******************************************************************************** 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/EED.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr1:92270325-92270345 1.0000 20 chr3:189814220-189814240 1.0000 20 chr16:57375145-57375165 1.0000 20 chr1:161469662-161469682 1.0000 20 chr16:13535759-13535779 1.0000 20 chr10:6172011-6172031 1.0000 20 chr5:150531587-150531607 1.0000 20 chr8:10646435-10646455 1.0000 20 chr1:59479089-59479109 1.0000 20 chr10:3852486-3852506 1.0000 20 chr17:70026707-70026727 1.0000 20 chr16:19139318-19139338 1.0000 20 chr15:67426454-67426474 1.0000 20 chr16:15993619-15993639 1.0000 20 chr10:126303020-12630304 1.0000 20 chr7:24768298-24768318 1.0000 20 chr19:50872100-50872120 1.0000 20 chr2:60743063-60743083 1.0000 20 chr1:92338350-92338370 1.0000 20 chr10:73648720-73648740 1.0000 20 chr10:74052133-74052153 1.0000 20 chr7:131305541-131305561 1.0000 20 chr6:32209671-32209691 1.0000 20 chr11:65341924-65341944 1.0000 20 chr8:18704580-18704600 1.0000 20 chr18:9069900-9069920 1.0000 20 chr8:42360634-42360654 1.0000 20 chr10:30716683-30716703 1.0000 20 chr15:74692333-74692353 1.0000 20 chr22:44845452-44845472 1.0000 20 chr12:46459712-46459732 1.0000 20 chr16:31363007-31363027 1.0000 20 chr16:70462125-70462145 1.0000 20 chr20:414510-414530 1.0000 20 chr2:231818723-231818743 1.0000 20 chr22:30711072-30711092 1.0000 20 chr6:159488613-159488633 1.0000 20 chr20:62359919-62359939 1.0000 20 chr21:45592743-45592763 1.0000 20 chr6:42391163-42391183 1.0000 20 chr13:111128068-11112808 1.0000 20 chr3:185972685-185972705 1.0000 20 chr2:31479269-31479289 1.0000 20 chr10:85299822-85299842 1.0000 20 chr16:89390913-89390933 1.0000 20 chr19:45225721-45225741 1.0000 20 chr3:149294157-149294177 1.0000 20 chr14:52311352-52311372 1.0000 20 chr4:141712179-141712199 1.0000 20 chr20:19928695-19928715 1.0000 20 chr8:56798288-56798308 1.0000 20 chr7:83428039-83428059 1.0000 20 chr16:10336937-10336957 1.0000 20 chr16:87814492-87814512 1.0000 20 chr6:137040882-137040902 1.0000 20 chr5:176727452-176727472 1.0000 20 chr8:119208358-119208378 1.0000 20 chr5:157029672-157029692 1.0000 20 chr6:14666307-14666327 1.0000 20 chr5:173216163-173216183 1.0000 20 chr15:40408159-40408179 1.0000 20 chr16:10915145-10915165 1.0000 20 chr7:77022754-77022774 1.0000 20 chr10:121276198-12127621 1.0000 20 chr12:111837327-11183734 1.0000 20 chr4:40765454-40765474 1.0000 20 chr5:18698722-18698742 1.0000 20 chr20:52228292-52228312 1.0000 20 chr16:77361777-77361797 1.0000 20 chr1:182592460-182592480 1.0000 20 chr22:32313440-32313460 1.0000 20 chr10:81026656-81026676 1.0000 20 chr20:35899118-35899138 1.0000 20 chr16:10847162-10847182 1.0000 20 chr1:15742608-15742628 1.0000 20 chr22:44725484-44725504 1.0000 20 chr2:103052970-103052990 1.0000 20 chr16:11456011-11456031 1.0000 20 chr16:81850470-81850490 1.0000 20 chr15:66683219-66683239 1.0000 20 chr1:12139533-12139553 1.0000 20 chr3:137707178-137707198 1.0000 20 chr19:33771493-33771513 1.0000 20 chr1:41275262-41275282 1.0000 20 chrX:13770932-13770952 1.0000 20 chr2:45918410-45918430 1.0000 20 chr19:6556663-6556683 1.0000 20 chr9:137295962-137295982 1.0000 20 chr17:65566120-65566140 1.0000 20 chr16:68390485-68390505 1.0000 20 chr14:91708356-91708376 1.0000 20 chr8:101485385-101485405 1.0000 20 chr4:40579246-40579266 1.0000 20 chr8:56835607-56835627 1.0000 20 chr6:31705946-31705966 1.0000 20 chr2:99076406-99076426 1.0000 20 chr6:4902082-4902102 1.0000 20 chr6:157018515-157018535 1.0000 20 chr1:160752169-160752189 1.0000 20 chr7:56119262-56119282 1.0000 20 chr1:183562682-183562702 1.0000 20 chr6:112314237-112314257 1.0000 20 chr7:90561504-90561524 1.0000 20 chr19:42375848-42375868 1.0000 20 chr16:85981635-85981655 1.0000 20 chr5:73872898-73872918 1.0000 20 chr1:112019804-112019824 1.0000 20 chr6:35336418-35336438 1.0000 20 chr14:90147533-90147553 1.0000 20 chr2:11884328-11884348 1.0000 20 chr3:118491749-118491769 1.0000 20 chr6:119907875-119907895 1.0000 20 chr16:86045309-86045329 1.0000 20 chr15:40339997-40340017 1.0000 20 chr17:43410644-43410664 1.0000 20 chr3:72361724-72361744 1.0000 20 chr9:93589660-93589680 1.0000 20 chr12:124875346-12487536 1.0000 20 chr3:169975124-169975144 1.0000 20 chr3:16416545-16416565 1.0000 20 chr12:123372204-12337222 1.0000 20 chrX:70838416-70838436 1.0000 20 chr19:4369317-4369337 1.0000 20 chr8:66863909-66863929 1.0000 20 chr1:247570784-247570804 1.0000 20 chrX:118772988-118773008 1.0000 20 chr1:11000340-11000360 1.0000 20 chr3:185255274-185255294 1.0000 20 chr7:43796390-43796410 1.0000 20 chr20:37491886-37491906 1.0000 20 chr13:99964874-99964894 1.0000 20 chr20:49158438-49158458 1.0000 20 chr17:32307467-32307487 1.0000 20 chr4:89300533-89300553 1.0000 20 chr8:134539058-134539078 1.0000 20 chr21:42733795-42733815 1.0000 20 chr11:1876417-1876437 1.0000 20 chr7:50484313-50484333 1.0000 20 chr20:62330674-62330694 1.0000 20 chr19:56111002-56111022 1.0000 20 chr8:103569508-103569528 1.0000 20 chr2:8656306-8656326 1.0000 20 chr14:65676984-65677004 1.0000 20 chr8:141519390-141519410 1.0000 20 chr19:14495250-14495270 1.0000 20 chr1:32420469-32420489 1.0000 20 chr10:30876637-30876657 1.0000 20 chrX:13023854-13023874 1.0000 20 chr19:2529743-2529763 1.0000 20 chr2:29540117-29540137 1.0000 20 chr12:53594378-53594398 1.0000 20 chr19:10987492-10987512 1.0000 20 chr1:51750870-51750890 1.0000 20 chr19:38570837-38570857 1.0000 20 chr19:39468705-39468725 1.0000 20 chr3:15313513-15313533 1.0000 20 