******************************************************************************** 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/NFXL1.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr1:27930380-27930400 1.0000 20 chr12:133164529-13316454 1.0000 20 chr17:80185492-80185512 1.0000 20 chr12:131574153-13157417 1.0000 20 chr1:117338221-117338241 1.0000 20 chr5:176790153-176790173 1.0000 20 chr6:157100006-157100026 1.0000 20 chr22:39417791-39417811 1.0000 20 chr9:109625834-109625854 1.0000 20 chr22:39473659-39473679 1.0000 20 chr9:135450535-135450555 1.0000 20 chr3:195887390-195887410 1.0000 20 chr16:29606365-29606385 1.0000 20 chr7:105650092-105650112 1.0000 20 chr20:44651615-44651635 1.0000 20 chr12:111866890-11186691 1.0000 20 chr7:73704970-73704990 1.0000 20 chr8:50064176-50064196 1.0000 20 chr11:742739-742759 1.0000 20 chr19:2056518-2056538 1.0000 20 chr12:131530482-13153050 1.0000 20 chr20:62151309-62151329 1.0000 20 chr2:158732794-158732814 1.0000 20 chr22:39437273-39437293 1.0000 20 chr20:32450523-32450543 1.0000 20 chr1:26201738-26201758 1.0000 20 chr5:1472384-1472404 1.0000 20 chr13:24846305-24846325 1.0000 20 chr10:71078621-71078641 1.0000 20 chr8:71316142-71316162 1.0000 20 chr12:122237888-12223790 1.0000 20 chr9:134151372-134151392 1.0000 20 chr15:91397600-91397620 1.0000 20 chr22:38200982-38201002 1.0000 20 chr18:46468292-46468312 1.0000 20 chr10:125785708-12578572 1.0000 20 chr8:128751162-128751182 1.0000 20 chr9:140428872-140428892 1.0000 20 chr5:77409673-77409693 1.0000 20 chr1:994453-994473 1.0000 20 chr16:49384483-49384503 1.0000 20 chr17:73238749-73238769 1.0000 20 chr5:394975-394995 1.0000 20 chr2:242144697-242144717 1.0000 20 chr14:21539682-21539702 1.0000 20 chr1:205473879-205473899 1.0000 20 chr19:18526398-18526418 1.0000 20 chr10:135132197-13513221 1.0000 20 chr9:126774067-126774087 1.0000 20 chr2:191492733-191492753 1.0000 20 chr7:1115936-1115956 1.0000 20 chr17:45609320-45609340 1.0000 20 chr22:42680091-42680111 1.0000 20 chr17:36412457-36412477 1.0000 20 chr1:180980981-180981001 1.0000 20 chr18:77492147-77492167 1.0000 20 chr5:944674-944694 1.0000 20 chr14:90701799-90701819 1.0000 20 chr2:162095412-162095432 1.0000 20 chr19:35167791-35167811 1.0000 20 chr6:3457229-3457249 1.0000 20 chr11:47398069-47398089 1.0000 20 chr5:1471785-1471805 1.0000 20 chr3:48541720-48541740 1.0000 20 chr7:38385338-38385358 1.0000 20 chr9:139429859-139429879 1.0000 20 chr5:1473173-1473193 1.0000 20 chrX:9982886-9982906 1.0000 20 chr16:616978-616998 1.0000 20 chr2:106361174-106361194 1.0000 20 chr16:1426311-1426331 1.0000 20 chr4:48212472-48212492 1.0000 20 chr20:52358814-52358834 1.0000 20 chr20:52410713-52410733 1.0000 20 chr6:32981553-32981573 1.0000 20 chr7:44347053-44347073 1.0000 20 chr18:77492778-77492798 1.0000 20 chr20:52524696-52524716 1.0000 20 chr7:38398790-38398810 1.0000 20 chr7:38389618-38389638 1.0000 20 chr3:53839688-53839708 1.0000 20 chr20:52234628-52234648 1.0000 20 chr7:75619616-75619636 1.0000 20 chr17:6366204-6366224 1.0000 20 chr22:32960951-32960971 1.0000 20 chr20:52198535-52198555 1.0000 20 chr6:163835760-163835780 1.0000 20 chr20:52557005-52557025 1.0000 20 chr19:4145749-4145769 1.0000 20 chr20:52560250-52560270 1.0000 20 chr10:104504456-10450447 1.0000 20 chr15:81592142-81592162 1.0000 20 chr19:4081561-4081581 1.0000 20 chr10:133579292-13357931 1.0000 20 chr20:52244794-52244814 1.0000 20 chr19:42432617-42432637 1.0000 20 chr15:22892598-22892618 1.0000 20 chr17:59896815-59896835 1.0000 20 chr19:17531464-17531484 1.0000 20 chr20:52237935-52237955 1.0000 20 chr17:65822310-65822330 1.0000 20 chr20:52210711-52210731 1.0000 20 chr7:100397323-100397343 1.0000 20 chr20:52394733-52394753 1.0000 20 chr20:52308001-52308021 1.0000 20 chr20:52309431-52309451 1.0000 20 chr22:46421261-46421281 1.0000 20 chr17:59787041-59787061 1.0000 20 chr22:45088361-45088381 1.0000 20 chr16:9185799-9185819 1.0000 20 chr9:139887370-139887390 1.0000 20 chr17:59849791-59849811 1.0000 20 chr20:52319339-52319359 1.0000 20 chr17:59631608-59631628 1.0000 20 chr7:5494965-5494985 1.0000 20 chr20:52213324-52213344 1.0000 20 chr20:11871436-11871456 1.0000 20 chr20:43940318-43940338 1.0000 20 chr12:19592931-19592951 1.0000 20 chr17:59782485-59782505 1.0000 20 chr20:52201843-52201863 1.0000 20 chr20:52185733-52185753 1.0000 20 chr5:49962748-49962768 1.0000 20 chr13:21871271-21871291 1.0000 20 chr20:52423737-52423757 1.0000 20 chr20:52224287-52224307 1.0000 20 chr20:52362245-52362265 1.0000 20 chr12:105086054-10508607 1.0000 20 chr20:46020153-46020173 1.0000 20 chr5:6322737-6322757 1.0000 20 chr19:39014092-39014112 1.0000 20 chr19:4241963-4241983 1.0000 20 chr9:73027875-73027895 1.0000 20 chr17:7121219-7121239 1.0000 20 chr10:105455580-10545560 1.0000 20 chr17:994569-994589 1.0000 20 chr20:55832219-55832239 1.0000 20 chr12:125978351-12597837 1.0000 20 chr6:2989214-2989234 1.0000 20 chr19:3647339-3647359 1.0000 20 chr14:70015000-70015020 1.0000 20 chr17:59837624-59837644 1.0000 20 chr10:105211378-10521139 1.0000 20 chr20:52292522-52292542 1.0000 20 chr20:52245481-52245501 1.0000 20 chr12:2034524-2034544 1.0000 20 chr20:52430695-52430715 1.0000 20 chr20:52457733-52457753 1.0000 20 chr17:59696540-59696560 1.0000 20 chr21:40177886-40177906 1.0000 20 chr19:3646880-3646900 1.0000 20 chr17:57909785-57909805 1.0000 20 chr20:35089898-35089918 1.0000 20 chr3:64017364-64017384 1.0000 20 chr17:59890270-59890290 1.0000 20 chr12:108991827-10899184 1.0000 20 chr20:52475757-52475777 1.0000 20 chr17:59916187-59916207 1.0000 20 chr14:75895184-75895204 1.0000 20 