******************************************************************************** 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/HDAC3.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr8:22842829-22842909 1.0000 80 chr16:89884102-89884182 1.0000 80 chr21:45118658-45118738 1.0000 80 chr1:213218672-213218752 1.0000 80 chr1:120838268-120838348 1.0000 80 chr21:45158579-45158659 1.0000 80 chrX:2035564-2035644 1.0000 80 chr3:119813383-119813463 1.0000 80 chr6:28778239-28778319 1.0000 80 chr9:103361127-103361207 1.0000 80 chr5:77541056-77541136 1.0000 80 chr5:56111276-56111356 1.0000 80 chr17:7145862-7145942 1.0000 80 chr1:206137674-206137754 1.0000 80 chr6:91006627-91006707 1.0000 80 chr9:126031179-126031259 1.0000 80 chr11:72533278-72533358 1.0000 80 chr4:187125453-187125533 1.0000 80 chr7:150694249-150694329 1.0000 80 chr8:21777043-21777123 1.0000 80 chr5:141468604-141468684 1.0000 80 chr6:41863210-41863290 1.0000 80 chr8:144152511-144152591 1.0000 80 chr11:77532155-77532235 1.0000 80 chr19:14318446-14318526 1.0000 80 chr19:38806449-38806529 1.0000 80 chr10:97416489-97416569 1.0000 80 chr9:2241970-2242050 1.0000 80 chr17:29035799-29035879 1.0000 80 chr9:129428859-129428939 1.0000 80 chr3:167452440-167452520 1.0000 80 chr12:69201591-69201671 1.0000 80 chr12:6603477-6603557 1.0000 80 chr9:19161761-19161841 1.0000 80 chr12:30908071-30908151 1.0000 80 chrX:108780672-108780752 1.0000 80 chr9:102582418-102582498 1.0000 80 chr14:95623860-95623940 1.0000 80 chr2:27579219-27579299 1.0000 80 chr11:61447782-61447862 1.0000 80 chr2:196521784-196521864 1.0000 80 chr7:66395450-66395530 1.0000 80 chr2:149402906-149402986 1.0000 80 chr19:12947221-12947301 1.0000 80 chr3:137905896-137905976 1.0000 80 chr10:17272496-17272576 1.0000 80 chr11:64053203-64053283 1.0000 80 chrX:100075207-100075287 1.0000 80 chrX:129300125-129300205 1.0000 80 chr12:860444-860524 1.0000 80 chr2:69664716-69664796 1.0000 80 chr8:19674781-19674861 1.0000 80 chr22:38902431-38902511 1.0000 80 chr2:190648999-190649079 1.0000 80 chr1:85039956-85040036 1.0000 80 chr18:61034910-61034990 1.0000 80 chr8:128813037-128813117 1.0000 80 chr8:125029920-125030000 1.0000 80 chr12:53297253-53297333 1.0000 80 chr17:36754981-36755061 1.0000 80 chr1:30664089-30664169 1.0000 80 chr12:52430733-52430813 1.0000 80 chr10:43133716-43133796 1.0000 80 chr17:28054023-28054103 1.0000 80 chr6:30484381-30484461 1.0000 80 chr1:52869485-52869565 1.0000 80 chr4:166248470-166248550 1.0000 80 chr7:150015235-150015315 1.0000 80 chr2:55746582-55746662 1.0000 80 chr15:34875860-34875940 1.0000 80 chr11:63448659-63448739 1.0000 80 chr1:25566592-25566672 1.0000 80 chr1:234736069-234736149 1.0000 80 chr16:56496465-56496545 1.0000 80 chr16:20756319-20756399 1.0000 80 chr16:20685582-20685662 1.0000 80 chr2:75089581-75089661 1.0000 80 chr16:20693249-20693329 1.0000 80 chr14:97207832-97207912 1.0000 80 chr4:144940553-144940633 1.0000 80 chr1:195868172-195868252 1.0000 80 chr22:39915517-39915597 1.0000 80 chr3:146262354-146262434 1.0000 80 chr1:120930420-120930500 1.0000 80 chr20:443266-443346 1.0000 80 chr6:167412806-167412886 1.0000 80 chr17:56085059-56085139 1.0000 80 chr10:103929469-10392954 1.0000 80 chr9:139981322-139981402 1.0000 80 chr19:46149508-46149588 1.0000 80 chr16:53737964-53738044 1.0000 80 chr7:129882118-129882198 1.0000 80 chr17:61850905-61850985 1.0000 80 chr12:75724117-75724197 1.0000 80 chr7:35840719-35840799 1.0000 80 chr7:95238160-95238240 1.0000 80 chr4:25090250-25090330 1.0000 80 chr17:45955103-45955183 1.0000 80 chr1:27018818-27018898 1.0000 80 chr16:78133401-78133481 1.0000 80 chr6:134339229-134339309 1.0000 80 chr18:55785431-55785511 1.0000 80 chr7:23312929-23313009 1.0000 80 chr2:8817914-8817994 1.0000 80 chr2:9748149-9748229 1.0000 80 chr11:65138864-65138944 1.0000 80 chr7:157130546-157130626 1.0000 80 chr15:85078218-85078298 1.0000 80 chrX:55054634-55054714 1.0000 80 chr1:51985169-51985249 1.0000 80 chr15:45027803-45027883 1.0000 80 chr12:131834896-13183497 1.0000 80 chr8:98790771-98790851 1.0000 80 chr4:84417366-84417446 1.0000 80 chr12:112432673-11243275 1.0000 80 chr9:99736458-99736538 1.0000 80 chr7:77168103-77168183 1.0000 80 chr17:9424093-9424173 1.0000 80 chr2:86332989-86333069 1.0000 80 chr2:11606367-11606447 1.0000 80 chr15:64752639-64752719 1.0000 80 chrX:79768010-79768090 1.0000 80 chrX:47535523-47535603 1.0000 80 chr6:7975435-7975515 1.0000 80 chr14:73292881-73292961 1.0000 80 chr19:41370675-41370755 1.0000 80 chr11:61348990-61349070 1.0000 80 chr2:227637487-227637567 1.0000 80 chr18:11947290-11947370 1.0000 80 chrX:47572277-47572357 1.0000 80 chr9:116131433-116131513 1.0000 80 chr9:107537660-107537740 1.0000 80 chr19:58874224-58874304 1.0000 80 chr17:73851604-73851684 1.0000 80 chr1:45732148-45732228 1.0000 80 chr17:25856386-25856466 1.0000 80 chr15:65529474-65529554 1.0000 80 chr19:56698374-56698454 1.0000 80 chr12:109249771-10924985 1.0000 80 chr6:34360490-34360570 1.0000 80 chr21:47875802-47875882 1.0000 80 chr11:10830627-10830707 1.0000 80 chr1:154973411-154973491 1.0000 80 chr14:69087002-69087082 1.0000 80 chr4:185373033-185373113 1.0000 80 chr4:26322306-26322386 1.0000 80 chr20:52225339-52225419 1.0000 80 chr3:193721082-193721162 1.0000 80 chr12:14410809-14410889 1.0000 80 chr7:26240480-26240560 1.0000 80 chr18:51750941-51751021 1.0000 80 chr5:175624451-175624531 1.0000 80 chr12:80326334-80326414 1.0000 80 chr12:4262868-4262948 1.0000 80 chr1:197170616-197170696 1.0000 80 chr10:21419195-21419275 1.0000 80 chr8:126175788-126175868 1.0000 80 chr10:86284951-86285031 1.0000 80 chr1:204370131-204370211 1.0000 80 chrX:15693362-15693442 1.0000 80 