chr2:37851278-37851298 1.0000 20 chr5:139419409-139419429 1.0000 20 chr9:119713905-119713925 1.0000 20 chr19:16230500-16230520 1.0000 20 chr16:80617594-80617614 1.0000 20 chr16:19138661-19138681 1.0000 20 chr3:52278476-52278496 1.0000 20 chr19:36400355-36400375 1.0000 20 chr5:157030543-157030563 1.0000 20 chr14:106995741-10699576 1.0000 20 chr2:38373917-38373937 1.0000 20 chr1:26907578-26907598 1.0000 20 chr12:125030268-12503028 1.0000 20 chr22:31005458-31005478 1.0000 20 chr20:35994920-35994940 1.0000 20 chr12:123921200-12392122 1.0000 20 chr20:43118692-43118712 1.0000 20 chr14:50527874-50527894 1.0000 20 chr4:84096081-84096101 1.0000 20 chr9:102029062-102029082 1.0000 20 chr12:65054590-65054610 1.0000 20 chr6:75994552-75994572 1.0000 20 chr3:5020576-5020596 1.0000 20 chr11:65260765-65260785 1.0000 20 chr5:157289649-157289669 1.0000 20 chr10:25210480-25210500 1.0000 20 chr10:11239284-11239304 1.0000 20 chr6:157042148-157042168 1.0000 20 chr12:76577391-76577411 1.0000 20 chr9:92037278-92037298 1.0000 20 chr15:70772755-70772775 1.0000 20 chr1:21005294-21005314 1.0000 20 chr1:161676359-161676379 1.0000 20 chr20:43213854-43213874 1.0000 20 chr1:12139734-12139754 1.0000 20 chr6:159070923-159070943 1.0000 20 chr8:126525550-126525570 1.0000 20 chr17:76642097-76642117 1.0000 20 chr22:45631326-45631346 1.0000 20 chr11:48128864-48128884 1.0000 20 chr16:21285640-21285660 1.0000 20 chr4:120159450-120159470 1.0000 20 chr1:154779738-154779758 1.0000 20 chr19:3553073-3553093 1.0000 20 chr7:105752259-105752279 1.0000 20 chr12:14767905-14767925 1.0000 20 chr9:138831385-138831405 1.0000 20 chr15:67377879-67377899 1.0000 20 chr16:66558891-66558911 1.0000 20 chr1:12116642-12116662 1.0000 20 chr16:10874742-10874762 1.0000 20 chr3:185943605-185943625 1.0000 20 chr5:171416410-171416430 1.0000 20 chr11:6424025-6424045 1.0000 20 chr1:117370000-117370020 1.0000 20 chr6:341375-341395 1.0000 20 chr4:146981179-146981199 1.0000 20 chr5:142437398-142437418 1.0000 20 chr2:113881964-113881984 1.0000 20 chr12:101381922-10138194 1.0000 20 chr7:43204540-43204560 1.0000 20 chr18:10928183-10928203 1.0000 20 chr20:48955497-48955517 1.0000 20 chr3:16416345-16416365 1.0000 20 chr15:96517204-96517224 1.0000 20 chr7:50304755-50304775 1.0000 20 chr13:51905037-51905057 1.0000 20 chr10:86068673-86068693 1.0000 20 chr7:92271614-92271634 1.0000 20 chr10:8175249-8175269 1.0000 20 chr10:64374309-64374329 1.0000 20 chr12:93384199-93384219 1.0000 20 chr3:72150047-72150067 1.0000 20 chr10:70825632-70825652 1.0000 20 chr6:86353859-86353879 1.0000 20 chr8:82199103-82199123 1.0000 20 chr19:13958621-13958641 1.0000 20 chrX:7002283-7002303 1.0000 20 chr15:79296906-79296926 1.0000 20 chr7:55141953-55141973 1.0000 20 chr12:92757699-92757719 1.0000 20 chr11:60833631-60833651 1.0000 20 chr9:6185200-6185220 1.0000 20 chr13:42943399-42943419 1.0000 20 chr2:75283667-75283687 1.0000 20 chr1:25054193-25054213 1.0000 20 chr3:127469405-127469425 1.0000 20 chr17:18804316-18804336 1.0000 20 chr5:173164233-173164253 1.0000 20 chr6:225350-225370 1.0000 20 chr11:35294110-35294130 1.0000 20 chr1:101759167-101759187 1.0000 20 chr9:136819261-136819281 1.0000 20 chr7:136044251-136044271 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_EED/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/EED.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 0.231 C 0.269 G 0.264 T 0.235 Background letter frequencies (from file dataset with add-one prior applied): A 0.231 C 0.269 G 0.264 T 0.235 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF NSWGGRAR MEME-1 width = 8 sites = 48 llr = 295 E-value = 3.4e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif NSWGGRAR MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2:5:25a5 pos.-specific C 26:::::2 probability G 34:a85:4 matrix T 3:5::::: bits 2.1 * 1.9 * * 1.7 * * 1.5 * * Relative 1.3 ** * Entropy 1.1 ***** (8.9 bits) 0.8 ****** 0.6 ****** 0.4 ******* 0.2 ******* 0.0 -------- Multilevel TCTGGAAA consensus GGA G G sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NSWGGRAR MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr14:50527874-50527894 8 1.07e-04 AGGAGAC TCTGGGAA TTTCC chr4:40579246-40579266 9 1.07e-04 GTTTCAGT TCTGGGAA AGGG chr14:91708356-91708376 13 1.07e-04 agtttctacc tgtggaaa chr7:83428039-83428059 5 1.07e-04 ccca tgtggaaa aaccacat chr2:38373917-38373937 5 1.65e-04 TCAG CCTGGAAA CAACTTTT chr7:55141953-55141973 8 2.51e-04 AGGTCCA GGAGGAAA TTCGG chr1:51750870-51750890 12 2.51e-04 TGGCAGATGT GCTGGGAA G chr2:103052970-103052990 12 2.51e-04 TTCTTGGACC ACAGGAAA C chr16:68390485-68390505 7 3.12e-04 GGCAGG GCAGGAAG GAAGTG chr15:40408159-40408179 5 3.12e-04 ACCC GCAGGAAG CGGTCCAG chr6:137040882-137040902 6 3.12e-04 AGCTA GCTGGAAG TTTCACA chr15:79296906-79296926 12 4.35e-04 ttttgtggaa tgaggaag c chr19:2529743-2529763 10 4.35e-04 ATTCAGGTT TCAGGGAG AGG chr3:185255274-185255294 7 4.35e-04 CATGCT CCTGGGAA CATGCA chr19:6556663-6556683 8 4.35e-04 TCAGAGG CCAGGGAA GTTCT chr16:89390913-89390933 1 4.35e-04 . tgaggaag ctgccaaagg chr19:14495250-14495270 10 5.52e-04 CCCTTAGGC CCAGGAAG TGA chr1:247570784-247570804 10 5.52e-04 TTCTCCCAC ACTGGGAA CAG chr17:43410644-43410664 5 5.52e-04 TCTG CCTGGAAG GTCAGGGG chr16:10847162-10847182 1 5.52e-04 . ACTGGGAA CATTAGACCA chr8:66863909-66863929 9 6.50e-04 AGAAGCAA ACAGGAAG TGCC chr16:10915145-10915165 11 6.50e-04 GGGGATATTG GGAGGAAG GA chr7:136044251-136044271 2 7.44e-04 a tgtgggag acatttctac chr17:76642097-76642117 3 8.42e-04 CT CCTGGGAG AAAAGAGGAT chr19:4369317-4369337 