******************************************************************************** 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/SMAD5.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr22:23040407-23040427 1.0000 20 chr22:23249280-23249300 1.0000 20 chr14:106692314-10669233 1.0000 20 chr12:10705996-10706016 1.0000 20 chr19:42037879-42037899 1.0000 20 chr1:32801820-32801840 1.0000 20 chr14:20937590-20937610 1.0000 20 chr12:104301678-10430169 1.0000 20 chr12:49525122-49525142 1.0000 20 chr21:26937990-26938010 1.0000 20 chr1:159895245-159895265 1.0000 20 chr22:22380717-22380737 1.0000 20 chr1:207627722-207627742 1.0000 20 chr3:178254292-178254312 1.0000 20 chr17:4851742-4851762 1.0000 20 chr21:26938271-26938291 1.0000 20 chr5:73936515-73936535 1.0000 20 chr15:45019346-45019366 1.0000 20 chr9:113018732-113018752 1.0000 20 chr11:65222787-65222807 1.0000 20 chr22:23249485-23249505 1.0000 20 chr6:27776349-27776369 1.0000 20 chr6:30693789-30693809 1.0000 20 chr6:26217484-26217504 1.0000 20 chr4:36334143-36334163 1.0000 20 chr4:39628694-39628714 1.0000 20 chr14:23120453-23120473 1.0000 20 chr22:22385440-22385460 1.0000 20 chr8:96103497-96103517 1.0000 20 chr14:106329195-10632921 1.0000 20 chr14:106172040-10617206 1.0000 20 chr2:136875648-136875668 1.0000 20 chr2:192542877-192542897 1.0000 20 chr1:182573479-182573499 1.0000 20 chr5:172198164-172198184 1.0000 20 chr11:65899603-65899623 1.0000 20 chr11:65194204-65194224 1.0000 20 chr19:42055877-42055897 1.0000 20 chr12:49582834-49582854 1.0000 20 chr1:161677034-161677054 1.0000 20 chr2:30454420-30454440 1.0000 20 chr6:33043787-33043807 1.0000 20 chr19:35820109-35820129 1.0000 20 chr6:27841234-27841254 1.0000 20 chr5:149791268-149791288 1.0000 20 chr3:112100791-112100811 1.0000 20 chr12:56615830-56615850 1.0000 20 chr1:149514219-149514239 1.0000 20 chr14:96180427-96180447 1.0000 20 chr2:121832835-121832855 1.0000 20 chr22:23244032-23244052 1.0000 20 chr6:30583915-30583935 1.0000 20 chrX:41193450-41193470 1.0000 20 chr17:33700599-33700619 1.0000 20 chr5:149780030-149780050 1.0000 20 chr6:31543380-31543400 1.0000 20 chr10:32345275-32345295 1.0000 20 chr14:102553338-10255335 1.0000 20 chr14:51135365-51135385 1.0000 20 chr6:27835169-27835189 1.0000 20 chr6:34204465-34204485 1.0000 20 chrX:135962817-135962837 1.0000 20 chr20:2853955-2853975 1.0000 20 chr16:57392728-57392748 1.0000 20 chr1:46049746-46049766 1.0000 20 chr7:127032723-127032743 1.0000 20 chr8:94753203-94753223 1.0000 20 chr6:32605181-32605201 1.0000 20 chr6:26250711-26250731 1.0000 20 chr11:82868216-82868236 1.0000 20 chr12:92757411-92757431 1.0000 20 chr8:103876347-103876367 1.0000 20 chr21:26874041-26874061 1.0000 20 chr1:145443077-145443097 1.0000 20 chr8:101734293-101734313 1.0000 20 chr14:50359841-50359861 1.0000 20 chr14:53173709-53173729 1.0000 20 chr5:151138111-151138131 1.0000 20 chr2:232573468-232573488 1.0000 20 chr17:18967127-18967147 1.0000 20 chr6:26240697-26240717 1.0000 20 chr6:31324905-31324925 1.0000 20 chr7:28450283-28450303 1.0000 20 chr1:28996421-28996441 1.0000 20 chr5:133512605-133512625 1.0000 20 chr2:85132808-85132828 1.0000 20 chr17:39834949-39834969 1.0000 20 chr8:82598503-82598523 1.0000 20 chr5:149791051-149791071 1.0000 20 chr12:53601002-53601022 1.0000 20 chr6:27833452-27833472 1.0000 20 chrX:23801341-23801361 1.0000 20 chr7:5632455-5632475 1.0000 20 chr5:150593710-150593730 1.0000 20 chr6:146057098-146057118 1.0000 20 chr6:156973630-156973650 1.0000 20 chr2:37862435-37862455 1.0000 20 chr1:156698262-156698282 1.0000 20 chr3:49058889-49058909 1.0000 20 chr5:53606558-53606578 1.0000 20 chr2:191745559-191745579 1.0000 20 chr12:6643716-6643736 1.0000 20 chr17:38718371-38718391 1.0000 20 chr2:231815817-231815837 1.0000 20 chr2:86426599-86426619 1.0000 20 chr6:32557533-32557553 1.0000 20 chr11:61735034-61735054 1.0000 20 chr17:79479765-79479785 1.0000 20 chr2:68666144-68666164 1.0000 20 chr5:142594146-142594166 