******************************************************************************** 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/PRPF4.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr9:139422922-139423002 1.0000 80 chr17:7788851-7788931 1.0000 80 chr2:42796018-42796098 1.0000 80 chr8:103424291-103424371 1.0000 80 chr15:80352142-80352222 1.0000 80 chr11:117015242-11701532 1.0000 80 chr7:148580836-148580916 1.0000 80 chr11:68518932-68519012 1.0000 80 chr17:159276-159356 1.0000 80 chr9:100746051-100746131 1.0000 80 chr10:103577859-10357793 1.0000 80 chr20:362429-362509 1.0000 80 chr14:67708296-67708376 1.0000 80 chr1:36787997-36788077 1.0000 80 chr17:80055673-80055753 1.0000 80 chr17:79479406-79479486 1.0000 80 chr2:196522537-196522617 1.0000 80 chr19:2050255-2050335 1.0000 80 chr5:170815241-170815321 1.0000 80 chr11:64545900-64545980 1.0000 80 chr9:80912384-80912464 1.0000 80 chr3:73046376-73046456 1.0000 80 chr17:80054336-80054416 1.0000 80 chr1:149857799-149857879 1.0000 80 chr19:798600-798680 1.0000 80 chr5:137802117-137802197 1.0000 80 chr8:145236142-145236222 1.0000 80 chr20:362007-362087 1.0000 80 chr1:28833046-28833126 1.0000 80 chr12:6644008-6644088 1.0000 80 chr6:34202685-34202765 1.0000 80 chr16:2239349-2239429 1.0000 80 chr17:37557969-37558049 1.0000 80 chr19:3977535-3977615 1.0000 80 chr7:5568015-5568095 1.0000 80 chr12:31477363-31477443 1.0000 80 chrX:41193951-41194031 1.0000 80 chr2:232574365-232574445 1.0000 80 chr4:83294780-83294860 1.0000 80 chr15:41245740-41245820 1.0000 80 chr7:5596131-5596211 1.0000 80 chr14:75746652-75746732 1.0000 80 chr3:186501931-186502011 1.0000 80 chr5:137803091-137803171 1.0000 80 chr7:23510852-23510932 1.0000 80 chr18:8608896-8608976 1.0000 80 chr22:39916945-39917025 1.0000 80 chr2:114648141-114648221 1.0000 80 chr10:121410736-12141081 1.0000 80 chr12:6644305-6644385 1.0000 80 chr8:101963050-101963130 1.0000 80 chr17:77805736-77805816 1.0000 80 chr1:45271863-45271943 1.0000 80 chr20:44519347-44519427 1.0000 80 chr6:30881676-30881756 1.0000 80 chr12:51158214-51158294 1.0000 80 chr11:122932506-12293258 1.0000 80 chr12:46766073-46766153 1.0000 80 chr4:129732583-129732663 1.0000 80 chr1:153895124-153895204 1.0000 80 chr18:54305831-54305911 1.0000 80 chr7:100027396-100027476 1.0000 80 chr19:10765149-10765229 1.0000 80 chr12:7342298-7342378 1.0000 80 chr7:5566307-5566387 1.0000 80 chr14:24563579-24563659 1.0000 80 chr2:10587938-10588018 1.0000 80 chr1:35658318-35658398 1.0000 80 chr10:70092100-70092180 1.0000 80 chr17:7476429-7476509 1.0000 80 chr7:26241466-26241546 1.0000 80 chr19:3979771-3979851 1.0000 80 chr5:126113895-126113975 1.0000 80 chr15:50646882-50646962 1.0000 80 chr19:5691722-5691802 1.0000 80 chr1:167906081-167906161 1.0000 80 chr2:85766846-85766926 1.0000 80 chr1:203765047-203765127 1.0000 80 chr7:5569728-5569808 1.0000 80 chr5:137802685-137802765 1.0000 80 chr5:141255737-141255817 1.0000 80 chr9:80912123-80912203 1.0000 80 chr6:43739320-43739400 1.0000 80 chr17:4851321-4851401 1.0000 80 chr4:100870881-100870961 1.0000 80 chr7:148581042-148581122 1.0000 80 chr2:232328679-232328759 1.0000 80 chr10:97890226-97890306 1.0000 80 chr15:75871754-75871834 1.0000 80 chr9:91926081-91926161 1.0000 80 chr13:50655718-50655798 1.0000 80 chr6:74230178-74230258 1.0000 80 chr2:232574111-232574191 1.0000 80 chr6:160390663-160390743 1.0000 80 chr12:110719483-11071956 1.0000 80 chr12:64798404-64798484 1.0000 80 chr7:26239890-26239970 1.0000 80 chr16:2803072-2803152 1.0000 80 chr1:46050077-46050157 1.0000 80 chr7:74072512-74072592 1.0000 80 chr1:149859326-149859406 1.0000 80 chr6:155055080-155055160 1.0000 80 chr6:151711932-151712012 1.0000 80 chr6:26250696-26250776 1.0000 80 chr11:65547564-65547644 1.0000 80 chr9:132245009-132245089 1.0000 80 chr1:149857411-149857491 1.0000 80 chr22:29196448-29196528 1.0000 80 chr8:47529121-47529201 1.0000 80 chr17:79008968-79009048 1.0000 80 chr13:45914823-45914903 1.0000 80 chr1:89458235-89458315 1.0000 80 chr17:27620087-27620167 1.0000 80 chr6:26056178-26056258 1.0000 80 chr6:26033620-26033700 1.0000 80 chr9:86595066-86595146 1.0000 80 chr3:128902536-128902616 1.0000 80 chr11:65667317-65667397 1.0000 80 chr6:111196862-111196942 1.0000 80 chr14:21994332-21994412 1.0000 80 chr15:44829376-44829456 1.0000 80 chr8:101734349-101734429 1.0000 80 chr20:48808441-48808521 1.0000 80 chr16:31191899-31191979 1.0000 80 chr3:13461909-13461989 1.0000 80 chr19:12903179-12903259 1.0000 80 chr12:98987740-98987820 1.0000 80 chr8:103875518-103875598 1.0000 80 chrX:135962444-135962524 1.0000 80 chr1:32801794-32801874 1.0000 80 chr6:24720570-24720650 1.0000 80 chr17:62501898-62501978 1.0000 80 chr3:169482546-169482626 1.0000 80 chr17:17740079-17740159 1.0000 80 chr15:79165061-79165141 1.0000 80 chr15:69111043-69111123 1.0000 80 chr3:23852066-23852146 1.0000 80 chr10:70716201-70716281 1.0000 80 chr14:70234340-70234420 1.0000 80 chr11:18417699-18417779 1.0000 80 chr6:108279266-108279346 1.0000 80 chrX:24043129-24043209 1.0000 80 chr16:4233680-4233760 1.0000 80 chr12:49524648-49524728 1.0000 80 chr6:17706665-17706745 1.0000 80 chr21:44495377-44495457 1.0000 80 chr8:22926314-22926394 1.0000 80 chr11:190061-190141 1.0000 80 chr19:3367208-3367288 1.0000 80 chr17:17739871-17739951 1.0000 80 chr12:6976894-6976974 1.0000 80 chr22:18121790-18121870 1.0000 80 chr8:92053045-92053125 1.0000 80 chr12:6977143-6977223 1.0000 80 chr3:38207232-38207312 1.0000 80 chr2:70142358-70142438 1.0000 80 chr17:55038040-55038120 1.0000 80 chr12:111180579-11118065 1.0000 80 chr11:65625206-65625286 1.0000 80 chr5:126113436-126113516 1.0000 80 chrX:153627100-153627180 1.0000 80 chrX:39953928-39954008 1.0000 80 chr9:99180495-99180575 1.0000 80 chr12:123849382-12384946 1.0000 80 chr17:4269265-4269345 1.0000 80 chr2:174828739-174828819 1.0000 80 chr17:7211567-7211647 1.0000 80 chr14:102553298-10255337 1.0000 80 chr2:232575276-232575356 1.0000 80 chr17:62501655-62501735 