143751409-143751429 1.0000 20 chr14:100704397-10070441 1.0000 20 chr1:225654965-225654985 1.0000 20 chr11:36615960-36615980 1.0000 20 chr16:58768254-58768274 1.0000 20 chr19:56092310-56092330 1.0000 20 chr2:74517781-74517801 1.0000 20 chr9:116102637-116102657 1.0000 20 chr13:42535280-42535300 1.0000 20 chr8:28748947-28748967 1.0000 20 chr13:108870802-10887082 1.0000 20 chrX:119077750-119077770 1.0000 20 chr2:233415333-233415353 1.0000 20 chr7:141251166-141251186 1.0000 20 chr10:74870191-74870211 1.0000 20 chr19:52097770-52097790 1.0000 20 chr1:149982691-149982711 1.0000 20 chr19:58838655-58838675 1.0000 20 chr7:50132890-50132910 1.0000 20 chr11:46958205-46958225 1.0000 20 chr1:28836667-28836687 1.0000 20 chrX:130839131-130839151 1.0000 20 chrX:130956476-130956496 1.0000 20 chrX:115009429-115009449 1.0000 20 chr4:40994040-40994060 1.0000 20 chr13:53226985-53227005 1.0000 20 chr5:171615812-171615832 1.0000 20 chr7:139910230-139910250 1.0000 20 chr13:26796470-26796490 1.0000 20 chr19:56154915-56154935 1.0000 20 chr12:123459250-12345927 1.0000 20 chr14:69658205-69658225 1.0000 20 chr5:137688233-137688253 1.0000 20 chr9:37390903-37390923 1.0000 20 chr3:11888414-11888434 1.0000 20 chr20:62694407-62694427 1.0000 20 chrX:130875932-130875952 1.0000 20 chrX:119379110-119379130 1.0000 20 chr12:31835275-31835295 1.0000 20 chr4:146860079-146860099 1.0000 20 chr4:124697619-124697639 1.0000 20 chr16:1823143-1823163 1.0000 20 chr6:28072540-28072560 1.0000 20 chr18:9073790-9073810 1.0000 20 chrX:131352220-131352240 1.0000 20 chr14:20774144-20774164 1.0000 20 chr12:6961654-6961674 1.0000 20 chr19:4400704-4400724 1.0000 20 chr1:161719537-161719557 1.0000 20 chr6:117996503-117996523 1.0000 20 chr8:67525765-67525785 1.0000 20 chr11:60145993-60146013 1.0000 20 chr6:88639684-88639704 1.0000 20 chr4:120221797-120221817 1.0000 20 chr15:67358066-67358086 1.0000 20 chr19:9879384-9879404 1.0000 20 chr17:30771433-30771453 1.0000 20 chr20:19997954-19997974 1.0000 20 chr7:138818445-138818465 1.0000 20 chr18:56325611-56325631 1.0000 20 chr4:185276515-185276535 1.0000 20 chr11:65627866-65627886 1.0000 20 chr16:31085683-31085703 1.0000 20 chr21:33984853-33984873 1.0000 20 chrX:130950962-130950982 1.0000 20 chr1:100435505-100435525 1.0000 20 chrX:56791030-56791050 1.0000 20 chr3:44666530-44666550 1.0000 20 chr21:26950965-26950985 1.0000 20 chr7:129691209-129691229 1.0000 20 chr18:71815689-71815709 1.0000 20 chr21:36080439-36080459 1.0000 20 chr19:2819782-2819802 1.0000 20 chr7:96746870-96746890 1.0000 20 chr19:3435336-3435356 1.0000 20 chr16:67840654-67840674 1.0000 20 chr17:7259485-7259505 1.0000 20 chrX:130902361-130902381 1.0000 20 chr16:89307666-89307686 1.0000 20 chr7:102988064-102988084 1.0000 20 chr12:95397501-95397521 1.0000 20 chr14:100462223-10046224 1.0000 20 chr16:3156543-3156563 1.0000 20 chr19:18699557-18699577 1.0000 20 chr9:127474374-127474394 1.0000 20 chrX:12965082-12965102 1.0000 20 chr10:124713731-12471375 1.0000 20 chr13:53191593-53191613 1.0000 20 chr7:75831166-75831186 1.0000 20 chr5:43105963-43105983 1.0000 20 chr14:61201440-61201460 1.0000 20 chr22:41799974-41799994 1.0000 20 chr8:135724916-135724936 1.0000 20 chr3:127872216-127872236 1.0000 20 chr8:101225225-101225245 1.0000 20 chr18:33552586-33552606 1.0000 20 chr9:114393448-114393468 1.0000 20 chr3:195577941-195577961 1.0000 20 chr1:85086470-85086490 1.0000 20 chr14:75229879-75229899 1.0000 20 chr1:151882113-151882133 1.0000 20 chr16:89307457-89307477 1.0000 20 chrX:1620282-1620302 1.0000 20 chr11:31391343-31391363 1.0000 20 chr7:99214534-99214554 1.0000 20 chrX:130926515-130926535 1.0000 20 chr1:181111791-181111811 1.0000 20 chr11:66278047-66278067 1.0000 20 chr6:26045957-26045977 1.0000 20 