1.0000 20 chr17:37026358-37026378 1.0000 20 chr4:10118735-10118755 1.0000 20 chr6:31320643-31320663 1.0000 20 chr6:32977312-32977332 1.0000 20 chr13:95892476-95892496 1.0000 20 chr19:49996124-49996144 1.0000 20 chr2:70475695-70475715 1.0000 20 chr17:6939069-6939089 1.0000 20 chr1:182808517-182808537 1.0000 20 chr1:23885930-23885950 1.0000 20 chr3:194406626-194406646 1.0000 20 chr20:2633313-2633333 1.0000 20 chr6:391793-391813 1.0000 20 chr2:152685168-152685188 1.0000 20 chr13:99959638-99959658 1.0000 20 chr21:26946274-26946294 1.0000 20 chr14:106692514-10669253 1.0000 20 chr6:27107399-27107419 1.0000 20 chr1:203274680-203274700 1.0000 20 chr2:33702706-33702726 1.0000 20 chr19:59055831-59055851 1.0000 20 chr4:57845065-57845085 1.0000 20 chr11:122932797-12293281 1.0000 20 chr18:57567265-57567285 1.0000 20 chr8:74205806-74205826 1.0000 20 chr21:26942252-26942272 1.0000 20 chr1:150207263-150207283 1.0000 20 chr14:69259724-69259744 1.0000 20 chr7:5565132-5565152 1.0000 20 chr2:176046384-176046404 1.0000 20 chr17:56084551-56084571 1.0000 20 chr1:211556225-211556245 1.0000 20 chr1:109234895-109234915 1.0000 20 chr19:47291807-47291827 1.0000 20 chr1:148604913-148604933 1.0000 20 chrX:153626754-153626774 1.0000 20 chr6:44355486-44355506 1.0000 20 chr2:201729319-201729339 1.0000 20 chr1:147735923-147735943 1.0000 20 chr9:131314868-131314888 1.0000 20 chr11:615904-615924 1.0000 20 chr16:4303722-4303742 1.0000 20 chr17:11900972-11900992 1.0000 20 chr19:42382060-42382080 1.0000 20 chr7:44084138-44084158 1.0000 20 chr17:48943677-48943697 1.0000 20 chr4:185202117-185202137 1.0000 20 chr6:86388409-86388429 1.0000 20 chr11:93474624-93474644 1.0000 20 chr2:231808525-231808545 1.0000 20 chr5:43313445-43313465 1.0000 20 chr9:123688375-123688395 1.0000 20 chr17:28443888-28443908 1.0000 20 chr12:69004446-69004466 1.0000 20 chr17:18965565-18965585 1.0000 20 chr1:47069866-47069886 1.0000 20 chr5:72794250-72794270 1.0000 20 chr4:57333778-57333798 1.0000 20 chr19:50432502-50432522 1.0000 20 chr21:26936984-26937004 1.0000 20 chr7:98972372-98972392 1.0000 20 chr6:21593997-21594017 1.0000 20 chr3:52312607-52312627 1.0000 20 chr19:49956921-49956941 1.0000 20 chr10:70847886-70847906 1.0000 20 chr5:170814869-170814889 1.0000 20 chrX:100646036-100646056 1.0000 20 chr1:37940192-37940212 1.0000 20 chr6:31802697-31802717 1.0000 20 chr6:29910325-29910345 1.0000 20 chr19:5828374-5828394 1.0000 20 chr6:89790503-89790523 1.0000 20 chr10:73975827-73975847 1.0000 20 chr1:17222703-17222723 1.0000 20 chr9:74980080-74980100 1.0000 20 chr20:42086532-42086552 1.0000 20 chr5:141348767-141348787 1.0000 20 chr15:69745177-69745197 1.0000 20 chr5:34008361-34008381 1.0000 20 chr17:57915316-57915336 1.0000 20 chr7:39606042-39606062 1.0000 20 chr10:27444079-27444099 1.0000 20 chr17:25621161-25621181 1.0000 20 chrX:118602439-118602459 1.0000 20 chr17:56416569-56416589 1.0000 20 chr1:147994169-147994189 1.0000 20 chr1:76190455-76190475 1.0000 20 chr19:24270056-24270076 1.0000 20 chr17:57970509-57970529 1.0000 20 chr7:5566086-5566106 1.0000 20 chr12:9913464-9913484 1.0000 20 chr17:39845174-39845194 1.0000 20 chr21:40721656-40721676 1.0000 20 chr3:185655747-185655767 1.0000 20 chr3:156392412-156392432 1.0000 20 chr14:24564762-24564782 1.0000 20 chr21:26940734-26940754 1.0000 20 chr17:62502355-62502375 1.0000 20 chr6:28891752-28891772 1.0000 20 chr22:24200106-24200126 1.0000 20 chr19:1269343-1269363 1.0000 20 chr6:31239836-31239856 1.0000 20 chr1:76251966-76251986 1.0000 20 chrX:12995707-12995727 1.0000 20 chr17:34136522-34136542 1.0000 20 chr16:30546430-30546450 1.0000 20 chr11:71823957-71823977 1.0000 20 chr19:46195143-46195163 1.0000 20 chr2:220071354-220071374 1.0000 20 chr6:137112701-137112721 1.0000 20 chr3:150320944-150320964 1.0000 20 chr19:55919139-55919159 1.0000 20 chr7:98923398-98923418 1.0000 20 chr3:143690919-143690939 1.0000 20 chr13:103426241-10342626 1.0000 20 chr9:108320311-108320331 