1.0000 80 chr4:1040468-1040548 1.0000 80 chr19:49378947-49379027 1.0000 80 chr17:62223683-62223763 1.0000 80 chr6:18264592-18264672 1.0000 80 chr21:46495062-46495142 1.0000 80 chr7:73589089-73589169 1.0000 80 chr16:2806361-2806441 1.0000 80 chr3:176915606-176915686 1.0000 80 chr12:31477581-31477661 1.0000 80 chr19:47729888-47729968 1.0000 80 chr1:184006312-184006392 1.0000 80 chr2:70313981-70314061 1.0000 80 chr1:9778876-9778956 1.0000 80 chr5:32585970-32586050 1.0000 80 chr19:13229656-13229736 1.0000 80 chr13:45915029-45915109 1.0000 80 chr7:149468842-149468922 1.0000 80 chr7:105925300-105925380 1.0000 80 chr13:28713217-28713297 1.0000 80 chr8:135725003-135725083 1.0000 80 chr10:69644793-69644873 1.0000 80 chr9:110045472-110045552 1.0000 80 chr10:5855183-5855263 1.0000 80 chr11:118927701-11892778 1.0000 80 chr1:154193703-154193783 1.0000 80 chr21:36260921-36261001 1.0000 80 chr17:47647505-47647585 1.0000 80 chr2:157198573-157198653 1.0000 80 chr19:1269300-1269380 1.0000 80 chr17:16342524-16342604 1.0000 80 chr6:111197116-111197196 1.0000 80 chr4:24585775-24585855 1.0000 80 chr9:74980049-74980129 1.0000 80 chr19:3983002-3983082 1.0000 80 chr10:43902867-43902947 1.0000 80 chr6:27862877-27862957 1.0000 80 chr16:67597144-67597224 1.0000 80 chr3:100428798-100428878 1.0000 80 chr6:27101657-27101737 1.0000 80 chr3:23959036-23959116 1.0000 80 chr2:178128688-178128768 1.0000 80 chr11:65686486-65686566 1.0000 80 chr1:205718722-205718802 1.0000 80 chr2:44222882-44222962 1.0000 80 chr16:28835072-28835152 1.0000 80 chr10:102820870-10282095 1.0000 80 chr6:64346029-64346109 1.0000 80 chr1:26232367-26232447 1.0000 80 chr14:103987522-10398760 1.0000 80 chr20:34329916-34329996 1.0000 80 chr1:40041480-40041560 1.0000 80 chr17:56408433-56408513 1.0000 80 chr17:74732497-74732577 1.0000 80 chr17:40831779-40831859 1.0000 80 chr19:34269065-34269145 1.0000 80 chr17:66032161-66032241 1.0000 80 chr19:12903447-12903527 1.0000 80 chr14:74225656-74225736 1.0000 80 chr9:127631170-127631250 1.0000 80 chr22:38902028-38902108 1.0000 80 chr1:19923780-19923860 1.0000 80 chr1:245026578-245026658 1.0000 80 chr1:21113351-21113431 1.0000 80 chr19:47615299-47615379 1.0000 80 chr2:113403518-113403598 1.0000 80 chr5:137801622-137801702 1.0000 80 chr19:17973823-17973903 1.0000 80 chr14:75745579-75745659 1.0000 80 chr16:74700448-74700528 1.0000 80 chr19:33183092-33183172 1.0000 80 chr11:62648713-62648793 1.0000 80 chr2:198364413-198364493 1.0000 80 chr1:212782517-212782597 1.0000 80 chr9:33025248-33025328 1.0000 80 chrX:16805044-16805124 1.0000 80 chr5:81574109-81574189 1.0000 80 chr6:64282477-64282557 1.0000 80 chr11:95522736-95522816 1.0000 80 chr16:88905534-88905614 1.0000 80 chr22:29664377-29664457 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_PRPF4/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/K562/fasta/RankLinear0.6_40/PRPF4.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 0.136 C 0.373 G 0.356 T 0.135 Background letter frequencies (from file dataset with add-one prior applied): A 0.136 C 0.373 G 0.356 T 0.135 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CCTCCCCC MEME-1 width = 8 sites = 59 llr = 437 E-value = 7.8e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCTCCCCC MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::2::::: pos.-specific C aa:7a9a9 probability G :::1:::: matrix T ::82:1:1 bits 2.9 2.6 2.3 2.0 * Relative 1.7 * Entropy 1.4 *** * * (10.7 bits) 1.2 *** **** 0.9 *** **** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel CCTCCCCC consensus AT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCCCCC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr11:95522736-95522816 4 1.36e-04 cct cctccccc tccccctgcc chr1:21113351-21113431 50 1.36e-04 AGCTCCCCCT CCTCCCCC AAATCCAAAC chr1:245026578-245026658 49 1.36e-04 gcccgcggcT CCTCCCCC TACAGCGGCA chr6:64346029-64346109 72 1.36e-04 GCAATCCTCC CCTCCCCC A chr1:205718722-205718802 54 1.36e-04 ACTTCACACC CCTCCCCC TCCGGCCGCT chr17:4269265-4269345 7 1.36e-04 ACAGCC CCTCCCCC GCAACGTCCT chr12:123849382-12384946 10 1.36e-04 CTTGACGCC CCTCCCCC Agcccccccg chr21:44495377-44495457 47 1.36e-04 GCCCCGCGTC CCTCCCCC AGCGGGCACC chr6:17706665-17706745 28 1.36e-04 CCTTAGAGAG CCTccccc gccgcccggc chr15:79165061-79165141 5 1.36e-04 ggcc cctccccc acccgggggg chr16:31191899-31191979 50 1.36e-04 TCTGCGGGCC CCTCCCCC TTCGCGGCGC chr3:128902536-128902616 66 1.36e-04 GCGCCGGGCC CCTCCCCC AGCCCTC chr7:74072512-74072592 49 1.36e-04 GCCCGTGCCG CCTCCCCC TACCCCCACC chr16:2803072-2803152 69 1.36e-04 CGGCTTCACT CCTCCCCC CAAC chr13:50655718-50655798 26 1.36e-04 CTGCAGCTCC CCTCCCCC CACAGCCCCG chr1:203765047-203765127 27 1.36e-04 CGTAACGACC CCTCCCCC CCACCTCCCG chr1:167906081-167906161 22 1.36e-04 CCCCTCCTCC CCTCCCCC ACGCGGTGGT chr19:10765149-10765229 60 1.36e-04 CGCCTCTGCC CCTCCCCC CGCCCGCCCT chr11:122932506-12293258 3 1.36e-04 AC CCTCCCCC GCCACGCGGC chr17:77805736-77805816 13 1.36e-04 GCTGGGCTCC CCTCCCCC ACGTCCAGCC chr12:6644305-6644385 63 1.36e-04 CAGAGGAGCC CCTCCCCC ACGGCCTCCG chr17:37557969-37558049 58 1.36e-04 CGAGACCACC CCTCCCCC ACACGGGGCC chr19:2050255-2050335 7 1.36e-04 CCATCC CCTCCCCC ACGGCACAGG chr17:80055673-80055753 57 1.36e-04 GGGTCCGCGG CCTCCCCC ACGGGAAGCG chr10:103577859-10357793 41 1.36e-04 GGCTccttcc cctccccc tctgcccttc chr11:117015242-11701532 5 1.36e-04 GGCC CCTCCCCC CACGCCGCCC chr15:80352142-80352222 53 1.36e-04 cggcgctgcc cctccccc gcctgctccc chr8:103424291-103424371 73 1.36e-04 GAAGGGCGCC CCTCCCCC chr2:42796018-42796098 70 1.36e-04 CATCCCTTCC CCTCCCCC CAC chr15:69111043-69111123 63 1.85e-04 cgcTTGGCGC CCTTCCCC CTCCGCGCAG chr13:45914823-45914903 23 1.85e-04 GACCGACTCA CCTTCCCC TCCACCTCCA chr2:114648141-114648221 25 1.85e-04 CCCTCCCGGC CCTTCCCC CACTACGGTG chr14:67708296-67708376 47 1.85e-04 gccgggcTCC CCTTCCCC CACACGCTGC chr16:67597144-67597224 21 2.34e-04 TCGGGCTGCC CCTCCTCC AGCCAGCCCC chr19:47729888-47729968 7 2.34e-04 ACTGTT CCTCCTCC