chr8:11141874-11141894 1.0000 20 chr16:30538185-30538205 1.0000 20 chr2:88315933-88315953 1.0000 20 chr22:19419313-19419333 1.0000 20 chr5:140943894-140943914 1.0000 20 chr1:235492289-235492309 1.0000 20 chr19:1905822-1905842 1.0000 20 chr19:47354315-47354335 1.0000 20 chr6:26533150-26533170 1.0000 20 chr1:40781118-40781138 1.0000 20 chr17:47755416-47755436 1.0000 20 chr2:208890300-208890320 1.0000 20 chr13:113242506-11324252 1.0000 20 chr17:76250679-76250699 1.0000 20 chr5:36876818-36876838 1.0000 20 chr8:110346381-110346401 1.0000 20 chr15:76196207-76196227 1.0000 20 chr15:40675146-40675166 1.0000 20 chr2:70121043-70121063 1.0000 20 chr21:26938274-26938294 1.0000 20 chr9:140149702-140149722 1.0000 20 chrX:21857680-21857700 1.0000 20 chr9:35812301-35812321 1.0000 20 chr19:37958422-37958442 1.0000 20 chr4:114758769-114758789 1.0000 20 chr22:46731547-46731567 1.0000 20 chr10:123734758-12373477 1.0000 20 chr13:48669303-48669323 1.0000 20 chr1:27160265-27160285 1.0000 20 chr4:89444972-89444992 1.0000 20 chr6:112163226-112163246 1.0000 20 chr17:55320637-55320657 1.0000 20 chr17:79475939-79475959 1.0000 20 chr1:36396819-36396839 1.0000 20 chr1:150039784-150039804 1.0000 20 chr1:210547381-210547401 1.0000 20 chr1:147806767-147806787 1.0000 20 chr9:138392474-138392494 1.0000 20 chr20:40322160-40322180 1.0000 20 chr5:177027047-177027067 1.0000 20 chr5:180688120-180688140 1.0000 20 chr19:48922709-48922729 1.0000 20 chr2:198063790-198063810 1.0000 20 chr6:30923502-30923522 1.0000 20 chr12:860523-860543 1.0000 20 chr1:226899074-226899094 1.0000 20 chr15:45879542-45879562 1.0000 20 chr11:77790924-77790944 1.0000 20 chr20:49435030-49435050 1.0000 20 chr6:28109642-28109662 1.0000 20 chr13:21872187-21872207 1.0000 20 chr15:74731218-74731238 1.0000 20 chr20:52556609-52556629 1.0000 20 chr22:36877420-36877440 1.0000 20 chr1:19642186-19642206 1.0000 20 chr10:126480445-12648046 1.0000 20 chrX:130947330-130947350 1.0000 20 chr5:271513-271533 1.0000 20 chr10:11312723-11312743 1.0000 20 chr6:57181500-57181520 1.0000 20 chr13:41837691-41837711 1.0000 20 chr3:101237445-101237465 1.0000 20 chr17:79604129-79604149 1.0000 20 chr1:32800892-32800912 1.0000 20 chr15:71184859-71184879 1.0000 20 chr14:24912179-24912199 1.0000 20 chr1:235159358-235159378 1.0000 20 chr6:36270435-36270455 1.0000 20 chr19:42388357-42388377 1.0000 20 chr16:740432-740452 1.0000 20 chr20:1516576-1516596 1.0000 20 chr10:17243694-17243714 1.0000 20 chr1:193091020-193091040 1.0000 20 chr17:40925427-40925447 1.0000 20 chr12:34175339-34175359 1.0000 20 chr14:69821284-69821304 1.0000 20 chr7:40174271-40174291 1.0000 20 chr14:107147780-10714780 1.0000 20 chr6:28193042-28193062 1.0000 20 chr4:25314355-25314375 1.0000 20 chr8:66546624-66546644 1.0000 20 chr2:232578933-232578953 1.0000 20 chr1:224301813-224301833 1.0000 20 chr17:37793580-37793600 1.0000 20 chr1:36689937-36689957 1.0000 20 chr21:26952482-26952502 1.0000 20 chr10:27793158-27793178 1.0000 20 chr3:50265023-50265043 1.0000 20 chr9:5438973-5438993 1.0000 20 chr7:20257123-20257143 1.0000 20 chr3:183966767-183966787 1.0000 20 chr8:90738201-90738221 1.0000 20 chr17:80170754-80170774 1.0000 20 chr1:146556201-146556221 1.0000 20 chr1:46153784-46153804 1.0000 20 chr6:126277872-126277892 1.0000 20 chr17:16877246-16877266 1.0000 20 chr1:205180858-205180878 1.0000 20 chr17:79451458-79451478 1.0000 20 chr9:140473374-140473394 1.0000 20 chr5:133747623-133747643 1.0000 20 chr19:49148206-49148226 1.0000 20 chr20:33999823-33999843 1.0000 20 chr16:87812858-87812878 1.0000 20 chr12:75724121-75724141 1.0000 20 chr9:37800739-37800759 1.0000 20 chr17:48785287-48785307 1.0000 20 chr2:32390819-32390839 1.0000 20 chr8:33371096-33371116 1.0000 20 chr6:157012336-157012356 1.0000 