1.0000 20 chr21:15918605-15918625 1.0000 20 chr13:45915287-45915307 1.0000 20 chr11:124823837-12482385 1.0000 20 chr11:62432782-62432802 1.0000 20 chr2:32264954-32264974 1.0000 20 chr3:196255855-196255875 1.0000 20 chr16:2011156-2011176 1.0000 20 chr6:139695731-139695751 1.0000 20 chr5:86708642-86708662 1.0000 20 chr5:71604118-71604138 1.0000 20 chr4:37828330-37828350 1.0000 20 chr19:23457011-23457031 1.0000 20 chr10:120938256-12093827 1.0000 20 chr6:114179931-114179951 1.0000 20 chr3:9439090-9439110 1.0000 20 chr14:21776890-21776910 1.0000 20 chr1:160596862-160596882 1.0000 20 chr19:6531060-6531080 1.0000 20 chr10:74033707-74033727 1.0000 20 chr7:66093564-66093584 1.0000 20 chr6:43543945-43543965 1.0000 20 chr1:160604405-160604425 1.0000 20 chr2:232573249-232573269 1.0000 20 chr14:23001185-23001205 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_SMAD5/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/SMAD5.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 0.206 C 0.292 G 0.3 T 0.202 Background letter frequencies (from file dataset with add-one prior applied): A 0.206 C 0.292 G 0.3 T 0.202 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AGBCTYTC MEME-1 width = 8 sites = 18 llr = 133 E-value = 7.6e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGBCTYTC MEME-1 Description -------------------------------------------------------------------------------- Simplified A 81111::: pos.-specific C ::49:7:8 probability G :93::::2 matrix T 2:2:93a: bits 2.3 * 2.1 * 1.8 * * 1.6 * * * Relative 1.4 ** ** * Entropy 1.2 ** ** ** (10.6 bits) 0.9 ** ***** 0.7 ** ***** 0.5 ** ***** 0.2 ** ***** 0.0 -------- Multilevel AGCCTCTC consensus T G T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGBCTYTC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr14:69259724-69259744 1 1.83e-05 . AGCCTCTC CTGTCTGGAG chr14:96180427-96180447 11 1.83e-05 CAAGAGCCAG AGCCTCTC AA chr2:32264954-32264974 12 6.25e-05 TCAGTCCCCG AGGCTCTC T chr6:89790503-89790523 11 6.25e-05 CGATCTTCTC AGGCTCTC CT chr3:156392412-156392432 13 8.43e-05 AGCGCGGTCG AGGCTTTC chr7:127032723-127032743 7 9.73e-05 AAGCAG AGACTCTC CGGCAG chr6:31320643-31320663 7 1.49e-04 tcctca tgtctctc aaatct chr4:10118735-10118755 9 1.49e-04 GGGGTGGG TGCCTTTC TGTT chr19:24270056-24270076 6 1.86e-04 GGCCC AGCCTCTG TGGCGCT chr4:36334143-36334163 6 2.08e-04 GCAAT TGTCTTTC CGCTGCA chr1:149514219-149514239 13 2.84e-04 gtttgataat agtatctc chr10:120938256-12093827 1 3.16e-04 . AGCCACTC ACCGACGCTC chr10:73975827-73975847 12 3.16e-04 TGGTGAGCGC AGCCACTC A chr2:85132808-85132828 5 3.16e-04 CACC AGGATCTC GGGCTCGG chr12:9913464-9913484 6 3.38e-04 GTGAA AGTCTTTG CTGGAGC chr14:51135365-51135385 10 3.38e-04 CGGAGGCAG TGACTCTC TTT chr17:38718371-38718391 4 3.57e-04 agc aggctttg aaaccctcc chr17:18967127-18967147 9 4.95e-04 GAGGCGAA AACCTTTC TCGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGBCTYTC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr14:69259724-69259744 1.8e-05 [+1]_12 chr14:96180427-96180447 1.8e-05 10_[+1]_2 chr2:32264954-32264974 6.3e-05 11_[+1]_1 chr6:89790503-89790523 6.3e-05 10_[+1]_2 chr3:156392412-156392432 8.4e-05 12_[+1] chr7:127032723-127032743 9.7e-05 6_[+1]_6 chr6:31320643-31320663 0.00015 6_[+1]_6 chr4:10118735-10118755 0.00015 8_[+1]_4 chr19:24270056-24270076 0.00019 5_[+1]_7 chr4:36334143-36334163 0.00021 5_[+1]_7 chr1:149514219-149514239 0.00028 12_[+1] chr10:120938256-12093827 0.00032 [+1]_12 chr10:73975827-73975847 0.00032 11_[+1]_1 chr2:85132808-85132828 0.00032 4_[+1]_8 chr12:9913464-9913484 0.00034 5_[+1]_7 chr14:51135365-51135385 0.00034 9_[+1]_3 chr17:38718371-38718391 0.00036 3_[+1]_9 chr17:18967127-18967147 0.00049 8_[+1]_4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGBCTYTC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGBCTYTC width=8 seqs=18 chr14:69259724-69259744 ( 1) AGCCTCTC 1 chr14:96180427-96180447 ( 11) AGCCTCTC 1 chr2:32264954-32264974 ( 12) AGGCTCTC 1 chr6:89790503-89790523 ( 11) AGGCTCTC 1 chr3:156392412-156392432 ( 13) AGGCTTTC 1 chr7:127032723-127032743 ( 7) AGACTCTC 1 chr6:31320643-31320663 ( 7) TGTCTCTC 1 chr4:10118735-10118755 ( 9) TGCCTTTC 1 chr19:24270056-24270076 ( 6) AGCCTCTG 1 chr4:36334143-36334163 ( 6) TGTCTTTC 1 chr1:149514219-149514239 ( 13) AGTATCTC 1 chr10:120938256-12093827 ( 1) AGCCACTC 1 chr10:73975827-73975847 ( 12) AGCCACTC 1 chr2:85132808-85132828 ( 5) AGGATCTC 1 chr12:9913464-9913484 ( 6) AGTCTTTG 1 chr14:51135365-51135385 ( 10) TGACTCTC 1 chr17:38718371-38718391 ( 4) AGGCTTTG 1 chr17:18967127-18967147 ( 9) AACCTTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGBCTYTC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.33985 E= 7.6e+002 191 -1081 -1081 14 -189 -1081 166 -1081 -89 41 -11 14 -89 161 -1081 -1081 -89 -1081 -1081 214 -1081 119 -1081 72 -1081 -1081 -1081 231 -1081 151 -85 -1081 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGBCTYTC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 18 E= 7.6e+002 0.777778 0.000000 0.000000 0.222222 0.055556 0.000000 0.944444 0.000000 0.111111 0.388889 0.277778 0.222222 0.111111 0.888889 0.000000 0.000000 0.111111 0.000000 0.000000 0.888889 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.833333 0.166667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGBCTYTC MEME-1 regular expression -------------------------------------------------------------------------------- [AT]G[CGT]CT[CT]TC -------------------------------------------------------------------------------- Time 3.26 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTYATTT MEME-2 width = 8 sites = 2 llr = 24 E-value = 7.0e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTYATTT MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::::a::: pos.-specific C :::5:::: probability G :::::::: matrix T aaa5:aaa bits 2.3 *** **** 2.1 *** **** 1.8 *** **** 1.6 *** **** Relative 1.4 *** **** Entropy 1.2 ******** (17.2 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TTTCATTT consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTYATTT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr21:40721656-40721676 1 2.83e-06 . ttttattt gagacagggt chr6:33043787-33043807 4 6.91e-06 TCT TTTCATTT TGCCATCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTYATTT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr21:40721656-40721676 2.8e-06 [+2]_12 chr6:33043787-33043807 6.9e-06 3_[+2]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTYATTT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTYATTT width=8 seqs=2 chr21:40721656-40721676 ( 1) TTTTATTT 1 chr6:33043787-33043807 ( 4) TTTCATTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTYATTT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 7.0e+002 -765 -765 -765 230 -765 -765 -765 230 -765 -765 -765 230 -765 77 -765 130 227 -765 -765 -765 -765 -765 -765 230 -765 -765 -765 230 -765 -765 -765 230 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTYATTT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 7.0e+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 0.500000 0.000000 0.500000 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 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTYATTT MEME-2 regular expression -------------------------------------------------------------------------------- TTT[CT]ATTT -------------------------------------------------------------------------------- Time 4.04 secs. ******************************************************************************** ******************************************************************************** MOTIF CCATYTTT MEME-3 width = 8 sites = 3 llr = 33 E-value = 1.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCATYTTT MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::a::::: pos.