******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.3.3 (Release date: Sun Feb 7 15:39:52 2021 -0800) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** PRIMARY SEQUENCES= ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/ZNF622.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr17:43697638-43697658 1.0000 20 chr19:17420269-17420289 1.0000 20 chr17:44302797-44302817 1.0000 20 chr5:145583099-145583119 1.0000 20 chr1:156308123-156308143 1.0000 20 chrX:13402337-13402357 1.0000 20 chr20:40247091-40247111 1.0000 20 chr2:224817304-224817324 1.0000 20 chr3:179280678-179280698 1.0000 20 chr1:205719414-205719434 1.0000 20 chr15:43213066-43213086 1.0000 20 chr15:69113246-69113266 1.0000 20 chr8:107738282-107738302 1.0000 20 chr3:176850273-176850293 1.0000 20 chr14:64010121-64010141 1.0000 20 chr15:80364822-80364842 1.0000 20 chr1:205196989-205197009 1.0000 20 chr14:21905459-21905479 1.0000 20 chr18:67862729-67862749 1.0000 20 chr1:145028897-145028917 1.0000 20 chr17:45177677-45177697 1.0000 20 chr14:73925483-73925503 1.0000 20 chr15:81274881-81274901 1.0000 20 chr19:55987925-55987945 1.0000 20 chr9:127905927-127905947 1.0000 20 chrX:44732265-44732285 1.0000 20 chr17:36908971-36908991 1.0000 20 chr5:172484226-172484246 1.0000 20 chr17:16945594-16945614 1.0000 20 chr1:54872094-54872114 1.0000 20 chr7:72936643-72936663 1.0000 20 chr3:113415666-113415686 1.0000 20 chr1:16942062-16942082 1.0000 20 chr17:30264040-30264060 1.0000 20 chr9:23826372-23826392 1.0000 20 chr2:20365288-20365308 1.0000 20 chr11:10879662-10879682 1.0000 20 chr11:125462639-12546265 1.0000 20 chr15:49103304-49103324 1.0000 20 chr10:104005150-10400517 1.0000 20 chr1:150669699-150669719 1.0000 20 chr5:139781336-139781356 1.0000 20 chr1:41174934-41174954 1.0000 20 chr2:38120204-38120224 1.0000 20 chr2:91802851-91802871 1.0000 20 chrX:18443598-18443618 1.0000 20 chr7:25165005-25165025 1.0000 20 chr11:133826953-13382697 1.0000 20 chr17:45728041-45728061 1.0000 20 chr2:9771201-9771221 1.0000 20 chr1:16951111-16951131 1.0000 20 chr19:13049323-13049343 1.0000 20 chr6:108879811-108879831 1.0000 20 chr5:90676100-90676120 1.0000 20 chr4:13421150-13421170 1.0000 20 chr2:62932761-62932781 1.0000 20 chr14:21924340-21924360 1.0000 20 chr1:11120196-11120216 1.0000 20 chr14:91527022-91527042 1.0000 20 chr20:29616320-29616340 1.0000 20 chr2:97481986-97482006 1.0000 20 chr2:96874615-96874635 1.0000 20 chr1:151432019-151432039 1.0000 20 chr12:56367716-56367736 1.0000 20 chr1:27560941-27560961 1.0000 20 chr5:151151386-151151406 1.0000 20 chr2:178500710-178500730 1.0000 20 chr8:121881236-121881256 1.0000 20 chr1:206860300-206860320 1.0000 20 chr16:50775942-50775962 1.0000 20 chr13:28194771-28194791 1.0000 20 chr19:45394461-45394481 1.0000 20 chr9:96929060-96929080 1.0000 20 chr14:99947471-99947491 1.0000 20 chr1:145077258-145077278 1.0000 20 chr4:174255666-174255686 1.0000 20 chr14:24631891-24631911 1.0000 20 chr14:34801518-34801538 1.0000 20 chr8:57124279-57124299 1.0000 20 chr19:45394034-45394054 1.0000 20 chr3:114866675-114866695 1.0000 20 chr11:66725907-66725927 1.0000 20 chr5:142149928-142149948 1.0000 20 chrX:136520483-136520503 1.0000 20 chr8:23347183-23347203 1.0000 20 chr17:29058647-29058667 1.0000 20 chr2:27651492-27651512 1.0000 20 chr5:22998046-22998066 1.0000 20 chr14:36295520-36295540 1.0000 20 chr1:214776507-214776527 1.0000 20 chr6:26474366-26474386 1.0000 20 chr6:108880972-108880992 1.0000 20 chr9:96215907-96215927 1.0000 20 chr6:26123273-26123293 1.0000 20 chr1:24742188-24742208 1.0000 20 chr1:145082269-145082289 1.0000 20 chr1:32860306-32860326 1.0000 20 chr19:3094335-3094355 1.0000 20 chr21:35015043-35015063 1.0000 20 chr1:156470519-156470539 1.0000 20 chr6:108396735-108396755 1.0000 20 chr2:133025772-133025792 1.0000 20 