******************************************************************************** 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/SPI1.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr4:86647232-86647252 1.0000 20 chr2:225503165-225503185 1.0000 20 chr2:218113571-218113591 1.0000 20 chr6:36660183-36660203 1.0000 20 chr1:230286216-230286236 1.0000 20 chr6:3356681-3356701 1.0000 20 chr6:130427679-130427699 1.0000 20 chr4:24770434-24770454 1.0000 20 chr1:154131017-154131037 1.0000 20 chr12:108130871-10813089 1.0000 20 chr6:42335561-42335581 1.0000 20 chr12:124876024-12487604 1.0000 20 chr10:14650646-14650666 1.0000 20 chr1:79106363-79106383 1.0000 20 chr6:43651963-43651983 1.0000 20 chr1:59878609-59878629 1.0000 20 chr1:157087392-157087412 1.0000 20 chr8:145052831-145052851 1.0000 20 chr3:48717337-48717357 1.0000 20 chr9:78070755-78070775 1.0000 20 chr20:36432504-36432524 1.0000 20 chr12:107147439-10714745 1.0000 20 chr8:52365177-52365197 1.0000 20 chr12:115760213-11576023 1.0000 20 chr3:72572715-72572735 1.0000 20 chr15:49284895-49284915 1.0000 20 chr2:112761967-112761987 1.0000 20 chr17:55700354-55700374 1.0000 20 chr9:73013240-73013260 1.0000 20 chr3:107821474-107821494 1.0000 20 chr3:72678559-72678579 1.0000 20 chr2:58259568-58259588 1.0000 20 chr18:44946689-44946709 1.0000 20 chr15:61088261-61088281 1.0000 20 chr13:51385345-51385365 1.0000 20 chr1:200623983-200624003 1.0000 20 chr8:11716366-11716386 1.0000 20 chr22:32186298-32186318 1.0000 20 chr1:112048611-112048631 1.0000 20 chr7:100485388-100485408 1.0000 20 chr18:46242167-46242187 1.0000 20 chr17:6999177-6999197 1.0000 20 chr9:136343190-136343210 1.0000 20 chr1:21617358-21617378 1.0000 20 chr1:155940543-155940563 1.0000 20 chrX:54722432-54722452 1.0000 20 chr3:111886756-111886776 1.0000 20 chr9:140703662-140703682 1.0000 20 chr13:113238060-11323808 1.0000 20 chr9:137297505-137297525 1.0000 20 chr10:112627421-11262744 1.0000 20 chr5:131803551-131803571 1.0000 20 chr1:198101386-198101406 1.0000 20 chr15:69959383-69959403 1.0000 20 chr13:77014927-77014947 1.0000 20 chr14:25142408-25142428 1.0000 20 chr16:85089199-85089219 1.0000 20 chr2:8256975-8256995 1.0000 20 chr6:36973409-36973429 1.0000 20 chr7:25127696-25127716 1.0000 20 chr16:17621022-17621042 1.0000 20 chr9:567568-567588 1.0000 20 chr3:143314447-143314467 1.0000 20 chr19:15437851-15437871 1.0000 20 chr1:56938717-56938737 1.0000 20 chr12:47706734-47706754 1.0000 20 chr5:131823819-131823839 1.0000 20 chr6:44232113-44232133 1.0000 20 chr8:55421033-55421053 1.0000 20 chr18:45497274-45497294 1.0000 20 chr14:95700173-95700193 1.0000 20 chr15:41139701-41139721 1.0000 20 chr19:19555822-19555842 1.0000 20 chr2:225759219-225759239 1.0000 20 chr17:55945514-55945534 1.0000 20 chr1:110448965-110448985 1.0000 20 chr6:15288102-15288122 1.0000 20 chr1:28454326-28454346 1.0000 20 chr6:2659295-2659315 1.0000 20 chr6:24575263-24575283 1.0000 20 chr16:11862854-11862874 1.0000 20 chr16:81786017-81786037 1.0000 20 chr10:110610110-11061013 1.0000 20 chr1:112050360-112050380 1.0000 20 chr16:71953125-71953145 1.0000 20 chr1:226132807-226132827 1.0000 20 chr17:46372947-46372967 1.0000 20 chrX:68248404-68248424 1.0000 20 chr3:142841651-142841671 1.0000 20 chr12:932641-932661 1.0000 20 chr4:155406436-155406456 1.0000 20 chr2:240175139-240175159 1.0000 20 chr14:65785576-65785596 1.0000 20 chr1:184716601-184716621 1.0000 20 chr5:148211421-148211441 1.0000 20 chr7:20153218-20153238 1.0000 20 chr1:167469063-167469083 1.0000 20 chr8:29452131-29452151 1.0000 20 chr11:10783940-10783960 1.0000 20 chr17:26133078-26133098 1.0000 20 chr1:45189257-45189277 1.0000 20 chr11:123418119-12341813 1.0000 20 chr7:47640882-47640902 1.0000 20 chr17:56582537-56582557 1.0000 20 chr9:108147837-108147857 1.0000 20 chr2:62372915-62372935 1.0000 20 chr8:103942453-103942473 1.0000 20 chr20:53250595-53250615 1.0000 20 chr1:26199398-26199418 1.0000 20 chr1:206329088-206329108 1.0000 20 chr1:172154502-172154522 1.0000 20 chr3:6721427-6721447 1.0000 20 chr10:112477906-11247792 1.0000 20 chr1:32805315-32805335 1.0000 20 chr18:55682429-55682449 1.0000 20 chr2:105593116-105593136 1.0000 20 chr16:82685605-82685625 1.0000 20 chr8:18704614-18704634 1.0000 20 chr3:193559907-193559927 1.0000 20 chr15:52774260-52774280 1.0000 20 chr6:166756813-166756833 1.0000 20 chr17:73567479-73567499 1.0000 20 chr11:44372710-44372730 1.0000 20 chr6:133078987-133079007 1.0000 20 chr2:64488107-64488127 1.0000 20 chr20:9596932-9596952 1.0000 20 chr16:49433718-49433738 1.0000 20 chr1:21291555-21291575 1.0000 20 chr18:72885157-72885177 1.0000 20 chr7:76033579-76033599 1.0000 20 chrX:29549624-29549644 1.0000 20 chr13:33825682-33825702 1.0000 20 chr14:71270210-71270230 1.0000 20 chr13:107146089-10714610 1.0000 20 chr8:102972882-102972902 1.0000 20 chr5:56326199-56326219 1.0000 20 chr6:112045844-112045864 1.0000 20 chr3:115757527-115757547 1.0000 20 chr8:30182173-30182193 1.0000 20 chr3:169872439-169872459 1.0000 20 chr12:3732358-3732378 1.0000 20 chr12:68152085-68152105 1.0000 20 chrX:97164424-97164444 1.0000 20 chr1:161688767-161688787 1.0000 20 chr12:102335546-10233556 1.0000 20 chr7:24911571-24911591 1.0000 20 chr11:2548437-2548457 1.0000 20 chr10:52212550-52212570 1.0000 20 chr1:46509349-46509369 1.0000 20 chr6:1482758-1482778 1.0000 20 chr20:55297365-55297385 1.0000 20 chr5:114598176-114598196 1.0000 20 chr6:143273923-143273943 1.0000 20 chr9:77704020-77704040 1.0000 20 chr5:1490652-1490672 1.0000 20 chr5:6237118-6237138 1.0000 20 chr5:138430338-138430358 1.0000 20 chr7:30560179-30560199 1.0000 20 chr1:112158701-112158721 1.0000 20 chr2:148447311-148447331 1.0000 20 chr1:25889098-25889118 1.0000 20 chr21:43669538-43669558 1.0000 20 chr21:43481672-43481692 1.0000 20 chr5:106709747-106709767 1.0000 20 