CCGCGGACTC chr17:17740079-17740159 63 2.34e-04 GGCGCAGCCG CCTCCTCC GGGAGGCCCG chr7:23510852-23510932 59 2.34e-04 CTGGGCGACA CCTCCTCC GCCTCCGCCT chrX:16805044-16805124 16 2.52e-04 GCCAGGCGTT CCTTCTCC CAGTCACCGC chr11:118927701-11892778 17 3.88e-04 GCACCTCCAT CCACCCCC GCTACCTCTT chr8:135725003-135725083 43 3.88e-04 gcgccgcgcc ccACCCCC ACCCCGTCTC chr12:49524648-49524728 16 3.88e-04 CAGCTGCTTC CCACCCCC GCTTTTCGCG chr3:13461909-13461989 4 3.88e-04 ACC CCACCCCC AGCCCGGCCC chr7:148581042-148581122 55 3.88e-04 CCCTCACCCT CCACCCCC CGCACGCCTA chr5:141255737-141255817 14 3.88e-04 TCTGGCGGCC CCACCCCC ACCCCGGCAG chr10:102820870-10282095 1 4.38e-04 . CCATCCCC CCGCGAGCTG chr9:110045472-110045552 43 4.38e-04 CCGCCCGGCC CCATCCCC CCAGGTTTTT chr4:1040468-1040548 68 4.38e-04 ccttcccgag ccatcccc gagcc chr6:24720570-24720650 22 4.38e-04 CTGAGCCCCT CCATCCCC GCTGCAGTGC chr7:26239890-26239970 70 4.38e-04 TGAAAGCTCC CCATCCCC CAC chr1:9778876-9778956 4 6.16e-04 CGA CCTGCCCC GCATGGCCCG chr7:73589089-73589169 60 6.16e-04 GGCCACACGG CCTGCCCC GCTCCGGTCC chr12:98987740-98987820 3 6.16e-04 CT CCTCCCCT AGAAAGATGT chr1:149859326-149859406 1 6.16e-04 . CCTGCCCC GACCCGCTCC chr1:46050077-46050157 68 6.16e-04 GTATCCTTCG CCTGCCCC TCTCC chr7:26241466-26241546 72 6.16e-04 GCTCCCCTCC CCTCCCCT T chr17:79479406-79479486 73 6.16e-04 AAGCCTCGGC CCTGCCCC chr1:153895124-153895204 13 6.34e-04 ctcccagcct ccttccct tcctcgctcc chr10:70092100-70092180 27 7.01e-04 GCCTCCCCGA CCATCTCC CACTTCAGGG chr6:155055080-155055160 7 7.66e-04 GGTTCC CCTGCTCC TGCCCGCACC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCCCCC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr11:95522736-95522816 0.00014 3_[+1]_69 chr1:21113351-21113431 0.00014 49_[+1]_23 chr1:245026578-245026658 0.00014 48_[+1]_24 chr6:64346029-64346109 0.00014 71_[+1]_1 chr1:205718722-205718802 0.00014 53_[+1]_19 chr17:4269265-4269345 0.00014 6_[+1]_66 chr12:123849382-12384946 0.00014 9_[+1]_63 chr21:44495377-44495457 0.00014 46_[+1]_26 chr6:17706665-17706745 0.00014 27_[+1]_45 chr15:79165061-79165141 0.00014 4_[+1]_68 chr16:31191899-31191979 0.00014 49_[+1]_23 chr3:128902536-128902616 0.00014 65_[+1]_7 chr7:74072512-74072592 0.00014 48_[+1]_24 chr16:2803072-2803152 0.00014 68_[+1]_4 chr13:50655718-50655798 0.00014 25_[+1]_47 chr1:203765047-203765127 0.00014 26_[+1]_46 chr1:167906081-167906161 0.00014 21_[+1]_51 chr19:10765149-10765229 0.00014 59_[+1]_13 chr11:122932506-12293258 0.00014 2_[+1]_70 chr17:77805736-77805816 0.00014 12_[+1]_60 chr12:6644305-6644385 0.00014 62_[+1]_10 chr17:37557969-37558049 0.00014 57_[+1]_15 chr19:2050255-2050335 0.00014 6_[+1]_66 chr17:80055673-80055753 0.00014 56_[+1]_16 chr10:103577859-10357793 0.00014 40_[+1]_32 chr11:117015242-11701532 0.00014 4_[+1]_68 chr15:80352142-80352222 0.00014 52_[+1]_20 chr8:103424291-103424371 0.00014 72_[+1] chr2:42796018-42796098 0.00014 69_[+1]_3 chr15:69111043-69111123 0.00018 62_[+1]_10 chr13:45914823-45914903 0.00018 22_[+1]_50 chr2:114648141-114648221 0.00018 24_[+1]_48 chr14:67708296-67708376 0.00018 46_[+1]_26 chr16:67597144-67597224 0.00023 20_[+1]_52 chr19:47729888-47729968 0.00023 6_[+1]_66 chr17:17740079-17740159 0.00023 62_[+1]_10 chr7:23510852-23510932 0.00023 58_[+1]_14 chrX:16805044-16805124 0.00025 15_[+1]_57 chr11:118927701-11892778 0.00039 16_[+1]_56 chr8:135725003-135725083 0.00039 42_[+1]_30 chr12:49524648-49524728 0.00039 15_[+1]_57 chr3:13461909-13461989 0.00039 3_[+1]_69 chr7:148581042-148581122 0.00039 54_[+1]_18 chr5:141255737-141255817 0.00039 13_[+1]_59 chr10:102820870-10282095 0.00044 [+1]_72 chr9:110045472-110045552 0.00044 42_[+1]_30 chr4:1040468-1040548 0.00044 67_[+1]_5 chr6:24720570-24720650 0.00044 21_[+1]_51 chr7:26239890-26239970 0.00044 69_[+1]_3 chr1:9778876-9778956 0.00062 3_[+1]_69 chr7:73589089-73589169 0.00062 59_[+1]_13 chr12:98987740-98987820 0.00062 2_[+1]_70 chr1:149859326-149859406 0.00062 [+1]_72 chr1:46050077-46050157 0.00062 67_[+1]_5 chr7:26241466-26241546 0.00062 71_[+1]_1 chr17:79479406-79479486 0.00062 72_[+1] chr1:153895124-153895204 0.00063 12_[+1]_60 chr10:70092100-70092180 0.0007 26_[+1]_46 chr6:155055080-155055160 0.00077 6_[+1]_66 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCCCCC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCTCCCCC width=8 seqs=59 chr11:95522736-95522816 ( 4) CCTCCCCC 1 chr1:21113351-21113431 ( 50) CCTCCCCC 1 chr1:245026578-245026658 ( 49) CCTCCCCC 1 chr6:64346029-64346109 ( 72) CCTCCCCC 1 chr1:205718722-205718802 ( 54) CCTCCCCC 1 chr17:4269265-4269345 ( 7) CCTCCCCC 1 chr12:123849382-12384946 ( 10) CCTCCCCC 1 chr21:44495377-44495457 ( 47) CCTCCCCC 1 chr6:17706665-17706745 ( 28) CCTCCCCC 1 chr15:79165061-79165141 ( 5) CCTCCCCC 1 chr16:31191899-31191979 ( 50) CCTCCCCC 1 chr3:128902536-128902616 ( 66) CCTCCCCC 1 chr7:74072512-74072592 ( 49) CCTCCCCC 1 chr16:2803072-2803152 ( 69) CCTCCCCC 1 chr13:50655718-50655798 ( 26) CCTCCCCC 1 chr1:203765047-203765127 ( 27) CCTCCCCC 1 chr1:167906081-167906161 ( 22) CCTCCCCC 1 chr19:10765149-10765229 ( 60) CCTCCCCC 1 chr11:122932506-12293258 ( 3) CCTCCCCC 1 chr17:77805736-77805816 ( 13) CCTCCCCC 1 chr12:6644305-6644385 ( 63) CCTCCCCC 1 chr17:37557969-37558049 ( 58) CCTCCCCC 1 chr19:2050255-2050335 ( 7) CCTCCCCC 1 chr17:80055673-80055753 ( 57) CCTCCCCC 1 chr10:103577859-10357793 ( 41) CCTCCCCC 1 chr11:117015242-11701532 ( 5) CCTCCCCC 1 chr15:80352142-80352222 ( 53) CCTCCCCC 1 chr8:103424291-103424371 ( 73) CCTCCCCC 1 chr2:42796018-42796098 ( 70) CCTCCCCC 1 chr15:69111043-69111123 ( 63) CCTTCCCC 1 chr13:45914823-45914903 ( 23) CCTTCCCC 1 chr2:114648141-114648221 ( 25) CCTTCCCC 1 chr14:67708296-67708376 ( 47) CCTTCCCC 1 chr16:67597144-67597224 ( 21) CCTCCTCC 1 chr19:47729888-47729968 ( 7) CCTCCTCC 1 chr17:17740079-17740159 ( 63) CCTCCTCC 1 chr7:23510852-23510932 ( 59) CCTCCTCC 1 chrX:16805044-16805124 ( 16) CCTTCTCC 1 chr11:118927701-11892778 ( 17) CCACCCCC 1 chr8:135725003-135725083 ( 43) CCACCCCC 