******************************************************************************** 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/RBM14.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr19:2049084-2049164 1.0000 80 chr22:19593511-19593591 1.0000 80 chr22:21800828-21800908 1.0000 80 chr22:19675965-19676045 1.0000 80 chr22:21385686-21385766 1.0000 80 chr22:20130332-20130412 1.0000 80 chr22:22068482-22068562 1.0000 80 chr1:17051668-17051748 1.0000 80 chr7:128482599-128482679 1.0000 80 chr22:19644166-19644246 1.0000 80 chr22:20133466-20133546 1.0000 80 chr15:79104236-79104316 1.0000 80 chr22:19763401-19763481 1.0000 80 chr1:12123750-12123830 1.0000 80 chr7:129419039-129419119 1.0000 80 chr22:50920615-50920695 1.0000 80 chr22:20784952-20785032 1.0000 80 chr22:19787240-19787320 1.0000 80 chr2:172967037-172967117 1.0000 80 chr21:18984591-18984671 1.0000 80 chr22:19951066-19951146 1.0000 80 chr18:2846667-2846747 1.0000 80 chr1:68151469-68151549 1.0000 80 chr17:73839692-73839772 1.0000 80 chr22:20130672-20130752 1.0000 80 chr1:47902877-47902957 1.0000 80 chr22:20130974-20131054 1.0000 80 chr18:3452167-3452247 1.0000 80 chr2:32582747-32582827 1.0000 80 chr6:139695295-139695375 1.0000 80 chr17:72984183-72984263 1.0000 80 chr9:86536255-86536335 1.0000 80 chr19:10613016-10613096 1.0000 80 chr21:46273915-46273995 1.0000 80 chr7:158824345-158824425 1.0000 80 chr7:158824561-158824641 1.0000 80 chr22:21435053-21435133 1.0000 80 chr17:27620207-27620287 1.0000 80 chr16:578398-578478 1.0000 80 chr7:150652073-150652153 1.0000 80 chr2:60777005-60777085 1.0000 80 chr1:245027423-245027503 1.0000 80 chr6:64282694-64282774 1.0000 80 chr6:31649140-31649220 1.0000 80 chr8:124408058-124408138 1.0000 80 chr1:205498267-205498347 1.0000 80 chr13:91827491-91827571 1.0000 80 chr17:79075976-79076056 1.0000 80 chr1:28586675-28586755 1.0000 80 chr20:62497027-62497107 1.0000 80 chr7:99156746-99156826 1.0000 80 chr19:41770727-41770807 1.0000 80 chr16:30569362-30569442 1.0000 80 chr18:2847352-2847432 1.0000 80 chr4:83294730-83294810 1.0000 80 chr16:578598-578678 1.0000 80 chr5:34930058-34930138 1.0000 80 chr1:145075707-145075787 1.0000 80 chr22:22315576-22315656 1.0000 80 chr22:21327610-21327690 1.0000 80 chr11:44749274-44749354 1.0000 80 chr11:44749514-44749594 1.0000 80 chr7:128482398-128482478 1.0000 80 chr9:136150126-136150206 1.0000 80 chr2:133016812-133016892 1.0000 80 chr20:57581581-57581661 1.0000 80 chr22:19951272-19951352 1.0000 80 chr1:16399671-16399751 1.0000 80 chr1:1242866-1242946 1.0000 80 chr7:148480128-148480208 1.0000 80 chr13:50699143-50699223 1.0000 80 chr22:21327934-21328014 1.0000 80 chr5:137802049-137802129 1.0000 80 chr7:100492532-100492612 1.0000 80 chr19:662649-662729 1.0000 80 chr19:1080977-1081057 1.0000 80 chr19:1081185-1081265 1.0000 80 chr6:151712320-151712400 1.0000 80 chr22:19892139-19892219 1.0000 80 chr7:25019559-25019639 1.0000 80 chr17:49244448-49244528 1.0000 80 chr17:80054362-80054442 1.0000 80 chr11:64036935-64037015 1.0000 80 chr8:144465929-144466009 1.0000 80 chr1:228270813-228270893 1.0000 80 chr7:5468964-5469044 1.0000 80 chr11:118927597-11892767 1.0000 80 chr7:157261240-157261320 1.0000 80 chr4:153857080-153857160 1.0000 80 chr4:153857279-153857359 1.0000 80 chr2:32582538-32582618 1.0000 80 chr22:22318508-22318588 1.0000 80 chr17:46100954-46101034 1.0000 80 chr5:172754382-172754462 1.0000 80 chr17:19015253-19015333 1.0000 80 chr5:172754789-172754869 1.0000 80 chr7:150652288-150652368 1.0000 80 chr6:86352253-86352333 1.0000 80 chr1:28586421-28586501 1.0000 80 chr1:840520-840600 1.0000 80 chr6:154831092-154831172 1.0000 80 chr22:19738706-19738786 1.0000 80 chr1:36274133-36274213 1.0000 80 chr16:1662917-1662997 1.0000 80 chr1:36274333-36274413 1.0000 80 chr15:20545559-20545639 1.0000 80 chr8:127570265-127570345 1.0000 80 chr1:68151691-68151771 1.0000 80 chr22:20081936-20082016 