chr18:56204034-56204054 1.0000 20 chr11:93246324-93246344 1.0000 20 chr3:15092090-15092110 1.0000 20 chr11:131056631-13105665 1.0000 20 chr19:35950058-35950078 1.0000 20 chr1:100988735-100988755 1.0000 20 chr3:188139792-188139812 1.0000 20 chr10:6110513-6110533 1.0000 20 chr19:43001723-43001743 1.0000 20 chr17:45277567-45277587 1.0000 20 chr8:42189087-42189107 1.0000 20 chr16:2737385-2737405 1.0000 20 chr8:74748103-74748123 1.0000 20 chr10:65458348-65458368 1.0000 20 chr20:12990390-12990410 1.0000 20 chr15:84624876-84624896 1.0000 20 chr2:118813887-118813907 1.0000 20 chr13:46280263-46280283 1.0000 20 chr8:123095277-123095297 1.0000 20 chr2:197114736-197114756 1.0000 20 chr5:53765609-53765629 1.0000 20 chr6:109127206-109127226 1.0000 20 chr9:97920262-97920282 1.0000 20 chr8:124191295-124191315 1.0000 20 chr11:126944586-12694460 1.0000 20 chr11:45053873-45053893 1.0000 20 chr2:194969593-194969613 1.0000 20 chr19:14551026-14551046 1.0000 20 chr14:100763796-10076381 1.0000 20 chr20:32712449-32712469 1.0000 20 chr14:30327691-30327711 1.0000 20 chr22:42793449-42793469 1.0000 20 chr6:13397694-13397714 1.0000 20 chr14:23259653-23259673 1.0000 20 chr3:3130843-3130863 1.0000 20 chr20:62884246-62884266 1.0000 20 chr5:139664437-139664457 1.0000 20 chr2:187778796-187778816 1.0000 20 chrX:112004925-112004945 1.0000 20 chr3:47267329-47267349 1.0000 20 chr6:33029914-33029934 1.0000 20 chr1:226035918-226035938 1.0000 20 chr6:31695476-31695496 1.0000 20 chr18:12050461-12050481 1.0000 20 chr13:33685278-33685298 1.0000 20 chr5:141340529-141340549 1.0000 20 chr1:150738299-150738319 1.0000 20 chr2:55094333-55094353 1.0000 20 chr12:131363866-13136388 1.0000 20 chr12:29305345-29305365 1.0000 20 chr13:37547929-37547949 1.0000 20 chr10:116258554-11625857 1.0000 20 chr3:56951883-56951903 1.0000 20 chr6:47210459-47210479 1.0000 20 chr14:68429017-68429037 1.0000 20 chr15:91525087-91525107 1.0000 20 chr10:3078567-3078587 1.0000 20 chr5:169206197-169206217 1.0000 20 chr3:156059970-156059990 1.0000 20 chr17:29285430-29285450 1.0000 20 chr17:29818567-29818587 1.0000 20 chr13:97424435-97424455 1.0000 20 chr4:26887655-26887675 1.0000 20 chr2:102650085-102650105 1.0000 20 chr14:70160127-70160147 1.0000 20 chr18:54519209-54519229 1.0000 20 chr3:39297293-39297313 1.0000 20 chr4:55181957-55181977 1.0000 20 chr2:47563929-47563949 1.0000 20 chr16:10023408-10023428 1.0000 20 chr9:22030195-22030215 1.0000 20 chr6:134694767-134694787 1.0000 20 chr3:189538365-189538385 1.0000 20 chr15:89984830-89984850 1.0000 20 chr11:72526881-72526901 1.0000 20 chr14:100481861-10048188 1.0000 20 chr10:79409444-79409464 1.0000 20 chr22:40888441-40888461 1.0000 20 chr4:17597369-17597389 1.0000 20 chr19:1904482-1904502 1.0000 20 chr2:219014743-219014763 1.0000 20 chr16:50743344-50743364 1.0000 20 chr5:96232711-96232731 1.0000 20 chr11:65145874-65145894 1.0000 20 chr22:40446415-40446435 1.0000 20 chr11:63143081-63143101 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_SPI1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/SPI1.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 0.273 C 0.227 G 0.223 T 0.277 Background letter frequencies (from file dataset with add-one prior applied): A 0.273 C 0.227 G 0.223 T 0.277 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GAGGAAGT MEME-1 width = 8 sites = 38 llr = 351 E-value = 2.9e-049 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAGGAAGT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 17::aa:: pos.-specific C ::::::31 probability G 93aa::7: matrix T :::::::9 bits 2.2 * 1.9 ** * 1.7 * **** 1.5 * **** * Relative 1.3 * ****** Entropy 1.1 ******** (13.3 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GAGGAAGT consensus G C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGGAAGT MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr14:100481861-10048188 2 1.39e-05 A GAGGAAGT GAATCCAGAT chr11:72526881-72526901 4 1.39e-05 AAA GAGGAAGT GACTGTTGA chr3:56951883-56951903 4 1.39e-05 AAG GAGGAAGT GAAATCACT chr13:37547929-37547949 4 1.39e-05 aaa gaggaagt gaaaatagc chr6:31695476-31695496 4 1.39e-05 AAA GAGGAAGT GTTCGAGTC chr14:100763796-10076381 8 1.39e-05 CTGGAAA GAGGAAGT GAATG chr19:14551026-14551046 2 1.39e-05 A GAGGAAGT GGCAGCCGAG chr1:112158701-112158721 2 1.39e-05 a gaggaagt caggaagagg chr11:2548437-2548457 10 1.39e-05 CTTGGAAAG GAGGAAGT GAA chr7:76033579-76033599 10 1.39e-05 attcagaaa gaggaagt ggc chr11:10783940-10783960 10 1.39e-05 TAGAGAAAT GAGGAAGT GGT chr1:184716601-184716621 3 1.39e-05 AA GAGGAAGT GTAAATTCTA chr2:225759219-225759239 8 1.39e-05 TCAGAAA GAGGAAGT CCTGA chr8:55421033-55421053 2 1.39e-05 A GAGGAAGT GAGAGCCCTT chr12:47706734-47706754 10 1.39e-05 TCTTGGAAA GAGGAAGT GAA chr18:46242167-46242187 11 1.39e-05 aagatcaaaa gaggaagt gg chr11:131056631-13105665 6 2.53e-05 CAAAA GGGGAAGT GCGGGGA chr6:166756813-166756833 1 2.53e-05 . GGGGAAGT GGCATTTTTC chr6:42335561-42335581 11 2.53e-05 AGCACAGAAA GGGGAAGT GA chr6:36660183-36660203 10 2.53e-05 CACCAGAAA GGGGAAGT GCC chr15:89984830-89984850 8 3.95e-05 CTTGGga gaggaact gagag chr17:29818567-29818587 5 3.95e-05 aaaa gaggaact gcaagggc chr17:29285430-29285450 10 3.95e-05 aaagaaaaa gaggaaCT GAA chr10:116258554-11625857 8 3.95e-05 ggcaaaa gaggaact gatag chr20:9596932-9596952 13 3.95e-05 tattacagat gaggaact chr2:105593116-105593136 4 3.95e-05 att gaggaact gaaaaggca chr17:56582537-56582557 6 3.95e-05 CAAAA GAGGAACT GAGAAGC chr20:36432504-36432524 8 3.95e-05 AGCAAAA GAGGAACT GGCCT chr11:45053873-45053893 12 5.11e-05 aggtaaaaaa ggggaact g chr3:15092090-15092110 12 5.11e-05 TCAGTTGGGT GGGGAACT G chr4:26887655-26887675 10 6.82e-05 TTGACAAAC AAGGAAGT TGT chr18:45497274-45497294 4 7.96e-05 CAA GAGGAAGC TAAGAAAAA chr1:172154502-172154522 10 9.35e-05 ACAAGACAA AGGGAAGT GAA chr2:58259568-58259588 5 9.35e-05 gaaa