1 chr12:49524648-49524728 ( 16) CCACCCCC 1 chr3:13461909-13461989 ( 4) CCACCCCC 1 chr7:148581042-148581122 ( 55) CCACCCCC 1 chr5:141255737-141255817 ( 14) CCACCCCC 1 chr10:102820870-10282095 ( 1) CCATCCCC 1 chr9:110045472-110045552 ( 43) CCATCCCC 1 chr4:1040468-1040548 ( 68) CCATCCCC 1 chr6:24720570-24720650 ( 22) CCATCCCC 1 chr7:26239890-26239970 ( 70) CCATCCCC 1 chr1:9778876-9778956 ( 4) CCTGCCCC 1 chr7:73589089-73589169 ( 60) CCTGCCCC 1 chr12:98987740-98987820 ( 3) CCTCCCCT 1 chr1:149859326-149859406 ( 1) CCTGCCCC 1 chr1:46050077-46050157 ( 68) CCTGCCCC 1 chr7:26241466-26241546 ( 72) CCTCCCCT 1 chr17:79479406-79479486 ( 73) CCTGCCCC 1 chr1:153895124-153895204 ( 13) CCTTCCCT 1 chr10:70092100-70092180 ( 27) CCATCTCC 1 chr6:155055080-155055160 ( 7) CCTGCTCC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCCCCC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 8.92768 E= 7.8e-003 -1253 142 -1253 -1253 -1253 142 -1253 -1253 58 -1253 -1253 256 -1253 90 -181 59 -1253 142 -1253 -1253 -1253 124 -1253 -19 -1253 142 -1253 -1253 -1253 135 -1253 -141 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCCCCC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 59 E= 7.8e-003 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.203390 0.000000 0.000000 0.796610 0.000000 0.694915 0.101695 0.203390 0.000000 1.000000 0.000000 0.000000 0.000000 0.881356 0.000000 0.118644 0.000000 1.000000 0.000000 0.000000 0.000000 0.949153 0.000000 0.050847 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTCCCCC MEME-1 regular expression -------------------------------------------------------------------------------- CC[TA][CT]CCCC -------------------------------------------------------------------------------- Time 5.15 secs. ******************************************************************************** ******************************************************************************** MOTIF GAAAGAAA MEME-2 width = 8 sites = 14 llr = 143 E-value = 3.1e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAAAGAAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :998:979 pos.-specific C ::1:31:: probability G a1::7:11 matrix T :1:2::1: bits 2.9 2.6 2.3 * * 2.0 *** * * Relative 1.7 *** * * Entropy 1.4 **** *** (14.7 bits) 1.2 **** *** 0.9 **** *** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GAAAGAAA consensus TC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAAGAAA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr17:7476429-7476509 60 8.02e-07 CCTGGCGTGG GAAAGAAA GGTGGAGGCG chr19:2050255-2050335 70 8.02e-07 TGGGGATTCT GAAAGAAA GTC chr4:24585775-24585855 59 1.64e-06 AGCCCAGAGA GAAACAAA GGCTCGGGCT chr1:149857411-149857491 27 2.44e-06 CTTCGTTTTA GAATGAAA CAGACCCAAG chr19:5691722-5691802 66 4.07e-06 GCCTGGTCGT GAATCAAA AGCCGTG chr5:81574109-81574189 58 7.80e-06 GGGCCTGAGC GAAAGAGA GAAGCACCGC chr6:30881676-30881756 69 7.80e-06 GGAAGCGGCA GAAACATA GCTC chrX:24043129-24043209 51 9.90e-06 TAAGTCCTGG GAAAGAAG ACAGCGCTGA chrX:39953928-39954008 16 1.28e-05 ACCGCGGGCA GGAAGAAA GAGCGGGCTG chr17:62501655-62501735 38 1.36e-05 GCCGGGCGGG GTAACAAA GGCGCCGCCG chr9:86595066-86595146 55 2.02e-05 GTCGGAGCTA GACAGAAA ACGAGCGCAG chr9:100746051-100746131 70 2.02e-05 CGGTGTGGGG GAAAGCAA ACT chr21:36260921-36261001 66 2.61e-05 cTGGCTCTAT GAATGAGA GTGCCTG chr12:98987740-98987820 12 3.11e-05 TCCTCCCCTA GAAAGATG TTCTCGTCCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAAGAAA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:7476429-7476509 8e-07 59_[+2]_13 chr19:2050255-2050335 8e-07 69_[+2]_3 chr4:24585775-24585855 1.6e-06 58_[+2]_14 chr1:149857411-149857491 2.4e-06 26_[+2]_46 chr19:5691722-5691802 4.1e-06 65_[+2]_7 chr5:81574109-81574189 7.8e-06 57_[+2]_15 chr6:30881676-30881756 7.8e-06 68_[+2]_4 chrX:24043129-24043209 9.9e-06 50_[+2]_22 chrX:39953928-39954008 1.3e-05 15_[+2]_57 chr17:62501655-62501735 1.4e-05 37_[+2]_35 chr9:86595066-86595146 2e-05 54_[+2]_18 chr9:100746051-100746131 2e-05 69_[+2]_3 chr21:36260921-36261001 2.6e-05 65_[+2]_7 chr12:98987740-98987820 3.1e-05 11_[+2]_61 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAAGAAA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GAAAGAAA width=8 seqs=14 chr17:7476429-7476509 ( 60) GAAAGAAA 1 chr19:2050255-2050335 ( 70) GAAAGAAA 1 chr4:24585775-24585855 ( 59) GAAACAAA 1 chr1:149857411-149857491 ( 27) GAATGAAA 1 chr19:5691722-5691802 ( 66) GAATCAAA 1 chr5:81574109-81574189 ( 58) GAAAGAGA 1 chr6:30881676-30881756 ( 69) GAAACATA 1 chrX:24043129-24043209 ( 51) GAAAGAAG 1 chrX:39953928-39954008 ( 16) GGAAGAAA 1 chr17:62501655-62501735 ( 38) GTAACAAA 1 chr9:86595066-86595146 ( 55) GACAGAAA 1 chr9:100746051-100746131 ( 70) GAAAGCAA 1 chr21:36260921-36261001 ( 66) GAATGAGA 1 chr12:98987740-98987820 ( 12) GAAAGATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAAGAAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 10.9532 E= 3.1e-001 -1045 -1045 149 -1045 266 -1045 -231 -92 277 -238 -1045 -1045 253 -1045 -1045 66 -1045 -38 100 -1045 277 -238 -1045 -1045 239 -1045 -132 8 266 -1045 -132 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAAGAAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 14 E= 3.1e-001 0.000000 0.000000 1.000000 0.000000 0.857143 0.000000 0.071429 0.071429 0.928571 0.071429 0.000000 0.000000 0.785714 0.000000 0.000000 0.214286 0.000000 0.285714 0.714286 0.000000 0.928571 0.071429 0.000000 0.000000 0.714286 0.000000 0.142857 0.142857 0.857143 0.000000 0.142857 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAAGAAA MEME-2 regular expression -------------------------------------------------------------------------------- GAA[AT][GC]AAA -------------------------------------------------------------------------------- Time 8.87 secs. ******************************************************************************** ******************************************************************************** MOTIF GGRGGAGG MEME-3 width = 8 sites = 44 llr = 346 E-value = 5.