9 8.42e-04 GCTGCCGG AGAGGGAA ATGA chrX:70838416-70838436 9 8.42e-04 AGCCTCTT CCAGGGAG TTAC chr16:81850470-81850490 11 8.42e-04 TGTTATCATT AGTGGGAA AA chr15:74692333-74692353 2 8.42e-04 C AGTGGGAA GAGGCCTTCC chr3:16416545-16416565 10 9.72e-04 GAGGGAAGA GGAGGGAG ACT chr6:119907875-119907895 6 9.72e-04 GAGTG GGTGGGAG CTGAAAT chr22:45631326-45631346 1 1.13e-03 . CCAGGAAC CGAAAGAGGC chr7:90561504-90561524 2 1.13e-03 A TCTGAAAA GTCATTTCTG chr1:161469662-161469682 12 1.13e-03 ccaaacaact cctggaac a chr6:225350-225370 1 1.26e-03 . GGAGGAAC CAGGTTCCCG chr19:36400355-36400375 3 1.26e-03 AA GGAGGAAC CTGAGGTTAG chr1:112019804-112019824 10 1.32e-03 AAAGCAAAA GCTGAAAA CCA chr10:85299822-85299842 10 1.32e-03 CAGTCATCC TGTGGGAC CTG chr2:37851278-37851298 2 1.44e-03 T TCTGAGAA TGAGTGTACA chr5:73872898-73872918 7 1.44e-03 GAGAGC TCTGAGAA TGACAC chr17:65566120-65566140 9 1.44e-03 CCCAGGCT CCAGGGAC AGGC chr20:52228292-52228312 4 1.44e-03 GCA TGAGAAAA GCACCACTT chr2:31479269-31479289 7 1.44e-03 GCCAAA CGTGGAAC AGGTTT chr3:15313513-15313533 5 1.59e-03 CCCT GGTGGGAC GTCCCTAA chr19:42375848-42375868 8 1.59e-03 GCAATTG TCAGAAAG TGAGA chr2:45918410-45918430 5 1.59e-03 CCTC AGAGGAAC AGGCTGGG chr3:118491749-118491769 3 1.66e-03 CT GGAGAAAA AGCCCAGCCC chr1:160752169-160752189 12 1.75e-03 AAAACGCAGG TGTGAGAA A chr16:77361777-77361797 2 2.08e-03 A ACAGAAAG CACCATTTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NSWGGRAR MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr14:50527874-50527894 0.00011 7_[+1]_5 chr4:40579246-40579266 0.00011 8_[+1]_4 chr14:91708356-91708376 0.00011 12_[+1] chr7:83428039-83428059 0.00011 4_[+1]_8 chr2:38373917-38373937 0.00017 4_[+1]_8 chr7:55141953-55141973 0.00025 7_[+1]_5 chr1:51750870-51750890 0.00025 11_[+1]_1 chr2:103052970-103052990 0.00025 11_[+1]_1 chr16:68390485-68390505 0.00031 6_[+1]_6 chr15:40408159-40408179 0.00031 4_[+1]_8 chr6:137040882-137040902 0.00031 5_[+1]_7 chr15:79296906-79296926 0.00043 11_[+1]_1 chr19:2529743-2529763 0.00043 9_[+1]_3 chr3:185255274-185255294 0.00043 6_[+1]_6 chr19:6556663-6556683 0.00043 7_[+1]_5 chr16:89390913-89390933 0.00043 [+1]_12 chr19:14495250-14495270 0.00055 9_[+1]_3 chr1:247570784-247570804 0.00055 9_[+1]_3 chr17:43410644-43410664 0.00055 4_[+1]_8 chr16:10847162-10847182 0.00055 [+1]_12 chr8:66863909-66863929 0.00065 8_[+1]_4 chr16:10915145-10915165 0.00065 10_[+1]_2 chr7:136044251-136044271 0.00074 1_[+1]_11 chr17:76642097-76642117 0.00084 2_[+1]_10 chr19:4369317-4369337 0.00084 8_[+1]_4 chrX:70838416-70838436 0.00084 8_[+1]_4 chr16:81850470-81850490 0.00084 10_[+1]_2 chr15:74692333-74692353 0.00084 1_[+1]_11 chr3:16416545-16416565 0.00097 9_[+1]_3 chr6:119907875-119907895 0.00097 5_[+1]_7 chr22:45631326-45631346 0.0011 [+1]_12 chr7:90561504-90561524 0.0011 1_[+1]_11 chr1:161469662-161469682 0.0011 11_[+1]_1 chr6:225350-225370 0.0013 [+1]_12 chr19:36400355-36400375 0.0013 2_[+1]_10 chr1:112019804-112019824 0.0013 9_[+1]_3 chr10:85299822-85299842 0.0013 9_[+1]_3 chr2:37851278-37851298 0.0014 1_[+1]_11 chr5:73872898-73872918 0.0014 6_[+1]_6 chr17:65566120-65566140 0.0014 8_[+1]_4 chr20:52228292-52228312 0.0014 3_[+1]_9 chr2:31479269-31479289 0.0014 6_[+1]_6 chr3:15313513-15313533 0.0016 4_[+1]_8 chr19:42375848-42375868 0.0016 7_[+1]_5 chr2:45918410-45918430 0.0016 4_[+1]_8 chr3:118491749-118491769 0.0017 2_[+1]_10 chr1:160752169-160752189 0.0018 11_[+1]_1 chr16:77361777-77361797 0.0021 1_[+1]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NSWGGRAR MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF NSWGGRAR width=8 seqs=48 chr14:50527874-50527894 ( 8) TCTGGGAA 1 chr4:40579246-40579266 ( 9) TCTGGGAA 1 chr14:91708356-91708376 ( 13) TGTGGAAA 1 chr7:83428039-83428059 ( 5) TGTGGAAA 1 chr2:38373917-38373937 ( 5) CCTGGAAA 1 chr7:55141953-55141973 ( 8) GGAGGAAA 1 chr1:51750870-51750890 ( 12) GCTGGGAA 1 chr2:103052970-103052990 ( 12) ACAGGAAA 1 chr16:68390485-68390505 ( 7) GCAGGAAG 1 chr15:40408159-40408179 ( 5) GCAGGAAG 1 chr6:137040882-137040902 ( 6) GCTGGAAG 1 chr15:79296906-79296926 ( 12) TGAGGAAG 1 chr19:2529743-2529763 ( 10) TCAGGGAG 1 chr3:185255274-185255294 ( 7) CCTGGGAA 1 chr19:6556663-6556683 ( 8) CCAGGGAA 1 chr16:89390913-89390933 ( 1) TGAGGAAG 1 chr19:14495250-14495270 ( 10) CCAGGAAG 1 chr1:247570784-247570804 ( 10) ACTGGGAA 1 chr17:43410644-43410664 ( 5) CCTGGAAG 1 chr16:10847162-10847182 ( 1) ACTGGGAA 1 chr8:66863909-66863929 ( 9) ACAGGAAG 1 chr16:10915145-10915165 ( 11) GGAGGAAG 1 chr7:136044251-136044271 ( 2) TGTGGGAG 1 chr17:76642097-76642117 ( 3) CCTGGGAG 1 chr19:4369317-4369337 ( 9) AGAGGGAA 1 chrX:70838416-70838436 ( 9) CCAGGGAG 1 chr16:81850470-81850490 ( 11) AGTGGGAA 1 chr15:74692333-74692353 ( 2) AGTGGGAA 1 chr3:16416545-16416565 ( 10) GGAGGGAG 1 chr6:119907875-119907895 ( 6) GGTGGGAG 1 chr22:45631326-45631346 ( 1) CCAGGAAC 1 chr7:90561504-90561524 ( 2) TCTGAAAA 1 chr1:161469662-161469682 ( 12) CCTGGAAC 1 chr6:225350-225370 ( 1) GGAGGAAC 1 chr19:36400355-36400375 ( 3) GGAGGAAC 1 chr1:112019804-112019824 ( 10) GCTGAAAA 1 chr10:85299822-85299842 ( 10) TGTGGGAC 1 chr2:37851278-37851298 ( 2) TCTGAGAA 1 chr5:73872898-73872918 ( 7) TCTGAGAA 1 chr17:65566120-65566140 ( 9) CCAGGGAC 1 chr20:52228292-52228312 ( 4) TGAGAAAA 1 chr2:31479269-31479289 ( 7) CGTGGAAC 1 chr3:15313513-15313533 ( 5) GGTGGGAC 1 chr19:42375848-42375868 ( 8) TCAGAAAG 1 chr2:45918410-45918430 ( 5) AGAGGAAC 1 chr3:118491749-118491769 ( 3) GGAGAAAA 1 chr1:160752169-160752189 ( 12) TGTGAGAA 1 chr16:77361777-77361797 ( 2) ACAGAAAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NSWGGRAR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 6.51301 E= 3.4e-005 -30 -23 4 41 -1223 106 73 -1223 105 -1223 -1223 115 -1223 -1223 192 -1223 -30 -1223 162 -1223 123 -1223 79 -1223 211 -1223 -1223 -1223 99 -52 42 -1223 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NSWGGRAR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 48 E= 3.4e-005 0.187500 0.229167 0.270833 0.312500 0.000000 0.562500 0.437500 0.000000 0.479167 0.000000 0.000000 0.520833 0.000000 0.000000 1.000000 0.000000 0.187500 0.000000 0.812500 0.000000 0.541667 0.000000 0.458333 0.000000 1.000000 0.000000 0.000000 0.000000 0.458333 0.187500 0.354167 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NSWGGRAR MEME-1 regular expression -------------------------------------------------------------------------------- [TGC][CG][TA]GG[AG]A[AG] -------------------------------------------------------------------------------- Time 5.31 secs. ******************************************************************************** ******************************************************************************** MOTIF CNYTTCCM MEME-2 width = 8 sites = 50 llr = 290 E-value = 3.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif CNYTTCCM MEME-2 Description -------------------------------------------------------------------------------- Simplified A 12::::13 pos.-specific C 5453:a95 probability G 22:::::: matrix T 2257a::2 bits 2.1 * 1.9 ** 1.7 ** 1.5 *** Relative 1.3 **** Entropy 1.1 ***** (8.4 bits) 0.8 ***** 0.6 ***** 0.4 ****** 0.2 * ****** 0.0 -------- Multilevel CCCTTCCC consensus GGTC A sequence TT T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CNYTTCCM MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr16:19138661-19138681 12 1.83e-05 CACCAAACTT CCTTTCCC A chr19:56111002-56111022 1 1.83e-05 . cctttccc AGCCCTGGAG chr20:62330674-62330694 1 3.92e-05 . CCCTTCCC AGCAGCTCCT chr10:25210480-25210500 6 5.49e-05 CTTTT CCTTTCCA CTCCTGC chr9:93589660-93589680 6 1.41e-04 AAGCC CATTTCCC TAATTAC chr10:30716683-30716703 1 1.41e-04 . CATTTCCC TTGCTCAGTT chr20:35994920-35994940 6 1.93e-04 ctccc cacttccc cctaaac chr1:117370000-117370020 5 2.54e-04 TTAT CTCTTCCA AGGGTGAT chr15:40339997-40340017 3 3.39e-04 GT CGCTTCCA GTCAGCCCCA chr1:15742608-15742628 13 3.39e-04 GAGTCACCTC TCCTTCCC chr14:52311352-52311372 1 3.39e-04 . TCCTTCCC GGGAGAACCT chr11:65341924-65341944 7 3.39e-04 CTTCGG GCTTTCCC TGCCTG chr20:62359919-62359939 11 3.91e-04 AAGAGCCAGG CCCTTCCT GG chr10:126303020-12630304 13 3.91e-04 GGGCGCGGCG GCCTTCCC chr1:12139734-12139754 6 4.36e-04 GCTCC TCCTTCCA AGGGGAT chr8:56798288-56798308 3 4.36e-04 CT GCTTTCCA GGGGGAAGCT chr4:89300533-89300553 6 5.29e-04 GTTTC GTTTTCCC AACGCCC chr15:74692333-74692353 13 5.29e-04 GTGGGAAGAG GCCTTCCA chr3:72150047-72150067 5 6.71e-04 CGGA TGCTTCCC CAGCGGGC chr1:183562682-183562702 2 6.71e-04 C CTCttcct ccgcccatgt chr16:11456011-11456031 7 6.71e-04 GTTTGT GGTTTCCC CTTACT chr20:35899118-35899138 5 6.71e-04 GTCT TACTTCCC CTCTGTGG chr11:60833631-60833651 3 8.16e-04 GC CGCTTCCT GATTTCACAT chr1:32420469-32420489 3 8.16e-04 CT CACTTCCT CCTCTTTGGG chr8:119208358-119208378 11 9.26e-04 CTTTCCGTCA GGTTTCCA AA chr12:111837327-11183734 2 1.10e-03 g cttctccc agagtggatg chr1:161676359-161676379 9 1.18e-03 AGATTTTC TTTTTCCT CTAC chr6:31705946-31705966 10 1.18e-03 CCTTTTTCT CTCCTCCC GAC chr5:142437398-142437418 4 1.51e-03 TTC TCTCTCCC ACTATTGCA chr5:157030543-157030563 11 1.51e-03 GGCCACAGTT CTCCTCCA TA chrX:13023854-13023874 13 1.51e-03 CAGGCACGCA CATCTCCA chr7:77022754-77022774 1 1.51e-03 . catctcca aactccacct chr2:113881964-113881984 3 1.69e-03 AG AGCTTCCC TTGTCCCCTT chr19:3553073-3553093 1 1.69e-03 . CCTCTCCT GCTGGTTTCT chr1:11000340-11000360 11 1.69e-03 CCTGGATGCT GACTTCCT GT chr10:121276198-12127621 1 1.69e-03 . GGCTTCCT GTTTCACCCG chr5:139419409-139419429 8 1.79e-03 TGACGAC AGTTTCCA AGTGC chr6:159488613-159488633 9 1.79e-03 TGTGTGGG ATCTTCCA TCGT chrX:7002283-7002303 12 1.88e-03 TGTGGTTAGA AACTTCCA C chr10:11239284-11239304 11 2.00e-03 ATGCTCACTC CTTCTCCT GT chr16:85981635-85981655 10 2.00e-03 CTGAATCCA GCCCTCCA CGT chr8:82199103-82199123 1 2.18e-03 . tttctcca ctccttagag chr6:157042148-157042168 6 2.18e-03 CACTT TTTCTCCA CACTCTG chr8:18704580-18704600 11 2.18e-03 CTCGACACTG CCTTTCAC CT chr3:189814220-189814240 12 2.18e-03 ttcccatttg cctttcac t chr20:19928695-19928715 8 2.35e-03 ATCCCAG TGTCTCCA GATGA chr19:45225721-45225741 5 2.35e-03 AGCG GGCCTCCC AGAATGTC chr4:40765454-40765474 2 2.50e-03 C AGTTTCCT CGTGCTTCTC chr11:1876417-1876437 5 2.74e-03 TTCT CATTTCAC AAGGTGAC chr16:87814492-87814512 12 3.17e-03 TGCCCACAAG TCCTTCAC C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CNYTTCCM MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr16:19138661-19138681 1.8e-05 11_[+2]_1 chr19:56111002-56111022 1.8e-05 [+2]_12 chr20:62330674-62330694 3.9e-05 [+2]_12 chr10:25210480-25210500 5.5e-05 5_[+2]_7 chr9:93589660-93589680 0.00014 5_[+2]_7 chr10:30716683-30716703 0.00014 [+2]_12 chr20:35994920-35994940 0.00019 5_[+2]_7 chr1:117370000-117370020 0.00025 4_[+2]_8 chr15:40339997-40340017 0.00034 2_[+2]_10 chr1:15742608-15742628 0.00034 12_[+2] chr14:52311352-52311372 0.00034 [+2]_12 chr11:65341924-65341944 0.00034 6_[+2]_6 chr20:62359919-62359939 0.00039 10_[+2]_2 chr10:126303020-12630304 0.00039 12_[+2] chr1:12139734-12139754 0.00044 5_[+2]_7 chr8:56798288-56798308 0.00044 2_[+2]_10 chr4:89300533-89300553 0.00053 5_[+2]_7 chr15:74692333-74692353 