chr20:52531576-52531596 1.0000 20 chr20:52388999-52389019 1.0000 20 chr16:4365891-4365911 1.0000 20 chr12:125670890-12567091 1.0000 20 chr20:52339610-52339630 1.0000 20 chr20:52206025-52206045 1.0000 20 chr17:59912788-59912808 1.0000 20 chr10:121410587-12141060 1.0000 20 chr19:7571604-7571624 1.0000 20 chr17:59637625-59637645 1.0000 20 chr17:59915209-59915229 1.0000 20 chr2:231386284-231386304 1.0000 20 chr17:58847445-58847465 1.0000 20 chr7:128809062-128809082 1.0000 20 chr9:129466522-129466542 1.0000 20 chr12:48297922-48297942 1.0000 20 chr1:148176264-148176284 1.0000 20 chr20:52343392-52343412 1.0000 20 chr20:46124382-46124402 1.0000 20 chr17:59684173-59684193 1.0000 20 chr11:129309997-12931001 1.0000 20 chr6:143267092-143267112 1.0000 20 chr20:52447041-52447061 1.0000 20 chr17:59773309-59773329 1.0000 20 chr20:45981205-45981225 1.0000 20 chr17:59777696-59777716 1.0000 20 chr17:59913776-59913796 1.0000 20 chr10:121302210-12130223 1.0000 20 chr17:59660152-59660172 1.0000 20 chr2:73511440-73511460 1.0000 20 chr17:58472464-58472484 1.0000 20 chr20:52713151-52713171 1.0000 20 chr20:52429910-52429930 1.0000 20 chr1:181318846-181318866 1.0000 20 chr20:52207354-52207374 1.0000 20 chrX:109245663-109245683 1.0000 20 chr12:122241894-12224191 1.0000 20 chr21:36262525-36262545 1.0000 20 chr20:52515217-52515237 1.0000 20 chr15:41851362-41851382 1.0000 20 chr17:3599517-3599537 1.0000 20 chr20:49288191-49288211 1.0000 20 chr14:75721761-75721781 1.0000 20 chr17:59911951-59911971 1.0000 20 chr3:53876888-53876908 1.0000 20 chr17:59672177-59672197 1.0000 20 chr10:127925208-12792522 1.0000 20 chr4:40859297-40859317 1.0000 20 chr17:58463493-58463513 1.0000 20 chr15:41136574-41136594 1.0000 20 chr14:105144138-10514415 1.0000 20 chr6:158402823-158402843 1.0000 20 chr20:46189371-46189391 1.0000 20 chrX:47240452-47240472 1.0000 20 chr4:185395296-185395316 1.0000 20 chr20:45950900-45950920 1.0000 20 chr20:49350576-49350596 1.0000 20 chr7:24612978-24612998 1.0000 20 chr6:4136354-4136374 1.0000 20 chr19:51315051-51315071 1.0000 20 chr17:59652602-59652622 1.0000 20 chr20:49341084-49341104 1.0000 20 chr20:52512125-52512145 1.0000 20 chr17:58475980-58476000 1.0000 20 chrX:19851278-19851298 1.0000 20 chr20:52868416-52868436 1.0000 20 chr16:53087037-53087057 1.0000 20 chr20:55767543-55767563 1.0000 20 chr7:70159458-70159478 1.0000 20 chr20:52630106-52630126 1.0000 20 chr12:131531542-13153156 1.0000 20 chr17:59691765-59691785 1.0000 20 chr20:52381918-52381938 1.0000 20 chr17:59671430-59671450 1.0000 20 chr6:86303173-86303193 1.0000 20 chr4:8206507-8206527 1.0000 20 chr20:52387439-52387459 1.0000 20 chr2:224702298-224702318 1.0000 20 chr10:79398120-79398140 1.0000 20 chr19:51315253-51315273 1.0000 20 chr20:52716671-52716691 1.0000 20 chr7:5636041-5636061 1.0000 20 chr17:59397697-59397717 1.0000 20 chr2:73613116-73613136 1.0000 20 chr20:52331467-52331487 1.0000 20 chr20:55813307-55813327 1.0000 20 chr17:59437865-59437885 1.0000 20 chr17:59643302-59643322 1.0000 20 chr20:49293623-49293643 1.0000 20 chr20:46165898-46165918 1.0000 20 chr7:4875202-4875222 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_NFXL1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/NFXL1.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 0.209 C 0.278 G 0.289 T 0.224 Background letter frequencies (from file dataset with add-one prior applied): A 0.209 C 0.278 G 0.289 T 0.224 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF RRGGAGGA MEME-1 width = 8 sites = 43 llr = 317 E-value = 4.1e-024 ******************************************************************************** -------------------------------------------------------------------------------- Motif RRGGAGGA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 35::a:18 pos.-specific C 1:::::3: probability G 54aa:961 matrix T :::::::1 bits 2.3 * 2.0 * 1.8 *** 1.6 *** Relative 1.4 **** * Entropy 1.1 **** * (10.7 bits) 0.9 ***** * 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GAGGAGGA consensus AG C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRGGAGGA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chrX:47240452-47240472 11 1.84e-05 ggaagagcag gaggagga gg chr6:158402823-158402843 9 1.84e-05 CGAGTggg gaggagga ggaa chr10:121302210-12130223 7 1.84e-05 gaaggc gaggagga ggagga chr6:143267092-143267112 8 1.84e-05 CGCTgag gaggagga gaagg chr12:19592931-19592951 12 1.84e-05 ggaggacgac gaggagga g chr3:48541720-48541740 2 1.84e-05 g gaggagga aggaAGGAAG chr20:44651615-44651635 8 1.84e-05 agaggag gaggagga agagg chr6:157100006-157100026 4 1.84e-05 gag gaggagga ggcagcgga chr7:100397323-100397343 4 5.72e-05 gag ggggagga ctgcttgag chr20:62151309-62151329 13 5.72e-05 TCTGCGCTGG GGGGAGGA chr9:109625834-109625854 13 5.72e-05 agagcaggag ggggagga chr19:51315253-51315273 4 7.56e-05 GGC AGGGAGGA CCATCTCAG chr1:181318846-181318866 9 7.56e-05 GGCTGCAT AGGGAGGA CTCA chr20:35089898-35089918 6 7.56e-05 GCGTG AGGGAGGA GGGTGAG chr6:2989214-2989234 5 7.56e-05 CTCC AGGGAGGA CGGTTGCA chr13:21871271-21871291 8 7.56e-05 ggggcta agggagga tccgg chr7:1115936-1115956 6 7.56e-05 AGGCC AGGGAGGA GCACCGC chr5:1472384-1472404 3 7.56e-05 AG AGGGAGGA CTTTGACCAG chr1:180980981-180981001 4 9.33e-05 TGG GAGGAGCA CTTCACTTT chr17:994569-994589 9 1.06e-04 GGAGGGAG AAGGAGCA CCCT chr9:129466522-129466542 6 1.31e-04 CACTC GGGGAGCA CTCCCAC chr17:6366204-6366224 11 1.31e-04 ggagcaccat ggggagca cc chr7:75619616-75619636 5 1.31e-04 CTAT GGGGAGCA CTATGCCA chr12:2034524-2034544 1 1.48e-04 . AGGGAGCA CTCACCTGGG chr12:133164529-13316454 4 1.48e-04 GTG AGGGAGCA CCCTCCTGG