chr8:33330684-33330764 1.0000 80 chr10:89622170-89622250 1.0000 80 chr4:68418034-68418114 1.0000 80 chr18:21120964-21121044 1.0000 80 chr4:144826788-144826868 1.0000 80 chr9:80442447-80442527 1.0000 80 chr15:75459026-75459106 1.0000 80 chr20:30505858-30505938 1.0000 80 chr17:53894325-53894405 1.0000 80 chr6:134516879-134516959 1.0000 80 chr7:7082263-7082343 1.0000 80 chr12:23712364-23712444 1.0000 80 chrX:55147373-55147453 1.0000 80 chr1:28193886-28193966 1.0000 80 chr7:158317032-158317112 1.0000 80 chr6:26206308-26206388 1.0000 80 chr16:70471087-70471167 1.0000 80 chr2:216973919-216973999 1.0000 80 chr1:54519010-54519090 1.0000 80 chrX:65383984-65384064 1.0000 80 chr3:170496598-170496678 1.0000 80 chr3:32115880-32115960 1.0000 80 chr1:231120659-231120739 1.0000 80 chr12:27170420-27170500 1.0000 80 chr6:15018809-15018889 1.0000 80 chr9:97176151-97176231 1.0000 80 chrX:47543035-47543115 1.0000 80 chr9:140024224-140024304 1.0000 80 chr6:112408705-112408785 1.0000 80 chr6:125404386-125404466 1.0000 80 chr1:27019595-27019675 1.0000 80 chr21:9968655-9968735 1.0000 80 chr19:52097670-52097750 1.0000 80 chr7:150736638-150736718 1.0000 80 chr4:154415015-154415095 1.0000 80 chr10:98379052-98379132 1.0000 80 chr9:98637851-98637931 1.0000 80 chr11:876047-876127 1.0000 80 chr5:131758496-131758576 1.0000 80 chr19:53664595-53664675 1.0000 80 chr1:28851625-28851705 1.0000 80 chr9:96873352-96873432 1.0000 80 chr2:176800443-176800523 1.0000 80 chr9:37197237-37197317 1.0000 80 chr16:29701071-29701151 1.0000 80 chr12:123237307-12323738 1.0000 80 chr5:111884096-111884176 1.0000 80 chr17:7660452-7660532 1.0000 80 chr1:167832558-167832638 1.0000 80 chr1:160919210-160919290 1.0000 80 chr4:76439733-76439813 1.0000 80 chr19:35411473-35411553 1.0000 80 chr8:67967446-67967526 1.0000 80 chr1:27561014-27561094 1.0000 80 chr3:33014374-33014454 1.0000 80 chr8:15559447-15559527 1.0000 80 chr19:944268-944348 1.0000 80 chr14:31699062-31699142 1.0000 80 chrX:39710123-39710203 1.0000 80 chr14:36733961-36734041 1.0000 80 chr6:108899890-108899970 1.0000 80 chr10:7294265-7294345 1.0000 80 chr6:658413-658493 1.0000 80 chr5:133298964-133299044 1.0000 80 chr6:151409193-151409273 1.0000 80 chr7:70033915-70033995 1.0000 80 chr11:2799949-2800029 1.0000 80 chr10:73976043-73976123 1.0000 80 chr17:43242854-43242934 1.0000 80 chr18:46307749-46307829 1.0000 80 chr14:64108531-64108611 1.0000 80 chr5:139990813-139990893 1.0000 80 chr2:97304106-97304186 1.0000 80 chr17:58042319-58042399 1.0000 80 chr1:25739904-25739984 1.0000 80 chr17:61920122-61920202 1.0000 80 chr17:65852216-65852296 1.0000 80 chr22:30217478-30217558 1.0000 80 chr1:27013503-27013583 1.0000 80 chr8:94564262-94564342 1.0000 80 chr22:36764682-36764762 1.0000 80 chr2:160008758-160008838 1.0000 80 chr17:6897238-6897318 1.0000 80 chrX:102356711-102356791 1.0000 80 chr19:54714764-54714844 1.0000 80 chr2:198317951-198318031 1.0000 80 chr8:144629506-144629586 1.0000 80 chr13:95923486-95923566 1.0000 80 chr2:119496737-119496817 1.0000 80 chr5:124064194-124064274 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_HDAC3/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/K562/fasta/RankLinear0.6_40/HDAC3.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 0.235 C 0.265 G 0.269 T 0.231 Background letter frequencies (from file dataset with add-one prior applied): A 0.235 C 0.265 G 0.269 T 0.231 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AGATAAVV MEME-1 width = 8 sites = 32 llr = 277 E-value = 1.6e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGATAAVV MEME-1 Description -------------------------------------------------------------------------------- Simplified A 8:a:aa25 pos.-specific C ::::::33 probability G :a::::43 matrix T 3::a:::: bits 2.1 **** 1.9 ***** 1.7 ***** 1.5 ***** Relative 1.3 ****** Entropy 1.1 ****** (12.5 bits) 0.8 ****** 0.6 ****** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AGATAAGA consensus T CC sequence AG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATAAVV MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr8:15559447-15559527 57 1.20e-05 cagtTCTCAG AGATAAGA GGTTGTTGAT chr10:86284951-86285031 41 1.20e-05 acagcctcac agataaga gcggctatac chr8:125029920-125030000 2 1.20e-05 T AGATAAGA AGCGACTTAC chr22:36764682-36764762 15 2.38e-05 AATTTCTCTA AGATAACA GTGCTGGGAG chr7:150736638-150736718 40 2.38e-05 CTGTCTAGAC AGATAACA CTGTGGGTAT chr15:85078218-85078298 70 2.38e-05 caagggatcg agataaca gag chr2:8817914-8817994 57 2.38e-05 CTGCTAAACC AGATAACA GGACCGGGAA chr17:6897238-6897318 47 3.42e-05 ctgcttggct agataaaa gtgagacttc chr7:7082263-7082343 16 3.42e-05 agggacctat agataaaa ccccatctcc chr8:126175788-126175868 28 3.42e-05 gggcaattgt agataaaa cgagattgta chr1:195868172-195868252 1 3.42e-05 . agataaaa cccccatgtg chr2:119496737-119496817 56 6.15e-05 aggttcagag agataagg tttttgccag chrX:102356711-102356791 47 6.15e-05 gggtacacta agataagg aagctaaaag chr2:160008758-160008838 53 6.15e-05 ATTTATTCTG AGATAAGC AGATGACTTT chr18:21120964-21121044 54 6.15e-05 GAAAAACCAC AGATAAGC GCATACCACA chr7:23312929-23313009 39 6.15e-05 TCTAAATAGA AGATAAGC TGACCCAAAG chr2:75089581-75089661 11 6.15e-05 TGTGCTGGGG AGATAAGG CCCATGTAGA chr8:128813037-128813117 27 6.15e-05 tgggttagac agataagg aacagcagac chr10:7294265-7294345 44 1.00e-04 TGTGTCCCTG AGATAACC CTATCCACTC chr1:204370131-204370211 37 1.00e-04 TGTCTCTCTC TGATAAGA TTAAGGCGTC chr21:47875802-47875882 41 1.00e-04 tgtggaagag agataacc aatccccact chr3:137905896-137905976 6 1.00e-04 aatgg agataacg acgccgggag chr6:151409193-151409273 39 1.35e-04 GACAATCCTT TGATAACA GTTTTTTTTA chr9:80442447-80442527 28 1.35e-04 AGCCAGTGTC TGATAACA TTCTGATCTT chr1:45732148-45732228 