-specific C aa::7::: probability G :::::::: matrix T :::a3aaa bits 2.3 ** *** 2.1 ** *** 1.8 **** *** 1.6 **** *** Relative 1.4 **** *** Entropy 1.2 **** *** (16.1 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CCATCTTT consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCATYTTT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr2:232573249-232573269 9 8.54e-06 CTGAAAAG CCATCTTT GCAT chr1:150207263-150207283 4 8.54e-06 AAC CCATCTTT AAAGCACGA chr21:26936984-26937004 12 1.44e-05 GCTGGTGTCT CCATTTTT G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCATYTTT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr2:232573249-232573269 8.5e-06 8_[+3]_4 chr1:150207263-150207283 8.5e-06 3_[+3]_9 chr21:26936984-26937004 1.4e-05 11_[+3]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCATYTTT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCATYTTT width=8 seqs=3 chr2:232573249-232573269 ( 9) CCATCTTT 1 chr1:150207263-150207283 ( 4) CCATCTTT 1 chr21:26936984-26937004 ( 12) CCATTTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCATYTTT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.73854 E= 1.6e+003 -823 177 -823 -823 -823 177 -823 -823 227 -823 -823 -823 -823 -823 -823 230 -823 119 -823 72 -823 -823 -823 230 -823 -823 -823 230 -823 -823 -823 230 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCATYTTT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 1.6e+003 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 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 CCATYTTT MEME-3 regular expression -------------------------------------------------------------------------------- CCAT[CT]TTT -------------------------------------------------------------------------------- Time 5.44 secs. ******************************************************************************** ******************************************************************************** MOTIF AYCYAAAC MEME-4 width = 8 sites = 6 llr = 60 E-value = 1.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AYCYAAAC MEME-4 Description -------------------------------------------------------------------------------- Simplified A a:::aaa: pos.-specific C :7a3:::8 probability G :::::::: matrix T :3:7:::2 bits 2.3 * *** 2.1 * *** 1.8 * * *** 1.6 * * *** Relative 1.4 * * *** Entropy 1.2 * ****** (14.3 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel ACCTAAAC consensus T C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AYCYAAAC MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:161677034-161677054 4 9.06e-06 GAG ACCTAAAC ACAGTCACC chr1:147994169-147994189 5 1.53e-05 tatt atctaaac gaaggtgg chr5:149780030-149780050 4 1.53e-05 ggc atctaaac taaaggatg chr5:86708642-86708662 10 2.84e-05 CAGACGAGA ACCCAAAC GCA chr3:49058889-49058909 12 2.84e-05 CCGAACAGCC ACCCAAAC A chr5:34008361-34008381 12 3.47e-05 TTTTTGTGCA ACCTAAAT T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AYCYAAAC MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:161677034-161677054 9.1e-06 3_[+4]_9 chr1:147994169-147994189 1.5e-05 4_[+4]_8 chr5:149780030-149780050 1.5e-05 3_[+4]_9 chr5:86708642-86708662 2.8e-05 9_[+4]_3 chr3:49058889-49058909 2.8e-05 11_[+4]_1 chr5:34008361-34008381 3.5e-05 11_[+4]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AYCYAAAC MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AYCYAAAC width=8 seqs=6 chr1:161677034-161677054 ( 4) ACCTAAAC 1 chr1:147994169-147994189 ( 5) ATCTAAAC 1 chr5:149780030-149780050 ( 4) ATCTAAAC 1 chr5:86708642-86708662 ( 10) ACCCAAAC 1 chr3:49058889-49058909 ( 12) ACCCAAAC 1 chr5:34008361-34008381 ( 12) ACCTAAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AYCYAAAC MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.52677 E= 1.4e+003 227 -923 -923 -923 -923 119 -923 72 -923 177 -923 -923 -923 19 -923 172 227 -923 -923 -923 227 -923 -923 -923 227 -923 -923 -923 -923 151 -923 -28 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AYCYAAAC MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 1.4e+003 