chr19:3646880-3646900 12 1.66e-04 ggacgacaga caggagga c chr10:105211378-10521139 9 1.66e-04 aggaggac caggagga acaa chr10:125785708-12578572 12 2.30e-04 CAAATGCGGA CAGGAGCA C chr7:70159458-70159478 2 2.49e-04 C GGGGAGAA GCCGCCGCGC chr2:73613116-73613136 10 3.07e-04 GTGGTCGTG GAGGAGGT GGA chr14:75721761-75721781 4 3.07e-04 AGG AGGGAGAA GAGGAAGGA chr7:44347053-44347073 9 3.07e-04 TGTGTGAA GAGGAGGG TTTC chr5:1471785-1471805 1 3.07e-04 . GAGGAGGT TCCAGGAAGA chr19:18526398-18526418 2 3.07e-04 g gaggaggg agaggaagag chr16:4365891-4365911 9 5.36e-04 TTGCTGGG AGGGAGGG AGCG chr7:38398790-38398810 13 5.98e-04 AGGACCTGCA GAGGAGCT chr20:52224287-52224307 6 6.92e-04 gaggt caggagaa accccct chr9:134151372-134151392 6 6.92e-04 CGGTA GCGGAGCA CCACGCT chr4:8206507-8206527 6 7.18e-04 AGGCG ACGGAGCA CTGTTCC chr10:127925208-12792522 2 7.18e-04 G AAGGAACA CCCATAGGAA chr17:65822310-65822330 5 7.96e-04 TTCT GAGGACGA CGAGGAGG chr1:205473879-205473899 9 8.52e-04 TGCCCGGG AGGGAGCG GGCG chr20:52245481-52245501 5 1.00e-03 cggc caggaaga gttttcta -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRGGAGGA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chrX:47240452-47240472 1.8e-05 10_[+1]_2 chr6:158402823-158402843 1.8e-05 8_[+1]_4 chr10:121302210-12130223 1.8e-05 6_[+1]_6 chr6:143267092-143267112 1.8e-05 7_[+1]_5 chr12:19592931-19592951 1.8e-05 11_[+1]_1 chr3:48541720-48541740 1.8e-05 1_[+1]_11 chr20:44651615-44651635 1.8e-05 7_[+1]_5 chr6:157100006-157100026 1.8e-05 3_[+1]_9 chr7:100397323-100397343 5.7e-05 3_[+1]_9 chr20:62151309-62151329 5.7e-05 12_[+1] chr9:109625834-109625854 5.7e-05 12_[+1] chr19:51315253-51315273 7.6e-05 3_[+1]_9 chr1:181318846-181318866 7.6e-05 8_[+1]_4 chr20:35089898-35089918 7.6e-05 5_[+1]_7 chr6:2989214-2989234 7.6e-05 4_[+1]_8 chr13:21871271-21871291 7.6e-05 7_[+1]_5 chr7:1115936-1115956 7.6e-05 5_[+1]_7 chr5:1472384-1472404 7.6e-05 2_[+1]_10 chr1:180980981-180981001 9.3e-05 3_[+1]_9 chr17:994569-994589 0.00011 8_[+1]_4 chr9:129466522-129466542 0.00013 5_[+1]_7 chr17:6366204-6366224 0.00013 10_[+1]_2 chr7:75619616-75619636 0.00013 4_[+1]_8 chr12:2034524-2034544 0.00015 [+1]_12 chr12:133164529-13316454 0.00015 3_[+1]_9 chr19:3646880-3646900 0.00017 11_[+1]_1 chr10:105211378-10521139 0.00017 8_[+1]_4 chr10:125785708-12578572 0.00023 11_[+1]_1 chr7:70159458-70159478 0.00025 1_[+1]_11 chr2:73613116-73613136 0.00031 9_[+1]_3 chr14:75721761-75721781 0.00031 3_[+1]_9 chr7:44347053-44347073 0.00031 8_[+1]_4 chr5:1471785-1471805 0.00031 [+1]_12 chr19:18526398-18526418 0.00031 1_[+1]_11 chr16:4365891-4365911 0.00054 8_[+1]_4 chr7:38398790-38398810 0.0006 12_[+1] chr20:52224287-52224307 0.00069 5_[+1]_7 chr9:134151372-134151392 0.00069 5_[+1]_7 chr4:8206507-8206527 0.00072 5_[+1]_7 chr10:127925208-12792522 0.00072 1_[+1]_11 chr17:65822310-65822330 0.0008 4_[+1]_8 chr1:205473879-205473899 0.00085 8_[+1]_4 chr20:52245481-52245501 0.001 4_[+1]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRGGAGGA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RRGGAGGA width=8 seqs=43 chrX:47240452-47240472 ( 11) GAGGAGGA 1 chr6:158402823-158402843 ( 9) GAGGAGGA 1 chr10:121302210-12130223 ( 7) GAGGAGGA 1 chr6:143267092-143267112 ( 8) GAGGAGGA 1 chr12:19592931-19592951 ( 12) GAGGAGGA 1 chr3:48541720-48541740 ( 2) GAGGAGGA 1 chr20:44651615-44651635 ( 8) GAGGAGGA 1 chr6:157100006-157100026 ( 4) GAGGAGGA 1 chr7:100397323-100397343 ( 4) GGGGAGGA 1 chr20:62151309-62151329 ( 13) GGGGAGGA 1 chr9:109625834-109625854 ( 13) GGGGAGGA 1 chr19:51315253-51315273 ( 4) AGGGAGGA 1 chr1:181318846-181318866 ( 9) AGGGAGGA 1 chr20:35089898-35089918 ( 6) AGGGAGGA 1 chr6:2989214-2989234 ( 5) AGGGAGGA 1 chr13:21871271-21871291 ( 8) AGGGAGGA 1 chr7:1115936-1115956 ( 6) AGGGAGGA 1 chr5:1472384-1472404 ( 3) AGGGAGGA 1 chr1:180980981-180981001 ( 4) GAGGAGCA 1 chr17:994569-994589 ( 9) AAGGAGCA 1 chr9:129466522-129466542 ( 6) GGGGAGCA 1 chr17:6366204-6366224 ( 11) GGGGAGCA 1 chr7:75619616-75619636 ( 5) GGGGAGCA 1 chr12:2034524-2034544 ( 1) AGGGAGCA 1 chr12:133164529-13316454 ( 4) AGGGAGCA 1 chr19:3646880-3646900 ( 12) CAGGAGGA 1 chr10:105211378-10521139 ( 9) CAGGAGGA 1 chr10:125785708-12578572 ( 12) CAGGAGCA 1 chr7:70159458-70159478 ( 2) GGGGAGAA 1 chr2:73613116-73613136 ( 10) GAGGAGGT 1 chr14:75721761-75721781 ( 4) AGGGAGAA 1 chr7:44347053-44347073 ( 9) GAGGAGGG 1 chr5:1471785-1471805 ( 1) GAGGAGGT 1 chr19:18526398-18526418 ( 2) GAGGAGGG 1 chr16:4365891-4365911 ( 9) AGGGAGGG 1 chr7:38398790-38398810 ( 13) GAGGAGCT 1 chr20:52224287-52224307 ( 6) CAGGAGAA 1 chr9:134151372-134151392 ( 6) GCGGAGCA 1 chr4:8206507-8206527 ( 6) ACGGAGCA 1 chr10:127925208-12792522 ( 2) AAGGAACA 1 chr17:65822310-65822330 ( 5) GAGGACGA 1 chr1:205473879-205473899 ( 9) AGGGAGCG 1 chr20:52245481-52245501 ( 5) CAGGAAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRGGAGGA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 7.75266 E= 4.1e-024 74 -126 89 -1207 129 -258 61 -1207 -1207 -1207 179 -1207 -1207 -1207 179 -1207 226 -1207 -1207 -1207 -217 -358 169 -1207 -158 12 112 -1207 200 -1207 -164 -168 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRGGAGGA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 43 E= 4.1e-024 0.348837 0.116279 0.534884 0.000000 0.511628 0.046512 0.441860 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.046512 0.023256 0.930233 0.000000 0.069767 0.302326 0.627907 0.000000 0.837209 0.000000 0.093023 0.069767 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRGGAGGA MEME-1 regular expression -------------------------------------------------------------------------------- [GA][AG]GGAG[GC]A -------------------------------------------------------------------------------- Time 2.18 secs. ******************************************************************************** ******************************************************************************** MOTIF STSCTCCC MEME-2 width = 8 sites = 39 llr = 298 E-value = 8.6e-024 ******************************************************************************** -------------------------------------------------------------------------------- Motif STSCTCCC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::1::1: pos.