20 chr19:37157747-37157767 1.0000 20 chr1:23345819-23345839 1.0000 20 chr2:15731923-15731943 1.0000 20 chr13:41707001-41707021 1.0000 20 chr6:88032230-88032250 1.0000 20 chr3:64009208-64009228 1.0000 20 chr19:12721565-12721585 1.0000 20 chr1:17222681-17222701 1.0000 20 chr11:72865380-72865400 1.0000 20 ******************************************************************************** ******************************************************************************** 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/GM12878/inference_raw/MEME/RankLinear0.6_10_BCLAF1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/BCLAF1.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= 5000 N= 250 sample: seed= 0 hsfrac= 0 searchsize= 5000 norand= no csites= 1000 Letter frequencies in dataset: A 0.194 C 0.306 G 0.31 T 0.19 Background letter frequencies (from file dataset with add-one prior applied): A 0.194 C 0.306 G 0.31 T 0.19 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF RYTTCCRG MEME-1 width = 8 sites = 17 llr = 135 E-value = 5.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif RYTTCCRG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 6::::14: pos.-specific C :6:1a9:: probability G 3:::::6a matrix T 14a9::1: bits 2.4 * 2.2 * 1.9 * 1.7 *** * Relative 1.4 *** * Entropy 1.2 **** * (11.4 bits) 1.0 ****** * 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel ACTTCCGG consensus GT A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYTTCCRG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr16:89307457-89307477 11 1.93e-05 AGAGCGAGGG ACTTCCgg gg chr7:102988064-102988084 2 1.93e-05 T ACTTCCGG TGGGGAAGGG chr16:89307666-89307686 12 1.93e-05 agagcgaggg aCTTCCgg g chr6:57181500-57181520 4 5.08e-05 TTA ATTTCCAG TTCTCGAAA chr8:11141874-11141894 4 5.08e-05 GGC ATTTCCAG AGGACCTAG chr22:46731547-46731567 11 8.16e-05 AGCTGCCGCA GCTTCCGG CC chr3:127872216-127872236 7 8.16e-05 GCGGAA GCTTCCGG GCCGGA chr5:42756891-42756911 8 8.16e-05 GGATTCG GCTTCCGG AGGAG chr7:96746870-96746890 9 1.20e-04 GAGCTTGG GTTTCCGG GAGG chr9:37800739-37800759 12 1.32e-04 GGCGGCGCGG GTTTCCAG C chr6:157012336-157012356 12 2.02e-04 ATAGctttac atttcagg g chr8:33371096-33371116 4 2.02e-04 tga ACTTCAAG GATCGATTT chr10:124713731-12471375 4 2.02e-04 CTC TCTTCCAG TGCTTGAAT chr1:193091020-193091040 12 2.14e-04 GGAGGGGCAC TTTTCCAG G chr2:171786960-171786980 10 2.26e-04 AGAGAGTGC ACTTCCTG GTG chr13:41707001-41707021 4 2.64e-04 CGG ACTCCCGG GCCGAGACC chr1:150039784-150039804 11 2.64e-04 GGCTGCCCGG ACTCCCGG AA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYTTCCRG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr16:89307457-89307477 1.9e-05 10_[+1]_2 chr7:102988064-102988084 1.9e-05 1_[+1]_11 chr16:89307666-89307686 1.9e-05 11_[+1]_1 chr6:57181500-57181520 5.1e-05 3_[+1]_9 chr8:11141874-11141894 5.1e-05 3_[+1]_9 chr22:46731547-46731567 8.2e-05 10_[+1]_2 chr3:127872216-127872236 8.2e-05 6_[+1]_6 chr5:42756891-42756911 8.2e-05 7_[+1]_5 chr7:96746870-96746890 0.00012 8_[+1]_4 chr9:37800739-37800759 0.00013 11_[+1]_1 chr6:157012336-157012356 0.0002 11_[+1]_1 chr8:33371096-33371116 0.0002 3_[+1]_9 chr10:124713731-12471375 0.0002 3_[+1]_9 chr1:193091020-193091040 0.00021 11_[+1]_1 chr2:171786960-171786980 0.00023 9_[+1]_3 chr13:41707001-41707021 0.00026 3_[+1]_9 chr1:150039784-150039804 0.00026 10_[+1]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYTTCCRG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RYTTCCRG width=8 seqs=17 chr16:89307457-89307477 ( 11) ACTTCCGG 1 chr7:102988064-102988084 ( 2) ACTTCCGG 1 chr16:89307666-89307686 ( 12) ACTTCCGG 1 chr6:57181500-57181520 ( 4) ATTTCCAG 1 chr8:11141874-11141894 ( 4) ATTTCCAG 1 chr22:46731547-46731567 ( 11) GCTTCCGG 1 