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.666667 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 0.833333 0.000000 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AYCYAAAC MEME-4 regular expression -------------------------------------------------------------------------------- A[CT]C[TC]AAAC -------------------------------------------------------------------------------- Time 6.20 secs. ******************************************************************************** ******************************************************************************** MOTIF TCTCTGTT MEME-5 width = 8 sites = 2 llr = 23 E-value = 2.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCTCTGTT MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :a:a:::: probability G :::::a:: matrix T a:a:a:aa bits 2.3 * * * ** 2.1 * * * ** 1.8 ******** 1.6 ******** Relative 1.4 ******** Entropy 1.2 ******** (16.8 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TCTCTGTT consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTCTGTT MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:182808517-182808537 4 8.60e-06 GTT TCTCTGTT GTCTCGGTA chr11:65194204-65194224 1 8.60e-06 . TCTCTGTT GAGAGTTGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTCTGTT MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:182808517-182808537 8.6e-06 3_[+5]_9 chr11:65194204-65194224 8.6e-06 [+5]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTCTGTT MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCTCTGTT width=8 seqs=2 chr1:182808517-182808537 ( 4) TCTCTGTT 1 chr11:65194204-65194224 ( 1) TCTCTGTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTCTGTT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 2.2e+003 -765 -765 -765 230 -765 177 -765 -765 -765 -765 -765 230 -765 177 -765 -765 -765 -765 -765 230 -765 -765 173 -765 -765 -765 -765 230 -765 -765 -765 230 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTCTGTT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.2e+003 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTCTGTT MEME-5 regular expression -------------------------------------------------------------------------------- TCTCTGTT -------------------------------------------------------------------------------- Time 6.97 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr22:23040407-23040427 8.12e-01 20 chr22:23249280-23249300 3.41e-01 20 chr14:106692314-10669233 9.91e-01 20 chr12:10705996-10706016 1.33e-03 20 chr19:42037879-42037899 9.54e-01 20 chr1:32801820-32801840 9.26e-01 20 chr14:20937590-20937610 2.42e-01 20 chr12:104301678-10430169 5.32e-01 20 chr12:49525122-49525142 5.07e-01 20 chr21:26937990-26938010 3.47e-01 20 chr1:159895245-159895265 1.00e+00 20 chr22:22380717-22380737 7.70e-01 20 chr1:207627722-207627742 6.99e-01 20 chr3:178254292-178254312 1.31e-02 20 chr17:4851742-4851762 6.41e-01 20 chr21:26938271-26938291 4.74e-01 20 chr5:73936515-73936535 7.21e-01 20 chr15:45019346-45019366 2.36e-01 20 chr9:113018732-113018752 9.57e-01 20 chr11:65222787-65222807 9.97e-01 20 chr22:23249485-23249505 9.97e-01 20 chr6:27776349-27776369 8.82e-01 20 chr6:30693789-30693809 9.60e-01 20 chr6:26217484-26217504 2.81e-01 20 chr4:36334143-36334163 8.33e-04 20 chr4:39628694-39628714 9.66e-01 20 chr14:23120453-23120473 9.98e-01 20 chr22:22385440-22385460 5.83e-01 20 chr8:96103497-96103517 8.33e-01 20 chr14:106329195-10632921 7.38e-01 20 chr14:106172040-10617206 1.43e-01 20 chr2:136875648-136875668 9.84e-01 20 chr2:192542877-192542897 7.80e-01 20 chr1:182573479-182573499 9.26e-01 20 chr5:172198164-172198184 9.75e-01 20 chr11:65899603-65899623 8.96e-01 20 chr11:65194204-65194224 8.06e-03 [+5(8.60e-06)]_12 chr19:42055877-42055897 8.58e-01 20 chr12:49582834-49582854 4.72e-01 20 chr1:161677034-161677054 1.88e-02 3_[+4(9.06e-06)]_9 chr2:30454420-30454440 3.67e-01 20 chr6:33043787-33043807 1.20e-04 3_[+2(6.91e-06)]_9 chr19:35820109-35820129 9.34e-01 20 chr6:27841234-27841254 