******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.3.3 (Release date: Sun Feb 7 15:39:52 2021 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** PRIMARY SEQUENCES= ../result/final_prediction/K562/fasta/RankLinear0.6_40/U2AF1.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr7:142535567-142535647 1.0000 80 chr15:37425201-37425281 1.0000 80 chr11:62621935-62622015 1.0000 80 chr8:102319790-102319870 1.0000 80 chr8:130108759-130108839 1.0000 80 chr6:11927168-11927248 1.0000 80 chr2:173941019-173941099 1.0000 80 chr4:79569236-79569316 1.0000 80 chr1:28835477-28835557 1.0000 80 chr19:10224858-10224938 1.0000 80 chr6:84246514-84246594 1.0000 80 chrX:128741035-128741115 1.0000 80 chr9:136039130-136039210 1.0000 80 chr6:26623856-26623936 1.0000 80 chr7:26238915-26238995 1.0000 80 chr17:48284070-48284150 1.0000 80 chr17:73178603-73178683 1.0000 80 chr6:42430470-42430550 1.0000 80 chr1:61491184-61491264 1.0000 80 chr16:5083516-5083596 1.0000 80 chr7:143147027-143147107 1.0000 80 chr11:13468557-13468637 1.0000 80 chr19:10225064-10225144 1.0000 80 chr5:65214117-65214197 1.0000 80 chr1:71163231-71163311 1.0000 80 chr11:62620110-62620190 1.0000 80 chr11:5017804-5017884 1.0000 80 chr12:54394190-54394270 1.0000 80 chr7:128045854-128045934 1.0000 80 chr1:234776588-234776668 1.0000 80 chr9:77567448-77567528 1.0000 80 chr19:14583203-14583283 1.0000 80 chr17:79486389-79486469 1.0000 80 chr2:54907328-54907408 1.0000 80 chr17:17740053-17740133 1.0000 80 chr19:2270524-2270604 1.0000 80 chr7:100167844-100167924 1.0000 80 chr3:15248073-15248153 1.0000 80 chr6:157700731-157700811 1.0000 80 chr1:162362044-162362124 1.0000 80 chr19:55574321-55574401 1.0000 80 chr1:186918503-186918583 1.0000 80 chr10:84521544-84521624 1.0000 80 chr11:507777-507857 1.0000 80 chr1:228703136-228703216 1.0000 80 chr4:56502269-56502349 1.0000 80 chr12:93964211-93964291 1.0000 80 chr9:38068884-38068964 1.0000 80 chr14:50087879-50087959 1.0000 80 chr1:144920783-144920863 1.0000 80 chr12:18547866-18547946 1.0000 80 chr5:109025702-109025782 1.0000 80 chr11:47788558-47788638 1.0000 80 chr5:73981071-73981151 1.0000 80 chr19:12996466-12996546 1.0000 80 chr22:20785065-20785145 1.0000 80 chr10:76994793-76994873 1.0000 80 chr1:45266354-45266434 1.0000 80 chr11:394392-394472 1.0000 80 chr7:75707568-75707648 1.0000 80 chr2:65215928-65216008 1.0000 80 chr7:64024029-64024109 1.0000 80 chr1:26704291-26704371 1.0000 80 chr2:216153961-216154041 1.0000 80 chr8:145735038-145735118 1.0000 80 chr10:71992900-71992980 1.0000 80 chr1:1004921-1005001 1.0000 80 chr7:149570647-149570727 1.0000 80 chr1:16942295-16942375 1.0000 80 chr3:49059462-49059542 1.0000 80 chr7:93536547-93536627 1.0000 80 chr16:88701104-88701184 1.0000 80 chr20:50808367-50808447 1.0000 80 chr2:183902837-183902917 1.0000 80 chr11:1968809-1968889 1.0000 80 chr20:62257845-62257925 1.0000 80 chr6:157801888-157801968 1.0000 80 chr6:154831690-154831770 1.0000 80 chr16:47071807-47071887 1.0000 80 chr12:39928740-39928820 1.0000 80 chr6:35465392-35465472 1.0000 80 chr8:146012576-146012656 1.0000 80 chr3:155588434-155588514 1.0000 80 chr11:64884823-64884903 1.0000 80 chr15:38544450-38544530 1.0000 80 chr3:12705331-12705411 1.0000 80 chr11:406825-406905 1.0000 80 chr17:76836492-76836572 1.0000 80 chr4:104178428-104178508 1.0000 80 chr4:165805367-165805447 1.0000 80 chr5:138941145-138941225 1.0000 80 chr7:111179329-111179409 1.0000 80 chr1:179198633-179198713 1.0000 80 chr20:32078113-32078193 1.0000 80 chr9:131464857-131464937 1.0000 80 chr1:71446807-71446887 1.0000 80 chr3:128902516-128902596 1.0000 80 chr22:22103304-22103384 1.0000 80 chr5:150460435-150460515 1.0000 80 chr19:813449-813529 1.0000 80 chr16:58549676-58549756 1.0000 80 chr15:50646668-50646748 1.0000 80 chr1:68151800-68151880 1.0000 80 chr7:100027676-100027756 1.0000 80 chr10:87203694-87203774 1.0000 80 chr1:235667593-235667673 1.0000 80 chr3:19988951-19989031 1.0000 80 chr7:75831117-75831197 1.0000 80 chr9:101984011-101984091 1.0000 80 chr11:65625031-65625111 1.0000 80 chr5:96143505-96143585 1.0000 80 chr8:38239534-38239614 1.0000 80 chr3:183146407-183146487 1.0000 80 chr1:192084281-192084361 1.0000 80 chr1:32800909-32800989 1.0000 80 chr6:152501861-152501941 1.0000 80 chr1:168608194-168608274 1.0000 80 chr16:85904764-85904844 1.0000 80 chr3:12851709-12851789 1.0000 80 chr16:451999-452079 1.0000 80 chr19:860740-860820 1.0000 80 chr19:5687513-5687593 1.0000 80 chr12:94853742-94853822 1.0000 80 chr16:58059527-58059607 1.0000 80 chr19:47290980-47291060 1.0000 80 chr19:12903220-12903300 1.0000 80 chr12:120637578-12063765 1.0000 80 chr21:27599219-27599299 1.0000 80 chr15:68570420-68570500 1.0000 80 chr7:30518367-30518447 1.0000 80 chr2:178129102-178129182 1.0000 80 chr21:31070098-31070178 1.0000 80 chr3:44552000-44552080 1.0000 80 chr22:24666972-24667052 1.0000 80 chr1:36184392-36184472 1.0000 80 chr20:47896587-47896667 1.0000 80 chr8:37756806-37756886 1.0000 80 chr12:31477361-31477441 1.0000 80 chr7:124167056-124167136 1.0000 80 chr16:1543478-1543558 1.0000 80 chr3:193852258-193852338 1.0000 80 chr11:62368913-62368993 1.0000 80 chr18:23050908-23050988 1.0000 80 chr10:126480419-12648049 1.0000 80 chr17:77841600-77841680 1.0000 80 chr17:56161007-56161087 1.0000 80 chr19:1445303-1445383 1.0000 80 chr7:32982577-32982657 1.0000 80 chr1:28052614-28052694 1.0000 80 chr8:59571791-59571871 1.0000 80 chr7:73082110-73082190 1.0000 80 chr9:35732195-35732275 1.0000 80 chr15:40574559-40574639 1.0000 80 chr9:131085202-131085282 1.0000 80 chr17:74723224-74723304 1.0000 80 chr11:59322453-59322533 1.0000 80 chr13:91234326-91234406 1.0000 80 chr1:22109431-22109511 1.0000 80 chr18:60190013-60190093 1.0000 80 chr17:4890785-4890865 1.0000 80 chr11:34937743-34937823 1.0000 80 chr6:3119026-3119106 1.0000 80 chr17:3749563-3749643 1.0000 80 chr2:95787508-95787588 1.0000 80 chr20:62152483-62152563 1.0000 80 chr17:66287946-66288026 1.0000 80 chr8:143820828-143820908 1.0000 80 chr3:183735281-183735361 