9 1.35e-04 catggctg tgataaca agtggagtta chr8:98790771-98790851 69 1.35e-04 tgtgtccggt tgataaca ccca chr17:45955103-45955183 36 1.35e-04 AAGGCCAGAC AGATAAAC ACAGATGGAG chr16:20693249-20693329 10 1.35e-04 tcactagac agataaac tcaagttgta chr16:20685582-20685662 58 1.35e-04 gtcactagac agataaac ccaagttgca chr19:54714764-54714844 37 1.72e-04 GGCAATGTGC TGATAAGG ATTCTAAGTG chr8:67967446-67967526 51 1.72e-04 gtgcagtctg tgataagg actaaggatc chr2:227637487-227637567 11 1.72e-04 CTTATCATGC TGATAAGG ATATTTACAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATAAVV MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr8:15559447-15559527 1.2e-05 56_[+1]_16 chr10:86284951-86285031 1.2e-05 40_[+1]_32 chr8:125029920-125030000 1.2e-05 1_[+1]_71 chr22:36764682-36764762 2.4e-05 14_[+1]_58 chr7:150736638-150736718 2.4e-05 39_[+1]_33 chr15:85078218-85078298 2.4e-05 69_[+1]_3 chr2:8817914-8817994 2.4e-05 56_[+1]_16 chr17:6897238-6897318 3.4e-05 46_[+1]_26 chr7:7082263-7082343 3.4e-05 15_[+1]_57 chr8:126175788-126175868 3.4e-05 27_[+1]_45 chr1:195868172-195868252 3.4e-05 [+1]_72 chr2:119496737-119496817 6.1e-05 55_[+1]_17 chrX:102356711-102356791 6.1e-05 46_[+1]_26 chr2:160008758-160008838 6.1e-05 52_[+1]_20 chr18:21120964-21121044 6.1e-05 53_[+1]_19 chr7:23312929-23313009 6.1e-05 38_[+1]_34 chr2:75089581-75089661 6.1e-05 10_[+1]_62 chr8:128813037-128813117 6.1e-05 26_[+1]_46 chr10:7294265-7294345 0.0001 43_[+1]_29 chr1:204370131-204370211 0.0001 36_[+1]_36 chr21:47875802-47875882 0.0001 40_[+1]_32 chr3:137905896-137905976 0.0001 5_[+1]_67 chr6:151409193-151409273 0.00014 38_[+1]_34 chr9:80442447-80442527 0.00014 27_[+1]_45 chr1:45732148-45732228 0.00014 8_[+1]_64 chr8:98790771-98790851 0.00014 68_[+1]_4 chr17:45955103-45955183 0.00014 35_[+1]_37 chr16:20693249-20693329 0.00014 9_[+1]_63 chr16:20685582-20685662 0.00014 57_[+1]_15 chr19:54714764-54714844 0.00017 36_[+1]_36 chr8:67967446-67967526 0.00017 50_[+1]_22 chr2:227637487-227637567 0.00017 10_[+1]_62 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATAAVV MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGATAAVV width=8 seqs=32 chr8:15559447-15559527 ( 57) AGATAAGA 1 chr10:86284951-86285031 ( 41) AGATAAGA 1 chr8:125029920-125030000 ( 2) AGATAAGA 1 chr22:36764682-36764762 ( 15) AGATAACA 1 chr7:150736638-150736718 ( 40) AGATAACA 1 chr15:85078218-85078298 ( 70) AGATAACA 1 chr2:8817914-8817994 ( 57) AGATAACA 1 chr17:6897238-6897318 ( 47) AGATAAAA 1 chr7:7082263-7082343 ( 16) AGATAAAA 1 chr8:126175788-126175868 ( 28) AGATAAAA 1 chr1:195868172-195868252 ( 1) AGATAAAA 1 chr2:119496737-119496817 ( 56) AGATAAGG 1 chrX:102356711-102356791 ( 47) AGATAAGG 1 chr2:160008758-160008838 ( 53) AGATAAGC 1 chr18:21120964-21121044 ( 54) AGATAAGC 1 chr7:23312929-23313009 ( 39) AGATAAGC 1 chr2:75089581-75089661 ( 11) AGATAAGG 1 chr8:128813037-128813117 ( 27) AGATAAGG 1 chr10:7294265-7294345 ( 44) AGATAACC 1 chr1:204370131-204370211 ( 37) TGATAAGA 1 chr21:47875802-47875882 ( 41) AGATAACC 1 chr3:137905896-137905976 ( 6) AGATAACG 1 chr6:151409193-151409273 ( 39) TGATAACA 1 chr9:80442447-80442527 ( 28) TGATAACA 1 chr1:45732148-45732228 ( 9) TGATAACA 1 chr8:98790771-98790851 ( 69) TGATAACA 1 chr17:45955103-45955183 ( 36) AGATAAAC 1 chr16:20693249-20693329 ( 10) AGATAAAC 1 chr16:20685582-20685662 ( 58) AGATAAAC 1 chr19:54714764-54714844 ( 37) TGATAAGG 1 chr8:67967446-67967526 ( 51) TGATAAGG 1 chr2:227637487-227637567 ( 11) TGATAAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATAAVV MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.15308 E= 1.6e-004 168 -1164 -1164 11 -1164 -1164 190 -1164 209 -1164 -1164 -1164 -1164 -1164 -1164 211 209 -1164 -1164 -1164 209 -1164 -1164 -1164 -10 37 70 -1164 109 -9 -10 -1164 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATAAVV MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 32 E= 1.6e-004 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.218750 0.343750 0.437500 0.000000 0.500000 0.250000 0.250000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATAAVV MEME-1 regular expression -------------------------------------------------------------------------------- [AT]GATAA[GCA][ACG] -------------------------------------------------------------------------------- Time 4.81 secs. ******************************************************************************** ******************************************************************************** MOTIF STTATCTS MEME-2 width = 8 sites = 29 llr = 248 E-value = 1.1e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif STTATCTS MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1::a::3: pos.-specific C 5::::a:3 probability G 2::::::6 matrix T 2aa:a:71 bits 2.1 **** 1.9 ***** 1.7 ***** 1.5 ***** Relative 1.3 ****** Entropy 1.1 ****** (12.4 bits) 0.8 ****** 0.6 ******* 0.4 ******* 0.2 ******** 0.0 -------- Multilevel CTTATCTG consensus G AC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STTATCTS MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr5:139990813-139990893 1 1.26e-05 . cttatctg ggaggcacag chr19:53664595-53664675 8 1.26e-05 caagttg cttatctg ggctctcaag chr7:150736638-150736718 59 1.26e-05 TGTGGGTATA CTTATCTG CAGGGCAAGC chrX:55147373-55147453 60 1.26e-05 ctttgtcctg cttatctg ggagggagag chr2:227637487-227637567 68 1.26e-05 TTTTAAGTAT CTTATCTG TAAGA chr22:30217478-30217558 29 2.51e-05 gatgacagca cttatctc acagggctgc chr3:33014374-33014454 1 2.51e-05 . cttatctc tcctccctta chr9:37197237-37197317 53 2.51e-05 GGAAGCAGCT CTTATCTC TCCAGACCTG chr14:73292881-73292961 44 2.51e-05 ATAAATTTTC CTTATCTC TCTAAGACAT chr11:2799949-2800029 29 4.89e-05 CTACATGGAC TTTATCTG AAAGTAGCTG chrX:47543035-47543115 