0.00053 12_[+2] chr3:72150047-72150067 0.00067 4_[+2]_8 chr1:183562682-183562702 0.00067 1_[+2]_11 chr16:11456011-11456031 0.00067 6_[+2]_6 chr20:35899118-35899138 0.00067 4_[+2]_8 chr11:60833631-60833651 0.00082 2_[+2]_10 chr1:32420469-32420489 0.00082 2_[+2]_10 chr8:119208358-119208378 0.00093 10_[+2]_2 chr12:111837327-11183734 0.0011 1_[+2]_11 chr1:161676359-161676379 0.0012 8_[+2]_4 chr6:31705946-31705966 0.0012 9_[+2]_3 chr5:142437398-142437418 0.0015 3_[+2]_9 chr5:157030543-157030563 0.0015 10_[+2]_2 chrX:13023854-13023874 0.0015 12_[+2] chr7:77022754-77022774 0.0015 [+2]_12 chr2:113881964-113881984 0.0017 2_[+2]_10 chr19:3553073-3553093 0.0017 [+2]_12 chr1:11000340-11000360 0.0017 10_[+2]_2 chr10:121276198-12127621 0.0017 [+2]_12 chr5:139419409-139419429 0.0018 7_[+2]_5 chr6:159488613-159488633 0.0018 8_[+2]_4 chrX:7002283-7002303 0.0019 11_[+2]_1 chr10:11239284-11239304 0.002 10_[+2]_2 chr16:85981635-85981655 0.002 9_[+2]_3 chr8:82199103-82199123 0.0022 [+2]_12 chr6:157042148-157042168 0.0022 5_[+2]_7 chr8:18704580-18704600 0.0022 10_[+2]_2 chr3:189814220-189814240 0.0022 11_[+2]_1 chr20:19928695-19928715 0.0024 7_[+2]_5 chr19:45225721-45225741 0.0024 4_[+2]_8 chr4:40765454-40765474 0.0025 1_[+2]_11 chr11:1876417-1876437 0.0027 4_[+2]_8 chr16:87814492-87814512 0.0032 11_[+2]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CNYTTCCM MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CNYTTCCM width=8 seqs=50 chr16:19138661-19138681 ( 12) CCTTTCCC 1 chr19:56111002-56111022 ( 1) CCTTTCCC 1 chr20:62330674-62330694 ( 1) CCCTTCCC 1 chr10:25210480-25210500 ( 6) CCTTTCCA 1 chr9:93589660-93589680 ( 6) CATTTCCC 1 chr10:30716683-30716703 ( 1) CATTTCCC 1 chr20:35994920-35994940 ( 6) CACTTCCC 1 chr1:117370000-117370020 ( 5) CTCTTCCA 1 chr15:40339997-40340017 ( 3) CGCTTCCA 1 chr1:15742608-15742628 ( 13) TCCTTCCC 1 chr14:52311352-52311372 ( 1) TCCTTCCC 1 chr11:65341924-65341944 ( 7) GCTTTCCC 1 chr20:62359919-62359939 ( 11) CCCTTCCT 1 chr10:126303020-12630304 ( 13) GCCTTCCC 1 chr1:12139734-12139754 ( 6) TCCTTCCA 1 chr8:56798288-56798308 ( 3) GCTTTCCA 1 chr4:89300533-89300553 ( 6) GTTTTCCC 1 chr15:74692333-74692353 ( 13) GCCTTCCA 1 chr3:72150047-72150067 ( 5) TGCTTCCC 1 chr1:183562682-183562702 ( 2) CTCTTCCT 1 chr16:11456011-11456031 ( 7) GGTTTCCC 1 chr20:35899118-35899138 ( 5) TACTTCCC 1 chr11:60833631-60833651 ( 3) CGCTTCCT 1 chr1:32420469-32420489 ( 3) CACTTCCT 1 chr8:119208358-119208378 ( 11) GGTTTCCA 1 chr12:111837327-11183734 ( 2) CTTCTCCC 1 chr1:161676359-161676379 ( 9) TTTTTCCT 1 chr6:31705946-31705966 ( 10) CTCCTCCC 1 chr5:142437398-142437418 ( 4) TCTCTCCC 1 chr5:157030543-157030563 ( 11) CTCCTCCA 1 chrX:13023854-13023874 ( 13) CATCTCCA 1 chr7:77022754-77022774 ( 1) CATCTCCA 1 chr2:113881964-113881984 ( 3) AGCTTCCC 1 chr19:3553073-3553093 ( 1) CCTCTCCT 1 chr1:11000340-11000360 ( 11) GACTTCCT 1 chr10:121276198-12127621 ( 1) GGCTTCCT 1 chr5:139419409-139419429 ( 8) AGTTTCCA 1 chr6:159488613-159488633 ( 9) ATCTTCCA 1 chrX:7002283-7002303 ( 12) AACTTCCA 1 chr10:11239284-11239304 ( 11) CTTCTCCT 1 chr16:85981635-85981655 ( 10) GCCCTCCA 1 chr8:82199103-82199123 ( 1) TTTCTCCA 1 chr6:157042148-157042168 ( 6) TTTCTCCA 1 chr8:18704580-18704600 ( 11) CCTTTCAC 1 chr3:189814220-189814240 ( 12) CCTTTCAC 1 chr20:19928695-19928715 ( 8) TGTCTCCA 1 chr19:45225721-45225741 ( 5) GGCCTCCC 1 chr4:40765454-40765474 ( 2) AGTTTCCT 1 chr11:1876417-1876437 ( 5) CATTTCAC 1 chr16:87814492-87814512 ( 12) TCCTTCAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CNYTTCCM MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 7.14511 E= 3.3e+000 -121 77 -26 -10 -21 42 -26 -10 -1229 89 -1229 109 -1229 -5 -1229 165 -1229 -1229 -1229 209 -1229 189 -1229 -1229 -153 177 -1229 -1229 55 77 -1229 -24 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CNYTTCCM MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 50 E= 3.3e+000 0.100000 0.460000 0.220000 0.220000 0.200000 0.360000 0.220000 0.220000 0.000000 0.500000 0.000000 0.500000 0.000000 0.260000 0.000000 0.740000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.080000 0.920000 0.000000 0.000000 0.340000 0.460000 0.000000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CNYTTCCM MEME-2 regular expression -------------------------------------------------------------------------------- [CGT][CGTA][CT][TC]TCC[CAT] -------------------------------------------------------------------------------- Time 8.30 secs. ******************************************************************************** ******************************************************************************** MOTIF AAAAATGT MEME-3 width = 8 sites = 2 llr = 23 E-value = 2.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAAATGT MEME-3 Description -------------------------------------------------------------------------------- Simplified A aaaaa::: pos.