agggaagt gagccctc chr14:25142408-25142428 12 1.20e-04 GAAGTGGAAA GGGGAAGC A chr11:123418119-12341813 1 1.32e-04 . GAGGGAGT CTGGACTGAG chr2:118813887-118813907 2 1.75e-04 A AGGGAACT GAAACTTGTT chr3:143314447-143314467 6 2.19e-04 ATGTA GGTGAAGT ATAGAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGGAAGT MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr14:100481861-10048188 1.4e-05 1_[+1]_11 chr11:72526881-72526901 1.4e-05 3_[+1]_9 chr3:56951883-56951903 1.4e-05 3_[+1]_9 chr13:37547929-37547949 1.4e-05 3_[+1]_9 chr6:31695476-31695496 1.4e-05 3_[+1]_9 chr14:100763796-10076381 1.4e-05 7_[+1]_5 chr19:14551026-14551046 1.4e-05 1_[+1]_11 chr1:112158701-112158721 1.4e-05 1_[+1]_11 chr11:2548437-2548457 1.4e-05 9_[+1]_3 chr7:76033579-76033599 1.4e-05 9_[+1]_3 chr11:10783940-10783960 1.4e-05 9_[+1]_3 chr1:184716601-184716621 1.4e-05 2_[+1]_10 chr2:225759219-225759239 1.4e-05 7_[+1]_5 chr8:55421033-55421053 1.4e-05 1_[+1]_11 chr12:47706734-47706754 1.4e-05 9_[+1]_3 chr18:46242167-46242187 1.4e-05 10_[+1]_2 chr11:131056631-13105665 2.5e-05 5_[+1]_7 chr6:166756813-166756833 2.5e-05 [+1]_12 chr6:42335561-42335581 2.5e-05 10_[+1]_2 chr6:36660183-36660203 2.5e-05 9_[+1]_3 chr15:89984830-89984850 4e-05 7_[+1]_5 chr17:29818567-29818587 4e-05 4_[+1]_8 chr17:29285430-29285450 4e-05 9_[+1]_3 chr10:116258554-11625857 4e-05 7_[+1]_5 chr20:9596932-9596952 4e-05 12_[+1] chr2:105593116-105593136 4e-05 3_[+1]_9 chr17:56582537-56582557 4e-05 5_[+1]_7 chr20:36432504-36432524 4e-05 7_[+1]_5 chr11:45053873-45053893 5.1e-05 11_[+1]_1 chr3:15092090-15092110 5.1e-05 11_[+1]_1 chr4:26887655-26887675 6.8e-05 9_[+1]_3 chr18:45497274-45497294 8e-05 3_[+1]_9 chr1:172154502-172154522 9.4e-05 9_[+1]_3 chr2:58259568-58259588 9.4e-05 4_[+1]_8 chr14:25142408-25142428 0.00012 11_[+1]_1 chr11:123418119-12341813 0.00013 [+1]_12 chr2:118813887-118813907 0.00017 1_[+1]_11 chr3:143314447-143314467 0.00022 5_[+1]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGGAAGT MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAGGAAGT width=8 seqs=38 chr14:100481861-10048188 ( 2) GAGGAAGT 1 chr11:72526881-72526901 ( 4) GAGGAAGT 1 chr3:56951883-56951903 ( 4) GAGGAAGT 1 chr13:37547929-37547949 ( 4) GAGGAAGT 1 chr6:31695476-31695496 ( 4) GAGGAAGT 1 chr14:100763796-10076381 ( 8) GAGGAAGT 1 chr19:14551026-14551046 ( 2) GAGGAAGT 1 chr1:112158701-112158721 ( 2) GAGGAAGT 1 chr11:2548437-2548457 ( 10) GAGGAAGT 1 chr7:76033579-76033599 ( 10) GAGGAAGT 1 chr11:10783940-10783960 ( 10) GAGGAAGT 1 chr1:184716601-184716621 ( 3) GAGGAAGT 1 chr2:225759219-225759239 ( 8) GAGGAAGT 1 chr8:55421033-55421053 ( 2) GAGGAAGT 1 chr12:47706734-47706754 ( 10) GAGGAAGT 1 chr18:46242167-46242187 ( 11) GAGGAAGT 1 chr11:131056631-13105665 ( 6) GGGGAAGT 1 chr6:166756813-166756833 ( 1) GGGGAAGT 1 chr6:42335561-42335581 ( 11) GGGGAAGT 1 chr6:36660183-36660203 ( 10) GGGGAAGT 1 chr15:89984830-89984850 ( 8) GAGGAACT 1 chr17:29818567-29818587 ( 5) GAGGAACT 1 chr17:29285430-29285450 ( 10) GAGGAACT 1 chr10:116258554-11625857 ( 8) GAGGAACT 1 chr20:9596932-9596952 ( 13) GAGGAACT 1 chr2:105593116-105593136 ( 4) GAGGAACT 1 chr17:56582537-56582557 ( 6) GAGGAACT 1 chr20:36432504-36432524 ( 8) GAGGAACT 1 chr11:45053873-45053893 ( 12) GGGGAACT 1 chr3:15092090-15092110 ( 12) GGGGAACT 1 chr4:26887655-26887675 ( 10) AAGGAAGT 1 chr18:45497274-45497294 ( 4) GAGGAAGC 1 chr1:172154502-172154522 ( 10) AGGGAAGT 1 chr2:58259568-58259588 ( 5) AGGGAAGT 1 chr14:25142408-25142428 ( 12) GGGGAAGC 1 chr11:123418119-12341813 ( 1) GAGGGAGT 1 chr2:118813887-118813907 ( 2) AGGGAACT 1 chr3:143314447-143314467 ( 6) GGTGAAGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGGAAGT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 7.30664 E= 2.9e-049 -137 -1189 200 -1189 138 -1189 38 -1189 -1189 -1189 213 -339 -1189 -1189 216 -1189 183 -1189 -308 -1189 187 -1189 -1189 -1189 -1189 35 167 -1189 -1189 -211 -1189 177 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGGAAGT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 2.9e-049 0.105263 0.000000 0.894737 0.000000 0.710526 0.000000 0.289474 0.000000 0.000000 0.000000 0.973684 0.026316 0.000000 0.000000 1.000000 0.000000 0.973684 0.000000 0.026316 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.289474 0.710526 0.000000 0.000000 0.052632 0.000000 0.947368 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAGGAAGT MEME-1 regular expression -------------------------------------------------------------------------------- G[AG]GGAA[GC]T -------------------------------------------------------------------------------- Time 2.03 secs. ******************************************************************************** ******************************************************************************** MOTIF TCACTTCC MEME-2 width = 8 sites = 38 llr = 324 E-value = 1.0e-036 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCACTTCC MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::9::::: pos.