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGRGGAGG MEME-3 Description -------------------------------------------------------------------------------- Simplified A ::3::a:: pos.-specific C 3:1::::: probability G 8a5aa:aa matrix T :::::::: bits 2.9 * 2.6 * 2.3 * 2.0 * Relative 1.7 * Entropy 1.4 * **** (11.3 bits) 1.2 * ***** 0.9 * ***** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel GGGGGAGG consensus C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGRGGAGG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:19923780-19923860 54 3.77e-05 GTTGCAGCCC GGAGGAGG TGGTCGGGGT chr19:13229656-13229736 73 3.77e-05 CCTGGGCGCT GGAGGAGG chr4:100870881-100870961 42 3.77e-05 GCCCGCGAGC GGAGGAGG AACGGAGAAT chr6:43739320-43739400 11 3.77e-05 GGGAGCCGGA GGAGGAGG CCGAGGGGGC chr18:54305831-54305911 53 3.77e-05 ggaggggaga ggaggagg atgggaaggC chr10:121410736-12141081 60 3.77e-05 GGGAGGGGCG GGAGGAGG TGGGGGAGGG chr2:198364413-198364493 64 1.36e-04 GCAGGAGCCG GGGGGAGG TGGTGCGGG chr10:43902867-43902947 66 1.36e-04 GGCGGCCTTG GGGGGAGG GCGAGTC chr9:110045472-110045552 66 1.36e-04 TTTTTCGCGT GGGGGAGG GGGCACG chr17:4269265-4269345 35 1.36e-04 ACAGAACGGT GGGGGAGG GGACCTCCTC chr12:123849382-12384946 44 1.36e-04 cgggaggggc gggggAGG GGCAACGGAT chr12:6977143-6977223 43 1.36e-04 GCGGGAGACC GGGGGAGG CTGGGCCGCG chr19:3367208-3367288 21 1.36e-04 TGTGCATGGA GGGGGAGG GGGCAGGAGA chr16:2803072-2803152 41 1.36e-04 CCTTGGTGAG GGGGGAGG GCGCGCGCCT chr12:51158214-51158294 21 1.36e-04 cgcagcggca gggggagg ggcCGCCCGC chr8:101963050-101963130 25 1.36e-04 AGCTGCAGGT GGGGGAGG GGACGAGAGC chr17:37557969-37558049 8 1.36e-04 CCCGGGA GGGGGAGG GGCGGGAGGG chr8:145236142-145236222 64 1.36e-04 GCCCGGTGAT GGGGGAGG GGCCGGTGA chr3:73046376-73046456 64 1.36e-04 CGTCTGGGCT GGGGGAGG GGAGCCGGG chr11:64545900-64545980 34 1.36e-04 AAGCCTCCCG GGGGGAGG GGACCCGAAT chr14:67708296-67708376 21 1.36e-04 GGAgcgcggc gggggagg ggcgggcggc chr9:100746051-100746131 49 1.36e-04 ggggcggccg gggggAGG CAGCGGTGTG chr11:68518932-68519012 73 1.36e-04 caggaacctg gggggagg chr8:103424291-103424371 46 1.36e-04 CACGGCCCGT GGGGGAGG GGAGGGAGGG chr17:7788851-7788931 14 1.36e-04 ACGGCGGCGT GGGGGAGG GGCACGTGGG chr1:205718722-205718802 15 1.76e-04 GGGACGGCCC CGAGGAGG TGGGGCCTCT chr10:69644793-69644873 73 1.76e-04 acgacgaggg cgaggagg chr6:18264592-18264672 63 1.76e-04 CGCGAGGGCA CGAGGAGG TTCTGGGAGG chr17:27620087-27620167 11 1.76e-04 AGCGGCCCCG CGAGGAGG AGAGAACATT chr8:47529121-47529201 11 1.76e-04 CCAGAGCACG CGAGGAGG GTGCTGCGCG chr12:110719483-11071956 63 1.76e-04 GAGGCGGAGG CGAGGAGG CCGCGGGGAC chr15:75871754-75871834 34 1.76e-04 AAGCTGGCGG CGAGGAGG GCCCGGCGGA chr15:50646882-50646962 20 1.76e-04 ATGCTAGGGC CGAGGAGG GGGCGGCGGC chr14:103987522-10398760 35 2.79e-04 GCGGAGGTAG CGGGGAGG GAGGACGCCG chr7:148581042-148581122 28 2.79e-04 CAGCTCCTTC CGGGGAGG GGGGCTCTCC chr17:80055673-80055753 10 2.79e-04 TTGTGGGCG CGGGGAGG CCGAGCCGGG chr9:33025248-33025328 51 3.82e-04 CTCGGTGAGA GGCGGAGG AGCGGTAACT chr13:28713217-28713297 40 3.82e-04 gggccgcggc ggcggAGG GCAGGCCTGG chr6:17706665-17706745 10 3.82e-04 AGAGGCAGA GGCGGAGG CCTTAGAGAG chr16:4233680-4233760 53 3.82e-04 GGCGTGAAGC GGCGGAGG TCAGCAGCGA chr9:132245009-132245089 57 3.82e-04 GCGGCGGCCG GGCGGAGG GCGGGGGACC chr12:64798404-64798484 57 3.82e-04 CTGCGGCCGT GGCGGAGG ACTACGGCGA chr8:101734349-101734429 70 3.97e-04 CGCCggagta ggaggaga cgc chr4:129732583-129732663 12 4.34e-04 GGAGGGAACC GGGGGAGA CTCGGGAGCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGRGGAGG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:19923780-19923860 3.8e-05 53_[+3]_19 chr19:13229656-13229736 3.8e-05 72_[+3] chr4:100870881-100870961 3.8e-05 41_[+3]_31 chr6:43739320-43739400 3.8e-05 10_[+3]_62 chr18:54305831-54305911 3.8e-05 52_[+3]_20 chr10:121410736-12141081 3.8e-05 59_[+3]_13 chr2:198364413-198364493 0.00014 63_[+3]_9 chr10:43902867-43902947 0.00014 65_[+3]_7 chr9:110045472-110045552 0.00014 65_[+3]_7 chr17:4269265-4269345 0.00014 34_[+3]_38 chr12:123849382-12384946 0.00014 43_[+3]_29 chr12:6977143-6977223 0.00014 42_[+3]_30 chr19:3367208-3367288 0.00014 20_[+3]_52 chr16:2803072-2803152 0.00014 40_[+3]_32 chr12:51158214-51158294 0.00014 20_[+3]_52 chr8:101963050-101963130 0.00014 24_[+3]_48 chr17:37557969-37558049 0.00014 7_[+3]_65 chr8:145236142-145236222 0.00014 63_[+3]_9 chr3:73046376-73046456 0.00014 63_[+3]_9 chr11:64545900-64545980 0.00014 33_[+3]_39 chr14:67708296-67708376 0.00014 20_[+3]_52 chr9:100746051-100746131 0.00014 48_[+3]_24 chr11:68518932-68519012 0.00014 72_[+3] chr8:103424291-103424371 0.00014 45_[+3]_27 chr17:7788851-7788931 0.00014 13_[+3]_59 chr1:205718722-205718802 0.00018 14_[+3]_58 chr10:69644793-69644873 0.00018 72_[+3] chr6:18264592-18264672 0.00018 62_[+3]_10 chr17:27620087-27620167 0.00018 10_[+3]_62 chr8:47529121-47529201 0.00018 10_[+3]_62 chr12:110719483-11071956 0.00018 62_[+3]_10 chr15:75871754-75871834 0.00018 33_[+3]_39 chr15:50646882-50646962 0.00018 19_[+3]_53 chr14:103987522-10398760 0.00028 34_[+3]_38 chr7:148581042-148581122 0.00028 27_[+3]_45 chr17:80055673-80055753 0.00028 9_[+3]_63 chr9:33025248-33025328 0.00038 50_[+3]_22 chr13:28713217-28713297 0.00038 39_[+3]_33 chr6:17706665-17706745 0.00038 9_[+3]_63 chr16:4233680-4233760 0.00038 52_[+3]_20 chr9:132245009-132245089 0.00038 56_[+3]_16 chr12:64798404-64798484 0.00038 56_[+3]_16 chr8:101734349-101734429 0.0004 69_[+3]_3 chr4:129732583-129732663 0.00043 11_[+3]_61 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGRGGAGG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGRGGAGG width=8 seqs=44 chr1:19923780-19923860 ( 54) GGAGGAGG 1 chr19:13229656-13229736 ( 73) GGAGGAGG 1 chr4:100870881-100870961 ( 42) GGAGGAGG 1 chr6:43739320-43739400 ( 11) GGAGGAGG 1 chr18:54305831-54305911 ( 53) GGAGGAGG 1 chr10:121410736-12141081 ( 60) GGAGGAGG 1 chr2:198364413-198364493 ( 64) GGGGGAGG 1 chr10:43902867-43902947 ( 