66 4.89e-05 tgtataagca gttatctg ggtcgac chr1:28193886-28193966 17 4.89e-05 gtgacttgag tttatctg cctagtgacc chr12:131834896-13183497 41 4.89e-05 gcgacttgag tttatctg tctggtgacc chr9:19161761-19161841 3 4.89e-05 CA TTTATCTG TCTTATCATA chr8:94564262-94564342 54 6.18e-05 GAAAACTTCC CTTATCAG GCATTTCTGA chr6:134516879-134516959 43 6.18e-05 TTCCAGGAAG CTTATCAG TTTTGTGTCT chr5:124064194-124064274 70 7.27e-05 TGGCCTTCTG CTTATCTT CGT chr22:36764682-36764762 43 9.62e-05 GTGGAGGAGT GTTATCTC CCCACCCTTA chr3:32115880-32115960 37 9.62e-05 tcctttactc tttatctc cagaacccag chr1:195868172-195868252 58 1.09e-04 aataaacatt cttatcac cagacacagg chr1:28851625-28851705 41 1.33e-04 gcatgcactg gttatcag aacggaacag chr12:109249771-10924985 33 1.33e-04 CCTCCCCCGT GTTATCAG TCAACTTCCC chr11:65138864-65138944 22 1.33e-04 GTTTGCTCAA GTTATCAG CTCTTTGCAA chr1:231120659-231120739 28 1.44e-04 tgaaatgctg attatctg tttacccagg chr17:6897238-6897318 3 1.65e-04 ag tttatctt gagaacacat chr15:75459026-75459106 5 1.65e-04 tggg gttatctt ggggctagca chr17:65852216-65852296 38 1.76e-04 ttctgacttt cttatcat ttctctccag chr17:28054023-28054103 17 2.00e-04 ATGTCATTTT GTTATCAC ACATGTCTAT chr5:131758496-131758576 11 2.11e-04 ACTGGCTTGC ATTATCTC CAGACACAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STTATCTS MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr5:139990813-139990893 1.3e-05 [+2]_72 chr19:53664595-53664675 1.3e-05 7_[+2]_65 chr7:150736638-150736718 1.3e-05 58_[+2]_14 chrX:55147373-55147453 1.3e-05 59_[+2]_13 chr2:227637487-227637567 1.3e-05 67_[+2]_5 chr22:30217478-30217558 2.5e-05 28_[+2]_44 chr3:33014374-33014454 2.5e-05 [+2]_72 chr9:37197237-37197317 2.5e-05 52_[+2]_20 chr14:73292881-73292961 2.5e-05 43_[+2]_29 chr11:2799949-2800029 4.9e-05 28_[+2]_44 chrX:47543035-47543115 4.9e-05 65_[+2]_7 chr1:28193886-28193966 4.9e-05 16_[+2]_56 chr12:131834896-13183497 4.9e-05 40_[+2]_32 chr9:19161761-19161841 4.9e-05 2_[+2]_70 chr8:94564262-94564342 6.2e-05 53_[+2]_19 chr6:134516879-134516959 6.2e-05 42_[+2]_30 chr5:124064194-124064274 7.3e-05 69_[+2]_3 chr22:36764682-36764762 9.6e-05 42_[+2]_30 chr3:32115880-32115960 9.6e-05 36_[+2]_36 chr1:195868172-195868252 0.00011 57_[+2]_15 chr1:28851625-28851705 0.00013 40_[+2]_32 chr12:109249771-10924985 0.00013 32_[+2]_40 chr11:65138864-65138944 0.00013 21_[+2]_51 chr1:231120659-231120739 0.00014 27_[+2]_45 chr17:6897238-6897318 0.00016 2_[+2]_70 chr15:75459026-75459106 0.00016 4_[+2]_68 chr17:65852216-65852296 0.00018 37_[+2]_35 chr17:28054023-28054103 0.0002 16_[+2]_56 chr5:131758496-131758576 0.00021 10_[+2]_62 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STTATCTS MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF STTATCTS width=8 seqs=29 chr5:139990813-139990893 ( 1) CTTATCTG 1 chr19:53664595-53664675 ( 8) CTTATCTG 1 chr7:150736638-150736718 ( 59) CTTATCTG 1 chrX:55147373-55147453 ( 60) CTTATCTG 1 chr2:227637487-227637567 ( 68) CTTATCTG 1 chr22:30217478-30217558 ( 29) CTTATCTC 1 chr3:33014374-33014454 ( 1) CTTATCTC 1 chr9:37197237-37197317 ( 53) CTTATCTC 1 chr14:73292881-73292961 ( 44) CTTATCTC 1 chr11:2799949-2800029 ( 29) TTTATCTG 1 chrX:47543035-47543115 ( 66) GTTATCTG 1 chr1:28193886-28193966 ( 17) TTTATCTG 1 chr12:131834896-13183497 ( 41) TTTATCTG 1 chr9:19161761-19161841 ( 3) TTTATCTG 1 chr8:94564262-94564342 ( 54) CTTATCAG 1 chr6:134516879-134516959 ( 43) CTTATCAG 1 chr5:124064194-124064274 ( 70) CTTATCTT 1 chr22:36764682-36764762 ( 43) GTTATCTC 1 chr3:32115880-32115960 ( 37) TTTATCTC 1 chr1:195868172-195868252 ( 58) CTTATCAC 1 chr1:28851625-28851705 ( 41) GTTATCAG 1 chr12:109249771-10924985 ( 33) GTTATCAG 1 chr11:65138864-65138944 ( 22) GTTATCAG 1 chr1:231120659-231120739 ( 28) ATTATCTG 1 chr17:6897238-6897318 ( 3) TTTATCTT 1 chr15:75459026-75459106 ( 5) GTTATCTT 1 chr17:65852216-65852296 ( 38) CTTATCAT 1 chr17:28054023-28054103 ( 17) GTTATCAC 1 chr5:131758496-131758576 ( 11) ATTATCTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STTATCTS MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.5458 E= 1.1e-001 -177 86 -15 -16 -1150 -1150 -1150 211 -1150 -1150 -1150 211 209 -1150 -1150 -1150 -1150 -1150 -1150 211 -1150 191 -1150 -1150 23 -1150 -1150 165 -1150 23 104 -75 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STTATCTS MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 29 E= 1.1e-001 0.068966 0.482759 0.241379 0.206897 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.275862 0.000000 0.000000 0.724138 0.000000 0.310345 0.551724 0.137931 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STTATCTS MEME-2 regular expression -------------------------------------------------------------------------------- [CGT]TTATC[TA][GC] -------------------------------------------------------------------------------- Time 8.48 secs. ******************************************************************************** ******************************************************************************** MOTIF TTCCAKGA MEME-3 width = 8 sites = 20 llr = 181 E-value = 1.3e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTCCAKGA MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::821a pos.