1.0000 80 chr9:138392449-138392529 1.0000 80 chr18:23806763-23806843 1.0000 80 chr8:144373378-144373458 1.0000 80 chr5:177659558-177659638 1.0000 80 chr16:4852788-4852868 1.0000 80 chr1:51984716-51984796 1.0000 80 chr4:2845307-2845387 1.0000 80 chr12:125348219-12534829 1.0000 80 chr1:161696509-161696589 1.0000 80 chr6:20402720-20402800 1.0000 80 chr11:59383119-59383199 1.0000 80 chr10:47656040-47656120 1.0000 80 chr21:36262275-36262355 1.0000 80 chr10:80828926-80829006 1.0000 80 chr7:93460039-93460119 1.0000 80 chr14:24563588-24563668 1.0000 80 chr3:150264040-150264120 1.0000 80 chr6:160114192-160114272 1.0000 80 chr1:46767754-46767834 1.0000 80 chr10:102822503-10282258 1.0000 80 chr15:96900378-96900458 1.0000 80 chr15:44829536-44829616 1.0000 80 chr11:119210744-11921082 1.0000 80 chr1:248070208-248070288 1.0000 80 chr3:127794548-127794628 1.0000 80 chr9:140195959-140196039 1.0000 80 chr16:57318538-57318618 1.0000 80 chr11:64781836-64781916 1.0000 80 chr7:127032260-127032340 1.0000 80 chr22:20849954-20850034 1.0000 80 chr7:98476630-98476710 1.0000 80 chr2:146375101-146375181 1.0000 80 chr2:10091857-10091937 1.0000 80 chr22:21213205-21213285 1.0000 80 chr3:141944393-141944473 1.0000 80 chr6:26205889-26205969 1.0000 80 chr6:17706714-17706794 1.0000 80 chr4:37687819-37687899 1.0000 80 chr1:1243429-1243509 1.0000 80 chr10:75203120-75203200 1.0000 80 chr17:21220061-21220141 1.0000 80 chr5:36241969-36242049 1.0000 80 chr17:38279203-38279283 1.0000 80 chr2:74781430-74781510 1.0000 80 chr6:43422490-43422570 1.0000 80 chr19:17622779-17622859 1.0000 80 chr7:32997150-32997230 1.0000 80 chr19:10531575-10531655 1.0000 80 chr1:16939898-16939978 1.0000 80 chr19:3360575-3360655 1.0000 80 chr22:46374893-46374973 1.0000 80 chr10:119135127-11913520 1.0000 80 chr1:223316565-223316645 1.0000 80 chr7:12726636-12726716 1.0000 80 chr6:35436560-35436640 1.0000 80 chr7:26437858-26437938 1.0000 80 chr6:161412802-161412882 1.0000 80 chr2:133015239-133015319 1.0000 80 chr1:51746102-51746182 1.0000 80 chr16:577283-577363 1.0000 80 chr15:57210805-57210885 1.0000 80 chr5:179050212-179050292 1.0000 80 chr1:19639005-19639085 1.0000 80 chr1:25870423-25870503 1.0000 80 chr11:9406377-9406457 1.0000 80 chr3:195163446-195163526 1.0000 80 chr5:19035579-19035659 1.0000 80 chr5:149737245-149737325 1.0000 80 chr7:100033516-100033596 1.0000 80 chr16:66864707-66864787 1.0000 80 chr16:85203350-85203430 1.0000 80 chr5:137368612-137368692 1.0000 80 chr5:137802913-137802993 1.0000 80 chr8:59571992-59572072 1.0000 80 chr1:27023368-27023448 1.0000 80 chr6:30882057-30882137 1.0000 80 chr3:194315677-194315757 1.0000 80 chr17:79995443-79995523 1.0000 80 chr1:174128782-174128862 1.0000 80 chr1:227448415-227448495 1.0000 80 chr7:148845243-148845323 1.0000 80 chr15:63519945-63520025 1.0000 80 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -oc ../result/final_prediction/K562/inference_raw/MEME/RankLinear0.6_40_U2AF1/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/K562/fasta/RankLinear0.6_40/U2AF1.fasta model: mod= zoops nmotifs= 5 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + width: minw= 8 maxw= 8 nsites: minsites= 2 maxsites= 250 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 20000 N= 250 sample: seed= 0 hsfrac= 0 searchsize= 20000 norand= no csites= 1000 Letter frequencies in dataset: A 0.184 C 0.33 G 0.317 T 0.17 Background letter frequencies (from file dataset with add-one prior applied): A 0.184 C 0.33 G 0.317 T 0.17 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AAAAKAAA MEME-1 width = 8 sites = 51 llr = 429 E-value = 1.1e-019 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAAKAAA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 7788189a pos.-specific C ::1::::: probability G 331:51:: matrix T 1::2411: bits 2.6 * 2.3 * 2.0 ** 1.8 * ** Relative 1.5 * *** Entropy 1.3 *** *** (12.1 bits) 1.0 **** *** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AAAAGAAA consensus GG T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAKAAA MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3:194315677-194315757 60 1.21e-06 CCCCAGCCta aaaataaa taaaattata chr7:93536547-93536627 26 1.21e-06 GATAAGCAAT AAAATAAA TATACGCATG chr1:144920783-144920863 19 1.21e-06 tcaaaaataa aaaataaa aaaCAGGGCT chr10:84521544-84521624 2 1.21e-06 C aaaataaa aaaattaagt chr11:5017804-5017884 49 1.21e-06 GGCATGGGGT AAAATAAA CTACTTCTCC chr2:146375101-146375181 30 3.48e-06 aaagagaaag aaaagaaa agtatcccca chr11:59322453-59322533 3 3.48e-06 ga aaaagaaa aTAGTGAAAA chr18:23050908-23050988 16 3.48e-06 aaaggaaagg aaaagaaa agaaagaGAC chr1:186918503-186918583 25 3.48e-06 agaaaaaaga aaaagaaa gaagaaagaa chr8:102319790-102319870 7 3.48e-06 aagaga aaaagaaa gaaagaaaag chr7:64024029-64024109 5 5.91e-06 ttgg aaaaaaaa ttaaaactat chr11:62620110-62620190 54 5.91e-06 CTGCAGAGGT AAAAAAAA AAGTTCTTAT chr21:31070098-31070178 5 1.01e-05 AAGC AGAATAAA GGGGCACACA chr10:75203120-75203200 29 1.22e-05 GAACCAAGTG AAATGAAA TTGTGAAGTC chr7:93460039-93460119 23 1.22e-05 ACTAAGTAGT AAATGAAA CAGAACTAGA chr6:152501861-152501941 3 2.00e-05 ga agaagaaa aggaagaaaa chr1:192084281-192084361 19 2.00e-05 aaagagaaag aGAAGAAA GGTGGGAACT chr4:165805367-165805447 21 2.00e-05 ggaagagaag gaaagaaa gaagagttcc chr12:39928740-39928820 2 2.00e-05 a gaaagaaa gaaaACAAAG chr7:75707568-75707648 16 2.00e-05 aagagagaaa gaaagaaa gaaaATAGGT chr1:61491184-61491264 7 2.00e-05 aagaaa gaaagaaa gaGGAAATCT chr2:74781430-74781510 53 2.22e-05 ccggccAGGG TAAATAAA GCCCCGGAGG chr1:71163231-71163311 7 2.85e-05 ATTGGA AAGATAAA ATATTGTAGA chr7:26238915-26238995 55 2.85e-05 ACAAAATGAG AAAAGTAA CAAAGTTCAA chr15:63519945-63520025 17 3.56e-05 AGATGAGTTA AAAATATA ACAAAACAAA chr5:65214117-65214197 29 4.07e-05 attacacaag agattaaa tgatttatcc chr15:57210805-57210885 68 5.34e-05 CCGCCTCAGC GAAAAAAA TGTCC chr12:120637578-12063765 12 5.34e-05 AACAGGATAA AAAAGGAA TGTTCCAAGT chr10:87203694-87203774 28 5.34e-05 AATCTTTTAG GAAAAAAA CATTTTTCTA chr1:234776588-234776668 