9.08e-02 20 chr5:149791268-149791288 9.31e-01 20 chr3:112100791-112100811 5.75e-02 20 chr12:56615830-56615850 6.26e-01 20 chr1:149514219-149514239 3.72e-02 20 chr14:96180427-96180447 2.09e-02 10_[+1(1.83e-05)]_2 chr2:121832835-121832855 5.33e-01 20 chr22:23244032-23244052 9.37e-02 20 chr6:30583915-30583935 2.57e-02 20 chrX:41193450-41193470 8.45e-02 20 chr17:33700599-33700619 6.51e-01 20 chr5:149780030-149780050 3.98e-03 3_[+4(1.53e-05)]_9 chr6:31543380-31543400 8.90e-01 20 chr10:32345275-32345295 8.61e-01 20 chr14:102553338-10255335 9.97e-01 20 chr14:51135365-51135385 4.23e-04 20 chr6:27835169-27835189 7.30e-01 20 chr6:34204465-34204485 8.75e-01 20 chrX:135962817-135962837 9.94e-01 20 chr20:2853955-2853975 9.94e-01 20 chr16:57392728-57392748 7.12e-01 20 chr1:46049746-46049766 8.79e-02 20 chr7:127032723-127032743 7.73e-02 6_[+1(9.73e-05)]_6 chr8:94753203-94753223 9.89e-01 20 chr6:32605181-32605201 2.70e-01 20 chr6:26250711-26250731 7.11e-01 20 chr11:82868216-82868236 6.76e-01 20 chr12:92757411-92757431 5.70e-01 20 chr8:103876347-103876367 6.45e-01 20 chr21:26874041-26874061 3.90e-03 20 chr1:145443077-145443097 6.51e-01 20 chr8:101734293-101734313 9.61e-01 20 chr14:50359841-50359861 1.00e+00 20 chr14:53173709-53173729 9.25e-01 20 chr5:151138111-151138131 9.95e-01 20 chr2:232573468-232573488 1.00e+00 20 chr17:18967127-18967147 2.43e-02 20 chr6:26240697-26240717 7.98e-01 20 chr6:31324905-31324925 1.00e+00 20 chr7:28450283-28450303 3.22e-01 20 chr1:28996421-28996441 1.00e+00 20 chr5:133512605-133512625 8.35e-01 20 chr2:85132808-85132828 7.45e-02 20 chr17:39834949-39834969 6.99e-01 20 chr8:82598503-82598523 3.09e-02 20 chr5:149791051-149791071 6.88e-01 20 chr12:53601002-53601022 2.41e-01 20 chr6:27833452-27833472 7.81e-01 20 chrX:23801341-23801361 9.61e-01 20 chr7:5632455-5632475 1.00e+00 20 chr5:150593710-150593730 2.22e-01 20 chr6:146057098-146057118 5.94e-02 20 chr6:156973630-156973650 6.28e-02 20 chr2:37862435-37862455 4.37e-02 20 chr1:156698262-156698282 9.99e-01 20 chr3:49058889-49058909 2.20e-02 11_[+4(2.84e-05)]_1 chr5:53606558-53606578 5.37e-01 20 chr2:191745559-191745579 9.99e-01 20 chr12:6643716-6643736 1.04e-02 20 chr17:38718371-38718391 3.49e-02 20 chr2:231815817-231815837 9.90e-01 20 chr2:86426599-86426619 9.95e-01 20 chr6:32557533-32557553 1.00e+00 20 chr11:61735034-61735054 9.79e-01 20 chr17:79479765-79479785 9.56e-01 20 chr2:68666144-68666164 9.93e-01 20 chr5:142594146-142594166 9.37e-01 20 chr17:37026358-37026378 9.88e-01 20 chr4:10118735-10118755 6.52e-05 12_[+5(7.04e-05)] chr6:31320643-31320663 8.21e-04 20 chr6:32977312-32977332 7.88e-02 20 chr13:95892476-95892496 1.06e-01 20 chr19:49996124-49996144 6.45e-01 20 chr2:70475695-70475715 2.97e-01 20 chr17:6939069-6939089 7.25e-01 20 chr1:182808517-182808537 1.71e-03 3_[+5(8.60e-06)]_9 chr1:23885930-23885950 7.45e-01 20 chr3:194406626-194406646 9.13e-01 20 chr20:2633313-2633333 9.97e-01 20 chr6:391793-391813 1.00e+00 20 chr2:152685168-152685188 9.99e-01 20 chr13:99959638-99959658 1.54e-01 20 chr21:26946274-26946294 5.02e-01 20 chr14:106692514-10669253 4.76e-01 20 chr6:27107399-27107419 2.47e-02 20 chr1:203274680-203274700 5.33e-01 20 chr2:33702706-33702726 1.29e-01 20 chr19:59055831-59055851 1.00e+00 20 chr4:57845065-57845085 5.45e-01 20 chr11:122932797-12293281 8.89e-01 20 chr18:57567265-57567285 9.94e-01 20 chr8:74205806-74205826 8.17e-01 20 chr21:26942252-26942272 9.40e-01 20 chr1:150207263-150207283 2.47e-03 3_[+3(8.54e-06)]_9 chr14:69259724-69259744 3.67e-03 [+1(1.83e-05)]_12 chr7:5565132-5565152 1.51e-01 20 chr2:176046384-176046404 1.00e+00 20 chr17:56084551-56084571 1.00e+00 20 chr1:211556225-211556245 3.93e-01 20 chr1:109234895-109234915 1.00e+00 20 chr19:47291807-47291827 9.56e-01 20 chr1:148604913-148604933 9.56e-01 20 chrX:153626754-153626774 3.79e-01 20 chr6:44355486-44355506 3.33e-01 20 chr2:201729319-201729339 4.08e-01 20 chr1:147735923-147735943 7.41e-01 20 