chr3:127872216-127872236 ( 7) GCTTCCGG 1 chr5:42756891-42756911 ( 8) GCTTCCGG 1 chr7:96746870-96746890 ( 9) GTTTCCGG 1 chr9:37800739-37800759 ( 12) GTTTCCAG 1 chr6:157012336-157012356 ( 12) ATTTCAGG 1 chr8:33371096-33371116 ( 4) ACTTCAAG 1 chr10:124713731-12471375 ( 4) TCTTCCAG 1 chr1:193091020-193091040 ( 12) TTTTCCAG 1 chr2:171786960-171786980 ( 10) ACTTCCTG 1 chr13:41707001-41707021 ( 4) ACTCCCGG 1 chr1:150039784-150039804 ( 11) ACTCCCGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYTTCCRG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.36909 E= 5.4e+000 160 -1073 -7 -69 -1073 108 -1073 89 -1073 -1073 -1073 239 -1073 -138 -1073 221 -1073 171 -1073 -1073 -72 153 -1073 -1073 86 -1073 92 -169 -1073 -1073 169 -1073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYTTCCRG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 17 E= 5.4e+000 0.588235 0.000000 0.294118 0.117647 0.000000 0.647059 0.000000 0.352941 0.000000 0.000000 0.000000 1.000000 0.000000 0.117647 0.000000 0.882353 0.000000 1.000000 0.000000 0.000000 0.117647 0.882353 0.000000 0.000000 0.352941 0.000000 0.588235 0.058824 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RYTTCCRG MEME-1 regular expression -------------------------------------------------------------------------------- [AG][CT]TTCC[GA]G -------------------------------------------------------------------------------- Time 2.17 secs. ******************************************************************************** ******************************************************************************** MOTIF TGCTCTTT MEME-2 width = 8 sites = 3 llr = 36 E-value = 1.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGCTCTTT MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C ::a:a::: probability G :a:::::: matrix T a::a:aaa bits 2.4 * * *** 2.2 * * *** 1.9 * * *** 1.7 ******** Relative 1.4 ******** Entropy 1.2 ******** (17.1 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TGCTCTTT consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTCTTT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:112163226-112163246 5 7.19e-06 TTCT TGCTCTTT CTCTCCCT chr14:61201440-61201460 10 7.19e-06 CCTTGCCGG TGCTCTTT CGC chr18:3297562-3297582 1 7.19e-06 . tgctcttt ggcaagcgcc -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTCTTT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:112163226-112163246 7.2e-06 4_[+2]_8 chr14:61201440-61201460 7.2e-06 9_[+2]_3 chr18:3297562-3297582 7.2e-06 [+2]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTCTTT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TGCTCTTT width=8 seqs=3 chr6:112163226-112163246 ( 5) TGCTCTTT 1 chr14:61201440-61201460 ( 10) TGCTCTTT 1 chr18:3297562-3297582 ( 1) TGCTCTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTCTTT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.73854 E= 1.5e+002 -823 -823 -823 239 -823 -823 169 -823 -823 171 -823 -823 -823 -823 -823 239 -823 171 -823 -823 -823 -823 -823 239 -823 -823 -823 239 -823 -823 -823 239 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTCTTT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 1.5e+002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCTCTTT MEME-2 regular expression -------------------------------------------------------------------------------- TGCTCTTT -------------------------------------------------------------------------------- Time 4.11 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTTTTTS MEME-3 width = 8 sites = 2 llr = 24 E-value = 4.