1 5.70e-05 . ggaataaa gaaggaacaa chr6:26623856-26623936 6 6.42e-05 TGTAA AGATGAAA TAGATAGGAA chr5:19035579-19035659 64 7.70e-05 cacaaacctt ggaagaaa tgtgtttcc chr16:85904764-85904844 16 7.70e-05 GTtgttcttg ggaagaaa gagtcacatt chr13:91234326-91234406 27 9.11e-05 TGATCCAAGG AAGTTAAA ACATCATAGA chr12:18547866-18547946 3 1.11e-04 ta agaagtaa aaggcttagt chr7:142535567-142535647 22 1.18e-04 atgagtaggt aaattata gtaaattata chr17:77841600-77841680 13 1.47e-04 agaaggaaga gagagaaa ggccaattgc chr1:16942295-16942375 57 1.47e-04 gaagttacat gagagaaa tttctgggtg chr22:22103304-22103384 59 1.59e-04 gtaagcagaa aaatggaa gccttaagag chr7:124167056-124167136 38 1.72e-04 ATGAGTTAGC AAAATACA TGAGCATCAC chr6:26205889-26205969 53 2.08e-04 ctgaggcagg aactgaaa caccagatca chr1:162362044-162362124 70 2.08e-04 AGTTTCTGGT AACTGAAA GGA chr21:27599219-27599299 13 2.30e-04 AAATGCTTAC AAAATTTA GTGCCCTTCA chr8:38239534-38239614 17 3.24e-04 GTGCTGCGGG AAGAGGAA GGCTCGGGAG chr2:54907328-54907408 2 3.24e-04 C TACAGAAA CAATTGTTTT chr6:157801888-157801968 32 3.41e-04 GCTGCTGCGC GGGATAAA CCCGGAAGAA chr10:71992900-71992980 69 4.18e-04 GCAAGGCCCG GGAATGAA TGGG chr8:130108759-130108839 10 4.18e-04 ACCTTGCTG AAGTTTAA TATAAGCACC chr11:9406377-9406457 14 4.94e-04 GCCAGCTCAA TGAAGTAA GGACGCCCGG chr5:179050212-179050292 44 4.94e-04 ccccccACGG AGCAAAAA CCGGGCGGAT chr7:12726636-12726716 1 5.91e-04 . TGAATGAA GAAGAGGGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAKAAA MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3:194315677-194315757 1.2e-06 59_[+1]_13 chr7:93536547-93536627 1.2e-06 25_[+1]_47 chr1:144920783-144920863 1.2e-06 18_[+1]_54 chr10:84521544-84521624 1.2e-06 1_[+1]_71 chr11:5017804-5017884 1.2e-06 48_[+1]_24 chr2:146375101-146375181 3.5e-06 29_[+1]_43 chr11:59322453-59322533 3.5e-06 2_[+1]_70 chr18:23050908-23050988 3.5e-06 15_[+1]_57 chr1:186918503-186918583 3.5e-06 24_[+1]_48 chr8:102319790-102319870 3.5e-06 6_[+1]_66 chr7:64024029-64024109 5.9e-06 4_[+1]_68 chr11:62620110-62620190 5.9e-06 53_[+1]_19 chr21:31070098-31070178 1e-05 4_[+1]_68 chr10:75203120-75203200 1.2e-05 28_[+1]_44 chr7:93460039-93460119 1.2e-05 22_[+1]_50 chr6:152501861-152501941 2e-05 2_[+1]_70 chr1:192084281-192084361 2e-05 18_[+1]_54 chr4:165805367-165805447 2e-05 20_[+1]_52 chr12:39928740-39928820 2e-05 1_[+1]_71 chr7:75707568-75707648 2e-05 15_[+1]_57 chr1:61491184-61491264 2e-05 6_[+1]_66 chr2:74781430-74781510 2.2e-05 52_[+1]_20 chr1:71163231-71163311 2.9e-05 6_[+1]_66 chr7:26238915-26238995 2.9e-05 54_[+1]_18 chr15:63519945-63520025 3.6e-05 16_[+1]_56 chr5:65214117-65214197 4.1e-05 28_[+1]_44 chr15:57210805-57210885 5.3e-05 67_[+1]_5 chr12:120637578-12063765 5.3e-05 11_[+1]_61 chr10:87203694-87203774 5.3e-05 27_[+1]_45 chr1:234776588-234776668 5.7e-05 [+1]_72 chr6:26623856-26623936 6.4e-05 5_[+1]_67 chr5:19035579-19035659 7.7e-05 63_[+1]_9 chr16:85904764-85904844 7.7e-05 15_[+1]_57 chr13:91234326-91234406 9.1e-05 26_[+1]_46 chr12:18547866-18547946 0.00011 2_[+1]_70 chr7:142535567-142535647 0.00012 21_[+1]_51 chr17:77841600-77841680 0.00015 12_[+1]_60 chr1:16942295-16942375 0.00015 56_[+1]_16 chr22:22103304-22103384 0.00016 58_[+1]_14 chr7:124167056-124167136 0.00017 37_[+1]_35 chr6:26205889-26205969 0.00021 52_[+1]_20 chr1:162362044-162362124 0.00021 69_[+1]_3 chr21:27599219-27599299 0.00023 12_[+1]_60 chr8:38239534-38239614 0.00032 16_[+1]_56 chr2:54907328-54907408 0.00032 1_[+1]_71 chr6:157801888-157801968 0.00034 31_[+1]_41 chr10:71992900-71992980 0.00042 68_[+1]_4 chr8:130108759-130108839 0.00042 9_[+1]_63 chr11:9406377-9406457 0.00049 13_[+1]_59 chr5:179050212-179050292 0.00049 43_[+1]_29 chr7:12726636-12726716 0.00059 [+1]_72 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAKAAA MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAAAKAAA width=8 seqs=51 chr3:194315677-194315757 ( 60) AAAATAAA 1 chr7:93536547-93536627 ( 26) AAAATAAA 1 chr1:144920783-144920863 ( 19) AAAATAAA 1 chr10:84521544-84521624 ( 2) AAAATAAA 1 chr11:5017804-5017884 ( 49) AAAATAAA 1 chr2:146375101-146375181 ( 30) AAAAGAAA 1 chr11:59322453-59322533 ( 3) AAAAGAAA 1 chr18:23050908-23050988 ( 16) AAAAGAAA 1 chr1:186918503-186918583 ( 25) AAAAGAAA 1 chr8:102319790-102319870 ( 7) AAAAGAAA 1 chr7:64024029-64024109 ( 5) AAAAAAAA 1 chr11:62620110-62620190 ( 54) AAAAAAAA 1 chr21:31070098-31070178 ( 5) AGAATAAA 1 chr10:75203120-75203200 ( 29) AAATGAAA 1 chr7:93460039-93460119 ( 23) AAATGAAA 1 chr6:152501861-152501941 ( 3) AGAAGAAA 1 chr1:192084281-192084361 ( 19) AGAAGAAA 1 chr4:165805367-165805447 ( 21) GAAAGAAA 1 chr12:39928740-39928820 ( 2) GAAAGAAA 1 chr7:75707568-75707648 ( 16) GAAAGAAA 1 chr1:61491184-61491264 ( 7) GAAAGAAA 1 chr2:74781430-74781510 ( 53) TAAATAAA 1 chr1:71163231-71163311 ( 7) AAGATAAA 1 chr7:26238915-26238995 ( 55) AAAAGTAA 1 chr15:63519945-63520025 ( 17) AAAATATA 1 chr5:65214117-65214197 ( 29) AGATTAAA 1 chr15:57210805-57210885 ( 68) GAAAAAAA 1 chr12:120637578-12063765 ( 12) AAAAGGAA 1 chr10:87203694-87203774 ( 28) GAAAAAAA 1 chr1:234776588-234776668 ( 1) GGAATAAA 1 chr6:26623856-26623936 ( 6) AGATGAAA 1 chr5:19035579-19035659 ( 64) GGAAGAAA 1 chr16:85904764-85904844 ( 16) GGAAGAAA 1 chr13:91234326-91234406 ( 27) AAGTTAAA 1 chr12:18547866-18547946 ( 3) AGAAGTAA 1 chr7:142535567-142535647 ( 22) AAATTATA 1 chr17:77841600-77841680 ( 13) GAGAGAAA 1 chr1:16942295-16942375 ( 57) GAGAGAAA 1 chr22:22103304-22103384 ( 59) AAATGGAA 1 chr7:124167056-124167136 ( 38) AAAATACA 1 chr6:26205889-26205969 ( 53) AACTGAAA 1 chr1:162362044-162362124 ( 70) AACTGAAA 1 chr21:27599219-27599299 ( 13) AAAATTTA 1 chr8:38239534-38239614 ( 17) AAGAGGAA 1 chr2:54907328-54907408 ( 2) TACAGAAA 1 chr6:157801888-157801968 ( 32) GGGATAAA 1 chr10:71992900-71992980 ( 69) GGAATGAA 1 chr8:130108759-130108839 ( 10) AAGTTTAA 1 chr11:9406377-9406457 ( 14) TGAAGTAA 1 chr5:179050212-179050292 ( 44) AGCAAAAA 1 chr7:12726636-12726716 ( 1) TGAATGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAKAAA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 