-specific C ::a9:::: probability G :::::5a: matrix T aa:223:: bits 2.1 ** * 1.9 *** * 1.7 *** ** 1.5 *** * ** Relative 1.3 ***** ** Entropy 1.1 ***** ** (13.1 bits) 0.8 ***** ** 0.6 ***** ** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TTCCAGGA consensus TT sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCAKGA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr8:144629506-144629586 38 1.50e-05 ctcatgagtt ttccagga aaggggtggg chr2:176800443-176800523 28 1.50e-05 TAAGACTTCT TTCCAGGA ATTTCAGACA chr12:23712364-23712444 32 1.50e-05 GATGAAACAC TTCCAGGA AAAGTAAAGA chr6:134516879-134516959 33 1.50e-05 ATATGTCTAT TTCCAGGA AGCTTATCAG chr12:4262868-4262948 30 1.50e-05 CCCACACTGA TTCCAGGA AGCCTGCCTG chr1:30664089-30664169 66 1.50e-05 TCAGAGCAGC TTCCAGGA ACTGACA chr9:96873352-96873432 32 2.78e-05 TCGTTCTGGA TTCCATGA AAACCACCAT chr3:170496598-170496678 70 2.78e-05 tagcttggat ttccatga att chrX:129300125-129300205 63 2.78e-05 GATCCAGTTT TTCCATGA GTCCGAGGCG chr1:27013503-27013583 45 4.09e-05 TCCCACTCAC TTCCAAGA AGAACACCTC chr5:133298964-133299044 36 4.09e-05 ttaaaagaac ttccaaga acgaccagaa chr17:9424093-9424173 27 4.09e-05 TAGCAGTGAA TTCCAAGA AGTAGCTTTC chr8:94564262-94564342 4 6.87e-05 CAT TTCTAGGA AGAGGAGGAA chr6:15018809-15018889 37 6.87e-05 aaacagCAAC TTCTAGGA AATAAGGCTG chr9:116131433-116131513 10 6.87e-05 AGGCTGTGT TTCTAGGA CACGTCCAAT chr8:15559447-15559527 5 8.13e-05 agat ttccttga ataaactact chr19:41370675-41370755 18 8.13e-05 aaatatgccg ttccttga aaagtaagaa chr16:20693249-20693329 38 8.13e-05 aaacatgttt ttccttga aaagtaagaa chr1:160919210-160919290 48 1.05e-04 atacctggct ttcctaga cagaggtccc chr12:14410809-14410889 52 1.30e-04 CAGTGGCCTC TTCCAGAA AGAGAAATCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCAKGA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr8:144629506-144629586 1.5e-05 37_[+3]_35 chr2:176800443-176800523 1.5e-05 27_[+3]_45 chr12:23712364-23712444 1.5e-05 31_[+3]_41 chr6:134516879-134516959 1.5e-05 32_[+3]_40 chr12:4262868-4262948 1.5e-05 29_[+3]_43 chr1:30664089-30664169 1.5e-05 65_[+3]_7 chr9:96873352-96873432 2.8e-05 31_[+3]_41 chr3:170496598-170496678 2.8e-05 69_[+3]_3 chrX:129300125-129300205 2.8e-05 62_[+3]_10 chr1:27013503-27013583 4.1e-05 44_[+3]_28 chr5:133298964-133299044 4.1e-05 35_[+3]_37 chr17:9424093-9424173 4.1e-05 26_[+3]_46 chr8:94564262-94564342 6.9e-05 3_[+3]_69 chr6:15018809-15018889 6.9e-05 36_[+3]_36 chr9:116131433-116131513 6.9e-05 9_[+3]_63 chr8:15559447-15559527 8.1e-05 4_[+3]_68 chr19:41370675-41370755 8.1e-05 17_[+3]_55 chr16:20693249-20693329 8.1e-05 37_[+3]_35 chr1:160919210-160919290 0.00011 47_[+3]_25 chr12:14410809-14410889 0.00013 51_[+3]_21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCAKGA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTCCAKGA width=8 seqs=20 chr8:144629506-144629586 ( 38) TTCCAGGA 1 chr2:176800443-176800523 ( 28) TTCCAGGA 1 chr12:23712364-23712444 ( 32) TTCCAGGA 1 chr6:134516879-134516959 ( 33) TTCCAGGA 1 chr12:4262868-4262948 ( 30) TTCCAGGA 1 chr1:30664089-30664169 ( 66) TTCCAGGA 1 chr9:96873352-96873432 ( 32) TTCCATGA 1 chr3:170496598-170496678 ( 70) TTCCATGA 1 chrX:129300125-129300205 ( 63) TTCCATGA 1 chr1:27013503-27013583 ( 45) TTCCAAGA 1 chr5:133298964-133299044 ( 36) TTCCAAGA 1 chr17:9424093-9424173 ( 27) TTCCAAGA 1 chr8:94564262-94564342 ( 4) TTCTAGGA 1 chr6:15018809-15018889 ( 37) TTCTAGGA 1 chr9:116131433-116131513 ( 10) TTCTAGGA 1 chr8:15559447-15559527 ( 5) TTCCTTGA 1 chr19:41370675-41370755 ( 18) TTCCTTGA 1 chr16:20693249-20693329 ( 38) TTCCTTGA 1 chr1:160919210-160919290 ( 48) TTCCTAGA 1 chr12:14410809-14410889 ( 52) TTCCAGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCAKGA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.0839 E= 1.3e+002 -1097 -1097 -1097 211 -1097 -1097 -1097 211 -1097 191 -1097 -1097 -1097 168 -1097 -63 177 -1097 -1097 -21 -23 -1097 90 37 -223 -1097 182 -1097 209 -1097 -1097 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCAKGA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 20 E= 1.3e+002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.850000 0.000000 0.150000 0.800000 0.000000 0.000000 0.200000 0.200000 0.000000 0.500000 0.300000 0.050000 0.000000 0.950000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCAKGA MEME-3 regular expression -------------------------------------------------------------------------------- TTCC[AT][GTA]GA -------------------------------------------------------------------------------- Time 12.10 secs. ******************************************************************************** ******************************************************************************** MOTIF CCKGGTTT MEME-4 width = 8 sites = 22 llr = 194 E-value = 1.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCKGGTTT MEME-4 Description -------------------------------------------------------------------------------- Simplified A 3::::::: pos.-specific C 7a:::2:: probability G ::4a7::: matrix T ::6:38aa bits 2.1 ** 1.9 * * ** 1.7 * * ** 1.5 * * *** Relative 1.3 * * *** Entropy 1.1 ******** (12.7 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CCTGGTTT consensus A G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCKGGTTT MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3:146262354-146262434 72 1.45e-05 ACCCGCGGCT CCTGGTTT C chr19:12947221-12947301 69 1.45e-05 AGAGGGAAAA CCTGGTTT GGAT chr2:27579219-27579299 46 1.45e-05 GGAGAGGAGC CCTGGTTT TTCTAACAAG chr9:97176151-97176231 23 2.73e-05 atgtctgtta actggTTT GTCTGTGAGG chr5:175624451-175624531 70 2.73e-05 attaaggccc actggttt acc chr10:73976043-73976123 5 4.41e-05 CAGG CCGGGTTT GACCGAGTGC chrX:65383984-65384064 66 4.41e-05 AAGAACCATC CCGGGTTT TGTATCA chr8:33330684-33330764 58 4.41e-05 CAGCCTGGAT CCGGGTTT TCACTCGTGC chr1:197170616-197170696 60 4.41e-05 ATCCGTTACT CCGGGTTT TCGCAGTGGC chr15:64752639-64752719 38 4.41e-05 CATCCAGGTT CCGGGTTT CCCCTGCGCT chr9:2241970-2242050 32 4.41e-05 AAGATCCACT CCGGGTTT TGCCTAGCGC chr4:76439733-76439813 16 5.66e-05 TCTTAGGTTG CCTGTTTT CCCCCAATCG chr2:227637487-227637567 54 5.66e-05 ACCACTGCTT CCTGTTTT AAGTATCTTA chr14:31699062-31699142 15 7.15e-05 AATGTAAACC ACGGGTTT ATCATTCCCA