66) GGGGGAGG 1 chr9:110045472-110045552 ( 66) GGGGGAGG 1 chr17:4269265-4269345 ( 35) GGGGGAGG 1 chr12:123849382-12384946 ( 44) GGGGGAGG 1 chr12:6977143-6977223 ( 43) GGGGGAGG 1 chr19:3367208-3367288 ( 21) GGGGGAGG 1 chr16:2803072-2803152 ( 41) GGGGGAGG 1 chr12:51158214-51158294 ( 21) GGGGGAGG 1 chr8:101963050-101963130 ( 25) GGGGGAGG 1 chr17:37557969-37558049 ( 8) GGGGGAGG 1 chr8:145236142-145236222 ( 64) GGGGGAGG 1 chr3:73046376-73046456 ( 64) GGGGGAGG 1 chr11:64545900-64545980 ( 34) GGGGGAGG 1 chr14:67708296-67708376 ( 21) GGGGGAGG 1 chr9:100746051-100746131 ( 49) GGGGGAGG 1 chr11:68518932-68519012 ( 73) GGGGGAGG 1 chr8:103424291-103424371 ( 46) GGGGGAGG 1 chr17:7788851-7788931 ( 14) GGGGGAGG 1 chr1:205718722-205718802 ( 15) CGAGGAGG 1 chr10:69644793-69644873 ( 73) CGAGGAGG 1 chr6:18264592-18264672 ( 63) CGAGGAGG 1 chr17:27620087-27620167 ( 11) CGAGGAGG 1 chr8:47529121-47529201 ( 11) CGAGGAGG 1 chr12:110719483-11071956 ( 63) CGAGGAGG 1 chr15:75871754-75871834 ( 34) CGAGGAGG 1 chr15:50646882-50646962 ( 20) CGAGGAGG 1 chr14:103987522-10398760 ( 35) CGGGGAGG 1 chr7:148581042-148581122 ( 28) CGGGGAGG 1 chr17:80055673-80055753 ( 10) CGGGGAGG 1 chr9:33025248-33025328 ( 51) GGCGGAGG 1 chr13:28713217-28713297 ( 40) GGCGGAGG 1 chr6:17706665-17706745 ( 10) GGCGGAGG 1 chr16:4233680-4233760 ( 53) GGCGGAGG 1 chr9:132245009-132245089 ( 57) GGCGGAGG 1 chr12:64798404-64798484 ( 57) GGCGGAGG 1 chr8:101734349-101734429 ( 70) GGAGGAGA 1 chr4:129732583-129732663 ( 12) GGGGGAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGRGGAGG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 9.72094 E= 5.9e-001 -1210 -58 107 -1210 -1210 -1210 149 -1210 133 -145 55 -1210 -1210 -1210 149 -1210 -1210 -1210 149 -1210 288 -1210 -1210 -1210 -1210 -1210 149 -1210 -158 -1210 142 -1210 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGRGGAGG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 44 E= 5.9e-001 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.340909 0.136364 0.522727 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 0.045455 0.000000 0.954545 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGRGGAGG MEME-3 regular expression -------------------------------------------------------------------------------- [GC]G[GA]GGAGG -------------------------------------------------------------------------------- Time 12.53 secs. ******************************************************************************** ******************************************************************************** MOTIF ATWHAKAA MEME-4 width = 8 sites = 5 llr = 60 E-value = 3.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATWHAKAA MEME-4 Description -------------------------------------------------------------------------------- Simplified A a264a:8a pos.-specific C :::2:::: probability G :::::4:: matrix T :844:62: bits 2.9 * * * 2.6 * * * 2.3 * * * 2.0 *** * ** Relative 1.7 *** * ** Entropy 1.4 *** **** (17.3 bits) 1.2 ******** 0.9 ******** 0.6 ******** 0.3 ******** 0.0 -------- Multilevel ATAAATAA consensus ATT GT sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATWHAKAA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:32801794-32801874 64 2.30e-07 CGAGCTGCCT ATATATAA GCGCCCGGA chr6:27862877-27862957 60 1.52e-06 CCCCTCTTCA ATAAATTA CTTCTATTGT chr4:100870881-100870961 58 1.52e-06 GGAACGGAGA ATATAGAA TTACCAAGgc chr8:103875518-103875598 3 3.21e-06 CC ATTCATAA CCAGGACCCC chr7:26239890-26239970 2 7.55e-06 G AATAAGAA TTCCCGCCTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATWHAKAA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:32801794-32801874 2.3e-07 63_[+4]_9 chr6:27862877-27862957 1.5e-06 59_[+4]_13 chr4:100870881-100870961 1.5e-06 57_[+4]_15 chr8:103875518-103875598 3.2e-06 2_[+4]_70 chr7:26239890-26239970 7.6e-06 1_[+4]_71 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATWHAKAA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ATWHAKAA width=8 seqs=5 chr1:32801794-32801874 ( 64) ATATATAA 1 chr6:27862877-27862957 ( 60) ATAAATTA 1 chr4:100870881-100870961 ( 58) ATATAGAA 1 chr8:103875518-103875598 ( 3) ATTCATAA 1 chr7:26239890-26239970 ( 2) AATAAGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATWHAKAA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 12.7769 E= 3.3e+003 288 -897 -897 -897 56 -897 -897 256 214 -897 -897 156 156 -90 -897 156 288 -897 -897 -897 -897 -897 17 215 256 -897 -897 56 288 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATWHAKAA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 3.3e+003 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.800000 0.600000 0.000000 0.000000 0.400000 0.400000 0.200000 0.000000 0.400000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.400000 0.600000 0.800000 0.000000 0.000000 0.200000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATWHAKAA MEME-4 regular expression -------------------------------------------------------------------------------- A[TA][AT][ATC]A[TG][AT]A -------------------------------------------------------------------------------- Time 16.08 secs. ******************************************************************************** ******************************************************************************** MOTIF AACTTTWN MEME-5 width = 8 sites = 7 llr = 78 E-value = 7.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AACTTTWN MEME-5 Description -------------------------------------------------------------------------------- Simplified A aa::::43 pos.