chr2:98280604-98280624 1.0000 20 chr19:49325364-49325384 1.0000 20 chr2:120110021-120110041 1.0000 20 chr6:27791800-27791820 1.0000 20 chr2:99773864-99773884 1.0000 20 chr12:56727790-56727810 1.0000 20 chr1:154154756-154154776 1.0000 20 chr16:71017169-71017189 1.0000 20 chr12:57030779-57030799 1.0000 20 chr19:4815378-4815398 1.0000 20 chr1:144988088-144988108 1.0000 20 chr19:3572744-3572764 1.0000 20 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme -oc ../result/final_prediction/GM12878/inference_raw/MEME/RankLinear0.6_10_ZNF622/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/GM12878/fasta/RankLinear0.6_10/ZNF622.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= 114 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= 2280 N= 114 sample: seed= 0 hsfrac= 0 searchsize= 2280 norand= no csites= 1000 Letter frequencies in dataset: A 0.211 C 0.294 G 0.286 T 0.208 Background letter frequencies (from file dataset with add-one prior applied): A 0.211 C 0.294 G 0.286 T 0.208 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CCAATGRC MEME-1 width = 8 sites = 19 llr = 136 E-value = 1.7e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCAATGRC MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::a7::41 pos.-specific C 8a:::216 probability G :::::652 matrix T 2::3a2:2 bits 2.3 * * 2.0 * * 1.8 ** * 1.6 ** * Relative 1.4 **** Entropy 1.1 ***** (10.3 bits) 0.9 ***** 0.7 ***** * 0.5 ******* 0.2 ******** 0.0 -------- Multilevel CCAATGGC consensus T CA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAATGRC MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr14:21924340-21924360 6 1.92e-05 ATCCG CCAATGGC AGCACCG chr17:43697638-43697658 3 1.92e-05 AG CCAATGGC GCTCACGATG chr19:13049323-13049343 6 3.34e-05 ATAGA CCAATGAC AAAGTGG chr5:139781336-139781356 11 7.11e-05 GTCACTTTGG CCAATGAT CT chr5:151151386-151151406 9 1.20e-04 GTCAGTGC CCAATTAC TGTT chr1:205196989-205197009 5 1.20e-04 CTTC CCATTGGC CGGTTGCC chr17:44302797-44302817 1 1.20e-04 . CCATTGGC TGAGCAATGG chr15:80364822-80364842 4 1.49e-04 TAT CCAATCAC AATTATCAG chr1:41174934-41174954 9 1.81e-04 CAGTTCAG CCAATGGG ACCA chr17:36908971-36908991 10 2.29e-04 GCCTATCAG CCAATGAA GAG chr7:25165005-25165025 10 2.49e-04 GCTCCAGTC CCAATGCC TGC chr17:45728041-45728061 9 2.93e-04 CCTGCCGC CCAATCGT TGCG chr2:98280604-98280624 9 5.04e-04 CTGGCCAG CCAATTGA GGTC chr15:49103304-49103324 8 5.04e-04 GCATCCT TCAATCGC CGACT chr17:45177677-45177697 8 5.04e-04 CTGGCGC TCATTGGC CCTTC chr20:40247091-40247111 1 5.04e-04 . CCATTGGG CTTCGCCGGT chr11:10879662-10879682 4 5.88e-04 CGC CCAATCAG CGCCAGATT chr8:23347183-23347203 5 6.69e-04 ggaa ccaattcc ggacacaG chr1:156308123-156308143 8 8.74e-04 ACCCATC TCATTGAT CGGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAATGRC MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr14:21924340-21924360 1.9e-05 5_[+1]_7 chr17:43697638-43697658 1.9e-05 2_[+1]_10 chr19:13049323-13049343 3.3e-05 5_[+1]_7 chr5:139781336-139781356 7.1e-05 10_[+1]_2 chr5:151151386-151151406 0.00012 8_[+1]_4 chr1:205196989-205197009 0.00012 4_[+1]_8 chr17:44302797-44302817 0.00012 [+1]_12 chr15:80364822-80364842 0.00015 3_[+1]_9 chr1:41174934-41174954 0.00018 8_[+1]_4 chr17:36908971-36908991 0.00023 9_[+1]_3 chr7:25165005-25165025 0.00025 9_[+1]_3 chr17:45728041-45728061 0.00029 8_[+1]_4 chr2:98280604-98280624 0.0005 8_[+1]_4 chr15:49103304-49103324 0.0005 7_[+1]_5 chr17:45177677-45177697 0.0005 7_[+1]_5 chr20:40247091-40247111 0.0005 [+1]_12 chr11:10879662-10879682 0.00059 3_[+1]_9 chr8:23347183-23347203 0.00067 4_[+1]_8 chr1:156308123-156308143 0.00087 7_[+1]_5 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAATGRC MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CCAATGRC width=8 seqs=19 chr14:21924340-21924360 ( 6) CCAATGGC 1 