chr12:27170420-27170500 32 8.25e-05 actaaggccc actgtttt actggggccc chr20:30505858-30505938 24 8.25e-05 attaagatct actgtttt actggggccc chrX:79768010-79768090 34 8.25e-05 actaaggccc actgtttt taccggtatg chr4:26322306-26322386 2 9.70e-05 T CCGGTTTT CCTCAGTCTC chr1:167832558-167832638 57 1.14e-04 tcacgtaccc cctggctt actcaatcga chr16:29701071-29701151 72 1.14e-04 tcacgtaccc cctggctt g chr16:56496465-56496545 7 1.14e-04 TCCGGT CCTGGCTT TCTGATATTT chr5:131758496-131758576 1 1.41e-04 . ACTGGCTT GCATTATCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCKGGTTT MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3:146262354-146262434 1.4e-05 71_[+4]_1 chr19:12947221-12947301 1.4e-05 68_[+4]_4 chr2:27579219-27579299 1.4e-05 45_[+4]_27 chr9:97176151-97176231 2.7e-05 22_[+4]_50 chr5:175624451-175624531 2.7e-05 69_[+4]_3 chr10:73976043-73976123 4.4e-05 4_[+4]_68 chrX:65383984-65384064 4.4e-05 65_[+4]_7 chr8:33330684-33330764 4.4e-05 57_[+4]_15 chr1:197170616-197170696 4.4e-05 59_[+4]_13 chr15:64752639-64752719 4.4e-05 37_[+4]_35 chr9:2241970-2242050 4.4e-05 31_[+4]_41 chr4:76439733-76439813 5.7e-05 15_[+4]_57 chr2:227637487-227637567 5.7e-05 53_[+4]_19 chr14:31699062-31699142 7.2e-05 14_[+4]_58 chr12:27170420-27170500 8.3e-05 31_[+4]_41 chr20:30505858-30505938 8.3e-05 23_[+4]_49 chrX:79768010-79768090 8.3e-05 33_[+4]_39 chr4:26322306-26322386 9.7e-05 1_[+4]_71 chr1:167832558-167832638 0.00011 56_[+4]_16 chr16:29701071-29701151 0.00011 71_[+4]_1 chr16:56496465-56496545 0.00011 6_[+4]_66 chr5:131758496-131758576 0.00014 [+4]_72 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCKGGTTT MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCKGGTTT width=8 seqs=22 chr3:146262354-146262434 ( 72) CCTGGTTT 1 chr19:12947221-12947301 ( 69) CCTGGTTT 1 chr2:27579219-27579299 ( 46) CCTGGTTT 1 chr9:97176151-97176231 ( 23) ACTGGTTT 1 chr5:175624451-175624531 ( 70) ACTGGTTT 1 chr10:73976043-73976123 ( 5) CCGGGTTT 1 chrX:65383984-65384064 ( 66) CCGGGTTT 1 chr8:33330684-33330764 ( 58) CCGGGTTT 1 chr1:197170616-197170696 ( 60) CCGGGTTT 1 chr15:64752639-64752719 ( 38) CCGGGTTT 1 chr9:2241970-2242050 ( 32) CCGGGTTT 1 chr4:76439733-76439813 ( 16) CCTGTTTT 1 chr2:227637487-227637567 ( 54) CCTGTTTT 1 chr14:31699062-31699142 ( 15) ACGGGTTT 1 chr12:27170420-27170500 ( 32) ACTGTTTT 1 chr20:30505858-30505938 ( 24) ACTGTTTT 1 chrX:79768010-79768090 ( 34) ACTGTTTT 1 chr4:26322306-26322386 ( 2) CCGGTTTT 1 chr1:167832558-167832638 ( 57) CCTGGCTT 1 chr16:29701071-29701151 ( 72) CCTGGCTT 1 chr16:56496465-56496545 ( 7) CCTGGCTT 1 chr5:131758496-131758576 ( 1) ACTGGCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCKGGTTT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.0499 E= 1.8e+003 44 136 -1110 -1110 -1110 191 -1110 -1110 -1110 -1110 44 146 -1110 -1110 190 -1110 -1110 -1110 144 24 -1110 -55 -1110 182 -1110 -1110 -1110 211 -1110 -1110 -1110 211 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCKGGTTT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 1.8e+003 0.318182 0.681818 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.363636 0.636364 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.727273 0.272727 0.000000 0.181818 0.000000 0.818182 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCKGGTTT MEME-4 regular expression -------------------------------------------------------------------------------- [CA]C[TG]G[GT]TTT -------------------------------------------------------------------------------- Time 15.70 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTARCTT MEME-5 width = 8 sites = 8 llr = 84 E-value = 6.0e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTARCTT MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::a4::: pos.-specific C ::::1a:: probability G ::::5::: matrix T aaa:::aa bits 2.1 **** ** 1.9 **** *** 1.7 **** *** 1.5 **** *** Relative 1.3 **** *** Entropy 1.1 **** *** (15.1 bits) 0.8 **** *** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TTTAGCTT consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTARCTT MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr4:68418034-68418114 40 1.10e-05 cgagtctgct tttagctt ccctatctta chr5:175624451-175624531 14 1.10e-05 ccgagtctgc tttagctt ccctatctta chr4:84417366-84417446 49 1.10e-05 caagtctgct tttagctt ctctatctta chr1:120930420-120930500 26 1.10e-05 CTCAAATATC TTTAGCTT TGGTGGAAAG chr1:27013503-27013583 8 2.06e-05 ATAAGCC TTTAACTT TCCTTTCCTC chr5:141468604-141468684 8 2.06e-05 gcgtatc tttaactt atcggagagt chr8:22842829-22842909 66 2.06e-05 acagcgtatc tttaactt atcggag chr1:45732148-45732228 65 3.15e-05 actctggatg tttacctt ggcctatt -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTARCTT MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr4:68418034-68418114 1.1e-05 39_[+5]_33 chr5:175624451-175624531 1.1e-05 13_[+5]_59 chr4:84417366-84417446 1.1e-05 48_[+5]_24 chr1:120930420-120930500 1.1e-05 25_[+5]_47 chr1:27013503-27013583 2.1e-05 7_[+5]_65 chr5:141468604-141468684 2.1e-05 7_[+5]_65 chr8:22842829-22842909 2.1e-05 65_[+5]_7 chr1:45732148-45732228 3.1e-05 64_[+5]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTARCTT MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTARCTT width=8 seqs=8 chr4:68418034-68418114 ( 40) TTTAGCTT 1 chr5:175624451-175624531 ( 14) TTTAGCTT 1 chr4:84417366-84417446 ( 49) TTTAGCTT 1 chr1:120930420-120930500 ( 26) TTTAGCTT 1 chr1:27013503-27013583 ( 8) TTTAACTT 1 chr5:141468604-141468684 ( 8) TTTAACTT 1 chr8:22842829-22842909 ( 66) TTTAACTT 1 chr1:45732148-45732228 ( 65) TTTACCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTARCTT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.155 E= 6.0e+003 -965 -965 -965 