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTTTTTS MEME-3 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :::::::5 probability G :::::::5 matrix T aaaaaaa: bits 2.4 ******* 2.2 ******* 1.9 ******* 1.7 ******* Relative 1.4 ******* Entropy 1.2 ******* (17.4 bits) 1.0 ******* 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TTTTTTTC consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTTTS MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:17222681-17222701 4 5.51e-06 ATC TTTTTTTG TTTTGGTTT chrX:130947330-130947350 11 5.51e-06 TTAGTGGTGG TTTTTTTC AG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTTTS MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:17222681-17222701 5.5e-06 3_[+3]_9 chrX:130947330-130947350 5.5e-06 10_[+3]_2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTTTS MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTTTTTS width=8 seqs=2 chr1:17222681-17222701 ( 4) TTTTTTTG 1 chrX:130947330-130947350 ( 11) TTTTTTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTTTS MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 4.4e+002 -765 -765 -765 239 -765 -765 -765 239 -765 -765 -765 239 -765 -765 -765 239 -765 -765 -765 239 -765 -765 -765 239 -765 -765 -765 239 -765 71 69 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTTTS MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 4.4e+002 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 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTTTS MEME-3 regular expression -------------------------------------------------------------------------------- TTTTTTT[CG] -------------------------------------------------------------------------------- Time 6.99 secs. ******************************************************************************** ******************************************************************************** MOTIF GATWTTTT MEME-4 width = 8 sites = 2 llr = 24 E-value = 1.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GATWTTTT MEME-4 Description -------------------------------------------------------------------------------- Simplified A :a:5:::: pos.-specific C :::::::: probability G a::::::: matrix T ::a5aaaa bits 2.4 ** **** 2.2 ** **** 1.9 ** **** 1.7 *** **** Relative 1.4 ******** Entropy 1.2 ******** (17.4 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GATATTTT consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATWTTTT MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr17:48785287-48785307 9 5.72e-06 CTGACCCA GATATTTT CCGT chr21:26952482-26952502 2 5.72e-06 a gatttttt tctttttgag -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATWTTTT MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:48785287-48785307 5.7e-06 8_[+4]_4 chr21:26952482-26952502 5.7e-06 1_[+4]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATWTTTT MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GATWTTTT width=8 seqs=2 chr17:48785287-48785307 ( 9) GATATTTT 1 chr21:26952482-26952502 ( 2) GATTTTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATWTTTT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 1.3e+003 -765 -765 169 -765 236 -765 -765 -765 -765 -765 -765 239 136 -765 -765 139 -765 -765 -765 239 -765 -765 -765 239 -765 -765 -765 239 -765 -765 -765 239 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATWTTTT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.3e+003 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.000000 0.500000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATWTTTT MEME-4 regular expression -------------------------------------------------------------------------------- GAT[AT]TTTT -------------------------------------------------------------------------------- Time 10.09 secs. ******************************************************************************** ******************************************************************************** MOTIF CAAATTTC MEME-5 width = 8 sites = 2 llr = 25 E-value = 1.