chr17:43697638-43697658 ( 3) CCAATGGC 1 chr19:13049323-13049343 ( 6) CCAATGAC 1 chr5:139781336-139781356 ( 11) CCAATGAT 1 chr5:151151386-151151406 ( 9) CCAATTAC 1 chr1:205196989-205197009 ( 5) CCATTGGC 1 chr17:44302797-44302817 ( 1) CCATTGGC 1 chr15:80364822-80364842 ( 4) CCAATCAC 1 chr1:41174934-41174954 ( 9) CCAATGGG 1 chr17:36908971-36908991 ( 10) CCAATGAA 1 chr7:25165005-25165025 ( 10) CCAATGCC 1 chr17:45728041-45728061 ( 9) CCAATCGT 1 chr2:98280604-98280624 ( 9) CCAATTGA 1 chr15:49103304-49103324 ( 8) TCAATCGC 1 chr17:45177677-45177697 ( 8) TCATTGGC 1 chr20:40247091-40247111 ( 1) CCATTGGG 1 chr11:10879662-10879682 ( 4) CCAATCAG 1 chr8:23347183-23347203 ( 5) CCAATTCC 1 chr1:156308123-156308143 ( 8) TCATTGAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAATGRC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1482 bayes= 6.46397 E= 1.7e-002 -1089 152 -1089 -40 -1089 176 -1089 -1089 224 -1089 -1089 -1089 180 -1089 -1089 34 -1089 -1089 -1089 226 -1089 -48 114 -40 80 -148 88 -1089 -101 98 -86 -40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAATGRC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 1.7e-002 0.000000 0.842105 0.000000 0.157895 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.736842 0.000000 0.000000 0.263158 0.000000 0.000000 0.000000 1.000000 0.000000 0.210526 0.631579 0.157895 0.368421 0.105263 0.526316 0.000000 0.105263 0.578947 0.157895 0.157895 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAATGRC MEME-1 regular expression -------------------------------------------------------------------------------- CCA[AT]T[GC][GA]C -------------------------------------------------------------------------------- Time 0.67 secs. ******************************************************************************** ******************************************************************************** MOTIF GGGCGGGR MEME-2 width = 8 sites = 7 llr = 63 E-value = 4.4e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGCGGGR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 3::::::6 pos.-specific C :::a:::: probability G 7aa:aaa4 matrix T :::::::: bits 2.3 2.0 1.8 ****** 1.6 ****** Relative 1.4 ****** Entropy 1.1 ******** (12.9 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel GGGCGGGA consensus A G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGGGR MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr13:28194771-28194791 12 3.39e-05 AGGTAGCACA GGGCGGGA G chr19:55987925-55987945 8 3.39e-05 GGTCCGG GGGCGGGA ACTCG chr17:29058647-29058667 1 1.05e-04 . GGGCGGGG GAAGTGGGCG chr19:45394461-45394481 12 1.05e-04 GGGCTAGGTG Gggcgggg c chrX:18443598-18443618 5 1.05e-04 GTAA AGGCGGGA TCGGGCAA chrX:44732265-44732285 12 1.05e-04 CGGCCTCGGT GGGCGGGG C chr15:69113246-69113266 5 1.05e-04 GTGG AGGCGGGA TCTGCGGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGGGR MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr13:28194771-28194791 3.4e-05 11_[+2]_1 chr19:55987925-55987945 3.4e-05 7_[+2]_5 chr17:29058647-29058667 0.00011 [+2]_12 chr19:45394461-45394481 0.00011 11_[+2]_1 chrX:18443598-18443618 0.00011 4_[+2]_8 chrX:44732265-44732285 0.00011 11_[+2]_1 chr15:69113246-69113266 0.00011 4_[+2]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGGGR MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GGGCGGGR width=8 seqs=7 chr13:28194771-28194791 ( 12) GGGCGGGA 1 chr19:55987925-55987945 ( 8) GGGCGGGA 1 chr17:29058647-29058667 ( 1) GGGCGGGG 1 chr19:45394461-45394481 ( 12) GGGCGGGG 1 chrX:18443598-18443618 ( 5) AGGCGGGA 1 chrX:44732265-44732285 ( 12) GGGCGGGG 1 chr15:69113246-69113266 ( 5) AGGCGGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGGGR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1482 bayes= 7.56224 E= 4.4e+001 43 -945 132 -945 -945 -945 180 -945 -945 -945 180 -945 -945 176 -945 -945 -945 -945 180 -945 -945 -945 180 -945 -945 -945 180 -945 143 -945 58 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGGGR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7 E= 4.4e+001 0.285714 0.000000 0.714286 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.571429 0.000000 0.428571 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGCGGGR MEME-2 regular expression -------------------------------------------------------------------------------- [GA]GGCGGG[AG] -------------------------------------------------------------------------------- Time 1.09 secs. ******************************************************************************** ******************************************************************************** MOTIF AGGKTGAG MEME-3 width = 8 sites = 3 llr = 32 E-value = 1.8e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGGKTGAG MEME-3 Description -------------------------------------------------------------------------------- Simplified A a:::::a: pos.-specific C :::::::: probability G :aa3:a:a matrix T :::7a::: bits 2.3 * * * 2.0 * * * 1.8 *** **** 1.6 *** **** Relative 1.4 *** **** Entropy 1.1 ******** (15.2 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel AGGTTGAG consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGKTGAG MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:108880972-108880992 1 1.29e-05 . AGGTTGAG GCGCCCTGCG chr1:150669699-150669719 1 1.29e-05 . AGGTTGAG TCCCGCCAAT chr17:30264040-30264060 2 3.06e-05 T AGGGTGAG CGGCCTCCGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGKTGAG MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:108880972-108880992 1.3e-05 [+3]_12 chr1:150669699-150669719 1.3e-05 [+3]_12 chr17:30264040-30264060 3.1e-05 1_[+3]_11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGKTGAG MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGGKTGAG width=8 seqs=3 chr6:108880972-108880992 ( 1) AGGTTGAG 1 chr1:150669699-150669719 ( 1) AGGTTGAG 1 chr17:30264040-30264060 ( 2) AGGGTGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGKTGAG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1482 bayes= 8.60363 E= 1.8e+003 224 -823 -823 -823 -823 -823 180 -823 -823 -823 180 -823 -823 -823 22 167 -823 -823 -823 226 -823 -823 180 -823 224 -823 -823 -823 -823 -823 180 -823 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGKTGAG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 3 E= 1.8e+003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGGKTGAG MEME-3 regular expression -------------------------------------------------------------------------------- AGG[TG]TGAG -------------------------------------------------------------------------------- Time 1.50 secs. ******************************************************************************** ******************************************************************************** MOTIF YWTTCTTT MEME-4 width = 8 sites = 2 llr = 21 E-value = 2.1e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif YWTTCTTT MEME-4 Description -------------------------------------------------------------------------------- Simplified A :5:::::: pos.-specific C 5:::a::: probability G :::::::: matrix T 55aa:aaa bits 2.3 ** *** 2.0 ** *** 1.8 ****** 1.6 ****** Relative 1.4 ******* Entropy 1.1 ******* (15.3 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel CATTCTTT consensus TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YWTTCTTT MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3:176850273-176850293 10 9.98e-06 TCATGTGAC TTTTCTTT AGC chr19:4815378-4815398 12 2.41e-05 ttcactcgtt cattcttt c -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YWTTCTTT MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3:176850273-176850293 1e-05 9_[+4]_3 