211 -965 -965 -965 211 -965 -965 -965 211 209 -965 -965 -965 68 -108 90 -965 -965 191 -965 -965 -965 -965 -965 211 -965 -965 -965 211 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTARCTT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 6.0e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.375000 0.125000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTARCTT MEME-5 regular expression -------------------------------------------------------------------------------- TTTA[GA]CTT -------------------------------------------------------------------------------- Time 19.21 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr8:22842829-22842909 5.17e-03 65_[+5(2.06e-05)]_7 chr16:89884102-89884182 7.00e-01 80 chr21:45118658-45118738 5.17e-02 80 chr1:213218672-213218752 3.69e-01 80 chr1:120838268-120838348 7.55e-01 80 chr21:45158579-45158659 1.25e-01 80 chrX:2035564-2035644 3.73e-01 80 chr3:119813383-119813463 9.95e-01 80 chr6:28778239-28778319 2.95e-01 80 chr9:103361127-103361207 5.75e-01 80 chr5:77541056-77541136 2.59e-01 80 chr5:56111276-56111356 1.00e+00 80 chr17:7145862-7145942 9.46e-01 80 chr1:206137674-206137754 9.34e-02 80 chr6:91006627-91006707 8.90e-01 80 chr9:126031179-126031259 9.80e-01 80 chr11:72533278-72533358 1.00e+00 80 chr4:187125453-187125533 1.00e+00 80 chr7:150694249-150694329 1.00e+00 80 chr8:21777043-21777123 1.00e+00 80 chr5:141468604-141468684 2.17e-03 7_[+5(2.06e-05)]_65 chr6:41863210-41863290 7.19e-01 80 chr8:144152511-144152591 1.00e+00 80 chr11:77532155-77532235 3.30e-01 80 chr19:14318446-14318526 7.06e-01 80 chr19:38806449-38806529 9.98e-01 80 chr10:97416489-97416569 5.64e-01 80 chr9:2241970-2242050 7.65e-03 31_[+4(4.41e-05)]_41 chr17:29035799-29035879 2.38e-01 80 chr9:129428859-129428939 2.12e-01 80 chr3:167452440-167452520 9.44e-01 80 chr12:69201591-69201671 3.15e-01 80 chr12:6603477-6603557 5.80e-01 80 chr9:19161761-19161841 3.09e-03 2_[+2(4.89e-05)]_70 chr12:30908071-30908151 9.99e-01 80 chrX:108780672-108780752 9.00e-01 80 chr9:102582418-102582498 9.77e-01 80 chr14:95623860-95623940 9.64e-01 80 chr2:27579219-27579299 6.54e-03 45_[+4(1.45e-05)]_27 chr11:61447782-61447862 6.81e-01 80 chr2:196521784-196521864 9.82e-01 80 chr7:66395450-66395530 3.64e-01 80 chr2:149402906-149402986 4.00e-01 80 chr19:12947221-12947301 8.79e-02 68_[+4(1.45e-05)]_4 chr3:137905896-137905976 1.55e-01 80 chr10:17272496-17272576 9.93e-01 80 chr11:64053203-64053283 9.03e-01 80 chrX:100075207-100075287 9.23e-01 80 chrX:129300125-129300205 7.38e-03 62_[+3(2.78e-05)]_10 chr12:860444-860524 8.95e-01 80 chr2:69664716-69664796 8.09e-01 80 chr8:19674781-19674861 8.56e-02 80 chr22:38902431-38902511 6.23e-01 80 chr2:190648999-190649079 9.99e-01 80 chr1:85039956-85040036 9.75e-01 80 chr18:61034910-61034990 9.82e-01 80 chr8:128813037-128813117 3.21e-02 26_[+1(6.15e-05)]_46 chr8:125029920-125030000 1.70e-02 1_[+1(1.20e-05)]_71 chr12:53297253-53297333 2.00e-01 80 chr17:36754981-36755061 4.95e-01 80 chr1:30664089-30664169 4.98e-02 65_[+3(1.50e-05)]_7 chr12:52430733-52430813 6.30e-01 80 chr10:43133716-43133796 7.62e-01 80 chr17:28054023-28054103 1.50e-01 80 chr6:30484381-30484461 9.69e-01 80 chr1:52869485-52869565 2.87e-01 80 chr4:166248470-166248550 9.55e-01 80 chr7:150015235-150015315 1.17e-01 80 chr2:55746582-55746662 9.24e-02 80 chr15:34875860-34875940 9.42e-01 80 chr11:63448659-63448739 7.28e-01 80 chr1:25566592-25566672 9.98e-01 80 chr1:234736069-234736149 3.38e-01 80 chr16:56496465-56496545 1.34e-02 80 chr16:20756319-20756399 3.73e-01 80 chr16:20685582-20685662 1.68e-02 80 chr2:75089581-75089661 2.58e-01 10_[+1(6.15e-05)]_62 chr16:20693249-20693329 3.69e-04 37_[+3(8.13e-05)]_35 chr14:97207832-97207912 7.42e-01 80 chr4:144940553-144940633 3.44e-01 80 chr1:195868172-195868252 1.50e-03 [+1(3.42e-05)]_72 chr22:39915517-39915597 5.60e-01 80 chr3:146262354-146262434 5.74e-03 71_[+4(1.45e-05)]_1 chr1:120930420-120930500 4.35e-03 25_[+5(1.10e-05)]_47 chr20:443266-443346 9.00e-01 80 chr6:167412806-167412886 9.97e-01 80 chr17:56085059-56085139 4.13e-01 80 chr10:103929469-10392954 2.20e-01 80 chr9:139981322-139981402 1.00e+00 80 chr19:46149508-46149588 5.58e-01 80 chr16:53737964-53738044 6.21e-01 80 chr7:129882118-129882198 1.61e-01 80 chr17:61850905-61850985 8.49e-01 80 chr12:75724117-75724197 8.95e-01 80 chr7:35840719-35840799 9.98e-01 80 chr7:95238160-95238240 6.97e-01 80 chr4:25090250-25090330 7.62e-01 80 chr17:45955103-45955183 6.45e-02 80 chr1:27018818-27018898 1.53e-01 80 chr16:78133401-78133481 9.33e-01 80 chr6:134339229-134339309 6.71e-01 80 chr18:55785431-55785511 3.73e-01 80 chr7:23312929-23313009 9.23e-02 38_[+1(6.15e-05)]_34 chr2:8817914-8817994 2.29e-02 56_[+1(2.38e-05)]_16 chr2:9748149-9748229 1.38e-01 80 chr11:65138864-65138944 1.31e-02 80 chr7:157130546-157130626 2.78e-01 80 chr15:85078218-85078298 1.64e-01 69_[+1(2.38e-05)]_3 chrX:55054634-55054714 1.31e-01 80 chr1:51985169-51985249 2.91e-01 80 chr15:45027803-45027883 3.25e-01 80 chr12:131834896-13183497 7.98e-04 40_[+2(4.89e-05)]_32 chr8:98790771-98790851 1.27e-02 80 chr4:84417366-84417446 1.50e-03 48_[+5(1.10e-05)]_24 chr12:112432673-11243275 2.45e-01 80 chr9:99736458-99736538 4.65e-01 80 chr7:77168103-77168183 9.97e-01 80 chr17:9424093-9424173 5.38e-03 26_[+3(4.09e-05)]_46 chr2:86332989-86333069 5.86e-01 80 chr2:11606367-11606447 8.95e-01 80 chr15:64752639-64752719 1.87e-02 37_[+4(4.41e-05)]_35 chrX:79768010-79768090 6.96e-02 33_[+4(8.25e-05)]_39 chrX:47535523-47535603 2.55e-01 80 chr6:7975435-7975515 2.70e-01 80 chr14:73292881-73292961 6.07e-03 43_[+2(2.51e-05)]_29 chr19:41370675-41370755 4.86e-02 17_[+3(8.13e-05)]_55 chr11:61348990-61349070 