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAAATTTC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :aaa:::: pos.-specific C a::::::a probability G :::::::: matrix T ::::aaa: bits 2.4 ****** 2.2 ****** 1.9 ****** 1.7 ******** Relative 1.4 ******** Entropy 1.2 ******** (17.7 bits) 1.0 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CAAATTTC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAATTTC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr15:71184859-71184879 4 4.69e-06 ATA CAAATTTC GCGCGGGCA chr1:147806767-147806787 12 4.69e-06 attgtgcagc caaatttc t -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAATTTC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr15:71184859-71184879 4.7e-06 3_[+5]_9 chr1:147806767-147806787 4.7e-06 11_[+5]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAATTTC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CAAATTTC width=8 seqs=2 chr15:71184859-71184879 ( 4) CAAATTTC 1 chr1:147806767-147806787 ( 12) CAAATTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAATTTC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 1.7e+003 -765 170 -765 -765 236 -765 -765 -765 236 -765 -765 -765 236 -765 -765 -765 -765 -765 -765 239 -765 -765 -765 239 -765 -765 -765 239 -765 170 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAATTTC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.7e+003 0.000000 1.000000 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAATTTC MEME-5 regular expression -------------------------------------------------------------------------------- CAAATTTC -------------------------------------------------------------------------------- Time 13.36 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr5:42756891-42756911 5.42e-02 7_[+1(8.16e-05)]_5 chr6:6584260-6584280 2.99e-02 20 chr7:2178166-2178186 8.83e-01 20 chr6:27356745-27356765 7.87e-01 20 chr13:114103657-11410367 7.05e-01 20 chr13:50510493-50510513 9.97e-01 20 chr16:2771154-2771174 1.00e+00 20 chr2:171786960-171786980 1.66e-02 20 chrX:130845177-130845197 8.73e-01 20 chr18:3297562-3297582 1.21e-03 [+2(7.19e-06)]_12 chr20:62259809-62259829 2.60e-01 20 chr11:43333473-43333493 9.64e-01 20 chr18:43355282-43355302 1.00e+00 20 chr6:28220058-28220078 7.94e-01 20 chr1:241715478-241715498 1.00e+00 20 chr12:50478886-50478906 9.99e-01 20 chr9:130218072-130218092 5.14e-02 20 chrX:130897932-130897952 1.71e-01 20 chr2:232646340-232646360 5.81e-01 20 chr7:133977893-133977913 1.00e+00 20 chr1:155113027-155113047 9.63e-02 20 chr2:157192221-157192241 9.99e-01 20 chr8:143751409-143751429 9.50e-01 20 chr14:100704397-10070441 6.93e-01 20 chr1:225654965-225654985 8.19e-02 20 chr11:36615960-36615980 9.62e-04 20 chr16:58768254-58768274 1.00e+00 20 chr19:56092310-56092330 7.37e-01 20 chr2:74517781-74517801 1.00e+00 20 chr9:116102637-116102657 9.97e-01 20 chr13:42535280-42535300 9.96e-01 20 chr8:28748947-28748967 4.12e-02 20 chr13:108870802-10887082 1.63e-01 20 chrX:119077750-119077770 5.67e-01 20 chr2:233415333-233415353 9.72e-01 20 chr7:141251166-141251186 1.00e+00 20 chr10:74870191-74870211 4.58e-01 20 chr19:52097770-52097790 1.00e+00 20 chr1:149982691-149982711 9.94e-01 20 chr19:58838655-58838675 9.83e-01 20 chr7:50132890-50132910 9.43e-01 20 chr11:46958205-46958225 7.86e-02 20 chr1:28836667-28836687 3.07e-01 20 chrX:130839131-130839151 5.32e-03 20 chrX:130956476-130956496 9.97e-02 20 chrX:115009429-115009449 3.51e-01 20 chr4:40994040-40994060 2.41e-01 20 chr13:53226985-53227005 9.99e-01 20 chr5:171615812-171615832 5.79e-01 20 chr7:139910230-139910250 9.98e-01 20 chr13:26796470-26796490 9.88e-01 20 chr19:56154915-56154935 9.54e-02 20 chr12:123459250-12345927 7.51e-01 20 chr14:69658205-69658225 9.45e-01 20 