-specific C 2a18::a8 probability G 1::1:::: matrix T 7::2aa:2 bits 2.2 1.9 * ** 1.7 * *** 1.5 ** **** Relative 1.3 ** **** Entropy 1.1 ******* (12.3 bits) 0.9 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TCACTTCC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCACTTCC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr13:33685278-33685298 13 1.54e-05 TTTATTATTT TCACTTCC chr2:187778796-187778816 9 1.54e-05 ataattga tcacttcc tctt chr5:139664437-139664457 9 1.54e-05 CTGCTATT TCACTTCC TCAT chr8:124191295-124191315 9 1.54e-05 gagaacag tcacttcc tctt chr13:46280263-46280283 3 1.54e-05 TT TCACTTCC CCTTTTCCTT chr3:193559907-193559927 6 1.54e-05 TCATC TCACTTCC TCATTTG chr8:18704614-18704634 1 1.54e-05 . TCACTTCC GCTGCTGAGG chr12:932641-932661 10 1.54e-05 tgtacagtt tcacttcc tat chr1:112050360-112050380 4 1.54e-05 TGC TCACTTCC TCTTGGCCC chr6:2659295-2659315 5 1.54e-05 attc tcacttcc tgtttttc chrX:54722432-54722452 8 1.54e-05 AAGCCTT TCACTTCC TCTTT chr8:11716366-11716386 4 1.54e-05 TTT TCACTTCC CTTTATATA chr15:49284895-49284915 13 1.54e-05 TCATCTGGCT TCACTTCC chr3:72572715-72572735 6 1.54e-05 CCATG TCACTTCC TCTTTCC chr1:79106363-79106383 1 1.54e-05 . TCACTTCC TCTTTTTCTT chr2:102650085-102650105 1 2.80e-05 . CCACTTCC TCATTCTTCA chr16:81786017-81786037 13 2.80e-05 TGGCTTCTGA CCACTTCC chr6:36973409-36973429 5 2.80e-05 GGGA CCACTTCC TCTTTCTT chr16:85089199-85089219 12 2.80e-05 tcagccctca ccacttcc c chr4:17597369-17597389 11 6.56e-05 TTGATTTGTT TCACTTCT GC chr3:156059970-156059990 5 6.56e-05 CCTT TCACTTCT GCATTTCT chr12:131363866-13136388 2 9.36e-05 T TCAGTTCC CCTCCTTGAA chr5:138430338-138430358 13 9.36e-05 ttactcagtt tcagttcc chr14:71270210-71270230 5 9.36e-05 CTAT TCCCTTCC TTACTCAG chr1:21617358-21617378 3 9.36e-05 TT TCAGTTCC CCTTTCTAGC chr15:41139701-41139721 12 1.06e-04 GGAGCAGCTT GCACTTcc t chr2:225503165-225503185 6 1.06e-04 CTTCA GCACTTCC TCATTTT chr16:50743344-50743364 4 1.21e-04 TCC CCATTTCC TGAAAGGGG chr11:65145874-65145894 9 1.37e-04 CACAGTCC CCACTTCT GCTT chr9:22030195-22030215 8 1.52e-04 AGACAAT ACACTTCC TCTTT chr6:13397694-13397714 5 1.88e-04 TCTT TCACCTCC AGGCCCTC chr6:109127206-109127226 3 2.26e-04 CC TCATTTCT ACTTCACCAG chr16:71953125-71953145 8 2.26e-04 ccctttt tcatttct tacca chr10:110610110-11061013 11 2.26e-04 gagctagttt tCATTTCT TT chr5:131823819-131823839 7 2.26e-04 AAAGGC TGACTTCC CCTTTT chr2:55094333-55094353 8 2.60e-04 CTCTTTC TCCTTTCC CCTAA chr9:137297505-137297525 13 2.60e-04 GTGCGTGAGT TCCTTTCC chr2:47563929-47563949 3 4.16e-04 GA CCACTTTC CACAAATTTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCACTTCC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr13:33685278-33685298 1.5e-05 12_[+2] chr2:187778796-187778816 1.5e-05 8_[+2]_4 chr5:139664437-139664457 1.5e-05 8_[+2]_4 chr8:124191295-124191315 1.5e-05 8_[+2]_4 chr13:46280263-46280283 1.5e-05 2_[+2]_10 chr3:193559907-193559927 1.5e-05 5_[+2]_7 chr8:18704614-18704634 1.5e-05 [+2]_12 chr12:932641-932661 1.5e-05 9_[+2]_3 chr1:112050360-112050380 1.5e-05 3_[+2]_9 chr6:2659295-2659315 1.5e-05 4_[+2]_8 chrX:54722432-54722452 1.5e-05 7_[+2]_5 chr8:11716366-11716386 1.5e-05 3_[+2]_9 chr15:49284895-49284915 1.5e-05 12_[+2] chr3:72572715-72572735 1.5e-05 5_[+2]_7 chr1:79106363-79106383 1.5e-05 [+2]_12 chr2:102650085-102650105 2.8e-05 [+2]_12 chr16:81786017-81786037 2.8e-05 12_[+2] chr6:36973409-36973429 2.8e-05 4_[+2]_8 chr16:85089199-85089219 2.8e-05 11_[+2]_1 chr4:17597369-17597389 6.6e-05 10_[+2]_2 chr3:156059970-156059990 6.6e-05 4_[+2]_8 chr12:131363866-13136388 9.4e-05 1_[+2]_11 chr5:138430338-138430358 9.4e-05 12_[+2] chr14:71270210-71270230 9.4e-05 4_[+2]_8 chr1:21617358-21617378 9.4e-05 2_[+2]_10 chr15:41139701-41139721 0.00011 11_[+2]_1 chr2:225503165-225503185 0.00011 5_[+2]_7 chr16:50743344-50743364 0.00012 3_[+2]_9 chr11:65145874-65145894 0.00014 8_[+2]_4 chr9:22030195-22030215 0.00015 7_[+2]_5 chr6:13397694-13397714 0.00019 4_[+2]_8 chr6:109127206-109127226 0.00023 2_[+2]_10 chr16:71953125-71953145 0.00023 7_[+2]_5 chr10:110610110-11061013 0.00023 10_[+2]_2 chr5:131823819-131823839 0.00023 6_[+2]_6 chr2:55094333-55094353 0.00026 7_[+2]_5 chr9:137297505-137297525 0.00026 12_[+2] chr2:47563929-47563949 0.00042 2_[+2]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCACTTCC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCACTTCC width=8 seqs=38 chr13:33685278-33685298 ( 13) TCACTTCC 1 chr2:187778796-187778816 ( 9) TCACTTCC 1 chr5:139664437-139664457 ( 9) TCACTTCC 1 chr8:124191295-124191315 ( 9) TCACTTCC 1 chr13:46280263-46280283 ( 3) TCACTTCC 1 chr3:193559907-193559927 ( 6) TCACTTCC 1 chr8:18704614-18704634 ( 1) TCACTTCC 1 chr12:932641-932661 ( 10) TCACTTCC 1 chr1:112050360-112050380 ( 4) TCACTTCC 1 chr6:2659295-2659315 ( 5) TCACTTCC 1 chrX:54722432-54722452 ( 8) TCACTTCC 1 chr8:11716366-11716386 ( 4) TCACTTCC 1 chr15:49284895-49284915 ( 13) TCACTTCC 1 chr3:72572715-72572735 ( 6) TCACTTCC 1 chr1:79106363-79106383 ( 1) TCACTTCC 1 chr2:102650085-102650105 ( 1) CCACTTCC 1 chr16:81786017-81786037 ( 13) CCACTTCC 1 chr6:36973409-36973429 ( 5) CCACTTCC 1 chr16:85089199-85089219 ( 12) CCACTTCC 1 chr4:17597369-17597389 ( 11) TCACTTCT 1 chr3:156059970-156059990 ( 5) TCACTTCT 1 chr12:131363866-13136388 ( 2) TCAGTTCC 1 chr5:138430338-138430358 ( 13) TCAGTTCC 1 chr14:71270210-71270230 ( 5) TCCCTTCC 1 chr1:21617358-21617378 ( 3) TCAGTTCC 1 chr15:41139701-41139721 ( 12) GCACTTCC 1 chr2:225503165-225503185 ( 6) GCACTTCC 1 chr16:50743344-50743364 ( 4) CCATTTCC 1 chr11:65145874-65145894 ( 9) CCACTTCT 1 chr9:22030195-22030215 ( 8) ACACTTCC 1 chr6:13397694-13397714 ( 5) TCACCTCC 1 chr6:109127206-109127226 ( 3) TCATTTCT 1 chr16:71953125-71953145 ( 8) TCATTTCT 1 chr10:110610110-11061013 ( 11) TCATTTCT 1 chr5:131823819-131823839 ( 7) TGACTTCC 1 chr2:55094333-55094353 ( 8) TCCTTTCC 1 chr9:137297505-137297525 ( 13) TCCTTTCC 1 chr2:47563929-47563949 ( 3) CCACTTTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCACTTCC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 7.85264 E= 1.0e-036 -337 -30 -208 141 -1189 210 -308 -1189 175 -152 -1189 -1189 -1189 175 -150 -81 -1189 -311 -1189 181 -1189 -1189 -1189 185 -1189 210 -1189 -339 -1189 189 -1189 -81 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCACTTCC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 38 E= 1.0e-036 0.026316 0.184211 0.052632 0.736842 0.000000 0.973684 0.026316 0.000000 0.921053 0.078947 0.000000 0.000000 0.000000 0.763158 0.078947 0.157895 0.000000 0.026316 0.000000 0.973684 0.000000 0.000000 0.000000 1.000000 0.000000 0.973684 0.000000 0.026316 0.000000 0.842105 0.000000 0.157895 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCACTTCC MEME-2 regular expression -------------------------------------------------------------------------------- TCACTTCC -------------------------------------------------------------------------------- Time 3.14 secs. ******************************************************************************** ******************************************************************************** MOTIF TTCCTCTT MEME-3 width = 8 sites = 15 llr = 141 E-value = 1.4e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTCCTCTT MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::::::21 pos.