chr19:4815378-4815398 2.4e-05 11_[+4]_1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YWTTCTTT MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF YWTTCTTT width=8 seqs=2 chr3:176850273-176850293 ( 10) TTTTCTTT 1 chr19:4815378-4815398 ( 12) CATTCTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YWTTCTTT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1482 bayes= 9.53138 E= 2.1e+003 -765 76 -765 126 124 -765 -765 126 -765 -765 -765 226 -765 -765 -765 226 -765 176 -765 -765 -765 -765 -765 226 -765 -765 -765 226 -765 -765 -765 226 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YWTTCTTT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 2.1e+003 0.000000 0.500000 0.000000 0.500000 0.500000 0.000000 0.000000 0.500000 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 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YWTTCTTT MEME-4 regular expression -------------------------------------------------------------------------------- [CT][AT]TTCTTT -------------------------------------------------------------------------------- Time 1.92 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTTRCTT MEME-5 width = 8 sites = 2 llr = 23 E-value = 4.7e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTTRCTT MEME-5 Description -------------------------------------------------------------------------------- Simplified A ::::5::: pos.-specific C :::::a:: probability G ::::5::: matrix T aaaa::aa bits 2.3 **** ** 2.0 **** ** 1.8 **** *** 1.6 **** *** Relative 1.4 **** *** Entropy 1.1 ******** (16.4 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ******** 0.0 -------- Multilevel TTTTACTT consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTRCTT MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr3:114866675-114866695 5 5.02e-06 CTGC TTTTACTT TCTACGCA chr1:156470519-156470539 10 1.18e-05 TTGTTGATA TTTTGCTT CCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTRCTT MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr3:114866675-114866695 5e-06 4_[+5]_8 chr1:156470519-156470539 1.2e-05 9_[+5]_3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTRCTT MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTTTRCTT width=8 seqs=2 chr3:114866675-114866695 ( 5) TTTTACTT 1 chr1:156470519-156470539 ( 10) TTTTGCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTRCTT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1482 bayes= 9.53138 E= 4.7e+002 -765 -765 -765 226 -765 -765 -765 226 -765 -765 -765 226 -765 -765 -765 226 124 -765 80 -765 -765 176 -765 -765 -765 -765 -765 226 -765 -765 -765 226 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTRCTT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 4.7e+002 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.500000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTRCTT MEME-5 regular expression -------------------------------------------------------------------------------- TTTT[AG]CTT -------------------------------------------------------------------------------- Time 2.83 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:43697638-43697658 5.32e-02 2_[+1(1.92e-05)]_10 chr19:17420269-17420289 9.36e-01 20 chr17:44302797-44302817 3.28e-03 20 chr5:145583099-145583119 6.02e-01 20 chr1:156308123-156308143 7.15e-02 20 chrX:13402337-13402357 3.72e-01 20 chr20:40247091-40247111 4.72e-02 20 chr2:224817304-224817324 5.30e-01 20 chr3:179280678-179280698 3.26e-01 20 chr1:205719414-205719434 4.93e-01 20 chr15:43213066-43213086 6.56e-01 20 chr15:69113246-69113266 1.42e-01 20 chr8:107738282-107738302 9.91e-02 20 chr3:176850273-176850293 3.20e-04 9_[+4(9.98e-06)]_3 chr14:64010121-64010141 4.49e-01 20 chr15:80364822-80364842 6.48e-02 20 chr1:205196989-205197009 1.27e-02 20 chr14:21905459-21905479 2.96e-01 20 chr18:67862729-67862749 