8.99089 E= 1.1e-019 186 -1232 -31 -111 198 -1232 -21 -1232 209 -207 -121 -1232 213 -1232 -1232 21 -90 -1232 74 114 213 -1232 -169 -79 233 -407 -1232 -153 245 -1232 -1232 -1232 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAKAAA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 51 E= 1.1e-019 0.666667 0.000000 0.254902 0.078431 0.725490 0.000000 0.274510 0.000000 0.784314 0.078431 0.137255 0.000000 0.803922 0.000000 0.000000 0.196078 0.098039 0.000000 0.529412 0.372549 0.803922 0.000000 0.098039 0.098039 0.921569 0.019608 0.000000 0.058824 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAKAAA MEME-1 regular expression -------------------------------------------------------------------------------- [AG][AG]AA[GT]AAA -------------------------------------------------------------------------------- Time 4.85 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTTYTTT MEME-2 width = 8 sites = 41 llr = 364 E-value = 3.5e-018 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTTYTTT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 21122:31 pos.-specific C 1:::41:: probability G ::1::::: matrix T 79884979 bits 2.6 2.3 2.0 * * 1.8 * * * * Relative 1.5 *** *** Entropy 1.3 **** *** (12.8 bits) 1.0 **** *** 0.8 **** *** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel TTTTCTTT consensus AT A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTYTTT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr18:23050908-23050988 59 6.98e-07 GCTCTTTGTT TTTTTTTT TTCAAttttt chr6:157700731-157700811 59 6.98e-07 TCTATTATAG TTTttttt ctgttttctt chr12:18547866-18547946 60 2.05e-06 tctttctttc ttttcttt ctctttcttt chr1:228703136-228703216 70 2.05e-06 CTCTTCCCAG TTTTCTTT Ttc chr10:84521544-84521624 69 2.05e-06 AATTGTATTT Ttttcttt ttcc chr1:71163231-71163311 57 2.05e-06 AATTCATAAA Ttttcttt cttctttctc chr8:130108759-130108839 58 2.05e-06 CCCTTCtctt ttttcttt tttcctttct chr10:87203694-87203774 39 6.54e-06 AAAAAAACAT TTTTCTAT ATTACCCAAG chr6:11927168-11927248 54 6.54e-06 AAACTACTGA ATTTTTTT AAAATGTTGT chr7:142535567-142535647 52 7.35e-06 atggaatatc ttttatat ttcaaaactt chr4:104178428-104178508 62 1.10e-05 taataACATT Atttcttt ctttctttct chr7:93536547-93536627 65 1.10e-05 GCATTTTGTT TTTACTTT TCTAAACT chr1:144920783-144920863 1 1.48e-05 . tttattat tcaaaaataa chr15:37425201-37425281 27 1.48e-05 CCATCATTTG ATTTTTAT TCTTGGACAT chr6:42430470-42430550 11 1.72e-05 tttcctgatt tttaattt ggttgttttc chr6:26623856-26623936 45 1.72e-05 CTTCAGAGCC TTTAATTT TTCTCATAGA chr7:93460039-93460119 54 2.15e-05 GGAATTTAGA TTTTCTTA ATGCTACTAA chr7:111179329-111179409 63 2.15e-05 CTTTTCTGTA TTTTTCTT CAATAAATCA chr1:51746102-51746182 61 2.89e-05 ttctttcttc ctttcttt ctctttctct chr7:124167056-124167136 9 2.89e-05 CCTAATGG ATTATTTT CTGGTACTTG chr11:59322453-59322533 62 3.56e-05 AAAATGTAGC CTTTTTAT CAGGTTATTT chr3:15248073-15248153 20 3.56e-05 CGAGGCGGTG TTTTATTA CAAGGTAGGG chr2:54907328-54907408 19 3.56e-05 ACAATTGTTT TTGTTTTT AGTAACTATC chr17:48284070-48284150 63 3.96e-05 ATTCCGTGCC TATTTTAT CCCAtttgct chr1:227448415-227448495 1 4.31e-05 . TTTTCCTT CTTCTCTTTC chr11:13468557-13468637 52 4.31e-05 TTAGAACAAT TTTTCCTT ACTCTACATA chr16:85904764-85904844 58 4.79e-05 tccccataaa ttatctat caatgtaatg chr11:5017804-5017884 29 4.79e-05 AAAACATGGA ATATTTTT CTGGCATGGG chr11:62621935-62622015 11 4.79e-05 AATGGCTAAG TTATCTAT TAGATAATAG chr6:84246514-84246594 54 6.67e-05 GTCATATAAC TATATTTT GTTCTGAACT chr5:65214117-65214197 1 6.90e-05 . ttttataa atcatgaagc chr12:39928740-39928820 32 7.20e-05 AAAATATTGA CTTTATAT CTCGTTGTCT chr1:26704291-26704371 72 9.37e-05 ATTCATTCAC ATATTTAT T chr10:75203120-75203200 10 1.14e-04 aaaagagca cttattAT GGAACCAAGT chr1:71446807-71446887 48 1.14e-04 ACTCCAGTTG TTGATTTT CAGGATCTTA chr5:19035579-19035659 31 1.32e-04 aagaaggcag ttatctta ccacttttca chr7:64024029-64024109 27 1.32e-04 aactatgtat tttacctt tctaccacat chr1:234776588-234776668 70 1.56e-04 accgcccctg ctttctta aag chr2:216153961-216154041 56 2.10e-04 agtcactgtg tagttttt aggtgggtgt chr3:194315677-194315757 71 2.18e-04 aaataaataa aattatat aG chr21:31070098-31070178 56 2.38e-04 CTCCTTCGGT CTTTCCTT CTCTCCTTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTYTTT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr18:23050908-23050988 7e-07 58_[+2]_14 chr6:157700731-157700811 7e-07 58_[+2]_14 chr12:18547866-18547946 2.1e-06 59_[+2]_13 chr1:228703136-228703216 2.1e-06 69_[+2]_3 chr10:84521544-84521624 2.1e-06 68_[+2]_4 chr1:71163231-71163311 2.1e-06 56_[+2]_16 chr8:130108759-130108839 2.1e-06 57_[+2]_15 chr10:87203694-87203774 6.5e-06 38_[+2]_34 chr6:11927168-11927248 6.5e-06 53_[+2]_19 chr7:142535567-142535647 7.4e-06 51_[+2]_21 chr4:104178428-104178508 1.1e-05 61_[+2]_11 chr7:93536547-93536627 1.1e-05 64_[+2]_8 chr1:144920783-144920863 1.5e-05 [+2]_72 chr15:37425201-37425281 1.5e-05 26_[+2]_46 chr6:42430470-42430550 1.7e-05 10_[+2]_62 chr6:26623856-26623936 1.7e-05 44_[+2]_28 chr7:93460039-93460119 2.1e-05 53_[+2]_19 chr7:111179329-111179409 2.1e-05 62_[+2]_10 chr1:51746102-51746182 2.9e-05 60_[+2]_12 chr7:124167056-124167136 2.9e-05 8_[+2]_64 chr11:59322453-59322533 3.6e-05 61_[+2]_11 chr3:15248073-15248153 3.6e-05 19_[+2]_53 chr2:54907328-54907408 3.6e-05 18_[+2]_54 chr17:48284070-48284150 4e-05 62_[+2]_10 chr1:227448415-227448495 4.3e-05 [+2]_72 chr11:13468557-13468637 4.3e-05 51_[+2]_21 chr16:85904764-85904844 4.8e-05 57_[+2]_15 chr11:5017804-5017884 4.8e-05 28_[+2]_44 chr11:62621935-62622015 4.8e-05 10_[+2]_62 chr6:84246514-84246594 6.7e-05 53_[+2]_19 chr5:65214117-65214197 6.9e-05 [+2]_72 chr12:39928740-39928820 7.2e-05 31_[+2]_41 chr1:26704291-26704371 9.4e-05 71_[+2]_1 chr10:75203120-75203200 0.00011 9_[+2]_63 chr1:71446807-71446887 0.00011 47_[+2]_25 chr5:19035579-19035659 0.00013 30_[+2]_42 chr7:64024029-64024109 0.00013 26_[+2]_46 chr1:234776588-234776668 0.00016 69_[+2]_3 chr2:216153961-216154041 0.00021 55_[+2]_17 chr3:194315677-194315757 0.00022 70_[+2]_2 chr21:31070098-31070178 