-specific C 4:59:a97 probability G 6:5::::: matrix T 1a::a:13 bits 2.3 * 2.0 * * 1.8 * ** 1.6 * *** Relative 1.4 * **** Entropy 1.1 * **** (11.0 bits) 0.9 ****** 0.7 ******* 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GTCCTCCC consensus C G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STSCTCCC MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr12:131531542-13153156 6 2.41e-05 TCAGT GTCCTCCC TGGTGAG chr12:125978351-12597837 11 2.41e-05 CCTCCTCTCC GTCCTCCC TG chr11:47398069-47398089 5 2.41e-05 CTGA Gtcctccc tatcctcc chr4:40859297-40859317 2 4.91e-05 G GTGCTCCC GCCAGATGCT chr3:53876888-53876908 6 4.91e-05 CAGGA GTGCTCCC AACAGTT chr5:944674-944694 6 4.91e-05 TCCTG GTGCTCCC CATACTC chr18:46468292-46468312 9 4.91e-05 TGTTGGCA GTGCTCCC ACCC chr22:39437273-39437293 1 4.91e-05 . GTGCTCCC TCTGTGTTCT chr12:131530482-13153050 10 4.91e-05 CCCTGGTTG GTGCTCCC TCC chr9:135450535-135450555 10 4.91e-05 GTCCTCCGG GTGCTCCC AGC chr22:39473659-39473679 11 4.91e-05 CCCTGGGAGG GTGCTCCC TC chr12:131574153-13157417 12 4.91e-05 TACCTGATGG GTGCTCCC G chr15:41851362-41851382 1 7.23e-05 . ctcctccc tcccgctccc chr11:129309997-12931001 9 7.23e-05 AGCACTCC CTCCTCCC ACAG chr12:125670890-12567091 12 7.23e-05 cctcctcctc ctcctccc c chr22:45088361-45088381 2 7.23e-05 C CTCCTCCC AGGGCTCCTC chr19:4081561-4081581 2 7.23e-05 C CTCCTCCC TTCTCCTTGA chr3:53839688-53839708 11 7.23e-05 AAGCCTTAtc ctcctccc tc chr16:616978-616998 10 7.23e-05 TGCCAGTGG CTCCTCCC ACT chrX:19851278-19851298 5 1.16e-04 cacg gtcctcct ctccttcc chr22:32960951-32960971 6 1.36e-04 AAACA GTGCTCCT GGACTGC chr17:73238749-73238769 11 1.36e-04 GGAAGCTATT GTGCTCCT CC chr8:50064176-50064196 10 1.36e-04 gctcccatg gtgctcct atg chr16:53087037-53087057 11 1.55e-04 cctcctgctc ctcctcct cc chr5:49962748-49962768 12 1.55e-04 cctccccctc ctcctcct c chr1:26201738-26201758 2 1.55e-04 G CTCCTCCT TCCTGCGCCC chr10:133579292-13357931 13 1.74e-04 gctccttctt ctgctcct chr19:39014092-39014112 10 1.93e-04 ccctctccc ttcctccc cag chr10:79398120-79398140 10 2.27e-04 CGCTCGCTC TTCCTCCT TGC chr19:42432617-42432637 5 2.27e-04 cctc ttcctcct cttcctcc chr7:4875202-4875222 5 2.98e-04 CCAA GTCATCCC CAAAACTG chr11:742739-742759 7 3.56e-04 TGGGCA GTGATCCC TTTGTA chr10:135132197-13513221 6 4.28e-04 GCCCG CTCCTCAC ACGGACG chr5:1473173-1473193 4 5.02e-04 CTC CTGCTCTC TGGCCAGAG chr14:90701799-90701819 5 5.02e-04 ACAA GTGCTCCA CAGAGCAC chr8:128751162-128751182 13 5.02e-04 CTCGGATTCT CTGCTCTC chr5:77409673-77409693 7 5.72e-04 ACTGCT GTCCTCAT TGCTGT chr15:41136574-41136594 5 6.62e-04 TGGG GTGCTCCG GTCCCTCC chr21:40177886-40177906 13 7.93e-04 CTCCAGCTCA GAGCTCCC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STSCTCCC MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:131531542-13153156 2.4e-05 5_[+2]_7 chr12:125978351-12597837 2.4e-05 10_[+2]_2 chr11:47398069-47398089 2.4e-05 4_[+2]_8 chr4:40859297-40859317 4.9e-05 1_[+2]_11 chr3:53876888-53876908 4.9e-05 5_[+2]_7 chr5:944674-944694 4.9e-05 5_[+2]_7 chr18:46468292-46468312 4.9e-05 8_[+2]_4 chr22:39437273-39437293 4.9e-05 [+2]_12 chr12:131530482-13153050 4.9e-05 9_[+2]_3 chr9:135450535-135450555 4.9e-05 9_[+2]_3 chr22:39473659-39473679 4.9e-05 10_[+2]_2 chr12:131574153-13157417 4.9e-05 11_[+2]_1 chr15:41851362-41851382 7.2e-05 [+2]_12 chr11:129309997-12931001 7.2e-05 8_[+2]_4 chr12:125670890-12567091 7.2e-05 11_[+2]_1 chr22:45088361-45088381 7.2e-05 1_[+2]_11 chr19:4081561-4081581 7.2e-05 1_[+2]_11 chr3:53839688-53839708 7.2e-05 10_[+2]_2 chr16:616978-616998 7.2e-05 9_[+2]_3 chrX:19851278-19851298 0.00012 4_[+2]_8 chr22:32960951-32960971 0.00014 5_[+2]_7 chr17:73238749-73238769 0.00014 10_[+2]_2 chr8:50064176-50064196 0.00014 9_[+2]_3 chr16:53087037-53087057 0.00015 10_[+2]_2 chr5:49962748-49962768 0.00015 11_[+2]_1 chr1:26201738-26201758 0.00015 1_[+2]_11 chr10:133579292-13357931 0.00017 12_[+2] chr19:39014092-39014112 0.00019 9_[+2]_3 chr10:79398120-79398140 0.00023 9_[+2]_3 chr19:42432617-42432637 0.00023 4_[+2]_8 chr7:4875202-4875222 0.0003 4_[+2]_8 chr11:742739-742759 0.00036 6_[+2]_6 chr10:135132197-13513221 0.00043 5_[+2]_7 chr5:1473173-1473193 0.0005 3_[+2]_9 chr14:90701799-90701819 0.0005 4_[+2]_8 chr8:128751162-128751182 0.0005 12_[+2] chr5:77409673-77409693 0.00057 6_[+2]_6 chr15:41136574-41136594 0.00066 4_[+2]_8 chr21:40177886-40177906 0.00079 12_[+2] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STSCTCCC MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF STSCTCCC width=8 seqs=39 chr12:131531542-13153156 ( 6) GTCCTCCC 1 chr12:125978351-12597837 ( 11) GTCCTCCC 1 chr11:47398069-47398089 ( 5) GTCCTCCC 1 chr4:40859297-40859317 ( 2) GTGCTCCC 1 chr3:53876888-53876908 ( 6) GTGCTCCC 1 chr5:944674-944694 ( 6) GTGCTCCC 1 chr18:46468292-46468312 ( 9) GTGCTCCC 1 chr22:39437273-39437293 ( 1) GTGCTCCC 1 chr12:131530482-13153050 ( 10) GTGCTCCC 1 chr9:135450535-135450555 ( 10) GTGCTCCC 1 chr22:39473659-39473679 ( 11) GTGCTCCC 1 chr12:131574153-13157417 ( 12) GTGCTCCC 1 chr15:41851362-41851382 ( 1) CTCCTCCC 