chr5:137688233-137688253 1.00e+00 20 chr9:37390903-37390923 3.42e-01 20 chr3:11888414-11888434 8.38e-01 20 chr20:62694407-62694427 1.00e+00 20 chrX:130875932-130875952 1.02e-01 20 chrX:119379110-119379130 9.97e-01 20 chr12:31835275-31835295 4.24e-02 20 chr4:146860079-146860099 2.93e-01 20 chr4:124697619-124697639 3.67e-01 20 chr16:1823143-1823163 9.66e-01 20 chr6:28072540-28072560 3.54e-01 20 chr18:9073790-9073810 9.69e-01 20 chrX:131352220-131352240 7.08e-01 20 chr14:20774144-20774164 9.94e-01 20 chr12:6961654-6961674 7.04e-01 20 chr19:4400704-4400724 1.00e+00 20 chr1:161719537-161719557 4.22e-01 20 chr6:117996503-117996523 9.85e-01 20 chr8:67525765-67525785 9.97e-01 20 chr11:60145993-60146013 5.67e-01 20 chr6:88639684-88639704 9.97e-01 20 chr4:120221797-120221817 9.83e-01 20 chr15:67358066-67358086 7.39e-01 20 chr19:9879384-9879404 8.74e-01 20 chr17:30771433-30771453 1.00e+00 20 chr20:19997954-19997974 9.89e-01 20 chr7:138818445-138818465 9.99e-01 20 chr18:56325611-56325631 8.83e-01 20 chr4:185276515-185276535 8.31e-01 20 chr11:65627866-65627886 9.13e-01 20 chr16:31085683-31085703 5.44e-02 20 chr21:33984853-33984873 9.99e-01 20 chrX:130950962-130950982 1.88e-01 20 chr1:100435505-100435525 1.00e+00 20 chrX:56791030-56791050 7.98e-01 20 chr3:44666530-44666550 1.53e-01 20 chr21:26950965-26950985 3.30e-01 20 chr7:129691209-129691229 3.50e-01 20 chr18:71815689-71815709 2.66e-01 20 chr21:36080439-36080459 8.43e-01 20 chr19:2819782-2819802 9.48e-01 20 chr7:96746870-96746890 1.48e-02 20 chr19:3435336-3435356 6.16e-01 20 chr16:67840654-67840674 1.69e-01 20 chr17:7259485-7259505 8.23e-01 20 chrX:130902361-130902381 6.18e-01 20 chr16:89307666-89307686 3.37e-02 11_[+1(1.93e-05)]_1 chr7:102988064-102988084 6.30e-02 1_[+1(1.93e-05)]_11 chr12:95397501-95397521 9.07e-01 20 chr14:100462223-10046224 1.68e-02 20 chr16:3156543-3156563 9.60e-01 20 chr19:18699557-18699577 9.90e-01 20 chr9:127474374-127474394 9.79e-01 20 chrX:12965082-12965102 8.69e-01 20 chr10:124713731-12471375 1.65e-02 20 chr13:53191593-53191613 1.00e+00 20 chr7:75831166-75831186 9.66e-01 20 chr5:43105963-43105983 9.88e-01 20 chr14:61201440-61201460 4.87e-04 9_[+2(7.19e-06)]_3 chr22:41799974-41799994 9.33e-01 20 chr8:135724916-135724936 7.44e-01 20 chr3:127872216-127872236 2.57e-02 6_[+1(8.16e-05)]_6 chr8:101225225-101225245 7.97e-01 20 chr18:33552586-33552606 8.58e-01 20 chr9:114393448-114393468 3.56e-01 20 chr3:195577941-195577961 8.59e-01 20 chr1:85086470-85086490 3.73e-01 20 chr14:75229879-75229899 5.62e-01 20 chr1:151882113-151882133 6.19e-01 20 chr16:89307457-89307477 3.37e-02 10_[+1(1.93e-05)]_2 chrX:1620282-1620302 1.60e-01 20 chr11:31391343-31391363 9.93e-01 20 chr7:99214534-99214554 1.25e-02 20 chrX:130926515-130926535 1.00e+00 20 chr1:181111791-181111811 7.58e-01 20 chr11:66278047-66278067 3.20e-01 20 chr6:26045957-26045977 1.09e-01 20 chr8:11141874-11141894 7.85e-03 3_[+1(5.08e-05)]_9 chr16:30538185-30538205 9.05e-01 20 chr2:88315933-88315953 5.47e-02 20 chr22:19419313-19419333 1.00e+00 20 chr5:140943894-140943914 7.71e-01 20 chr1:235492289-235492309 1.00e+00 20 chr19:1905822-1905842 7.96e-01 20 chr19:47354315-47354335 1.00e+00 20 chr6:26533150-26533170 8.97e-01 20 chr1:40781118-40781138 1.00e+00 20 chr17:47755416-47755436 9.96e-01 20 chr2:208890300-208890320 9.96e-01 20 chr13:113242506-11324252 9.74e-01 20 chr17:76250679-76250699 9.97e-01 20 chr5:36876818-36876838 9.20e-01 20 chr8:110346381-110346401 5.70e-01 20 chr15:76196207-76196227 5.50e-01 20 chr15:40675146-40675166 9.82e-01 20 chr2:70121043-70121063 4.72e-01 20 chr21:26938274-26938294 9.71e-01 20 chr9:140149702-140149722 9.97e-01 20 chrX:21857680-21857700 8.91e-01 20 chr9:35812301-35812321 9.79e-01 20 chr19:37958422-37958442 8.47e-01 20 