0.00024 55_[+2]_17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTYTTT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTTYTTT width=8 seqs=41 chr18:23050908-23050988 ( 59) TTTTTTTT 1 chr6:157700731-157700811 ( 59) TTTTTTTT 1 chr12:18547866-18547946 ( 60) TTTTCTTT 1 chr1:228703136-228703216 ( 70) TTTTCTTT 1 chr10:84521544-84521624 ( 69) TTTTCTTT 1 chr1:71163231-71163311 ( 57) TTTTCTTT 1 chr8:130108759-130108839 ( 58) TTTTCTTT 1 chr10:87203694-87203774 ( 39) TTTTCTAT 1 chr6:11927168-11927248 ( 54) ATTTTTTT 1 chr7:142535567-142535647 ( 52) TTTTATAT 1 chr4:104178428-104178508 ( 62) ATTTCTTT 1 chr7:93536547-93536627 ( 65) TTTACTTT 1 chr1:144920783-144920863 ( 1) TTTATTAT 1 chr15:37425201-37425281 ( 27) ATTTTTAT 1 chr6:42430470-42430550 ( 11) TTTAATTT 1 chr6:26623856-26623936 ( 45) TTTAATTT 1 chr7:93460039-93460119 ( 54) TTTTCTTA 1 chr7:111179329-111179409 ( 63) TTTTTCTT 1 chr1:51746102-51746182 ( 61) CTTTCTTT 1 chr7:124167056-124167136 ( 9) ATTATTTT 1 chr11:59322453-59322533 ( 62) CTTTTTAT 1 chr3:15248073-15248153 ( 20) TTTTATTA 1 chr2:54907328-54907408 ( 19) TTGTTTTT 1 chr17:48284070-48284150 ( 63) TATTTTAT 1 chr1:227448415-227448495 ( 1) TTTTCCTT 1 chr11:13468557-13468637 ( 52) TTTTCCTT 1 chr16:85904764-85904844 ( 58) TTATCTAT 1 chr11:5017804-5017884 ( 29) ATATTTTT 1 chr11:62621935-62622015 ( 11) TTATCTAT 1 chr6:84246514-84246594 ( 54) TATATTTT 1 chr5:65214117-65214197 ( 1) TTTTATAA 1 chr12:39928740-39928820 ( 32) CTTTATAT 1 chr1:26704291-26704371 ( 72) ATATTTAT 1 chr10:75203120-75203200 ( 10) CTTATTAT 1 chr1:71446807-71446887 ( 48) TTGATTTT 1 chr5:19035579-19035659 ( 31) TTATCTTA 1 chr7:64024029-64024109 ( 27) TTTACCTT 1 chr1:234776588-234776668 ( 70) CTTTCTTA 1 chr2:216153961-216154041 ( 56) TAGTTTTT 1 chr3:194315677-194315757 ( 71) AATTATAT 1 chr21:31070098-31070178 ( 56) CTTTCCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTYTTT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.6437 E= 3.5e-018 -10 -117 -1200 201 -91 -1200 -1200 241 -59 -1200 -211 225 26 -1200 -1200 220 -10 41 -1200 120 -1200 -144 -1200 237 79 -1200 -1200 201 -59 -1200 -1200 237 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTYTTT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 41 E= 3.5e-018 0.170732 0.146341 0.000000 0.682927 0.097561 0.000000 0.000000 0.902439 0.121951 0.000000 0.073171 0.804878 0.219512 0.000000 0.000000 0.780488 0.170732 0.439024 0.000000 0.390244 0.000000 0.121951 0.000000 0.878049 0.317073 0.000000 0.000000 0.682927 0.121951 0.000000 0.000000 0.878049 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTYTTT MEME-2 regular expression -------------------------------------------------------------------------------- TTT[TA][CT]T[TA]T -------------------------------------------------------------------------------- Time 8.50 secs. ******************************************************************************** ******************************************************************************** MOTIF TATAAAHT MEME-3 width = 8 sites = 16 llr = 155 E-value = 1.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif TATAAAHT MEME-3 Description -------------------------------------------------------------------------------- Simplified A 17:9a631 pos.-specific C :3:::24: probability G :1:::::: matrix T 9:a1:249 bits 2.6 * * 2.3 * * * * 2.0 * * * * 1.8 * *** * Relative 1.5 * *** * Entropy 1.3 * *** * (14.0 bits) 1.0 ****** * 0.8 ****** * 0.5 ******** 0.3 ******** 0.0 -------- Multilevel TATAAACT consensus C T sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TATAAAHT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr10:84521544-84521624 55 9.57e-07 TATGCACAAA TATAAATT GTATTTTttt chr7:142535567-142535647 36 1.99e-06 tatagtaaat tataaaat ggaatatctt chr6:26623856-26623936 64 7.41e-06 TCTCATAGAG TATAATAT GAATACCAC chr17:77841600-77841680 32 9.13e-06 gccaattgcc tataatct tatgacacag chr10:87203694-87203774 15 9.13e-06 AAAACATGTT TATAATCT TTTAGGAAAA chr1:168608194-168608274 4 1.08e-05 gta tataactt gaagttttga chr1:71163231-71163311 43 1.17e-05 TGACATTTTA TATTAATT CATAAATttt chr6:84246514-84246594 19 1.17e-05 TGAACTAACC TATTAATT AACAACATAA chr1:234776588-234776668 44 1.36e-05 cagaacactt tctaaaat gtaactcaac chr7:93536547-93536627 73 1.69e-05 TTTTTACTTT TCTAAACT chr7:75707568-75707648 70 1.69e-05 TCTGAATATG TCTAAACT ACA chr4:79569236-79569316 25 1.88e-05 AAGACTCCTA TATAACAT ACAAAGCATG chr10:75203120-75203200 50 3.01e-05 TGAAGTCAAA TGTAAATT CATTCAAAAC chr5:36241969-36242049 24 4.68e-05 CGCCCGGGCC TCTAACTT CGCGCCGGAC chr6:11927168-11927248 1 4.68e-05 . AATAAACT GAACTGGGAA chr15:37425201-37425281 53 4.68e-05 ATGTGGATGC TATAAACA ATACAATGTA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TATAAAHT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr10:84521544-84521624 9.6e-07 54_[+3]_18 chr7:142535567-142535647 2e-06 35_[+3]_37 chr6:26623856-26623936 7.4e-06 63_[+3]_9 chr17:77841600-77841680 9.1e-06 31_[+3]_41 chr10:87203694-87203774 9.1e-06 14_[+3]_58 chr1:168608194-168608274 1.1e-05 3_[+3]_69 chr1:71163231-71163311 1.2e-05 42_[+3]_30 chr6:84246514-84246594 1.2e-05 18_[+3]_54 chr1:234776588-234776668 1.4e-05 43_[+3]_29 chr7:93536547-93536627 1.7e-05 72_[+3] chr7:75707568-75707648 1.7e-05 69_[+3]_3 chr4:79569236-79569316 1.9e-05 24_[+3]_48 chr10:75203120-75203200 3e-05 49_[+3]_23 chr5:36241969-36242049 4.7e-05 23_[+3]_49 chr6:11927168-11927248 4.7e-05 [+3]_72 chr15:37425201-37425281 4.7e-05 52_[+3]_20 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TATAAAHT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TATAAAHT width=8 seqs=16 chr10:84521544-84521624 ( 55) TATAAATT 1 chr7:142535567-142535647 ( 36) TATAAAAT 1 chr6:26623856-26623936 ( 64) TATAATAT 1 chr17:77841600-77841680 ( 32) TATAATCT 1 chr10:87203694-87203774 ( 15) TATAATCT 1 chr1:168608194-168608274 ( 4) TATAACTT 1 chr1:71163231-71163311 ( 43) TATTAATT 1 chr6:84246514-84246594 ( 19) TATTAATT 1 chr1:234776588-234776668 ( 44) TCTAAAAT 1 chr7:93536547-93536627 ( 73) TCTAAACT 1 chr7:75707568-75707648 ( 70) TCTAAACT 1 chr4:79569236-79569316 ( 25) TATAACAT 1 chr10:75203120-75203200 ( 50) TGTAAATT 1 chr5:36241969-36242049 ( 24) TCTAACTT 1 chr6:11927168-11927248 ( 1) AATAAACT 1 chr15:37425201-37425281 ( 53) TATAAACA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TATAAAHT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.477 E= 1.5e+000 -155 -1064 -1064 247 190 -40 -234 -1064 -1064 -1064 -1064 256 225 -1064 -1064 -44 244 -1064 -1064 -1064 177 -82 -1064 14 45 18 -1064 114 -155 -1064 -1064 247 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TATAAAHT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 16 E= 1.5e+000 0.062500 0.000000 0.000000 0.937500 0.687500 0.250000 0.062500 0.000000 0.000000 0.000000 0.000000 1.000000 0.875000 0.000000 0.000000 0.125000 1.000000 0.000000 0.000000 0.000000 0.625000 0.187500 0.000000 0.187500 0.250000 0.375000 0.000000 0.375000 0.062500 0.000000 0.000000 0.937500 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TATAAAHT MEME-3 regular expression -------------------------------------------------------------------------------- T[AC]TAAA[CTA]T -------------------------------------------------------------------------------- Time 12.09 secs. ******************************************************************************** ******************************************************************************** MOTIF RWAAABAT MEME-4 width = 8 sites = 21 llr = 191 E-value = 4.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif RWAAABAT MEME-4 Description -------------------------------------------------------------------------------- Simplified A 7688a:a2 pos.-specific C :::::3:: probability G 3::::3:: matrix T :322:4:8 bits 2.6 * * 2.3 * * 2.0 * * 1.8 *** ** Relative 1.5 *** ** Entropy 1.3 ***** ** (13.1 bits) 1.0 ***** ** 0.8 ***** ** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AAAAATAT consensus GT G A sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RWAAABAT MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr8:102319790-102319870 27 4.25e-06 aagaaaagag aaaAAgat cctccagcct chr1:144920783-144920863 11 7.64e-06 tttattattc aaaaataa aaaataaaaa chr12:39928740-39928820 21 9.57e-06 aaaACAAAGA GAAAATAT TGACTTTATA chr7:93536547-93536627 45 1.36e-05 ATACGCATGC AATAATAT AGGCATTTTG chr11:13468557-13468637 2 1.36e-05 A ATAAAGAT GTAGAGATTT chr7:143147027-143147107 69 1.36e-05 atttgctacc ataaagat gtta chr7:111179329-111179409 19 2.04e-05 CGATTACTAC ATATATAT CTGTATATTG chr10:84521544-84521624 34 2.04e-05 attataaaac atatatat GTGTATGCAC chr15:37425201-37425281 5 2.04e-05 CACT ATTAATAT TCTTCCATCA chr2:146375101-146375181 10 2.27e-05 aaacaaaga aaaaagaa agaaagagaa chr16:85904764-85904844 34 2.63e-05 gagtcacatt gaaaagat gtcaattccc chr11:62621935-62622015 43 3.25e-05 ATAGAATTCG AAAAACAA CTTACTGTAA chr10:87203694-87203774 4 3.62e-05 GAT GAAAACAT GTTTATAATC chr11:5017804-5017884 18 3.62e-05 AATTAAAGGA GAAAACAT GGAATATTTT chr4:104178428-104178508 53 4.03e-05 ctgaatctgt aataACAT TAtttctttc chr12:18547866-18547946 32 4.03e-05 atccctaagc aAATACAT ACtctccctt chr13:91234326-91234406 52 5.36e-05 AGACAGCGTG GAATATAT GCCACTGTTA chr1:168608194-168608274 67 6.75e-05 agctaagcta attaacat atccat chr20:62152483-62152563 60 7.13e-05 CCCCGCCTCG GTAAATAA CCCAGCGCGG chr6:152501861-152501941 16 8.15e-05 agaaaaggaa gaaaagaa gGGATGGAAG chr15:63519945-63520025 3 1.22e-04 AC AGAAAGAT GAGTTAAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RWAAABAT MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr8:102319790-102319870 4.2e-06 26_[+4]_46 chr1:144920783-144920863 7.6e-06 10_[+4]_62 chr12:39928740-39928820 9.6e-06 20_[+4]_52 chr7:93536547-93536627 1.4e-05 44_[+4]_28 chr11:13468557-13468637 1.4e-05 1_[+4]_71 chr7:143147027-143147107 1.4e-05 68_[+4]_4 chr7:111179329-111179409 2e-05 18_[+4]_54 chr10:84521544-84521624 2e-05 33_[+4]_39 chr15:37425201-37425281 2e-05 4_[+4]_68 chr2:146375101-146375181 2.3e-05 9_[+4]_63 chr16:85904764-85904844 2.6e-05 33_[+4]_39 chr11:62621935-62622015 3.2e-05 42_[+4]_30 chr10:87203694-87203774 3.6e-05 3_[+4]_69 chr11:5017804-5017884 3.6e-05 17_[+4]_55 chr4:104178428-104178508 4e-05 52_[+4]_20 chr12:18547866-18547946 4e-05 31_[+4]_41 chr13:91234326-91234406 5.4e-05 51_[+4]_21 chr1:168608194-168608274 6.7e-05 66_[+4]_6 chr20:62152483-62152563 7.1e-05 59_[+4]_13 chr6:152501861-152501941 8.2e-05 15_[+4]_57 chr15:63519945-63520025 0.00012 2_[+4]_70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RWAAABAT MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF RWAAABAT width=8 seqs=21 chr8:102319790-102319870 ( 27) AAAAAGAT 1 chr1:144920783-144920863 ( 11) AAAAATAA 1 chr12:39928740-39928820 ( 21) GAAAATAT 1 chr7:93536547-93536627 ( 45) AATAATAT 1 chr11:13468557-13468637 ( 2) ATAAAGAT 1 chr7:143147027-143147107 ( 69) ATAAAGAT 1 chr7:111179329-111179409 ( 19) ATATATAT 1 chr10:84521544-84521624 ( 34) ATATATAT 1 chr15:37425201-37425281 ( 5) ATTAATAT 1 chr2:146375101-146375181 ( 10) AAAAAGAA 1 chr16:85904764-85904844 ( 34) GAAAAGAT 1 chr11:62621935-62622015 ( 43) AAAAACAA 1 chr10:87203694-87203774 ( 4) GAAAACAT 1 chr11:5017804-5017884 ( 18) GAAAACAT 1 chr4:104178428-104178508 ( 53) AATAACAT 1 chr12:18547866-18547946 ( 32) AAATACAT 1 chr13:91234326-91234406 ( 52) GAATATAT 1 chr1:168608194-168608274 ( 67) ATTAACAT 1 chr20:62152483-62152563 ( 60) GTAAATAA 1 chr6:152501861-152501941 ( 16) GAAAAGAA 1 chr15:63519945-63520025 ( 3) AGAAAGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RWAAABAT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.6191 E= 4.0e+000 186 -1104 7 -1104 175 -1104 -273 97 214 -1104 -1104 17 214 -1104 -1104 17 244 -1104 -1104 -1104 -1104 -21 7 117 244 -1104 -1104 -1104 37 -1104 -1104 217 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RWAAABAT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 21 E= 4.0e+000 0.666667 0.000000 0.333333 0.000000 0.619048 0.000000 0.047619 0.333333 0.809524 0.000000 0.000000 0.190476 0.809524 0.000000 0.000000 0.190476 1.000000 0.000000 0.000000 0.000000 0.000000 0.285714 0.333333 0.380952 1.000000 0.000000 0.000000 0.000000 0.238095 0.000000 0.000000 0.761905 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RWAAABAT MEME-4 regular expression -------------------------------------------------------------------------------- [AG][AT]AAA[TGC]A[TA] -------------------------------------------------------------------------------- Time 15.64 secs. ******************************************************************************** ******************************************************************************** MOTIF TTCTTTYT MEME-5 width = 8 sites = 7 llr = 81 E-value = 6.8e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTCTTTYT MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::1:: pos.