-specific C ::a:3::1 probability G :::::1:3 matrix T :::a7963 bits 2.9 ** * 2.6 ** * 2.3 ** * 2.0 ** * ** Relative 1.7 ** **** Entropy 1.4 ******* (16.0 bits) 1.2 ******* 0.9 ******* 0.6 ******* 0.3 ******** 0.0 -------- Multilevel AACTTTTA consensus C AG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTTTWN MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr11:65686486-65686566 42 1.25e-06 CCTCAACAAC AACTTTAT AGACAGGCGC chr4:129732583-129732663 73 2.06e-06 CCCCGGGGCC AACTTTTG chr22:29196448-29196528 14 2.88e-06 ACAGAAGCAG AACTTTAG GGGTCCCGTC chr1:40041480-40041560 52 3.74e-06 CGCGGGGCTG AACTTTTC GTACAGCATG chr9:100746051-100746131 14 5.45e-06 CGCGAGGATT AACTCTTT gccgcccgcg chr1:28833046-28833126 4 8.04e-06 CCC AACTCTAA AGTACGCGTT chr10:69644793-69644873 41 9.68e-06 GCTGGCCGAC AACTTGTa cgacgaagac -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTTTWN MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr11:65686486-65686566 1.2e-06 41_[+5]_31 chr4:129732583-129732663 2.1e-06 72_[+5] chr22:29196448-29196528 2.9e-06 13_[+5]_59 chr1:40041480-40041560 3.7e-06 51_[+5]_21 chr9:100746051-100746131 5.5e-06 13_[+5]_59 chr1:28833046-28833126 8e-06 3_[+5]_69 chr10:69644793-69644873 9.7e-06 40_[+5]_32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTTTWN MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AACTTTWN width=8 seqs=7 chr11:65686486-65686566 ( 42) AACTTTAT 1 chr4:129732583-129732663 ( 73) AACTTTTG 1 chr22:29196448-29196528 ( 14) AACTTTAG 1 chr1:40041480-40041560 ( 52) AACTTTTC 1 chr9:100746051-100746131 ( 14) AACTCTTT 1 chr1:28833046-28833126 ( 4) AACTCTAA 1 chr10:69644793-69644873 ( 41) AACTTGTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTTTWN MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.9536 E= 7.5e+003 288 -945 -945 -945 288 -945 -945 -945 -945 142 -945 -945 -945 -945 -945 288 -945 -38 -945 240 -945 -945 -131 266 166 -945 -945 208 107 -138 -32 108 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTTTWN MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 7.5e+003 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.285714 0.000000 0.714286 0.000000 0.000000 0.142857 0.857143 0.428571 0.000000 0.000000 0.571429 0.285714 0.142857 0.285714 0.285714 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTTTWN MEME-5 regular expression -------------------------------------------------------------------------------- AACT[TC]T[TA][AGT] -------------------------------------------------------------------------------- Time 19.63 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr9:139422922-139423002 7.35e-01 80 chr17:7788851-7788931 4.72e-01 80 chr2:42796018-42796098 2.18e-01 80 chr8:103424291-103424371 2.31e-02 80 chr15:80352142-80352222 3.93e-01 80 chr11:117015242-11701532 1.50e-01 80 chr7:148580836-148580916 1.16e-01 80 chr11:68518932-68519012 8.27e-02 80 chr17:159276-159356 2.99e-01 80 chr9:100746051-100746131 5.31e-06 13_[+5(5.45e-06)]_48_[+2(2.02e-05)]_\ 3 chr10:103577859-10357793 2.65e-01 80 chr20:362429-362509 8.93e-01 80 chr14:67708296-67708376 2.54e-02 80 chr1:36787997-36788077 5.35e-01 80 chr17:80055673-80055753 7.19e-03 80 chr17:79479406-79479486 1.58e-01 80 chr2:196522537-196522617 6.26e-01 80 chr19:2050255-2050335 1.37e-05 69_[+2(8.02e-07)]_3 chr5:170815241-170815321 2.90e-01 80 chr11:64545900-64545980 1.30e-01 80 chr9:80912384-80912464 7.53e-01 80 chr3:73046376-73046456 1.77e-01 80 chr17:80054336-80054416 5.28e-01 80 chr1:149857799-149857879 8.66e-01 80 chr19:798600-798680 4.81e-01 80 chr5:137802117-137802197 9.22e-01 80 chr8:145236142-145236222 1.96e-01 80 chr20:362007-362087 6.40e-01 80 chr1:28833046-28833126 2.77e-03 3_[+5(8.04e-06)]_69 chr12:6644008-6644088 6.00e-01 80 chr6:34202685-34202765 9.00e-01 80 chr16:2239349-2239429 7.90e-01 80 chr17:37557969-37558049 4.52e-02 80 chr19:3977535-3977615 8.91e-01 80 chr7:5568015-5568095 2.63e-02 80 chr12:31477363-31477443 4.13e-01 80 chrX:41193951-41194031 9.52e-01 80 chr2:232574365-232574445 9.60e-01 80 chr4:83294780-83294860 4.85e-01 80 chr15:41245740-41245820 2.13e-01 80 chr7:5596131-5596211 1.54e-01 80 chr14:75746652-75746732 7.01e-01 80 chr3:186501931-186502011 3.50e-01 80 chr5:137803091-137803171 9.46e-01 80 chr7:23510852-23510932 1.02e-01 80 chr18:8608896-8608976 9.22e-01 80 chr22:39916945-39917025 8.01e-01 80 chr2:114648141-114648221 4.47e-01 80 chr10:121410736-12141081 6.31e-02 59_[+3(3.77e-05)]_13 chr12:6644305-6644385 6.59e-02 80 chr8:101963050-101963130 6.92e-02 80 chr17:77805736-77805816 1.43e-01 80 chr1:45271863-45271943 8.53e-01 80 chr20:44519347-44519427 9.98e-02 80 chr6:30881676-30881756 2.55e-03 68_[+2(7.80e-06)]_4 chr12:51158214-51158294 3.92e-01 80 chr11:122932506-12293258 1.20e-01 80 chr12:46766073-46766153 9.30e-01 80 chr4:129732583-129732663 1.16e-03 72_[+5(2.06e-06)] chr1:153895124-153895204 7.41e-01 80 chr18:54305831-54305911 1.27e-01 52_[+3(3.77e-05)]_20 chr7:100027396-100027476 7.79e-01 80 chr19:10765149-10765229 9.17e-02 80 chr12:7342298-7342378 7.68e-01 80 chr7:5566307-5566387 3.23e-01 80 chr14:24563579-24563659 9.69e-01 80 chr2:10587938-10588018 4.68e-02 15_[+2(6.94e-05)]_57 chr1:35658318-35658398 7.60e-01 80 chr10:70092100-70092180 2.68e-01 80 chr17:7476429-7476509 7.42e-04 59_[+2(8.02e-07)]_13 chr7:26241466-26241546 2.77e-01 80 chr19:3979771-3979851 7.31e-01 80 chr5:126113895-126113975 8.96e-01 80 chr15:50646882-50646962 1.13e-01 80 chr19:5691722-5691802 1.88e-03 65_[+2(4.07e-06)]_7 chr1:167906081-167906161 1.77e-01 80 chr2:85766846-85766926 7.85e-01 80 chr1:203765047-203765127 3.13e-01 80 chr7:5569728-5569808 9.62e-01 80 chr5:137802685-137802765 9.08e-02 80 chr5:141255737-141255817 1.93e-01 80 chr9:80912123-80912203 3.91e-02 80 chr6:43739320-43739400 2.04e-02 7_[+3(3.77e-05)]_65 chr17:4851321-4851401 4.59e-01 80 chr4:100870881-100870961 1.31e-04 41_[+3(3.77e-05)]_8_[+4(1.52e-06)]_\ 15 chr7:148581042-148581122 4.57e-02 80 chr2:232328679-232328759 5.66e-01 80 chr10:97890226-97890306 5.88e-01 80 chr15:75871754-75871834 6.53e-03 17_[+4(9.07e-05)]_55 chr9:91926081-91926161 5.50e-01 80 chr13:50655718-50655798 8.46e-02 80 chr6:74230178-74230258 3.00e-01 80 chr2:232574111-232574191 1.10e-01 80 chr6:160390663-160390743 4.30e-01 80 chr12:110719483-11071956 3.35e-01 80 chr12:64798404-64798484 3.85e-01 80 chr7:26239890-26239970 5.00e-04 1_[+4(7.55e-06)]_71 chr16:2803072-2803152 2.66e-02 80 chr1:46050077-46050157 