-specific C ::9a:a1: probability G ::1::::: matrix T aa::a:79 bits 2.2 * * 1.9 ** *** 1.7 ****** 1.5 ****** Relative 1.3 ****** * Entropy 1.1 ****** * (13.6 bits) 0.9 ****** * 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TTCCTCTT consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCTCTT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr10:79409444-79409464 1 1.91e-05 . ttcctctt tttagagtga chrX:112004925-112004945 6 1.91e-05 TTCTG TTCCTCTT GATTTGT chr9:97920262-97920282 3 1.91e-05 AT TTCCTCTT TTCAGATGAG chr3:115757527-115757547 2 1.91e-05 C TTCCTCTT TTAATTGAAG chr1:32805315-32805335 11 1.91e-05 CTGACTGGAG TTCCTCTT TC chr4:24770434-24770454 1 1.91e-05 . TTCCTCTT TTTGGAGCTT chr1:230286216-230286236 1 1.91e-05 . TTCCTCTT TCTGCCCGCT chr4:86647232-86647252 3 1.91e-05 AC TTCCTCTT TTCTAGTTTC chr9:136343190-136343210 1 3.79e-05 . TTCCTCAT TTCAGAGGAA chr2:112761967-112761987 4 3.79e-05 cac ttcctcat ttgaggatg chr3:47267329-47267349 1 5.35e-05 . ttcctcct ttatgttcag chr17:73567479-73567499 1 5.35e-05 . ttcctcct agagcagctg chr5:96232711-96232731 10 7.23e-05 CTTCCCTTT TTCCTCTA ACA chr15:91525087-91525107 11 9.10e-05 GTTCTTGATC TTGCTCTT GA chr22:40446415-40446435 4 1.10e-04 cag ttcctcaa attgcccaa -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCTCTT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr10:79409444-79409464 1.9e-05 [+3]_12 chrX:112004925-112004945 1.9e-05 5_[+3]_7 chr9:97920262-97920282 1.9e-05 2_[+3]_10 chr3:115757527-115757547 1.9e-05 1_[+3]_11 chr1:32805315-32805335 1.9e-05 10_[+3]_2 chr4:24770434-24770454 1.9e-05 [+3]_12 chr1:230286216-230286236 1.9e-05 [+3]_12 chr4:86647232-86647252 1.9e-05 2_[+3]_10 chr9:136343190-136343210 3.8e-05 [+3]_12 chr2:112761967-112761987 3.8e-05 3_[+3]_9 chr3:47267329-47267349 5.4e-05 [+3]_12 chr17:73567479-73567499 5.4e-05 [+3]_12 chr5:96232711-96232731 7.2e-05 9_[+3]_3 chr15:91525087-91525107 9.1e-05 10_[+3]_2 chr22:40446415-40446435 0.00011 3_[+3]_9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCTCTT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTCCTCTT width=8 seqs=15 chr10:79409444-79409464 ( 1) TTCCTCTT 1 chrX:112004925-112004945 ( 6) TTCCTCTT 1 chr9:97920262-97920282 ( 3) TTCCTCTT 1 chr3:115757527-115757547 ( 2) TTCCTCTT 1 chr1:32805315-32805335 ( 11) TTCCTCTT 1 chr4:24770434-24770454 ( 1) TTCCTCTT 1 chr1:230286216-230286236 ( 1) TTCCTCTT 1 chr4:86647232-86647252 ( 3) TTCCTCTT 1 chr9:136343190-136343210 ( 1) TTCCTCAT 1 chr2:112761967-112761987 ( 4) TTCCTCAT 1 chr3:47267329-47267349 ( 1) TTCCTCCT 1 chr17:73567479-73567499 ( 1) TTCCTCCT 1 chr5:96232711-96232731 ( 10) TTCCTCTA 1 chr15:91525087-91525107 ( 11) TTGCTCTT 1 chr22:40446415-40446435 ( 4) TTCCTCAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCTCTT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.42938 E= 1.4e-007 -1055 -1055 -1055 185 -1055 -1055 -1055 185 -1055 204 -174 -1055 -1055 214 -1055 -1055 -1055 -1055 -1055 185 -1055 214 -1055 -1055 -45 -77 -1055 127 -103 -1055 -1055 165 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCTCTT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 15 E= 1.4e-007 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.933333 0.066667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.133333 0.000000 0.666667 0.133333 0.000000 0.000000 0.866667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCCTCTT MEME-3 regular expression -------------------------------------------------------------------------------- TTCCTC[TA]T -------------------------------------------------------------------------------- Time 6.47 secs. ******************************************************************************** ******************************************************************************** MOTIF ARAAGAGG MEME-4 width = 8 sites = 22 llr = 177 E-value = 1.3e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif ARAAGAGG MEME-4 Description -------------------------------------------------------------------------------- Simplified A 76a8:7:: pos.-specific C :::::::: probability G 34::a29a matrix T :::2:11: bits 2.2 * 1.9 * * * 1.7 * * ** 1.5 * * ** Relative 1.3 * * ** Entropy 1.1 ***** ** (11.6 bits) 0.9 ***** ** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AAAAGAGG consensus GG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAAGAGG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr20:12990390-12990410 13 1.68e-05 CTTCAGAAGA AAAAGAGG chr10:52212550-52212570 11 1.68e-05 ttgctacacc aaaagagg aa chr13:33825682-33825702 12 1.68e-05 TTTGTATTTT AAAAGAGG A chr11:44372710-44372730 1 1.68e-05 . AAAAGAGG TGGCAAATGA chr16:11862854-11862874 12 1.68e-05 ATGTATTTAC AAAAGAGG A chrX:97164424-97164444 13 3.06e-05 CAGGAGGCAA AGAAGAGG chr5:169206197-169206217 13 4.43e-05 aaaaggccct gaaagagg chr1:59878609-59878629 10 4.43e-05 tattcacag gaaagagg aag chr1:112158701-112158721 12 5.55e-05 gaggaagtca ggaagagg a chrX:68248404-68248424 12 8.05e-05 ATCTGCCCAC AGAAGGGG A chr1:150738299-150738319 10 9.75e-05 AGGTACTCA AAATGAGG AAG chr16:50743344-50743364 13 1.26e-04 CCCATTTCCT GAAAGGGG chr3:189538365-189538385 11 1.26e-04 GACAAAAGGA GAAAGGGG AA chr6:43651963-43651983 4 1.40e-04 AAA AGATGAGG AGTGCAGGG chr2:64488107-64488127 