chr4:114758769-114758789 9.87e-01 20 chr22:46731547-46731567 4.80e-02 10_[+1(8.16e-05)]_2 chr10:123734758-12373477 4.32e-01 20 chr13:48669303-48669323 1.00e+00 20 chr1:27160265-27160285 2.44e-01 20 chr4:89444972-89444992 1.00e+00 20 chr6:112163226-112163246 2.04e-04 4_[+2(7.19e-06)]_8 chr17:55320637-55320657 2.61e-01 20 chr17:79475939-79475959 7.05e-01 20 chr1:36396819-36396839 8.57e-01 20 chr1:150039784-150039804 2.26e-01 20 chr1:210547381-210547401 5.95e-03 20 chr1:147806767-147806787 1.08e-03 11_[+5(4.69e-06)]_1 chr9:138392474-138392494 9.99e-01 20 chr20:40322160-40322180 9.17e-01 20 chr5:177027047-177027067 8.40e-01 20 chr5:180688120-180688140 9.76e-01 20 chr19:48922709-48922729 9.07e-01 20 chr2:198063790-198063810 9.73e-01 20 chr6:30923502-30923522 8.27e-01 20 chr12:860523-860543 9.50e-01 20 chr1:226899074-226899094 7.35e-01 20 chr15:45879542-45879562 3.50e-02 20 chr11:77790924-77790944 9.96e-01 20 chr20:49435030-49435050 1.57e-01 20 chr6:28109642-28109662 9.39e-01 20 chr13:21872187-21872207 1.00e+00 20 chr15:74731218-74731238 7.03e-01 20 chr20:52556609-52556629 9.74e-01 20 chr22:36877420-36877440 9.51e-01 20 chr1:19642186-19642206 8.92e-01 20 chr10:126480445-12648046 1.00e+00 20 chrX:130947330-130947350 3.03e-07 10_[+3(5.51e-06)]_2 chr5:271513-271533 3.97e-01 20 chr10:11312723-11312743 8.71e-01 20 chr6:57181500-57181520 1.64e-04 3_[+1(5.08e-05)]_9 chr13:41837691-41837711 9.99e-01 20 chr3:101237445-101237465 9.19e-01 20 chr17:79604129-79604149 8.88e-01 20 chr1:32800892-32800912 9.95e-01 20 chr15:71184859-71184879 8.47e-04 3_[+5(4.69e-06)]_9 chr14:24912179-24912199 9.84e-01 20 chr1:235159358-235159378 9.78e-01 20 chr6:36270435-36270455 5.32e-01 20 chr19:42388357-42388377 1.00e+00 20 chr16:740432-740452 7.50e-01 20 chr20:1516576-1516596 8.57e-01 20 chr10:17243694-17243714 7.17e-01 20 chr1:193091020-193091040 1.59e-04 20 chr17:40925427-40925447 9.72e-01 20 chr12:34175339-34175359 8.20e-01 20 chr14:69821284-69821304 7.13e-01 20 chr7:40174271-40174291 9.98e-01 20 chr14:107147780-10714780 3.84e-01 20 chr6:28193042-28193062 7.18e-03 20 chr4:25314355-25314375 2.33e-01 20 chr8:66546624-66546644 1.00e+00 20 chr2:232578933-232578953 8.44e-01 20 chr1:224301813-224301833 9.88e-01 20 chr17:37793580-37793600 7.85e-01 20 chr1:36689937-36689957 9.97e-01 20 chr21:26952482-26952502 3.84e-08 3_[+3(5.51e-06)]_9 chr10:27793158-27793178 9.78e-01 20 chr3:50265023-50265043 9.98e-01 20 chr9:5438973-5438993 9.93e-01 20 chr7:20257123-20257143 9.82e-01 20 chr3:183966767-183966787 6.24e-01 20 chr8:90738201-90738221 2.82e-01 20 chr17:80170754-80170774 9.99e-01 20 chr1:146556201-146556221 4.62e-01 20 chr1:46153784-46153804 7.98e-01 20 chr6:126277872-126277892 9.88e-01 20 chr17:16877246-16877266 2.66e-01 20 chr1:205180858-205180878 3.39e-01 20 chr17:79451458-79451478 1.00e+00 20 chr9:140473374-140473394 3.99e-01 20 chr5:133747623-133747643 1.00e+00 20 chr19:49148206-49148226 5.76e-01 20 chr20:33999823-33999843 3.25e-03 20 chr16:87812858-87812878 8.91e-01 20 chr12:75724121-75724141 1.00e+00 20 chr9:37800739-37800759 3.35e-02 20 chr17:48785287-48785307 2.59e-06 8_[+4(5.72e-06)]_4 chr2:32390819-32390839 1.00e+00 20 chr8:33371096-33371116 3.56e-03 20 chr6:157012336-157012356 4.64e-04 20 chr19:37157747-37157767 5.02e-01 20 chr1:23345819-23345839 5.46e-01 20 chr2:15731923-15731943 2.78e-01 20 chr13:41707001-41707021 2.61e-01 20 chr6:88032230-88032250 1.00e+00 20 chr3:64009208-64009228 9.70e-01 20 chr19:12721565-12721585 3.22e-01 20 chr1:17222681-17222701 3.98e-05 3_[+3(5.51e-06)]_9 chr11:72865380-72865400 4.94e-01 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c17n10.farnam.hpc.yale.internal ********************************************************************************