-specific C ::a::16: probability G :::::::: matrix T aa:aa74a bits 2.6 ** ** * 2.3 ** ** * 2.0 ** ** * 1.8 ** ** * Relative 1.5 ***** * Entropy 1.3 ****** * (16.7 bits) 1.0 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel TTCTTTCT consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCTTTYT MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:157700731-157700811 72 1.35e-06 tttttctgtt ttcttttt c chr1:51746102-51746182 51 3.98e-06 TGCAGCTTGC ttctttct tcctttcttt chr4:104178428-104178508 72 3.98e-06 Atttctttct ttctttct t chr1:71163231-71163311 66 3.98e-06 ATtttctttc ttctttct ctttctt chr8:130108759-130108839 72 3.98e-06 cttttttcct ttctttct c chr11:62620110-62620190 65 5.45e-06 AAAAAAAAAG TTCTTATT GGATTGGA chr1:227448415-227448495 54 1.09e-05 CATTCTACCA TTCTTCTT CTCCCTTATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCTTTYT MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:157700731-157700811 1.4e-06 71_[+5]_1 chr1:51746102-51746182 4e-06 50_[+5]_22 chr4:104178428-104178508 4e-06 71_[+5]_1 chr1:71163231-71163311 4e-06 65_[+5]_7 chr8:130108759-130108839 4e-06 71_[+5]_1 chr11:62620110-62620190 5.4e-06 64_[+5]_8 chr1:227448415-227448495 1.1e-05 53_[+5]_19 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCTTTYT MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTCTTTYT width=8 seqs=7 chr6:157700731-157700811 ( 72) TTCTTTTT 1 chr1:51746102-51746182 ( 51) TTCTTTCT 1 chr4:104178428-104178508 ( 72) TTCTTTCT 1 chr1:71163231-71163311 ( 66) TTCTTTCT 1 chr8:130108759-130108839 ( 72) TTCTTTCT 1 chr11:62620110-62620190 ( 65) TTCTTATT 1 chr1:227448415-227448495 ( 54) TTCTTCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCTTTYT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.9536 E= 6.8e+001 -945 -945 -945 256 -945 -945 -945 256 -945 160 -945 -945 -945 -945 -945 256 -945 -945 -945 256 -36 -121 -945 207 -945 79 -945 134 -945 -945 -945 256 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCTTTYT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 6.8e+001 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.142857 0.142857 0.000000 0.714286 0.000000 0.571429 0.000000 0.428571 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCTTTYT MEME-5 regular expression -------------------------------------------------------------------------------- TTCTTT[CT]T -------------------------------------------------------------------------------- Time 19.09 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:142535567-142535647 9.59e-09 35_[+3(1.99e-06)]_8_[+2(7.35e-06)]_\ 7_[+2(9.37e-05)]_6 chr15:37425201-37425281 8.27e-08 4_[+4(2.04e-05)]_14_[+2(1.48e-05)]_\ 18_[+3(4.68e-05)]_20 chr11:62621935-62622015 2.91e-05 10_[+2(4.79e-05)]_24_[+4(3.25e-05)]_\ 30 chr8:102319790-102319870 1.05e-04 6_[+1(3.48e-06)]_[+1(2.00e-05)]_4_\ [+4(4.25e-06)]_46 chr8:130108759-130108839 3.04e-08 12_[+2(3.96e-05)]_39_[+5(1.35e-06)]_\ 4_[+5(3.98e-06)]_1 chr6:11927168-11927248 2.84e-05 [+3(4.68e-05)]_45_[+2(6.54e-06)]_19 chr2:173941019-173941099 9.89e-01 80 chr4:79569236-79569316 2.90e-04 24_[+3(1.88e-05)]_48 chr1:28835477-28835557 2.11e-01 80 chr19:10224858-10224938 7.78e-01 80 chr6:84246514-84246594 4.95e-06 18_[+3(1.17e-05)]_27_[+2(6.67e-05)]_\ 19 chrX:128741035-128741115 6.71e-01 80 chr9:136039130-136039210 3.11e-01 80 chr6:26623856-26623936 1.13e-08 1_[+4(5.36e-05)]_1_[+4(3.25e-05)]_\ 26_[+2(1.72e-05)]_11_[+3(7.41e-06)]_9 chr7:26238915-26238995 1.64e-04 54_[+1(2.85e-05)]_18 chr17:48284070-48284150 1.03e-03 62_[+2(3.96e-05)]_10 chr17:73178603-73178683 8.53e-01 80 chr6:42430470-42430550 9.55e-04 10_[+2(1.72e-05)]_62 chr1:61491184-61491264 3.09e-04 2_[+1(2.00e-05)]_70 chr16:5083516-5083596 9.99e-01 80 chr7:143147027-143147107 9.35e-05 68_[+4(1.36e-05)]_4 chr11:13468557-13468637 4.47e-06 1_[+4(1.36e-05)]_42_[+2(4.31e-05)]_\ 21 chr19:10225064-10225144 9.72e-01 80 chr5:65214117-65214197 6.06e-05 [+2(6.90e-05)]_20_[+1(4.07e-05)]_44 chr1:71163231-71163311 7.62e-11 6_[+1(2.85e-05)]_23_[+2(7.35e-06)]_\ 11_[+2(2.05e-06)]_1_[+5(3.98e-06)]_7 chr11:62620110-62620190 8.01e-07 53_[+1(5.91e-06)]_3_[+5(5.45e-06)]_\ 8 chr11:5017804-5017884 4.80e-09 6_[+1(4.07e-05)]_3_[+4(3.62e-05)]_3_\ [+2(4.79e-05)]_12_[+1(1.21e-06)]_24 chr12:54394190-54394270 6.20e-01 80 chr7:128045854-128045934 9.99e-01 80 chr1:234776588-234776668 4.07e-08 3_[+4(4.67e-05)]_32_[+3(1.36e-05)]_\ 29 chr9:77567448-77567528 9.78e-01 80 chr19:14583203-14583283 9.88e-01 80 chr17:79486389-79486469 1.00e+00 80 chr2:54907328-54907408 1.06e-06 12_[+5(2.28e-05)]_60 chr17:17740053-17740133 9.93e-01 80 chr19:2270524-2270604 1.00e+00 80 chr7:100167844-100167924 9.91e-01 80 chr3:15248073-15248153 1.90e-03 19_[+2(3.56e-05)]_53 chr6:157700731-157700811 9.09e-07 58_[+2(6.98e-07)]_5_[+5(1.35e-06)]_\ 1 chr1:162362044-162362124 1.17e-02 80 chr19:55574321-55574401 2.30e-01 80 chr1:186918503-186918583 1.39e-05 3_[+1(2.00e-05)]_7_[+1(3.48e-06)]_5_\ [+1(2.00e-05)]_[+1(2.00e-05)]_7_[+1(2.00e-05)]_18 chr10:84521544-84521624 2.22e-14 1_[+1(1.21e-06)]_[+1(2.22e-05)]_16_\ [+4(2.04e-05)]_13_[+3(9.57e-07)]_8_[+5(1.35e-06)]_2 chr11:507777-507857 4.35e-01 80 chr1:228703136-228703216 2.10e-06 71_[+5(1.35e-06)]_1 chr4:56502269-56502349 