chr9:131314868-131314888 9.82e-01 20 chr11:615904-615924 8.08e-01 20 chr16:4303722-4303742 9.92e-01 20 chr17:11900972-11900992 2.52e-01 20 chr19:42382060-42382080 1.75e-02 20 chr7:44084138-44084158 6.69e-01 20 chr17:48943677-48943697 9.61e-01 20 chr4:185202117-185202137 9.81e-01 20 chr6:86388409-86388429 6.71e-01 20 chr11:93474624-93474644 9.64e-01 20 chr2:231808525-231808545 7.45e-01 20 chr5:43313445-43313465 6.76e-01 20 chr9:123688375-123688395 7.06e-03 20 chr17:28443888-28443908 9.97e-01 20 chr12:69004446-69004466 7.55e-01 20 chr17:18965565-18965585 1.81e-01 20 chr1:47069866-47069886 1.00e+00 20 chr5:72794250-72794270 7.40e-02 20 chr4:57333778-57333798 6.89e-01 20 chr19:50432502-50432522 3.30e-01 20 chr21:26936984-26937004 7.19e-05 11_[+3(1.44e-05)]_1 chr7:98972372-98972392 9.38e-01 20 chr6:21593997-21594017 3.87e-02 20 chr3:52312607-52312627 9.98e-01 20 chr19:49956921-49956941 9.58e-02 20 chr10:70847886-70847906 6.14e-01 20 chr5:170814869-170814889 6.10e-01 20 chrX:100646036-100646056 6.71e-01 20 chr1:37940192-37940212 9.63e-01 20 chr6:31802697-31802717 9.98e-01 20 chr6:29910325-29910345 8.35e-01 20 chr19:5828374-5828394 8.11e-01 20 chr6:89790503-89790523 1.08e-03 10_[+1(6.25e-05)]_2 chr10:73975827-73975847 2.28e-01 20 chr1:17222703-17222723 5.86e-02 20 chr9:74980080-74980100 7.87e-01 20 chr20:42086532-42086552 4.40e-01 20 chr5:141348767-141348787 6.96e-01 20 chr15:69745177-69745197 5.37e-01 20 chr5:34008361-34008381 1.84e-03 11_[+4(3.47e-05)]_1 chr17:57915316-57915336 1.91e-01 20 chr7:39606042-39606062 9.66e-01 20 chr10:27444079-27444099 1.62e-01 20 chr17:25621161-25621181 1.02e-01 20 chrX:118602439-118602459 9.71e-01 20 chr17:56416569-56416589 3.31e-01 20 chr1:147994169-147994189 9.04e-04 4_[+4(1.53e-05)]_8 chr1:76190455-76190475 8.72e-01 20 chr19:24270056-24270076 9.62e-03 20 chr17:57970509-57970529 8.17e-01 20 chr7:5566086-5566106 1.00e+00 20 chr12:9913464-9913484 5.02e-03 20 chr17:39845174-39845194 6.02e-01 20 chr21:40721656-40721676 1.38e-03 [+2(2.83e-06)]_12 chr3:185655747-185655767 5.88e-01 20 chr3:156392412-156392432 8.21e-02 12_[+1(8.43e-05)] chr14:24564762-24564782 3.07e-01 20 chr21:26940734-26940754 9.90e-01 20 chr17:62502355-62502375 9.58e-01 20 chr6:28891752-28891772 6.00e-01 20 chr22:24200106-24200126 7.88e-01 20 chr19:1269343-1269363 4.91e-01 20 chr6:31239836-31239856 9.98e-02 20 chr1:76251966-76251986 5.68e-01 20 chrX:12995707-12995727 4.93e-01 20 chr17:34136522-34136542 8.41e-02 20 chr16:30546430-30546450 9.00e-02 20 chr11:71823957-71823977 1.30e-01 20 chr19:46195143-46195163 9.43e-01 20 chr2:220071354-220071374 9.92e-01 20 chr6:137112701-137112721 9.01e-01 20 chr3:150320944-150320964 9.92e-01 20 chr19:55919139-55919159 9.23e-01 20 chr7:98923398-98923418 8.59e-01 20 chr3:143690919-143690939 1.00e+00 20 chr13:103426241-10342626 1.00e+00 20 chr9:108320311-108320331 9.95e-01 20 chr21:15918605-15918625 1.16e-01 20 chr13:45915287-45915307 1.00e+00 20 chr11:124823837-12482385 9.73e-01 20 chr11:62432782-62432802 9.97e-01 20 chr2:32264954-32264974 8.36e-02 11_[+1(6.25e-05)]_1 chr3:196255855-196255875 7.00e-01 20 chr16:2011156-2011176 9.95e-01 20 chr6:139695731-139695751 7.15e-01 20 chr5:86708642-86708662 9.23e-02 9_[+4(2.84e-05)]_3 chr5:71604118-71604138 9.96e-01 20 chr4:37828330-37828350 9.70e-01 20 chr19:23457011-23457031 9.31e-01 20 chr10:120938256-12093827 1.41e-01 20 chr6:114179931-114179951 3.80e-01 20 chr3:9439090-9439110 7.87e-01 20 chr14:21776890-21776910 8.09e-01 20 chr1:160596862-160596882 6.94e-01 20 chr19:6531060-6531080 5.89e-01 20 chr10:74033707-74033727 9.55e-01 20 chr7:66093564-66093584 8.95e-01 20 chr6:43543945-43543965 2.84e-01 20 chr1:160604405-160604425 3.11e-01 20 chr2:232573249-232573269 1.96e-03 8_[+3(8.54e-06)]_4 chr14:23001185-23001205 2.31e-01 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n04.farnam.hpc.yale.internal ********************************************************************************