-specific C :::::::: probability G ::::::a: matrix T :::::a:a bits 2.1 ****** * 1.9 ******** 1.7 ******** 1.5 ******** Relative 1.3 ******** Entropy 1.1 ******** (16.7 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AAAAATGT consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAATGT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:154779738-154779758 3 9.59e-06 GA AAAAATGT CCCCTGGTGG chr12:76577391-76577411 6 9.59e-06 GGGAT AAAAATGT CTATTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAATGT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:154779738-154779758 9.6e-06 2_[+3]_10 chr12:76577391-76577411 9.6e-06 5_[+3]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAATGT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAAAATGT width=8 seqs=2 chr1:154779738-154779758 ( 3) AAAAATGT 1 chr12:76577391-76577411 ( 6) AAAAATGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAATGT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.6653 E= 2.4e+003 211 -765 -765 -765 211 -765 -765 -765 211 -765 -765 -765 211 -765 -765 -765 211 -765 -765 -765 -765 -765 -765 208 -765 -765 192 -765 -765 -765 -765 208 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAATGT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.4e+003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAATGT MEME-3 regular expression -------------------------------------------------------------------------------- AAAAATGT -------------------------------------------------------------------------------- Time 10.72 secs. ******************************************************************************** ******************************************************************************** MOTIF RAAAGAGG MEME-4 width = 8 sites = 7 llr = 65 E-value = 1.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAAAGAGG MEME-4 Description -------------------------------------------------------------------------------- Simplified A 49aa:a11 pos.-specific C :1:::::: probability G 6:::a:99 matrix T :::::::: bits 2.1 ** * 1.9 **** 1.7 **** 1.5 ***** Relative 1.3 ******* Entropy 1.1 ******** (13.5 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GAAAGAGG consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAGAGG MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr22:45631326-45631346 10 1.38e-05 CCAGGAACC GAAAGAGG CTC chr10:73648720-73648740 8 1.38e-05 GAGAAGC GAAAGAGG ATCCG chr17:76642097-76642117 11 2.59e-05 CTCCTGGGAG AAAAGAGG AT chr16:19139318-19139338 1 2.59e-05 . AAAAGAGG CATCAGAGTC chr19:10987492-10987512 2 5.01e-05 G GAAAGAGA ACAGAACAAA chr17:32307467-32307487 5 5.01e-05 AAGT GAAAGAAG TGAAAGAA chr22:44725484-44725504 10 1.02e-04 GTTTCAGCC ACAAGAGG GGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAGAGG MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr22:45631326-45631346 1.4e-05 9_[+4]_3 chr10:73648720-73648740 1.4e-05 7_[+4]_5 chr17:76642097-76642117 2.6e-05 10_[+4]_2 chr16:19139318-19139338 2.6e-05 [+4]_12 chr19:10987492-10987512 5e-05 1_[+4]_11 chr17:32307467-32307487 5e-05 4_[+4]_8 chr22:44725484-44725504 0.0001 9_[+4]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAGAGG MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RAAAGAGG width=8 seqs=7 chr22:45631326-45631346 ( 10) GAAAGAGG 1 chr10:73648720-73648740 ( 8) GAAAGAGG 1 chr17:76642097-76642117 ( 11) AAAAGAGG 1 chr16:19139318-19139338 ( 1) AAAAGAGG 1 chr19:10987492-10987512 ( 2) GAAAGAGA 1 chr17:32307467-32307487 ( 5) GAAAGAAG 1 chr22:44725484-44725504 ( 10) ACAAGAGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAGAGG MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 10.0799 E= 1.5e+003 89 -945 111 -945 189 -91 -945 -945 211 -945 -945 -945 211 -945 -945 -945 -945 -945 192 -945 211 -945 -945 -945 -69 -945 170 -945 -69 -945 170 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAGAGG MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 1.5e+003 0.428571 0.000000 0.571429 0.000000 0.857143 0.142857 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 1.000000 0.000000 0.000000 0.000000 0.142857 0.000000 0.857143 0.000000 0.142857 0.000000 0.857143 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAGAGG MEME-4 regular expression -------------------------------------------------------------------------------- [GA]AAAGAGG -------------------------------------------------------------------------------- Time 11.44 secs. ******************************************************************************** ******************************************************************************** MOTIF GMAGGMCC MEME-5 width = 8 sites = 10 llr = 86 E-value = 3.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GMAGGMCC MEME-5 Description -------------------------------------------------------------------------------- Simplified A :6a::4:2 pos.-specific C :3:::5a8 probability G a::aa1:: matrix T :1:::::: bits 2.1 * 1.9 * *** * 1.7 * *** * 1.5 * *** * Relative 1.3 * *** ** Entropy 1.1 * *** ** (12.4 bits) 0.8 ***** ** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GAAGGCCC consensus C A A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GMAGGMCC MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr12:93384199-93384219 10 1.91e-05 AGAAGCTAG GAAGGCCC TGG chr20:43118692-43118712 10 1.91e-05 ACTGGAGAT GAAGGCCC CAG chr6:42391163-42391183 7 1.91e-05 AACCGA GAAGGCCC CATCAC chr6:341375-341395 7 3.55e-05 GCAATA GAAGGACC AGGACT chr1:182592460-182592480 9 3.55e-05 AATGAAAG GAAGGACC GGAA chr1:21005294-21005314 10 7.69e-05 AGTACGTGT GCAGGACC AGA chr5:173164233-173164253 1 1.26e-04 . GAAGGGCC TCAACCACAG chr1:92270325-92270345 1 1.46e-04 . GTAGGCCC TCACCGGCAG chr9:92037278-92037298 11 1.81e-04 CTTGGGGAGG GCAGGCCA CA chr11:35294110-35294130 6 1.98e-04 CCAAG GCAGGACA TGGGAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GMAGGMCC MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr12:93384199-93384219 1.9e-05 9_[+5]_3 chr20:43118692-43118712 1.9e-05 9_[+5]_3 chr6:42391163-42391183 1.9e-05 6_[+5]_6 chr6:341375-341395 3.6e-05 6_[+5]_6 chr1:182592460-182592480 3.6e-05 8_[+5]_4 chr1:21005294-21005314 7.7e-05 9_[+5]_3 chr5:173164233-173164253 0.00013 [+5]_12 