1 chr11:129309997-12931001 ( 9) CTCCTCCC 1 chr12:125670890-12567091 ( 12) CTCCTCCC 1 chr22:45088361-45088381 ( 2) CTCCTCCC 1 chr19:4081561-4081581 ( 2) CTCCTCCC 1 chr3:53839688-53839708 ( 11) CTCCTCCC 1 chr16:616978-616998 ( 10) CTCCTCCC 1 chrX:19851278-19851298 ( 5) GTCCTCCT 1 chr22:32960951-32960971 ( 6) GTGCTCCT 1 chr17:73238749-73238769 ( 11) GTGCTCCT 1 chr8:50064176-50064196 ( 10) GTGCTCCT 1 chr16:53087037-53087057 ( 11) CTCCTCCT 1 chr5:49962748-49962768 ( 12) CTCCTCCT 1 chr1:26201738-26201758 ( 2) CTCCTCCT 1 chr10:133579292-13357931 ( 13) CTGCTCCT 1 chr19:39014092-39014112 ( 10) TTCCTCCC 1 chr10:79398120-79398140 ( 10) TTCCTCCT 1 chr19:42432617-42432637 ( 5) TTCCTCCT 1 chr7:4875202-4875222 ( 5) GTCATCCC 1 chr11:742739-742759 ( 7) GTGATCCC 1 chr10:135132197-13513221 ( 6) CTCCTCAC 1 chr5:1473173-1473193 ( 4) CTGCTCTC 1 chr14:90701799-90701819 ( 5) GTGCTCCA 1 chr8:128751162-128751182 ( 13) CTGCTCTC 1 chr5:77409673-77409693 ( 7) GTCCTCAT 1 chr15:41136574-41136594 ( 5) GTGCTCCG 1 chr21:40177886-40177906 ( 13) GAGCTCCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STSCTCCC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 7.83209 E= 8.6e-024 -1193 37 96 -154 -303 -1193 -1193 212 -1193 88 75 -1193 -203 177 -1193 -1193 -1193 -1193 -1193 216 -1193 185 -1193 -1193 -203 169 -1193 -212 -303 126 -349 33 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STSCTCCC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 39 E= 8.6e-024 0.000000 0.358974 0.564103 0.076923 0.025641 0.000000 0.000000 0.974359 0.000000 0.512821 0.487179 0.000000 0.051282 0.948718 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.051282 0.897436 0.000000 0.051282 0.025641 0.666667 0.025641 0.282051 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif STSCTCCC MEME-2 regular expression -------------------------------------------------------------------------------- [GC]T[CG]CTCC[CT] -------------------------------------------------------------------------------- Time 2.89 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTTHHWT MEME-3 width = 8 sites = 25 llr = 176 E-value = 1.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTTHHWT MEME-3 Description -------------------------------------------------------------------------------- Simplified A 1:::3353 pos.-specific C ::2:34:: probability G :2:::::: matrix T 988a4357 bits 2.3 * 2.0 * 1.8 * 1.6 ** * Relative 1.4 **** * Entropy 1.1 **** ** (10.2 bits) 0.9 **** ** 0.7 **** ** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TTTTTCAT consensus C CTTA sequence AA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTHHWT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr20:52512125-52512145 8 1.33e-05 TGATTTC TTTTTTAT TATAA chr20:52531576-52531596 2 1.33e-05 C TTTTTCAT TTCGTAAATA chr17:59916187-59916207 12 3.30e-05 TATGGACTAC TTTTTTTT C chr20:52292522-52292542 10 3.30e-05 TAACtttta tttttttt gag chr20:52237935-52237955 3 5.13e-05 AT TTTTACAT AGGAAAACAA chr17:59913776-59913796 10 5.64e-05 AAAAACTAT TTTTAAAT CTG chr17:59696540-59696560 2 8.61e-05 T TTTTCCAT AAGTGTGGGT chr20:46020153-46020173 10 8.61e-05 TACCAATAT TTTTACTT GAG chr17:57909785-57909805 1 1.54e-04 . TTTTTCTA AGGCTTTCTC chr20:52358814-52358834 7 1.76e-04 GCCTCA TTTTAAAA ATGTGA chr20:52560250-52560270 1 2.04e-04 . TTTTATTA ACTGAGGTTA chr17:59787041-59787061 2 2.15e-04 G TTTTCAAA CTGCCTTGCT chr17:59643302-59643322 8 2.32e-04 cagtacc ttttctta tattt chr17:58463493-58463513 12 2.55e-04 CTTCCAAGAG TTCTTTAT T chr20:45950900-45950920 9 2.97e-04 agcctccc tgtttcat tgat chr17:59773309-59773329 12 2.97e-04 cctttctttc ttcttctt g chr20:52447041-52447061 1 2.97e-04 . TGTTTTAT CAGAAATAAA chr17:59849791-59849811 9 3.39e-04 gaacagag ttcttatt tggt chr19:4081561-4081581 10 5.46e-04 CCTCCTCCC TTCTCCTT GAT chr20:52234628-52234648 2 5.46e-04 T ATTTAAAT CCATTCTCTC chr20:52630106-52630126 4 6.15e-04 tgt atttccat ctctaagag chr22:39437273-39437293 13 6.55e-04 GCTCCCTCTG TGTTCTTT chr20:52185733-52185753 10 8.93e-04 ACCATTCGC TTCTCAAA GGA chr17:59671430-59671450 3 9.53e-04 AG TGTTACTA GAGTATGTTT chr17:59652602-59652622 6 1.07e-03 GAGAA ATTTCATA CAGAAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTHHWT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr20:52512125-52512145 1.3e-05 7_[+3]_5 chr20:52531576-52531596 1.3e-05 1_[+3]_11 chr17:59916187-59916207 3.3e-05 11_[+3]_1 chr20:52292522-52292542 3.3e-05 9_[+3]_3 chr20:52237935-52237955 5.1e-05 2_[+3]_10 chr17:59913776-59913796 5.6e-05 9_[+3]_3 chr17:59696540-59696560 8.6e-05 1_[+3]_11 chr20:46020153-46020173 8.6e-05 9_[+3]_3 chr17:57909785-57909805 0.00015 [+3]_12 chr20:52358814-52358834 0.00018 6_[+3]_6 chr20:52560250-52560270 0.0002 [+3]_12 chr17:59787041-59787061 0.00022 1_[+3]_11 chr17:59643302-59643322 0.00023 7_[+3]_5 chr17:58463493-58463513 0.00026 11_[+3]_1 chr20:45950900-45950920 0.0003 8_[+3]_4 chr17:59773309-59773329 0.0003 11_[+3]_1 chr20:52447041-52447061 0.0003 [+3]_12 chr17:59849791-59849811 0.00034 8_[+3]_4 chr19:4081561-4081581 0.00055 9_[+3]_3 chr20:52234628-52234648 0.00055 1_[+3]_11 chr20:52630106-52630126 0.00061 3_[+3]_9 chr22:39437273-39437293 0.00066 12_[+3] chr20:52185733-52185753 0.00089 9_[+3]_3 chr17:59671430-59671450 0.00095 2_[+3]_10 chr17:59652602-59652622 0.0011 5_[+3]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTHHWT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTTHHWT width=8 seqs=25 chr20:52512125-52512145 ( 8) TTTTTTAT 1 chr20:52531576-52531596 ( 2) TTTTTCAT 1 chr17:59916187-59916207 ( 12) TTTTTTTT 1 chr20:52292522-52292542 ( 10) TTTTTTTT 1 chr20:52237935-52237955 ( 3) TTTTACAT 1 chr17:59913776-59913796 ( 10) TTTTAAAT 1 chr17:59696540-59696560 ( 2) TTTTCCAT 1 chr20:46020153-46020173 ( 10) TTTTACTT 1 chr17:57909785-57909805 ( 1) TTTTTCTA 1 chr20:52358814-52358834 ( 7) TTTTAAAA 1 chr20:52560250-52560270 ( 1) TTTTATTA 1 chr17:59787041-59787061 ( 2) TTTTCAAA 1 chr17:59643302-59643322 ( 8) TTTTCTTA 1 chr17:58463493-58463513 ( 12) TTCTTTAT 1 chr20:45950900-45950920 ( 9) TGTTTCAT 1 chr17:59773309-59773329 ( 12) TTCTTCTT 1 chr20:52447041-52447061 ( 1) TGTTTTAT 1 chr17:59849791-59849811 ( 9) TTCTTATT 1 chr19:4081561-4081581 ( 10) TTCTCCTT 1 chr20:52234628-52234648 ( 2) ATTTAAAT 1 chr20:52630106-52630126 ( 4) ATTTCCAT 1 chr22:39437273-39437293 ( 13) TGTTCTTT 1 chr20:52185733-52185753 ( 10) TTCTCAAA 1 chr17:59671430-59671450 ( 3) TGTTACTA 1 chr17:59652602-59652622 ( 6) ATTTCATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTHHWT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.15019 E= 1.7e+001 -80 -1129 -1129 198 -1129 -1129 -85 191 -1129 -47 -1129 184 -1129 -1129 -1129 216 42 20 -1129 84 42 52 -1129 52 131 -1129 -1129 110 61 -1129 -1129 160 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTHHWT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 25 E= 1.7e+001 0.120000 0.000000 0.000000 0.880000 0.000000 0.000000 0.160000 0.840000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 1.000000 0.280000 0.320000 0.000000 0.400000 0.280000 0.400000 0.000000 0.320000 0.520000 0.000000 0.000000 0.480000 0.320000 0.000000 0.000000 0.680000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTHHWT MEME-3 regular expression -------------------------------------------------------------------------------- TT[TC]T[TCA][CTA][AT][TA] -------------------------------------------------------------------------------- Time 3.61 secs. ******************************************************************************** ******************************************************************************** MOTIF AVAAAYAA MEME-4 width = 8 sites = 7 llr = 67 E-value = 6.7e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif AVAAAYAA MEME-4 Description -------------------------------------------------------------------------------- Simplified A a4aaa:9a pos.-specific C :3:::4:: probability G :3:::1:: matrix T :::::41: bits 2.3 * *** * 2.0 * *** * 1.8 * *** * 1.6 * *** ** Relative 1.4 * *** ** Entropy 1.1 * *** ** (13.9 bits) 0.9 * *** ** 0.7 * *** ** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel AAAAACAA consensus C T sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVAAAYAA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr20:55832219-55832239 3 8.74e-06 TG AAAAACAA ACTTCTGGGA chr20:52213324-52213344 12 8.74e-06 ATGCCAGCAA AAAAACAA A chr17:59660152-59660172 6 1.93e-05 GGCAA ACAAATAA TCAGAAA chr20:52447041-52447061 10 1.93e-05 TGTTTTATC AGAAATAA ATA chr17:59684173-59684193 13 1.93e-05 atttgttgta acaaataa chr17:36412457-36412477 2 5.53e-05 A AGAAAGAA CTGAGTCAGG chr17:59913776-59913796 1 6.05e-05 . AAAAACTA TTTTTAAATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVAAAYAA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr20:55832219-55832239 8.7e-06 2_[+4]_10 chr20:52213324-52213344 8.7e-06 11_[+4]_1 chr17:59660152-59660172 1.9e-05 5_[+4]_7 chr20:52447041-52447061 1.9e-05 9_[+4]_3 chr17:59684173-59684193 1.9e-05 12_[+4] chr17:36412457-36412477 5.5e-05 1_[+4]_11 chr17:59913776-59913796 6.1e-05 [+4]_12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVAAAYAA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AVAAAYAA width=8 seqs=7 chr20:55832219-55832239 ( 3) AAAAACAA 1 chr20:52213324-52213344 ( 12) AAAAACAA 1 chr17:59660152-59660172 ( 6) ACAAATAA 1 chr20:52447041-52447061 ( 10) AGAAATAA 1 chr17:59684173-59684193 ( 13) ACAAATAA 1 chr17:36412457-36412477 ( 2) AGAAAGAA 1 chr17:59913776-59913796 ( 1) AAAAACTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVAAAYAA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.0799 E= 6.7e+001 226 -945 -945 -945 103 4 -2 -945 226 -945 -945 -945 226 -945 -945 -945 226 -945 -945 -945 -945 62 -102 94 203 -945 -945 -65 226 -945 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVAAAYAA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 6.7e+001 1.000000 0.000000 0.000000 0.000000 0.428571 0.285714 0.285714 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.428571 0.142857 0.428571 0.857143 0.000000 0.000000 0.142857 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVAAAYAA MEME-4 regular expression -------------------------------------------------------------------------------- A[ACG]AAA[CT]AA -------------------------------------------------------------------------------- Time 6.53 secs. ******************************************************************************** ******************************************************************************** MOTIF AAGAAAAG MEME-5 width = 8 sites = 2 llr = 24 E-value = 1.6e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAGAAAAG MEME-5 Description -------------------------------------------------------------------------------- Simplified A aa:aaaa: pos.