9.99e-01 80 chr12:93964211-93964291 9.23e-01 80 chr9:38068884-38068964 1.00e+00 80 chr14:50087879-50087959 8.67e-01 80 chr1:144920783-144920863 3.73e-10 [+2(1.48e-05)]_3_[+1(1.21e-06)]_\ [+1(3.68e-05)]_10_[+2(6.18e-05)]_35 chr12:18547866-18547946 7.58e-09 31_[+4(4.03e-05)]_9_[+5(3.98e-06)]_\ 3_[+2(2.05e-06)]_4_[+5(3.98e-06)]_1 chr5:109025702-109025782 2.64e-02 80 chr11:47788558-47788638 7.72e-01 80 chr5:73981071-73981151 9.99e-01 80 chr19:12996466-12996546 9.54e-01 80 chr22:20785065-20785145 9.67e-01 80 chr10:76994793-76994873 1.00e+00 80 chr1:45266354-45266434 3.50e-01 80 chr11:394392-394472 9.99e-01 80 chr7:75707568-75707648 4.14e-06 11_[+1(2.00e-05)]_[+1(2.00e-05)]_42_\ [+3(1.69e-05)]_3 chr2:65215928-65216008 1.00e+00 80 chr7:64024029-64024109 3.33e-06 9_[+1(4.60e-06)]_63 chr1:26704291-26704371 1.67e-03 71_[+2(9.37e-05)]_1 chr2:216153961-216154041 2.22e-03 80 chr8:145735038-145735118 1.00e+00 80 chr10:71992900-71992980 4.38e-01 80 chr1:1004921-1005001 1.00e+00 80 chr7:149570647-149570727 9.90e-01 80 chr1:16942295-16942375 5.46e-04 80 chr3:49059462-49059542 1.00e+00 80 chr7:93536547-93536627 2.30e-12 25_[+1(1.21e-06)]_11_[+4(1.36e-05)]_\ 12_[+2(1.10e-05)]_[+3(1.69e-05)] chr16:88701104-88701184 5.95e-01 80 chr20:50808367-50808447 9.94e-01 80 chr2:183902837-183902917 1.00e+00 80 chr11:1968809-1968889 9.96e-01 80 chr20:62257845-62257925 1.00e+00 80 chr6:157801888-157801968 4.34e-01 80 chr6:154831690-154831770 1.00e+00 80 chr16:47071807-47071887 9.44e-01 80 chr12:39928740-39928820 4.35e-07 1_[+1(2.00e-05)]_11_[+4(9.57e-06)]_\ 3_[+2(7.20e-05)]_41 chr6:35465392-35465472 5.94e-02 80 chr8:146012576-146012656 1.00e+00 80 chr3:155588434-155588514 6.19e-01 80 chr11:64884823-64884903 9.95e-01 80 chr15:38544450-38544530 9.97e-01 80 chr3:12705331-12705411 7.97e-01 80 chr11:406825-406905 9.97e-01 80 chr17:76836492-76836572 1.00e+00 80 chr4:104178428-104178508 2.50e-08 52_[+4(4.03e-05)]_1_[+2(1.10e-05)]_\ 2_[+5(3.98e-06)]_1 chr4:165805367-165805447 2.86e-03 20_[+1(2.00e-05)]_52 chr5:138941145-138941225 8.75e-01 80 chr7:111179329-111179409 2.30e-06 18_[+4(2.04e-05)]_36_[+2(2.15e-05)]_\ 10 chr1:179198633-179198713 1.00e+00 80 chr20:32078113-32078193 1.00e+00 80 chr9:131464857-131464937 9.99e-01 80 chr1:71446807-71446887 6.95e-03 80 chr3:128902516-128902596 9.92e-01 80 chr22:22103304-22103384 6.23e-02 80 chr5:150460435-150460515 9.99e-01 80 chr19:813449-813529 6.06e-01 80 chr16:58549676-58549756 6.31e-02 80 chr15:50646668-50646748 9.81e-01 80 chr1:68151800-68151880 9.95e-01 80 chr7:100027676-100027756 9.30e-01 80 chr10:87203694-87203774 1.11e-09 3_[+4(3.62e-05)]_3_[+3(9.13e-06)]_8_\ [+4(6.43e-06)]_[+2(6.54e-06)]_34 chr1:235667593-235667673 1.00e+00 80 chr3:19988951-19989031 9.96e-01 80 chr7:75831117-75831197 9.62e-01 80 chr9:101984011-101984091 8.14e-01 80 chr11:65625031-65625111 1.00e+00 80 chr5:96143505-96143585 9.99e-01 80 chr8:38239534-38239614 5.81e-01 80 chr3:183146407-183146487 5.78e-01 80 chr1:192084281-192084361 1.82e-04 9_[+1(3.56e-05)]_1_[+1(2.00e-05)]_\ 54 chr1:32800909-32800989 8.08e-01 80 chr6:152501861-152501941 4.91e-03 2_[+1(2.00e-05)]_1_[+1(7.70e-05)]_\ 61 chr1:168608194-168608274 4.01e-05 3_[+3(1.08e-05)]_55_[+4(6.75e-05)]_\ 6 chr16:85904764-85904844 1.44e-07 15_[+1(7.70e-05)]_10_[+4(2.63e-05)]_\ 16_[+2(4.79e-05)]_15 chr3:12851709-12851789 9.69e-01 80 chr16:451999-452079 9.88e-01 80 chr19:860740-860820 1.00e+00 80 chr19:5687513-5687593 8.78e-01 80 chr12:94853742-94853822 8.40e-01 80 chr16:58059527-58059607 9.96e-01 80 chr19:47290980-47291060 1.00e+00 80 chr19:12903220-12903300 9.99e-01 80 chr12:120637578-12063765 6.46e-03 11_[+1(5.34e-05)]_61 chr21:27599219-27599299 5.29e-03 80 chr15:68570420-68570500 9.92e-01 80 chr7:30518367-30518447 9.89e-01 80 chr2:178129102-178129182 9.64e-01 80 chr21:31070098-31070178 5.03e-06 4_[+1(1.01e-05)]_57_[+5(2.53e-05)]_\ 3 chr3:44552000-44552080 5.54e-01 80 chr22:24666972-24667052 7.94e-01 80 chr1:36184392-36184472 1.00e+00 80 chr20:47896587-47896667 2.11e-01 80 chr8:37756806-37756886 3.91e-01 80 chr12:31477361-31477441 9.92e-01 80 chr7:124167056-124167136 3.61e-06 8_[+2(2.89e-05)]_22_[+4(4.03e-05)]_\ 34 chr16:1543478-1543558 9.90e-01 80 chr3:193852258-193852338 8.87e-01 80 chr11:62368913-62368993 1.00e+00 80 chr18:23050908-23050988 1.39e-09 [+1(3.48e-06)]_7_[+1(3.48e-06)]_33_\ [+2(6.98e-07)]_7_[+2(3.20e-05)]_1 chr10:126480419-12648049 9.99e-01 80 chr17:77841600-77841680 6.51e-05 31_[+3(9.13e-06)]_41 chr17:56161007-56161087 1.00e+00 80 chr19:1445303-1445383 9.79e-01 80 chr7:32982577-32982657 9.99e-01 80 chr1:28052614-28052694 9.50e-01 80 chr8:59571791-59571871 9.94e-01 80 chr7:73082110-73082190 9.77e-01 80 chr9:35732195-35732275 8.70e-01 80 chr15:40574559-40574639 1.00e+00 80 chr9:131085202-131085282 3.05e-01 80 chr17:74723224-74723304 1.00e+00 80 chr11:59322453-59322533 1.81e-07 2_[+1(3.48e-06)]_51_[+2(3.56e-05)]_\ 11 chr13:91234326-91234406 9.13e-05 26_[+1(9.11e-05)]_17_[+4(5.36e-05)]_\ 21 chr1:22109431-22109511 1.00e+00 80 chr18:60190013-60190093 9.56e-01 80 chr17:4890785-4890865 1.00e+00 80 chr11:34937743-34937823 8.63e-01 80 chr6:3119026-3119106 1.00e+00 80 chr17:3749563-3749643 9.97e-01 80 chr2:95787508-95787588 1.00e+00 80 chr20:62152483-62152563 6.72e-02 59_[+4(7.13e-05)]_13 chr17:66287946-66288026 8.49e-01 80 chr8:143820828-143820908 7.46e-01 80 chr3:183735281-183735361 1.00e+00 80 chr9:138392449-138392529 1.00e+00 80 chr18:23806763-23806843 1.00e+00 80 chr8:144373378-144373458 7.67e-01 80 chr5:177659558-177659638 1.00e+00 80 chr16:4852788-4852868 9.91e-01 80 chr1:51984716-51984796 8.41e-01 80 chr4:2845307-2845387 8.97e-01 80 chr12:125348219-12534829 1.00e+00 80 chr1:161696509-161696589 1.00e+00 80 chr6:20402720-20402800 9.99e-01 80 chr11:59383119-59383199 2.22e-01 80 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******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c17n10.farnam.hpc.yale.internal ********************************************************************************