2.80e-01 80 chr7:74072512-74072592 4.66e-01 80 chr1:149859326-149859406 1.49e-01 80 chr6:155055080-155055160 6.65e-01 80 chr6:151711932-151712012 1.52e-01 80 chr6:26250696-26250776 8.03e-01 80 chr11:65547564-65547644 4.77e-01 80 chr9:132245009-132245089 1.57e-01 80 chr1:149857411-149857491 9.91e-04 26_[+2(2.44e-06)]_46 chr22:29196448-29196528 7.51e-05 13_[+5(2.88e-06)]_59 chr8:47529121-47529201 1.30e-01 80 chr17:79008968-79009048 9.50e-01 80 chr13:45914823-45914903 1.25e-02 80 chr1:89458235-89458315 9.65e-01 80 chr17:27620087-27620167 5.70e-02 80 chr6:26056178-26056258 7.68e-01 80 chr6:26033620-26033700 1.02e-01 80 chr9:86595066-86595146 5.71e-03 54_[+2(2.02e-05)]_18 chr3:128902536-128902616 2.85e-01 80 chr11:65667317-65667397 3.32e-01 80 chr6:111196862-111196942 5.89e-01 80 chr14:21994332-21994412 5.19e-01 80 chr15:44829376-44829456 3.33e-01 80 chr8:101734349-101734429 1.74e-01 80 chr20:48808441-48808521 4.25e-01 80 chr16:31191899-31191979 3.32e-01 80 chr3:13461909-13461989 3.18e-01 80 chr19:12903179-12903259 3.13e-01 80 chr12:98987740-98987820 3.63e-03 11_[+2(3.11e-05)]_61 chr8:103875518-103875598 2.18e-02 2_[+4(3.21e-06)]_70 chrX:135962444-135962524 7.42e-01 80 chr1:32801794-32801874 5.79e-03 63_[+4(2.30e-07)]_9 chr6:24720570-24720650 5.96e-01 80 chr17:62501898-62501978 5.17e-01 80 chr3:169482546-169482626 9.98e-01 80 chr17:17740079-17740159 2.69e-01 80 chr15:79165061-79165141 2.88e-02 80 chr15:69111043-69111123 4.38e-01 80 chr3:23852066-23852146 9.59e-01 80 chr10:70716201-70716281 9.92e-01 80 chr14:70234340-70234420 2.18e-02 80 chr11:18417699-18417779 8.72e-01 80 chr6:108279266-108279346 8.03e-01 80 chrX:24043129-24043209 7.64e-03 50_[+2(9.90e-06)]_22 chr16:4233680-4233760 2.99e-01 80 chr12:49524648-49524728 6.46e-02 80 chr6:17706665-17706745 9.41e-03 80 chr21:44495377-44495457 9.03e-02 80 chr8:22926314-22926394 8.15e-01 80 chr11:190061-190141 8.73e-01 80 chr19:3367208-3367288 1.68e-01 80 chr17:17739871-17739951 5.81e-01 80 chr12:6976894-6976974 6.74e-01 80 chr22:18121790-18121870 8.98e-01 80 chr8:92053045-92053125 2.40e-01 80 chr12:6977143-6977223 2.54e-01 80 chr3:38207232-38207312 9.51e-01 80 chr2:70142358-70142438 7.16e-01 80 chr17:55038040-55038120 7.58e-01 80 chr12:111180579-11118065 5.94e-01 80 chr11:65625206-65625286 9.17e-02 80 chr5:126113436-126113516 9.63e-01 80 chrX:153627100-153627180 8.34e-01 80 chrX:39953928-39954008 1.01e-02 15_[+2(1.28e-05)]_57 chr9:99180495-99180575 9.47e-02 80 chr12:123849382-12384946 5.97e-03 80 chr17:4269265-4269345 1.44e-03 80 chr2:174828739-174828819 5.66e-01 80 chr17:7211567-7211647 9.24e-01 80 chr14:102553298-10255337 8.93e-01 80 chr2:232575276-232575356 1.29e-01 80 chr17:62501655-62501735 1.03e-03 37_[+2(1.36e-05)]_35 chr4:1040468-1040548 5.58e-01 80 chr19:49378947-49379027 3.91e-01 80 chr17:62223683-62223763 9.14e-01 80 chr6:18264592-18264672 1.74e-01 80 chr21:46495062-46495142 4.50e-01 80 chr7:73589089-73589169 4.14e-01 80 chr16:2806361-2806441 3.53e-02 80 chr3:176915606-176915686 9.75e-01 80 chr12:31477581-31477661 8.17e-01 80 chr19:47729888-47729968 5.57e-01 80 chr1:184006312-184006392 7.51e-01 80 chr2:70313981-70314061 6.18e-01 80 chr1:9778876-9778956 7.22e-02 80 chr5:32585970-32586050 2.69e-01 80 chr19:13229656-13229736 1.52e-01 72_[+3(3.77e-05)] chr13:45915029-45915109 8.69e-01 80 chr7:149468842-149468922 8.46e-01 80 chr7:105925300-105925380 2.21e-01 80 chr13:28713217-28713297 1.22e-01 80 chr8:135725003-135725083 2.95e-01 80 chr10:69644793-69644873 1.93e-03 40_[+5(9.68e-06)]_32 chr9:110045472-110045552 2.51e-02 80 chr10:5855183-5855263 3.13e-01 80 chr11:118927701-11892778 7.81e-02 80 chr1:154193703-154193783 7.09e-01 80 chr21:36260921-36261001 1.46e-02 65_[+2(2.61e-05)]_7 chr17:47647505-47647585 8.24e-01 80 chr2:157198573-157198653 3.43e-01 80 chr19:1269300-1269380 5.92e-01 80 chr17:16342524-16342604 6.83e-01 80 chr6:111197116-111197196 9.09e-02 80 chr4:24585775-24585855 2.23e-03 58_[+2(1.64e-06)]_14 chr9:74980049-74980129 4.98e-01 80 chr19:3983002-3983082 9.02e-01 80 chr10:43902867-43902947 4.25e-01 80 chr6:27862877-27862957 6.18e-03 59_[+4(1.52e-06)]_13 chr16:67597144-67597224 1.34e-01 80 chr3:100428798-100428878 4.80e-01 80 chr6:27101657-27101737 6.95e-01 80 chr3:23959036-23959116 5.47e-01 80 chr2:178128688-178128768 4.34e-01 80 chr11:65686486-65686566 1.13e-03 41_[+5(1.25e-06)]_31 chr1:205718722-205718802 1.90e-02 80 chr2:44222882-44222962 9.04e-01 80 chr16:28835072-28835152 7.34e-01 80 chr10:102820870-10282095 3.05e-01 80 chr6:64346029-64346109 2.33e-01 80 chr1:26232367-26232447 1.28e-02 80 chr14:103987522-10398760 9.92e-02 80 chr20:34329916-34329996 7.07e-01 80 chr1:40041480-40041560 1.59e-02 51_[+5(3.74e-06)]_21 chr17:56408433-56408513 5.02e-01 80 chr17:74732497-74732577 7.07e-01 80 chr17:40831779-40831859 4.36e-01 80 chr19:34269065-34269145 9.65e-01 80 chr17:66032161-66032241 2.38e-01 80 chr19:12903447-12903527 3.92e-01 80 chr14:74225656-74225736 7.95e-01 80 chr9:127631170-127631250 4.35e-01 80 chr22:38902028-38902108 8.71e-01 80 chr1:19923780-19923860 1.74e-01 53_[+3(3.77e-05)]_19 chr1:245026578-245026658 2.53e-01 80 chr1:21113351-21113431 1.65e-03 80 chr19:47615299-47615379 7.15e-01 80 chr2:113403518-113403598 9.48e-01 80 chr5:137801622-137801702 1.79e-01 80 chr19:17973823-17973903 4.02e-01 80 chr14:75745579-75745659 5.72e-01 80 chr16:74700448-74700528 6.76e-01 80 chr19:33183092-33183172 8.33e-01 80 chr11:62648713-62648793 9.86e-01 80 chr2:198364413-198364493 1.41e-01 80 chr1:212782517-212782597 7.71e-01 80 chr9:33025248-33025328 1.53e-02 80 chrX:16805044-16805124 5.70e-01 80 chr5:81574109-81574189 1.22e-02 57_[+2(7.80e-06)]_15 chr6:64282477-64282557 8.58e-01 80 chr11:95522736-95522816 3.64e-01 80 chr16:88905534-88905614 6.52e-01 80 chr22:29664377-29664457 8.17e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n10.farnam.hpc.yale.internal ********************************************************************************