chr1:92270325-92270345 0.00015 [+5]_12 chr9:92037278-92037298 0.00018 10_[+5]_2 chr11:35294110-35294130 0.0002 5_[+5]_7 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GMAGGMCC MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GMAGGMCC width=8 seqs=10 chr12:93384199-93384219 ( 10) GAAGGCCC 1 chr20:43118692-43118712 ( 10) GAAGGCCC 1 chr6:42391163-42391183 ( 7) GAAGGCCC 1 chr6:341375-341395 ( 7) GAAGGACC 1 chr1:182592460-182592480 ( 9) GAAGGACC 1 chr1:21005294-21005314 ( 10) GCAGGACC 1 chr5:173164233-173164253 ( 1) GAAGGGCC 1 chr1:92270325-92270345 ( 1) GTAGGCCC 1 chr9:92037278-92037298 ( 11) GCAGGCCA 1 chr11:35294110-35294130 ( 6) GCAGGACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GMAGGMCC MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 3250 bayes= 8.5921 E= 3.1e+003 -997 -997 192 -997 137 16 -997 -123 211 -997 -997 -997 -997 -997 192 -997 -997 -997 192 -997 79 89 -140 -997 -997 189 -997 -997 -21 157 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GMAGGMCC MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 10 E= 3.1e+003 0.000000 0.000000 1.000000 0.000000 0.600000 0.300000 0.000000 0.100000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.500000 0.100000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GMAGGMCC MEME-5 regular expression -------------------------------------------------------------------------------- G[AC]AGG[CA]C[CA] -------------------------------------------------------------------------------- Time 12.10 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:92270325-92270345 2.66e-02 20 chr3:189814220-189814240 6.98e-01 20 chr16:57375145-57375165 8.64e-01 20 chr1:161469662-161469682 5.77e-02 20 chr16:13535759-13535779 1.37e-01 20 chr10:6172011-6172031 5.96e-01 20 chr5:150531587-150531607 7.66e-01 20 chr8:10646435-10646455 8.17e-01 20 chr1:59479089-59479109 6.39e-01 20 chr10:3852486-3852506 6.91e-01 20 chr17:70026707-70026727 8.11e-01 20 chr16:19139318-19139338 1.34e-02 [+4(2.59e-05)]_12 chr15:67426454-67426474 6.72e-01 20 chr16:15993619-15993639 7.10e-01 20 chr10:126303020-12630304 2.57e-01 20 chr7:24768298-24768318 8.89e-02 20 chr19:50872100-50872120 7.32e-01 20 chr2:60743063-60743083 2.54e-01 20 chr1:92338350-92338370 5.97e-02 20 chr10:73648720-73648740 5.58e-03 7_[+4(1.38e-05)]_5 chr10:74052133-74052153 6.10e-01 20 chr7:131305541-131305561 9.65e-01 20 chr6:32209671-32209691 2.93e-02 20 chr11:65341924-65341944 3.03e-01 20 chr8:18704580-18704600 5.92e-01 20 chr18:9069900-9069920 5.15e-01 20 chr8:42360634-42360654 5.07e-01 20 chr10:30716683-30716703 2.38e-01 20 chr15:74692333-74692353 2.63e-04 20 chr22:44845452-44845472 1.33e-01 20 chr12:46459712-46459732 8.05e-01 20 chr16:31363007-31363027 2.92e-01 20 chr16:70462125-70462145 8.04e-02 20 chr20:414510-414530 3.53e-01 20 chr2:231818723-231818743 9.91e-01 20 chr22:30711072-30711092 8.81e-01 20 chr6:159488613-159488633 9.72e-02 20 chr20:62359919-62359939 1.85e-02 20 chr21:45592743-45592763 9.99e-01 20 chr6:42391163-42391183 4.13e-03 6_[+5(1.91e-05)]_6 chr13:111128068-11112808 9.60e-01 20 chr3:185972685-185972705 5.71e-02 20 chr2:31479269-31479289 5.14e-02 20 chr10:85299822-85299842 5.39e-02 20 chr16:89390913-89390933 2.79e-02 20 chr19:45225721-45225741 2.66e-02 20 chr3:149294157-149294177 7.90e-01 20 chr14:52311352-52311372 1.05e-02 20 chr4:141712179-141712199 4.65e-01 20 chr20:19928695-19928715 4.61e-01 20 chr8:56798288-56798308 7.28e-02 20 chr7:83428039-83428059 4.82e-03 20 chr16:10336937-10336957 4.98e-01 20 chr16:87814492-87814512 4.22e-01 20 chr6:137040882-137040902 1.33e-02 20 chr5:176727452-176727472 9.78e-01 20 chr8:119208358-119208378 4.98e-01 20 chr5:157029672-157029692 8.43e-01 20 chr6:14666307-14666327 4.31e-01 20 chr5:173216163-173216183 7.76e-01 20 chr15:40408159-40408179 1.03e-02 20 chr16:10915145-10915165 1.09e-01 20 chr7:77022754-77022774 3.12e-01 20 chr10:121276198-12127621 6.14e-01 20 chr12:111837327-11183734 1.48e-01 20 chr4:40765454-40765474 7.29e-01 20 chr5:18698722-18698742 3.49e-01 20 chr20:52228292-52228312 1.55e-02 20 chr16:77361777-77361797 9.39e-03 20 chr1:182592460-182592480 1.38e-03 8_[+5(3.55e-05)]_4 chr22:32313440-32313460 9.13e-01 20 chr10:81026656-81026676 5.33e-01 20 chr20:35899118-35899138 4.75e-01 20 chr16:10847162-10847182 1.00e-01 20 chr1:15742608-15742628 2.24e-01 20 chr22:44725484-44725504 4.67e-02 20 chr2:103052970-103052990 2.35e-02 20 chr16:11456011-11456031 4.14e-01 20 chr16:81850470-81850490 1.45e-01 20 chr15:66683219-66683239 3.87e-01 20 chr1:12139533-12139553 1.19e-01 20 chr3:137707178-137707198 9.27e-01 20 chr19:33771493-33771513 9.96e-01 20 chr1:41275262-41275282 8.86e-01 20 chrX:13770932-13770952 1.35e-01 20 chr2:45918410-45918430 6.39e-02 20 chr19:6556663-6556683 5.81e-02 20 chr9:137295962-137295982 7.45e-01 20 chr17:65566120-65566140 1.15e-01 20 chr16:68390485-68390505 2.79e-04 20 chr14:91708356-91708376 7.08e-02 20 chr8:101485385-101485405 9.99e-01 20 chr4:40579246-40579266 1.04e-01 20 chr8:56835607-56835627 2.61e-02 20 chr6:31705946-31705966 5.93e-01 20 chr2:99076406-99076426 1.96e-01 20 chr6:4902082-4902102 8.45e-01 20 chr6:157018515-157018535 9.10e-01 20 chr1:160752169-160752189 4.43e-02 20 chr7:56119262-56119282 2.08e-01 20 chr1:183562682-183562702 3.90e-01 20 chr6:112314237-112314257 6.97e-01 20 chr7:90561504-90561524 4.16e-02 20 chr19:42375848-42375868 2.95e-02 20 chr16:85981635-85981655 4.92e-01 20 chr5:73872898-73872918 1.37e-02 20 chr1:112019804-112019824 2.24e-02 20 chr6:35336418-35336438 4.39e-01 