7.15e-02 20 chr1:145028897-145028917 3.74e-01 20 chr17:45177677-45177697 1.27e-01 20 chr14:73925483-73925503 4.75e-01 20 chr15:81274881-81274901 2.08e-01 20 chr19:55987925-55987945 6.54e-02 7_[+2(3.39e-05)]_5 chr9:127905927-127905947 9.73e-01 20 chrX:44732265-44732285 9.99e-02 20 chr17:36908971-36908991 1.07e-01 20 chr5:172484226-172484246 2.94e-01 20 chr17:16945594-16945614 9.92e-01 20 chr1:54872094-54872114 2.66e-01 20 chr7:72936643-72936663 4.60e-01 20 chr3:113415666-113415686 1.57e-01 20 chr1:16942062-16942082 2.74e-01 20 chr17:30264040-30264060 5.78e-02 1_[+3(3.06e-05)]_11 chr9:23826372-23826392 8.29e-01 20 chr2:20365288-20365308 9.82e-01 20 chr11:10879662-10879682 1.90e-01 20 chr11:125462639-12546265 8.30e-01 20 chr15:49103304-49103324 7.78e-02 20 chr10:104005150-10400517 9.98e-01 20 chr1:150669699-150669719 2.86e-02 [+3(1.29e-05)]_12 chr5:139781336-139781356 2.15e-02 10_[+1(7.11e-05)]_2 chr1:41174934-41174954 9.06e-02 20 chr2:38120204-38120224 9.11e-02 20 chr2:91802851-91802871 1.48e-01 20 chrX:18443598-18443618 1.19e-01 20 chr7:25165005-25165025 2.28e-01 20 chr11:133826953-13382697 6.04e-01 20 chr17:45728041-45728061 3.97e-02 20 chr2:9771201-9771221 1.00e+00 20 chr1:16951111-16951131 4.21e-01 20 chr19:13049323-13049343 1.10e-01 5_[+1(3.34e-05)]_7 chr6:108879811-108879831 4.55e-01 20 chr5:90676100-90676120 9.97e-01 20 chr4:13421150-13421170 9.90e-01 20 chr2:62932761-62932781 7.29e-01 20 chr14:21924340-21924360 3.53e-02 5_[+1(1.92e-05)]_7 chr1:11120196-11120216 8.38e-01 20 chr14:91527022-91527042 9.65e-01 20 chr20:29616320-29616340 4.80e-01 20 chr2:97481986-97482006 2.57e-01 20 chr2:96874615-96874635 3.19e-01 20 chr1:151432019-151432039 9.77e-01 20 chr12:56367716-56367736 7.70e-01 20 chr1:27560941-27560961 9.69e-01 20 chr5:151151386-151151406 3.30e-02 20 chr2:178500710-178500730 9.03e-01 20 chr8:121881236-121881256 7.72e-01 20 chr1:206860300-206860320 2.44e-01 20 chr16:50775942-50775962 5.19e-01 20 chr13:28194771-28194791 2.43e-02 11_[+2(3.39e-05)]_1 chr19:45394461-45394481 3.56e-02 20 chr9:96929060-96929080 9.45e-01 20 chr14:99947471-99947491 1.00e+00 20 chr1:145077258-145077278 9.51e-01 20 chr4:174255666-174255686 3.07e-01 20 chr14:24631891-24631911 6.46e-01 20 chr14:34801518-34801538 7.75e-01 20 chr8:57124279-57124299 5.16e-01 20 chr19:45394034-45394054 8.99e-01 20 chr3:114866675-114866695 4.54e-04 4_[+5(5.02e-06)]_8 chr11:66725907-66725927 9.59e-02 20 chr5:142149928-142149948 9.10e-01 20 chrX:136520483-136520503 3.60e-01 20 chr8:23347183-23347203 3.36e-01 20 chr17:29058647-29058667 1.26e-01 20 chr2:27651492-27651512 2.17e-01 20 chr5:22998046-22998066 3.34e-01 20 chr14:36295520-36295540 1.00e+00 20 chr1:214776507-214776527 2.92e-01 20 chr6:26474366-26474386 8.09e-01 20 chr6:108880972-108880992 2.71e-02 [+3(1.29e-05)]_12 chr9:96215907-96215927 2.10e-01 20 chr6:26123273-26123293 9.00e-01 20 chr1:24742188-24742208 4.85e-01 20 chr1:145082269-145082289 4.26e-01 20 chr1:32860306-32860326 7.01e-01 20 chr19:3094335-3094355 7.34e-01 20 chr21:35015043-35015063 5.91e-01 20 chr1:156470519-156470539 1.56e-03 9_[+5(1.18e-05)]_3 chr6:108396735-108396755 9.54e-01 20 chr2:133025772-133025792 1.36e-01 20 chr2:98280604-98280624 1.26e-01 20 chr19:49325364-49325384 9.76e-02 20 chr2:120110021-120110041 4.95e-02 20 chr6:27791800-27791820 3.10e-02 20 chr2:99773864-99773884 1.62e-01 20 chr12:56727790-56727810 7.99e-01 20 chr1:154154756-154154776 9.49e-01 20 chr16:71017169-71017189 9.93e-01 20 chr12:57030779-57030799 7.77e-01 20 chr19:4815378-4815398 4.15e-03 11_[+4(2.41e-05)]_1 chr1:144988088-144988108 9.93e-01 20 chr19:3572744-3572764 2.30e-01 20 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n05.farnam.hpc.yale.internal ********************************************************************************