13 1.63e-04 CTCGGAAAGC AGAAGTGG chr14:25142408-25142428 1 1.63e-04 . AGAAGTGG AAAGGGGAAG chr17:26133078-26133098 12 1.77e-04 atcaggaggg gaatgagg a chr5:141340529-141340549 1 2.13e-04 . GGAAGTGG GTGCCTGGGG chr19:35950058-35950078 10 2.34e-04 CCTTTCTGG AAAAGATG CTC chr4:155406436-155406456 3 2.34e-04 ga aaaagatg catgcaagaa chr9:78070755-78070775 8 2.77e-04 tctttac agatgggg ctcag chr8:102972882-102972902 6 3.97e-04 gtgat aGAAAAGG AACAATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAAGAGG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr20:12990390-12990410 1.7e-05 12_[+4] chr10:52212550-52212570 1.7e-05 10_[+4]_2 chr13:33825682-33825702 1.7e-05 11_[+4]_1 chr11:44372710-44372730 1.7e-05 [+4]_12 chr16:11862854-11862874 1.7e-05 11_[+4]_1 chrX:97164424-97164444 3.1e-05 12_[+4] chr5:169206197-169206217 4.4e-05 12_[+4] chr1:59878609-59878629 4.4e-05 9_[+4]_3 chr1:112158701-112158721 5.6e-05 11_[+4]_1 chrX:68248404-68248424 8e-05 11_[+4]_1 chr1:150738299-150738319 9.8e-05 9_[+4]_3 chr16:50743344-50743364 0.00013 12_[+4] chr3:189538365-189538385 0.00013 10_[+4]_2 chr6:43651963-43651983 0.00014 3_[+4]_9 chr2:64488107-64488127 0.00016 12_[+4] chr14:25142408-25142428 0.00016 [+4]_12 chr17:26133078-26133098 0.00018 11_[+4]_1 chr5:141340529-141340549 0.00021 [+4]_12 chr19:35950058-35950078 0.00023 9_[+4]_3 chr4:155406436-155406456 0.00023 2_[+4]_10 chr9:78070755-78070775 0.00028 7_[+4]_5 chr8:102972882-102972902 0.0004 5_[+4]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAAGAGG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ARAAGAGG width=8 seqs=22 chr20:12990390-12990410 ( 13) AAAAGAGG 1 chr10:52212550-52212570 ( 11) AAAAGAGG 1 chr13:33825682-33825702 ( 12) AAAAGAGG 1 chr11:44372710-44372730 ( 1) AAAAGAGG 1 chr16:11862854-11862874 ( 12) AAAAGAGG 1 chrX:97164424-97164444 ( 13) AGAAGAGG 1 chr5:169206197-169206217 ( 13) GAAAGAGG 1 chr1:59878609-59878629 ( 10) GAAAGAGG 1 chr1:112158701-112158721 ( 12) GGAAGAGG 1 chrX:68248404-68248424 ( 12) AGAAGGGG 1 chr1:150738299-150738319 ( 10) AAATGAGG 1 chr16:50743344-50743364 ( 13) GAAAGGGG 1 chr3:189538365-189538385 ( 11) GAAAGGGG 1 chr6:43651963-43651983 ( 4) AGATGAGG 1 chr2:64488107-64488127 ( 13) AGAAGTGG 1 chr14:25142408-25142428 ( 1) AGAAGTGG 1 chr17:26133078-26133098 ( 12) GAATGAGG 1 chr5:141340529-141340549 ( 1) GGAAGTGG 1 chr19:35950058-35950078 ( 10) AAAAGATG 1 chr4:155406436-155406456 ( 3) AAAAGATG 1 chr9:78070755-78070775 ( 8) AGATGGGG 1 chr8:102972882-102972902 ( 6) AGAAAAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAAGAGG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.22846 E= 1.3e-006 132 -1110 51 -1110 111 -1110 87 -1110 187 -1110 -1110 -1110 158 -1110 -1110 -61 -258 -1110 210 -1110 132 -1110 -29 -102 -1110 -1110 203 -160 -1110 -1110 216 -1110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAAGAGG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 22 E= 1.3e-006 0.681818 0.000000 0.318182 0.000000 0.590909 0.000000 0.409091 0.000000 1.000000 0.000000 0.000000 0.000000 0.818182 0.000000 0.000000 0.181818 0.045455 0.000000 0.954545 0.000000 0.681818 0.000000 0.181818 0.136364 0.000000 0.000000 0.909091 0.090909 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAAGAGG MEME-4 regular expression -------------------------------------------------------------------------------- [AG][AG]AAGAGG -------------------------------------------------------------------------------- Time 9.55 secs. ******************************************************************************** ******************************************************************************** MOTIF CWGSAGGG MEME-5 width = 8 sites = 9 llr = 82 E-value = 6.6e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CWGSAGGG MEME-5 Description -------------------------------------------------------------------------------- Simplified A :4::a::: pos.-specific C 8::4:::1 probability G 21a6:aa9 matrix T :4:::::: bits 2.2 * ** 1.9 * *** 1.7 * **** 1.5 * **** Relative 1.3 * * **** Entropy 1.1 * ****** (13.1 bits) 0.9 * ****** 0.6 * ****** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CAGGAGGG consensus GT C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGSAGGG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr5:53765609-53765629 9 1.88e-05 TTACTGGG CAGGAGGG TCTC chr17:26133078-26133098 4 1.88e-05 cat caggaggg gaatgagga chr10:14650646-14650666 6 1.88e-05 ccgtc caggaggg cgaaaga chr16:2737385-2737405 13 3.79e-05 AATGCTGTCG CTGCAGGG chr10:6110513-6110533 9 3.79e-05 GCTCACGT CTGCAGGG ATCC chr1:155940543-155940563 2 6.40e-05 T GTGGAGGG GCTGAGTCAA chr13:107146089-10714610 4 7.18e-05 CAG CGGCAGGG AAGAAAAAG chr6:43651963-43651983 13 9.06e-05 AAGATGAGGA GTGCAGGG chrX:97164424-97164444 3 1.10e-04 AG CAGGAGGC AAAGAAGAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGSAGGG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr5:53765609-53765629 1.9e-05 8_[+5]_4 chr17:26133078-26133098 1.9e-05 3_[+5]_9 chr10:14650646-14650666 1.9e-05 5_[+5]_7 chr16:2737385-2737405 3.8e-05 12_[+5] chr10:6110513-6110533 3.8e-05 8_[+5]_4 chr1:155940543-155940563 6.4e-05 1_[+5]_11 chr13:107146089-10714610 7.2e-05 3_[+5]_9 chr6:43651963-43651983 9.1e-05 12_[+5] chrX:97164424-97164444 0.00011 2_[+5]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGSAGGG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CWGSAGGG width=8 seqs=9 chr5:53765609-53765629 ( 9) CAGGAGGG 1 chr17:26133078-26133098 ( 4) CAGGAGGG 1 chr10:14650646-14650666 ( 6) CAGGAGGG 1 chr16:2737385-2737405 ( 13) CTGCAGGG 1 chr10:6110513-6110533 ( 9) CTGCAGGG 1 chr1:155940543-155940563 ( 2) GTGGAGGG 1 chr13:107146089-10714610 ( 4) CGGCAGGG 1 chr6:43651963-43651983 ( 13) GTGCAGGG 1 chrX:97164424-97164444 ( 3) CAGGAGGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGSAGGG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 