-specific C :::::::: probability G ::a::::a matrix T :::::::: bits 2.3 ** **** 2.0 ** **** 1.8 ******** 1.6 ******** Relative 1.4 ******** Entropy 1.1 ******** (17.1 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel AAGAAAAG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGAAAAG MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr17:59915209-59915229 2 6.96e-06 T AAGAAAAG GTACTGACAC chr20:52557005-52557025 8 6.96e-06 GCCATTC AAGAAAAG GGCAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGAAAAG MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:59915209-59915229 7e-06 1_[+5]_11 chr20:52557005-52557025 7e-06 7_[+5]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGAAAAG MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAGAAAAG width=8 seqs=2 chr17:59915209-59915229 ( 2) AAGAAAAG 1 chr20:52557005-52557025 ( 8) AAGAAAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGAAAAG MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 1.6e+003 225 -765 -765 -765 225 -765 -765 -765 -765 -765 178 -765 225 -765 -765 -765 225 -765 -765 -765 225 -765 -765 -765 225 -765 -765 -765 -765 -765 178 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGAAAAG MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.6e+003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGAAAAG MEME-5 regular expression -------------------------------------------------------------------------------- AAGAAAAG -------------------------------------------------------------------------------- Time 9.54 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:27930380-27930400 7.29e-03 20 chr12:133164529-13316454 6.49e-02 20 chr17:80185492-80185512 8.47e-01 20 chr12:131574153-13157417 9.43e-02 11_[+2(4.91e-05)]_1 chr1:117338221-117338241 4.34e-01 20 chr5:176790153-176790173 1.54e-01 20 chr6:157100006-157100026 2.33e-02 [+1(1.84e-05)]_12 chr22:39417791-39417811 9.88e-01 20 chr9:109625834-109625854 3.54e-02 12_[+1(5.72e-05)] chr22:39473659-39473679 1.17e-02 10_[+2(4.91e-05)]_2 chr9:135450535-135450555 2.72e-02 9_[+2(4.91e-05)]_3 chr3:195887390-195887410 8.99e-01 20 chr16:29606365-29606385 9.13e-01 20 chr7:105650092-105650112 7.58e-01 20 chr20:44651615-44651635 2.49e-03 1_[+1(1.84e-05)]_11 chr12:111866890-11186691 7.43e-01 20 chr7:73704970-73704990 7.80e-01 20 chr8:50064176-50064196 2.16e-02 20 chr11:742739-742759 1.39e-01 20 chr19:2056518-2056538 6.40e-01 20 chr12:131530482-13153050 5.47e-02 9_[+2(4.91e-05)]_3 chr20:62151309-62151329 7.21e-02 12_[+1(5.72e-05)] chr2:158732794-158732814 4.10e-01 20 chr22:39437273-39437293 6.96e-03 [+2(4.91e-05)]_12 chr20:32450523-32450543 8.91e-01 20 chr1:26201738-26201758 8.34e-02 20 chr5:1472384-1472404 4.46e-02 2_[+1(7.56e-05)]_10 chr13:24846305-24846325 8.94e-01 20 chr10:71078621-71078641 3.35e-01 20 chr8:71316142-71316162 5.34e-01 20 chr12:122237888-12223790 5.46e-01 20 chr9:134151372-134151392 1.67e-01 20 chr15:91397600-91397620 4.68e-01 20 chr22:38200982-38201002 9.68e-01 20 chr18:46468292-46468312 5.68e-02 8_[+2(4.91e-05)]_4 chr10:125785708-12578572 1.44e-01 20 chr8:128751162-128751182 3.21e-01 20 chr9:140428872-140428892 9.66e-01 20 chr5:77409673-77409693 1.74e-01 20 chr1:994453-994473 4.04e-01 20 chr16:49384483-49384503 3.81e-02 20 chr17:73238749-73238769 3.00e-02 20 chr5:394975-394995 9.64e-01 20 chr2:242144697-242144717 8.18e-01 20 chr14:21539682-21539702 8.49e-01 20 chr1:205473879-205473899 4.57e-01 20 chr19:18526398-18526418 1.76e-02 20 chr10:135132197-13513221 2.68e-01 20 chr9:126774067-126774087 9.98e-01 20 chr2:191492733-191492753 9.04e-01 20 chr7:1115936-1115956 4.80e-02 5_[+1(7.56e-05)]_7 chr17:45609320-45609340 7.56e-01 20 chr22:42680091-42680111 7.24e-01 20 chr17:36412457-36412477 1.92e-03 1_[+4(5.53e-05)]_11 chr1:180980981-180981001 1.41e-02 3_[+1(9.33e-05)]_9 chr18:77492147-77492167 1.59e-01 20 chr5:944674-944694 8.00e-02 5_[+2(4.91e-05)]_7 chr14:90701799-90701819 1.53e-02 20 chr2:162095412-162095432 9.99e-01 20 chr19:35167791-35167811 1.07e-01 20 chr6:3457229-3457249 6.88e-01 20 chr11:47398069-47398089 6.48e-02 4_[+2(2.41e-05)]_8 chr5:1471785-1471805 9.81e-03 20 chr3:48541720-48541740 2.24e-03 1_[+1(1.84e-05)]_11 chr7:38385338-38385358 3.47e-01 20 chr9:139429859-139429879 4.63e-01 20 chr5:1473173-1473193 1.79e-01 20 chrX:9982886-9982906 9.18e-01 20 chr16:616978-616998 1.23e-01 9_[+2(7.23e-05)]_3 chr2:106361174-106361194 8.87e-01 20 chr16:1426311-1426331 9.52e-01 20 chr4:48212472-48212492 6.06e-01 20 chr20:52358814-52358834 4.81e-03 20 chr20:52410713-52410733 5.35e-01 20 chr6:32981553-32981573 9.92e-01 20 chr7:44347053-44347073 2.49e-02 20 chr18:77492778-77492798 8.19e-02 20 chr20:52524696-52524716 2.54e-01 20 chr7:38398790-38398810 9.50e-02 20 chr7:38389618-38389638 4.54e-01 20 chr3:53839688-53839708 6.40e-02 10_[+2(7.23e-05)]_2 chr20:52234628-52234648 1.02e-01 20 chr7:75619616-75619636 3.60e-02 20 chr17:6366204-6366224 3.34e-02 20 chr22:32960951-32960971 2.85e-02 20 chr20:52198535-52198555 5.38e-01 20 chr6:163835760-163835780 9.54e-01 20 chr20:52557005-52557025 4.72e-03 7_[+5(6.96e-06)]_5 chr19:4145749-4145769 7.99e-01 20 chr20:52560250-52560270 7.17e-02 20 chr10:104504456-10450447 3.41e-01 20 chr15:81592142-81592162 3.93e-01 20 chr19:4081561-4081581 8.03e-03 1_[+2(7.23e-05)]_11 chr10:133579292-13357931 2.77e-02 20 chr20:52244794-52244814 4.40e-01 20 chr19:42432617-42432637 1.93e-01 20 chr15:22892598-22892618 5.79e-01 20 chr17:59896815-59896835 5.52e-01 20 chr19:17531464-17531484 9.88e-01 20 chr20:52237935-52237955 3.98e-05 2_[+3(5.13e-05)]_10 chr17:65822310-65822330 1.90e-01 20 chr20:52210711-52210731 3.85e-01 20 chr7:100397323-100397343 7.27e-02 3_[+1(5.72e-05)]_9 chr20:52394733-52394753 1.23e-01 20 chr20:52308001-52308021 7.80e-01 20 chr20:52309431-52309451 8.85e-01 20 chr22:46421261-46421281 9.77e-01 20 chr17:59787041-59787061 1.08e-01 20 chr22:45088361-45088381 1.33e-01 1_[+2(7.23e-05)]_11 chr16:9185799-9185819 9.72e-01 20 chr9:139887370-139887390 4.57e-01 20 chr17:59849791-59849811 4.13e-02 20 chr20:52319339-52319359 9.85e-01 20 chr17:59631608-59631628 