20 chr14:90147533-90147553 7.24e-01 20 chr2:11884328-11884348 9.72e-01 20 chr3:118491749-118491769 9.20e-03 20 chr6:119907875-119907895 2.95e-01 20 chr16:86045309-86045329 6.12e-01 20 chr15:40339997-40340017 1.01e-01 20 chr17:43410644-43410664 2.10e-02 20 chr3:72361724-72361744 9.63e-01 20 chr9:93589660-93589680 2.35e-01 20 chr12:124875346-12487536 8.40e-01 20 chr3:169975124-169975144 6.11e-01 20 chr3:16416545-16416565 1.10e-02 20 chr12:123372204-12337222 1.50e-01 20 chrX:70838416-70838436 1.73e-02 20 chr19:4369317-4369337 5.02e-02 20 chr8:66863909-66863929 4.12e-03 20 chr1:247570784-247570804 1.38e-01 20 chrX:118772988-118773008 4.46e-01 20 chr1:11000340-11000360 2.95e-01 20 chr3:185255274-185255294 6.32e-02 20 chr7:43796390-43796410 1.74e-01 20 chr20:37491886-37491906 7.26e-01 20 chr13:99964874-99964894 3.08e-01 20 chr20:49158438-49158458 8.66e-01 20 chr17:32307467-32307487 7.70e-04 4_[+4(5.01e-05)]_8 chr4:89300533-89300553 1.48e-01 20 chr8:134539058-134539078 6.59e-01 20 chr21:42733795-42733815 7.74e-01 20 chr11:1876417-1876437 1.55e-01 20 chr7:50484313-50484333 8.59e-01 20 chr20:62330674-62330694 2.40e-02 [+2(3.92e-05)]_12 chr19:56111002-56111022 1.17e-02 [+2(1.83e-05)]_12 chr8:103569508-103569528 1.33e-01 20 chr2:8656306-8656326 9.56e-01 20 chr14:65676984-65677004 7.40e-02 20 chr8:141519390-141519410 6.51e-01 20 chr19:14495250-14495270 2.06e-02 20 chr1:32420469-32420489 5.12e-01 20 chr10:30876637-30876657 2.72e-01 20 chrX:13023854-13023874 1.48e-02 20 chr19:2529743-2529763 4.46e-02 20 chr2:29540117-29540137 4.88e-02 20 chr12:53594378-53594398 6.55e-02 20 chr19:10987492-10987512 1.51e-02 1_[+4(5.01e-05)]_11 chr1:51750870-51750890 4.85e-02 20 chr19:38570837-38570857 9.74e-01 20 chr19:39468705-39468725 5.48e-01 20 chr3:15313513-15313533 1.03e-01 20 chr2:37851278-37851298 5.52e-02 20 chr5:139419409-139419429 2.82e-01 20 chr9:119713905-119713925 1.69e-01 20 chr19:16230500-16230520 3.21e-02 20 chr16:80617594-80617614 3.03e-01 20 chr16:19138661-19138681 3.04e-02 11_[+2(1.83e-05)]_1 chr3:52278476-52278496 1.47e-02 20 chr19:36400355-36400375 5.82e-02 20 chr5:157030543-157030563 4.20e-01 20 chr14:106995741-10699576 8.75e-01 20 chr2:38373917-38373937 1.31e-02 20 chr1:26907578-26907598 4.70e-01 20 chr12:125030268-12503028 6.06e-01 20 chr22:31005458-31005478 9.85e-01 20 chr20:35994920-35994940 2.60e-01 20 chr12:123921200-12392122 9.32e-01 20 chr20:43118692-43118712 4.93e-03 9_[+5(1.91e-05)]_3 chr14:50527874-50527894 6.91e-02 20 chr4:84096081-84096101 5.33e-01 20 chr9:102029062-102029082 8.18e-01 20 chr12:65054590-65054610 6.82e-01 20 chr6:75994552-75994572 1.34e-01 20 chr3:5020576-5020596 1.61e-01 20 chr11:65260765-65260785 9.70e-01 20 chr5:157289649-157289669 6.63e-01 20 chr10:25210480-25210500 1.48e-01 5_[+2(5.49e-05)]_7 chr10:11239284-11239304 6.86e-01 20 chr6:157042148-157042168 5.68e-01 20 chr12:76577391-76577411 7.38e-03 5_[+3(9.59e-06)]_7 chr9:92037278-92037298 8.15e-02 20 chr15:70772755-70772775 4.89e-01 20 chr1:21005294-21005314 3.36e-02 9_[+5(7.69e-05)]_3 chr1:161676359-161676379 5.83e-01 20 chr20:43213854-43213874 3.60e-01 20 chr1:12139734-12139754 5.26e-02 20 chr6:159070923-159070943 8.88e-01 20 chr8:126525550-126525570 6.72e-01 20 chr17:76642097-76642117 1.39e-03 10_[+4(2.59e-05)]_2 chr22:45631326-45631346 3.80e-04 9_[+4(1.38e-05)]_3 chr11:48128864-48128884 1.18e-01 20 chr16:21285640-21285660 9.97e-01 20 chr4:120159450-120159470 9.51e-01 20 chr1:154779738-154779758 1.22e-03 2_[+3(9.59e-06)]_10 chr19:3553073-3553093 6.35e-01 20 chr7:105752259-105752279 3.93e-01 20 chr12:14767905-14767925 3.20e-01 20 chr9:138831385-138831405 8.93e-01 20 chr15:67377879-67377899 9.96e-01 20 chr16:66558891-66558911 8.28e-01 20 chr1:12116642-12116662 7.00e-01 20 chr16:10874742-10874762 4.77e-01 20 chr3:185943605-185943625 2.74e-02 20 chr5:171416410-171416430 6.98e-01 20 chr11:6424025-6424045 6.90e-02 20 chr1:117370000-117370020 1.35e-01 20 chr6:341375-341395 3.52e-03 6_[+5(3.55e-05)]_6 chr4:146981179-146981199 1.80e-02 20 chr5:142437398-142437418 5.51e-01 20 chr2:113881964-113881984 6.07e-01 20 chr12:101381922-10138194 3.95e-01 20 chr7:43204540-43204560 1.42e-01 20 chr18:10928183-10928203 5.64e-01 20 chr20:48955497-48955517 7.25e-02 20 chr3:16416345-16416365 9.07e-01 20 chr15:96517204-96517224 9.94e-01 20 chr7:50304755-50304775 3.66e-01 20 chr13:51905037-51905057 9.78e-01 20 chr10:86068673-86068693 3.67e-02 20 chr7:92271614-92271634 9.31e-01 20 chr10:8175249-8175269 9.51e-01 20 chr10:64374309-64374329 3.26e-02 20 chr12:93384199-93384219 5.38e-03 9_[+5(1.91e-05)]_3 chr3:72150047-72150067 2.75e-01 20 chr10:70825632-70825652 5.67e-01 20 chr6:86353859-86353879 8.10e-01 20 chr8:82199103-82199123 4.28e-01 20 chr19:13958621-13958641 6.71e-01 20 chrX:7002283-7002303 5.56e-02 20 chr15:79296906-79296926 1.40e-02 20 chr7:55141953-55141973 2.46e-02 20 chr12:92757699-92757719 7.63e-01 20 chr11:60833631-60833651 5.03e-01 20 chr9:6185200-6185220 5.30e-01 20 chr13:42943399-42943419 1.84e-01 20 chr2:75283667-75283687 5.74e-01 20 chr1:25054193-25054213 8.96e-01 20 chr3:127469405-127469425 5.46e-02 20 chr17:18804316-18804336 1.00e+00 20 chr5:173164233-173164253 2.67e-02 20 chr6:225350-225370 6.44e-03 20 chr11:35294110-35294130 2.54e-02 20 chr1:101759167-101759187 5.20e-01 20 chr9:136819261-136819281 9.36e-01 20 chr7:136044251-136044271 1.99e-02 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c17n09.farnam.hpc.yale.internal ********************************************************************************