9.89918 E= 6.6e+001 -982 177 -1 -982 70 -982 -100 68 -982 -982 216 -982 -982 97 132 -982 187 -982 -982 -982 -982 -982 216 -982 -982 -982 216 -982 -982 -103 199 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGSAGGG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 6.6e+001 0.000000 0.777778 0.222222 0.000000 0.444444 0.000000 0.111111 0.444444 0.000000 0.000000 1.000000 0.000000 0.000000 0.444444 0.555556 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.111111 0.888889 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGSAGGG MEME-5 regular expression -------------------------------------------------------------------------------- [CG][AT]G[GC]AGGG -------------------------------------------------------------------------------- Time 12.41 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr4:86647232-86647252 1.74e-02 2_[+3(1.91e-05)]_10 chr2:225503165-225503185 9.43e-04 9_[+3(3.79e-05)]_3 chr2:218113571-218113591 8.73e-02 20 chr6:36660183-36660203 1.08e-04 9_[+1(2.53e-05)]_3 chr1:230286216-230286236 6.73e-03 [+3(1.91e-05)]_12 chr6:3356681-3356701 6.80e-01 20 chr6:130427679-130427699 5.25e-01 20 chr4:24770434-24770454 2.65e-03 [+3(1.91e-05)]_12 chr1:154131017-154131037 2.27e-01 20 chr12:108130871-10813089 4.59e-01 20 chr6:42335561-42335581 1.58e-04 10_[+1(2.53e-05)]_2 chr12:124876024-12487604 9.43e-01 20 chr10:14650646-14650666 1.69e-02 5_[+5(1.88e-05)]_7 chr1:79106363-79106383 2.13e-04 [+2(1.54e-05)]_12 chr6:43651963-43651983 1.30e-03 12_[+5(9.06e-05)] chr1:59878609-59878629 1.31e-02 9_[+4(4.43e-05)]_3 chr1:157087392-157087412 6.51e-01 20 chr8:145052831-145052851 5.14e-01 20 chr3:48717337-48717357 8.83e-01 20 chr9:78070755-78070775 1.36e-02 20 chr20:36432504-36432524 1.54e-04 3_[+4(1.68e-05)]_9 chr12:107147439-10714745 5.72e-01 20 chr8:52365177-52365197 5.13e-01 20 chr12:115760213-11576023 6.14e-01 20 chr3:72572715-72572735 1.72e-04 5_[+2(1.54e-05)]_7 chr15:49284895-49284915 7.23e-03 12_[+2(1.54e-05)] chr2:112761967-112761987 2.01e-02 3_[+3(3.79e-05)]_9 chr17:55700354-55700374 1.89e-01 20 chr9:73013240-73013260 7.52e-01 20 chr3:107821474-107821494 9.49e-01 20 chr3:72678559-72678579 4.01e-01 20 chr2:58259568-58259588 1.48e-03 4_[+1(9.35e-05)]_8 chr18:44946689-44946709 6.28e-01 20 chr15:61088261-61088281 4.70e-01 20 chr13:51385345-51385365 9.51e-01 20 chr1:200623983-200624003 1.70e-01 20 chr8:11716366-11716386 1.31e-02 3_[+2(1.54e-05)]_9 chr22:32186298-32186318 5.63e-01 20 chr1:112048611-112048631 6.73e-01 20 chr7:100485388-100485408 3.19e-01 20 chr18:46242167-46242187 3.71e-05 10_[+1(1.39e-05)]_2 chr17:6999177-6999197 3.74e-01 20 chr9:136343190-136343210 4.76e-04 [+3(3.79e-05)]_12 chr1:21617358-21617378 7.43e-03 2_[+2(9.36e-05)]_10 chr1:155940543-155940563 9.33e-03 1_[+5(6.40e-05)]_11 chrX:54722432-54722452 2.11e-04 7_[+2(1.54e-05)]_5 chr3:111886756-111886776 4.47e-01 20 chr9:140703662-140703682 2.46e-01 20 chr13:113238060-11323808 4.51e-01 20 chr9:137297505-137297525 2.22e-02 20 chr10:112627421-11262744 9.76e-01 20 chr5:131803551-131803571 2.20e-01 20 chr1:198101386-198101406 8.07e-01 20 chr15:69959383-69959403 3.18e-01 20 chr13:77014927-77014947 8.64e-02 20 chr14:25142408-25142428 4.25e-04 20 chr16:85089199-85089219 4.93e-02 11_[+2(2.80e-05)]_1 chr2:8256975-8256995 4.25e-01 20 chr6:36973409-36973429 2.55e-04 8_[+3(1.91e-05)]_4 chr7:25127696-25127716 1.40e-01 20 chr16:17621022-17621042 3.75e-01 20 chr9:567568-567588 3.55e-01 20 chr3:143314447-143314467 9.08e-02 20 chr19:15437851-15437871 3.31e-01 20 chr1:56938717-56938737 4.51e-01 20 chr12:47706734-47706754 9.35e-05 9_[+1(1.39e-05)]_3 chr5:131823819-131823839 3.09e-03 20 chr6:44232113-44232133 3.43e-01 20 chr8:55421033-55421053 1.76e-03 1_[+1(1.39e-05)]_11 chr18:45497274-45497294 1.10e-02 3_[+1(7.96e-05)]_9 chr14:95700173-95700193 2.72e-01 20 chr15:41139701-41139721 1.94e-03 20 chr19:19555822-19555842 3.14e-01 20 chr2:225759219-225759239 6.98e-05 7_[+1(1.39e-05)]_5 chr17:55945514-55945534 4.50e-01 20 chr1:110448965-110448985 6.28e-01 20 chr6:15288102-15288122 4.64e-01 20 chr1:28454326-28454346 8.33e-01 20 chr6:2659295-2659315 2.70e-03 4_[+2(1.54e-05)]_8 chr6:24575263-24575283 8.45e-01 20 chr16:11862854-11862874 1.16e-02 11_[+4(1.68e-05)]_1 chr16:81786017-81786037 3.79e-02 12_[+2(2.80e-05)] chr10:110610110-11061013 4.37e-02 20 chr1:112050360-112050380 1.60e-04 3_[+2(1.54e-05)]_9 chr16:71953125-71953145 1.05e-01 20 chr1:226132807-226132827 9.84e-01 20 chr17:46372947-46372967 9.05e-01 20 chrX:68248404-68248424 3.04e-03 11_[+4(8.05e-05)]_1 chr3:142841651-142841671 8.64e-02 20 chr12:932641-932661 9.07e-03 9_[+2(1.54e-05)]_3 chr4:155406436-155406456 7.44e-02 20 chr2:240175139-240175159 4.22e-02 20 chr14:65785576-65785596 6.76e-01 20 chr1:184716601-184716621 1.79e-03 2_[+1(1.39e-05)]_10 chr5:148211421-148211441 8.98e-01 20 chr7:20153218-20153238 8.00e-01 20 chr1:167469063-167469083 7.40e-02 20 chr8:29452131-29452151 5.22e-01 20 chr11:10783940-10783960 1.74e-04 9_[+1(1.39e-05)]_3 chr17:26133078-26133098 1.85e-04 3_[+5(1.88e-05)]_9 chr1:45189257-45189277 5.83e-01 20 chr11:123418119-12341813 3.69e-02 20 chr7:47640882-47640902 7.20e-01 20 chr17:56582537-56582557 1.96e-04 1_[+4(1.68e-05)]_11 chr9:108147837-108147857 8.77e-01 20 chr2:62372915-62372935 5.28e-01 20 chr8:103942453-103942473 3.86e-01 20 chr20:53250595-53250615 9.21e-01 20 chr1:26199398-26199418 1.89e-01 20 chr1:206329088-206329108 3.79e-01 20 chr1:172154502-172154522 1.50e-02 9_[+1(9.35e-05)]_3 chr3:6721427-6721447 1.86e-01 20 chr10:112477906-11247792 4.11e-01 20 chr1:32805315-32805335 1.28e-04 10_[+3(1.91e-05)]_2 chr18:55682429-55682449 7.52e-01 20 chr2:105593116-105593136 9.68e-03 3_[+1(3.95e-05)]_9 chr16:82685605-82685625 5.44e-01 20 chr8:18704614-18704634 5.25e-04 [+2(1.54e-05)]_12 