6.32e-01 80 chr2:227637487-227637567 4.70e-05 53_[+4(5.66e-05)]_6_[+2(1.26e-05)]_\ 5 chr18:11947290-11947370 5.62e-01 80 chrX:47572277-47572357 4.10e-01 80 chr9:116131433-116131513 1.83e-02 9_[+3(6.87e-05)]_63 chr9:107537660-107537740 1.53e-01 80 chr19:58874224-58874304 8.57e-01 80 chr17:73851604-73851684 4.24e-01 80 chr1:45732148-45732228 4.11e-03 64_[+5(3.15e-05)]_8 chr17:25856386-25856466 1.04e-02 80 chr15:65529474-65529554 4.33e-01 80 chr19:56698374-56698454 8.58e-01 80 chr12:109249771-10924985 1.57e-01 80 chr6:34360490-34360570 9.63e-01 80 chr21:47875802-47875882 2.89e-01 80 chr11:10830627-10830707 9.99e-01 80 chr1:154973411-154973491 2.68e-01 80 chr14:69087002-69087082 8.58e-01 80 chr4:185373033-185373113 2.69e-02 80 chr4:26322306-26322386 3.74e-02 1_[+4(9.70e-05)]_71 chr20:52225339-52225419 6.75e-01 80 chr3:193721082-193721162 5.52e-02 80 chr12:14410809-14410889 1.15e-01 80 chr7:26240480-26240560 9.13e-01 80 chr18:51750941-51751021 9.38e-01 80 chr5:175624451-175624531 4.55e-04 13_[+5(1.10e-05)]_48_[+4(2.73e-05)]_\ 3 chr12:80326334-80326414 7.51e-01 80 chr12:4262868-4262948 4.01e-03 29_[+3(1.50e-05)]_43 chr1:197170616-197170696 5.32e-02 59_[+4(4.41e-05)]_13 chr10:21419195-21419275 4.31e-01 80 chr8:126175788-126175868 2.81e-02 27_[+1(3.42e-05)]_45 chr10:86284951-86285031 3.96e-02 40_[+1(1.20e-05)]_32 chr1:204370131-204370211 8.55e-03 80 chrX:15693362-15693442 8.35e-01 80 chr8:33330684-33330764 6.65e-02 57_[+4(4.41e-05)]_15 chr10:89622170-89622250 9.99e-01 80 chr4:68418034-68418114 1.28e-02 39_[+5(1.10e-05)]_33 chr18:21120964-21121044 6.67e-03 53_[+1(6.15e-05)]_19 chr4:144826788-144826868 3.09e-01 80 chr9:80442447-80442527 3.31e-02 80 chr15:75459026-75459106 5.43e-02 80 chr20:30505858-30505938 4.04e-02 23_[+4(8.25e-05)]_49 chr17:53894325-53894405 2.27e-01 80 chr6:134516879-134516959 6.92e-05 32_[+3(1.50e-05)]_2_[+2(6.18e-05)]_\ 30 chr7:7082263-7082343 7.76e-02 15_[+1(3.42e-05)]_57 chr12:23712364-23712444 2.32e-02 31_[+3(1.50e-05)]_41 chrX:55147373-55147453 5.89e-03 59_[+2(1.26e-05)]_13 chr1:28193886-28193966 1.21e-02 16_[+2(4.89e-05)]_56 chr7:158317032-158317112 4.97e-01 80 chr6:26206308-26206388 4.38e-01 80 chr16:70471087-70471167 8.15e-01 80 chr2:216973919-216973999 9.80e-01 80 chr1:54519010-54519090 9.71e-01 80 chrX:65383984-65384064 7.98e-02 65_[+4(4.41e-05)]_7 chr3:170496598-170496678 2.39e-03 69_[+3(2.78e-05)]_3 chr3:32115880-32115960 1.41e-02 36_[+2(9.62e-05)]_36 chr1:231120659-231120739 6.52e-02 80 chr12:27170420-27170500 5.35e-02 31_[+4(8.25e-05)]_41 chr6:15018809-15018889 2.97e-02 36_[+3(6.87e-05)]_36 chr9:97176151-97176231 9.63e-03 22_[+4(2.73e-05)]_50 chrX:47543035-47543115 3.41e-02 65_[+2(4.89e-05)]_7 chr9:140024224-140024304 9.99e-01 80 chr6:112408705-112408785 7.61e-01 80 chr6:125404386-125404466 4.08e-02 80 chr1:27019595-27019675 1.61e-01 80 chr21:9968655-9968735 7.41e-01 80 chr19:52097670-52097750 9.32e-01 80 chr7:150736638-150736718 2.87e-04 39_[+1(2.38e-05)]_11_[+2(1.26e-05)]_\ 14 chr4:154415015-154415095 1.78e-02 80 chr10:98379052-98379132 3.48e-01 80 chr9:98637851-98637931 8.83e-01 80 chr11:876047-876127 4.05e-01 80 chr5:131758496-131758576 1.90e-02 80 chr19:53664595-53664675 1.64e-02 7_[+2(1.26e-05)]_65 chr1:28851625-28851705 7.98e-02 80 chr9:96873352-96873432 1.03e-02 31_[+3(2.78e-05)]_41 chr2:176800443-176800523 3.24e-02 27_[+3(1.50e-05)]_45 chr9:37197237-37197317 2.92e-02 52_[+2(2.51e-05)]_20 chr16:29701071-29701151 1.33e-01 80 chr12:123237307-12323738 5.96e-01 80 chr5:111884096-111884176 1.59e-01 80 chr17:7660452-7660532 9.19e-01 80 chr1:167832558-167832638 1.45e-01 80 chr1:160919210-160919290 1.11e-02 80 chr4:76439733-76439813 7.45e-02 15_[+4(5.66e-05)]_57 chr19:35411473-35411553 9.87e-01 80 chr8:67967446-67967526 1.38e-01 80 chr1:27561014-27561094 9.51e-01 80 chr3:33014374-33014454 1.96e-02 [+2(2.51e-05)]_72 chr8:15559447-15559527 9.93e-04 4_[+3(8.13e-05)]_44_[+1(1.20e-05)]_\ 16 chr19:944268-944348 9.03e-01 80 chr14:31699062-31699142 4.23e-03 14_[+4(7.15e-05)]_58 chrX:39710123-39710203 1.10e-01 80 chr14:36733961-36734041 6.56e-02 80 chr6:108899890-108899970 3.38e-01 80 chr10:7294265-7294345 6.09e-02 80 chr6:658413-658493 4.36e-02 80 chr5:133298964-133299044 6.43e-03 35_[+3(4.09e-05)]_37 chr6:151409193-151409273 2.73e-02 80 chr7:70033915-70033995 8.30e-02 80 chr11:2799949-2800029 2.70e-02 28_[+2(4.89e-05)]_44 chr10:73976043-73976123 2.65e-01 4_[+4(4.41e-05)]_68 chr17:43242854-43242934 9.27e-01 80 chr18:46307749-46307829 9.98e-01 80 chr14:64108531-64108611 7.59e-01 80 chr5:139990813-139990893 4.76e-03 [+2(1.26e-05)]_72 chr2:97304106-97304186 9.92e-01 80 chr17:58042319-58042399 5.75e-01 80 chr1:25739904-25739984 2.66e-02 80 chr17:61920122-61920202 1.54e-01 80 chr17:65852216-65852296 6.38e-02 80 chr22:30217478-30217558 1.86e-02 28_[+2(2.51e-05)]_44 chr1:27013503-27013583 4.45e-04 7_[+5(2.06e-05)]_29_[+3(4.09e-05)]_\ 28 chr8:94564262-94564342 5.35e-03 3_[+3(6.87e-05)]_42_[+2(6.18e-05)]_\ 19 chr22:36764682-36764762 1.63e-03 14_[+1(2.38e-05)]_20_[+2(9.62e-05)]_\ 30 chr2:160008758-160008838 5.69e-03 52_[+1(6.15e-05)]_20 chr17:6897238-6897318 5.94e-05 2_[+5(4.10e-05)]_36_[+1(3.42e-05)]_\ 26 chrX:102356711-102356791 5.65e-02 46_[+1(6.15e-05)]_26 chr19:54714764-54714844 4.89e-03 80 chr2:198317951-198318031 9.92e-01 80 chr8:144629506-144629586 2.89e-02 37_[+3(1.50e-05)]_13_[+3(5.56e-05)]_\ 14 chr13:95923486-95923566 5.17e-01 80 chr2:119496737-119496817 1.47e-02 55_[+1(6.15e-05)]_17 chr5:124064194-124064274 1.37e-03 69_[+2(7.27e-05)]_3 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c17n09.farnam.hpc.yale.internal ********************************************************************************