4.51e-02 20 chr7:5494965-5494985 4.43e-01 20 chr20:52213324-52213344 1.37e-04 11_[+4(8.74e-06)]_1 chr20:11871436-11871456 9.87e-01 20 chr20:43940318-43940338 3.79e-01 20 chr12:19592931-19592951 2.42e-02 11_[+1(1.84e-05)]_1 chr17:59782485-59782505 3.75e-01 20 chr20:52201843-52201863 9.69e-01 20 chr20:52185733-52185753 7.61e-02 20 chr5:49962748-49962768 1.97e-01 20 chr13:21871271-21871291 4.99e-02 7_[+1(7.56e-05)]_5 chr20:52423737-52423757 8.16e-01 20 chr20:52224287-52224307 2.91e-02 20 chr20:52362245-52362265 1.01e-01 20 chr12:105086054-10508607 9.72e-01 20 chr20:46020153-46020173 2.10e-02 9_[+3(8.61e-05)]_3 chr5:6322737-6322757 5.54e-01 20 chr19:39014092-39014112 1.86e-01 20 chr19:4241963-4241983 8.36e-01 20 chr9:73027875-73027895 9.95e-01 20 chr17:7121219-7121239 9.40e-01 20 chr10:105455580-10545560 9.68e-01 20 chr17:994569-994589 8.18e-03 20 chr20:55832219-55832239 3.84e-03 2_[+4(8.74e-06)]_10 chr12:125978351-12597837 6.50e-02 10_[+2(2.41e-05)]_2 chr6:2989214-2989234 1.13e-01 4_[+1(7.56e-05)]_8 chr19:3647339-3647359 6.83e-01 20 chr14:70015000-70015020 5.07e-01 20 chr17:59837624-59837644 6.83e-02 20 chr10:105211378-10521139 3.65e-03 20 chr20:52292522-52292542 8.12e-02 9_[+3(3.30e-05)]_3 chr20:52245481-52245501 4.91e-03 20 chr12:2034524-2034544 6.97e-02 20 chr20:52430695-52430715 9.83e-01 20 chr20:52457733-52457753 5.73e-02 20 chr17:59696540-59696560 8.19e-02 1_[+3(8.61e-05)]_11 chr21:40177886-40177906 2.26e-01 20 chr19:3646880-3646900 3.08e-02 20 chr17:57909785-57909805 9.16e-02 20 chr20:35089898-35089918 1.14e-01 5_[+1(7.56e-05)]_7 chr3:64017364-64017384 4.80e-01 20 chr17:59890270-59890290 2.78e-01 20 chr12:108991827-10899184 9.69e-01 20 chr20:52475757-52475777 3.80e-01 20 chr17:59916187-59916207 4.60e-02 11_[+3(3.30e-05)]_1 chr14:75895184-75895204 7.24e-01 20 chr20:52531576-52531596 8.95e-03 1_[+3(1.33e-05)]_11 chr20:52388999-52389019 5.33e-01 20 chr16:4365891-4365911 3.36e-01 20 chr12:125670890-12567091 1.31e-01 11_[+2(7.23e-05)]_1 chr20:52339610-52339630 1.64e-02 20 chr20:52206025-52206045 8.85e-01 20 chr17:59912788-59912808 9.84e-01 20 chr10:121410587-12141060 9.47e-01 20 chr19:7571604-7571624 3.45e-01 20 chr17:59637625-59637645 7.19e-01 20 chr17:59915209-59915229 8.65e-04 1_[+5(6.96e-06)]_11 chr2:231386284-231386304 2.00e-01 20 chr17:58847445-58847465 8.70e-01 20 chr7:128809062-128809082 1.00e+00 20 chr9:129466522-129466542 1.15e-01 20 chr12:48297922-48297942 4.13e-01 20 chr1:148176264-148176284 7.32e-01 20 chr20:52343392-52343412 5.43e-01 20 chr20:46124382-46124402 3.81e-01 20 chr17:59684173-59684193 1.85e-03 12_[+4(1.93e-05)] chr11:129309997-12931001 1.30e-01 8_[+2(7.23e-05)]_4 chr6:143267092-143267112 5.76e-03 4_[+1(1.84e-05)]_8 chr20:52447041-52447061 7.32e-05 9_[+4(1.93e-05)]_3 chr17:59773309-59773329 1.58e-01 20 chr20:45981205-45981225 7.70e-01 20 chr17:59777696-59777716 4.28e-01 20 chr17:59913776-59913796 4.20e-04 [+4(6.05e-05)]_1_[+3(5.64e-05)]_3 chr10:121302210-12130223 2.42e-02 6_[+1(1.84e-05)]_6 chr17:59660152-59660172 5.90e-03 5_[+4(1.93e-05)]_7 chr2:73511440-73511460 6.95e-01 20 chr17:58472464-58472484 7.62e-02 20 chr20:52713151-52713171 2.16e-01 20 chr20:52429910-52429930 5.03e-01 20 chr1:181318846-181318866 6.45e-02 8_[+1(7.56e-05)]_4 chr20:52207354-52207374 5.19e-01 20 chrX:109245663-109245683 6.50e-01 20 chr12:122241894-12224191 5.30e-01 20 chr21:36262525-36262545 1.00e+00 20 chr20:52515217-52515237 7.21e-01 20 chr15:41851362-41851382 1.23e-01 [+2(7.23e-05)]_12 chr17:3599517-3599537 7.72e-01 20 chr20:49288191-49288211 1.61e-01 20 chr14:75721761-75721781 1.47e-02 20 chr17:59911951-59911971 1.00e+00 20 chr3:53876888-53876908 8.44e-03 5_[+2(4.91e-05)]_7 chr17:59672177-59672197 5.61e-01 20 chr10:127925208-12792522 4.40e-02 20 chr4:40859297-40859317 8.76e-02 1_[+2(4.91e-05)]_11 chr17:58463493-58463513 7.87e-02 20 chr15:41136574-41136594 1.92e-01 20 chr14:105144138-10514415 6.30e-01 20 chr6:158402823-158402843 9.56e-03 8_[+1(1.84e-05)]_4 chr20:46189371-46189391 2.12e-02 20 chrX:47240452-47240472 4.27e-03 10_[+1(1.84e-05)]_2 chr4:185395296-185395316 1.82e-01 20 chr20:45950900-45950920 2.23e-01 20 chr20:49350576-49350596 7.03e-02 20 chr7:24612978-24612998 8.67e-01 20 chr6:4136354-4136374 6.95e-01 20 chr19:51315051-51315071 5.48e-01 20 chr17:59652602-59652622 5.05e-03 20 chr20:49341084-49341104 8.94e-01 20 chr20:52512125-52512145 2.44e-02 7_[+3(1.33e-05)]_5 chr17:58475980-58476000 7.15e-01 20 chrX:19851278-19851298 4.72e-02 20 chr20:52868416-52868436 2.97e-01 20 chr16:53087037-53087057 1.15e-01 20 chr20:55767543-55767563 9.03e-01 20 chr7:70159458-70159478 9.19e-02 20 chr20:52630106-52630126 1.79e-01 20 chr12:131531542-13153156 5.85e-02 5_[+2(2.41e-05)]_7 chr17:59691765-59691785 7.58e-01 20 chr20:52381918-52381938 1.49e-01 20 chr17:59671430-59671450 2.15e-01 20 chr6:86303173-86303193 9.32e-01 20 chr4:8206507-8206527 2.21e-01 20 chr20:52387439-52387459 8.95e-02 20 chr2:224702298-224702318 5.74e-01 20 chr10:79398120-79398140 1.04e-01 20 chr19:51315253-51315273 4.75e-02 3_[+1(7.56e-05)]_9 chr20:52716671-52716691 6.73e-01 20 chr7:5636041-5636061 1.00e+00 20 chr17:59397697-59397717 3.37e-01 20 chr2:73613116-73613136 1.77e-01 20 chr20:52331467-52331487 3.41e-02 20 chr20:55813307-55813327 1.01e-01 20 chr17:59437865-59437885 7.18e-01 20 chr17:59643302-59643322 1.00e-01 20 chr20:49293623-49293643 5.11e-01 20 chr20:46165898-46165918 4.66e-01 20 chr7:4875202-4875222 3.18e-02 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c17n09.farnam.hpc.yale.internal ********************************************************************************