chr3:193559907-193559927 3.58e-04 5_[+2(1.54e-05)]_7 chr15:52774260-52774280 9.78e-01 20 chr6:166756813-166756833 2.07e-05 [+1(2.53e-05)]_12 chr17:73567479-73567499 3.38e-03 [+3(5.35e-05)]_12 chr11:44372710-44372730 2.68e-03 [+4(1.68e-05)]_12 chr6:133078987-133079007 6.98e-01 20 chr2:64488107-64488127 1.44e-02 20 chr20:9596932-9596952 3.15e-04 12_[+1(3.95e-05)] chr16:49433718-49433738 8.43e-01 20 chr1:21291555-21291575 6.96e-01 20 chr18:72885157-72885177 1.97e-01 20 chr7:76033579-76033599 7.20e-05 9_[+1(1.39e-05)]_3 chrX:29549624-29549644 4.87e-01 20 chr13:33825682-33825702 1.97e-02 11_[+4(1.68e-05)]_1 chr14:71270210-71270230 5.09e-02 4_[+2(9.36e-05)]_8 chr13:107146089-10714610 3.92e-03 3_[+5(7.18e-05)]_9 chr8:102972882-102972902 4.67e-02 20 chr5:56326199-56326219 8.15e-01 20 chr6:112045844-112045864 8.95e-02 20 chr3:115757527-115757547 2.44e-03 1_[+3(1.91e-05)]_11 chr8:30182173-30182193 1.97e-01 20 chr3:169872439-169872459 9.11e-01 20 chr12:3732358-3732378 1.59e-01 20 chr12:68152085-68152105 1.40e-01 20 chrX:97164424-97164444 4.27e-04 12_[+4(3.06e-05)] chr1:161688767-161688787 1.49e-01 20 chr12:102335546-10233556 7.33e-01 20 chr7:24911571-24911591 7.48e-01 20 chr11:2548437-2548457 7.25e-04 9_[+1(1.39e-05)]_3 chr10:52212550-52212570 4.61e-03 10_[+4(1.68e-05)]_2 chr1:46509349-46509369 2.52e-01 20 chr6:1482758-1482778 3.08e-02 20 chr20:55297365-55297385 9.58e-01 20 chr5:114598176-114598196 4.97e-01 20 chr6:143273923-143273943 4.11e-02 20 chr9:77704020-77704040 7.58e-01 20 chr5:1490652-1490672 4.56e-01 20 chr5:6237118-6237138 2.69e-01 20 chr5:138430338-138430358 4.33e-02 12_[+2(9.36e-05)] chr7:30560179-30560199 9.81e-01 20 chr1:112158701-112158721 6.65e-05 1_[+1(1.39e-05)]_2_[+4(5.55e-05)]_1 chr2:148447311-148447331 5.97e-01 20 chr1:25889098-25889118 1.06e-01 20 chr21:43669538-43669558 6.51e-01 20 chr21:43481672-43481692 4.81e-01 20 chr5:106709747-106709767 3.34e-01 20 chr18:56204034-56204054 2.80e-01 20 chr11:93246324-93246344 1.57e-01 20 chr3:15092090-15092110 2.75e-03 11_[+1(5.11e-05)]_1 chr11:131056631-13105665 3.97e-05 5_[+1(2.53e-05)]_7 chr19:35950058-35950078 9.65e-02 20 chr1:100988735-100988755 3.49e-01 20 chr3:188139792-188139812 4.00e-01 20 chr10:6110513-6110533 2.77e-03 8_[+5(3.79e-05)]_4 chr19:43001723-43001743 9.79e-02 20 chr17:45277567-45277587 5.85e-01 20 chr8:42189087-42189107 4.38e-01 20 chr16:2737385-2737405 6.59e-03 12_[+5(3.79e-05)] chr8:74748103-74748123 3.57e-01 20 chr10:65458348-65458368 6.55e-02 20 chr20:12990390-12990410 1.85e-02 12_[+4(1.68e-05)] chr15:84624876-84624896 3.16e-01 20 chr2:118813887-118813907 5.78e-02 20 chr13:46280263-46280283 2.15e-03 2_[+2(1.54e-05)]_10 chr8:123095277-123095297 4.97e-01 20 chr2:197114736-197114756 3.70e-01 20 chr5:53765609-53765629 3.67e-03 8_[+5(1.88e-05)]_4 chr6:109127206-109127226 7.70e-02 20 chr9:97920262-97920282 8.13e-03 2_[+3(1.91e-05)]_10 chr8:124191295-124191315 2.19e-05 8_[+2(1.54e-05)]_4 chr11:126944586-12694460 3.99e-01 20 chr11:45053873-45053893 6.58e-04 11_[+1(5.11e-05)]_1 chr2:194969593-194969613 1.86e-01 20 chr19:14551026-14551046 2.25e-04 1_[+1(1.39e-05)]_11 chr14:100763796-10076381 6.42e-05 7_[+1(1.39e-05)]_5 chr20:32712449-32712469 1.27e-01 20 chr14:30327691-30327711 8.83e-01 20 chr22:42793449-42793469 1.22e-02 20 chr6:13397694-13397714 8.66e-03 20 chr14:23259653-23259673 3.25e-01 20 chr3:3130843-3130863 6.00e-01 20 chr20:62884246-62884266 3.32e-02 20 chr5:139664437-139664457 3.27e-04 8_[+2(1.54e-05)]_4 chr2:187778796-187778816 1.07e-04 8_[+2(1.54e-05)]_4 chrX:112004925-112004945 1.25e-02 5_[+3(1.91e-05)]_7 chr3:47267329-47267349 3.89e-02 [+3(5.35e-05)]_12 chr6:33029914-33029934 9.87e-01 20 chr1:226035918-226035938 2.35e-01 20 chr6:31695476-31695496 2.54e-03 3_[+1(1.39e-05)]_9 chr18:12050461-12050481 4.30e-01 20 chr13:33685278-33685298 1.30e-02 12_[+2(1.54e-05)] chr5:141340529-141340549 4.69e-02 20 chr1:150738299-150738319 2.97e-02 9_[+4(9.75e-05)]_3 chr2:55094333-55094353 3.08e-02 20 chr12:131363866-13136388 3.57e-02 1_[+2(9.36e-05)]_11 chr12:29305345-29305365 5.87e-01 20 chr13:37547929-37547949 3.31e-03 3_[+1(1.39e-05)]_9 chr10:116258554-11625857 1.85e-04 3_[+4(1.68e-05)]_9 chr3:56951883-56951903 1.57e-03 3_[+1(1.39e-05)]_9 chr6:47210459-47210479 1.36e-01 20 chr14:68429017-68429037 8.14e-01 20 chr15:91525087-91525107 8.92e-02 10_[+3(9.10e-05)]_2 chr10:3078567-3078587 3.25e-01 20 chr5:169206197-169206217 2.63e-02 12_[+4(4.43e-05)] chr3:156059970-156059990 2.29e-02 4_[+2(6.56e-05)]_8 chr17:29285430-29285450 2.04e-04 5_[+4(1.68e-05)]_7 chr17:29818567-29818587 1.11e-05 [+4(1.68e-05)]_12 chr13:97424435-97424455 8.77e-01 20 chr4:26887655-26887675 3.61e-03 9_[+1(6.82e-05)]_3 chr2:102650085-102650105 5.67e-04 [+2(2.80e-05)]_12 chr14:70160127-70160147 2.89e-01 20 chr18:54519209-54519229 1.61e-01 20 chr3:39297293-39297313 6.20e-01 20 chr4:55181957-55181977 3.63e-01 20 chr2:47563929-47563949 4.72e-02 20 chr16:10023408-10023428 7.87e-01 20 chr9:22030195-22030215 5.25e-04 11_[+3(1.91e-05)]_1 chr6:134694767-134694787 1.70e-01 20 chr3:189538365-189538385 2.25e-02 20 chr15:89984830-89984850 3.70e-03 7_[+1(3.95e-05)]_5 chr11:72526881-72526901 7.53e-04 3_[+1(1.39e-05)]_9 chr14:100481861-10048188 1.97e-03 1_[+1(1.39e-05)]_11 chr10:79409444-79409464 2.12e-03 [+3(1.91e-05)]_12 chr22:40888441-40888461 3.54e-01 20 chr4:17597369-17597389 2.98e-02 10_[+2(6.56e-05)]_2 chr19:1904482-1904502 8.56e-01 20 chr2:219014743-219014763 4.88e-01 20 chr16:50743344-50743364 3.11e-05 20 chr5:96232711-96232731 1.61e-02 9_[+3(7.23e-05)]_3 chr11:65145874-65145894 5.78e-02 20 chr22:40446415-40446435 1.29e-01 20 chr11:63143081-63143101 2.06e-01 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c17n10.farnam.hpc.yale.internal ********************************************************************************