1.0000 80 chr7:100027425-100027505 1.0000 80 chr15:79104436-79104516 1.0000 80 chr17:29815492-29815572 1.0000 80 chr17:79894760-79894840 1.0000 80 chr2:60776714-60776794 1.0000 80 chr7:66309574-66309654 1.0000 80 chr19:798323-798403 1.0000 80 chr5:72794702-72794782 1.0000 80 chr16:83987319-83987399 1.0000 80 chr17:79479410-79479490 1.0000 80 chr5:71403670-71403750 1.0000 80 chr19:2050426-2050506 1.0000 80 chr7:150652487-150652567 1.0000 80 chr16:30621399-30621479 1.0000 80 chr1:1225870-1225950 1.0000 80 chr20:32699692-32699772 1.0000 80 chr17:3867865-3867945 1.0000 80 chr2:112813397-112813477 1.0000 80 chr6:43739133-43739213 1.0000 80 chr6:64283024-64283104 1.0000 80 chr3:171758463-171758543 1.0000 80 chr1:46767457-46767537 1.0000 80 chr16:88947777-88947857 1.0000 80 chr6:34664188-34664268 1.0000 80 chr1:28199126-28199206 1.0000 80 chr5:172754588-172754668 1.0000 80 chr4:123300576-123300656 1.0000 80 chr1:150551587-150551667 1.0000 80 chr7:1498032-1498112 1.0000 80 chr21:46238461-46238541 1.0000 80 chr9:140173274-140173354 1.0000 80 chr22:20050870-20050950 1.0000 80 chr6:32134970-32135050 1.0000 80 chr11:2720573-2720653 1.0000 80 chr19:1605082-1605162 1.0000 80 chr8:145597883-145597963 1.0000 80 chr16:28834908-28834988 1.0000 80 chr22:19629728-19629808 1.0000 80 chr13:81281623-81281703 1.0000 80 chr16:22309209-22309289 1.0000 80 chr5:36877321-36877401 1.0000 80 chr22:21385960-21386040 1.0000 80 chr5:36877522-36877602 1.0000 80 chr9:19230903-19230983 1.0000 80 chr9:131465835-131465915 1.0000 80 chr12:98909758-98909838 1.0000 80 chr11:189786-189866 1.0000 80 chr1:36772151-36772231 1.0000 80 chr7:5467147-5467227 1.0000 80 chr6:136871023-136871103 1.0000 80 chr1:36786617-36786697 1.0000 80 chr6:168226721-168226801 1.0000 80 chr18:3262436-3262516 1.0000 80 chr20:52209758-52209838 1.0000 80 chr19:12902844-12902924 1.0000 80 chr20:60794551-60794631 1.0000 80 chr5:41925754-41925834 1.0000 80 chr22:20227686-20227766 1.0000 80 chr6:32940644-32940724 1.0000 80 chr5:180673941-180674021 1.0000 80 chr15:51200515-51200595 1.0000 80 chr4:1004450-1004530 1.0000 80 chr22:20939348-20939428 1.0000 80 chr4:1004065-1004145 1.0000 80 chr5:10565062-10565142 1.0000 80 chr5:10565536-10565616 1.0000 80 chr9:136242350-136242430 1.0000 80 chr5:71403465-71403545 1.0000 80 chr16:2285864-2285944 1.0000 80 chr2:111877944-111878024 1.0000 80 chr22:20308058-20308138 1.0000 80 chr4:24585825-24585905 1.0000 80 chr2:178128888-178128968 1.0000 80 chr1:120255071-120255151 1.0000 80 chr11:63581564-63581644 1.0000 80 chr5:137803178-137803258 1.0000 80 chr1:1208420-1208500 1.0000 80 chr17:41399889-41399969 1.0000 80 chr1:71512686-71512766 1.0000 80 chr19:46404640-46404720 1.0000 80 chr12:54412226-54412306 1.0000 80 chr8:145133758-145133838 1.0000 80 chr8:144466135-144466215 1.0000 80 chr17:73774856-73774936 1.0000 80 chr1:6479157-6479237 1.0000 80 chr11:65729497-65729577 1.0000 80 chr1:220101490-220101570 1.0000 80 chr1:840791-840871 1.0000 80 chr17:40828648-40828728 1.0000 80 chr1:2205519-2205599 1.0000 80 chr17:79827485-79827565 1.0000 80 chr1:228328341-228328421 1.0000 80 chr5:141016881-141016961 1.0000 80 chr17:80055195-80055275 1.0000 80 chr17:79825066-79825146 1.0000 80 chr11:34937685-34937765 1.0000 80 chr9:139562795-139562875 1.0000 80 chr11:34937897-34937977 1.0000 80 chr1:236558955-236559035 1.0000 80 chr6:42016279-42016359 1.0000 80 chr2:26101031-26101111 1.0000 80 chr10:62703595-62703675 1.0000 80 chr22:19810152-19810232 1.0000 80 chr6:137114038-137114118 1.0000 80 chr11:506488-506568 1.0000 80 chr5:137802906-137802986 1.0000 80 chr2:232573486-232573566 1.0000 80 chr1:178995615-178995695 1.0000 80 chr22:21798856-21798936 1.0000 80 chr22:19809948-19810028 1.0000 80 chr13:81278635-81278715 1.0000 80 chr7:25019758-25019838 1.0000 80 chr15:50646666-50646746 1.0000 80 chr1:44440911-44440991 1.0000 80 chr6:20402747-20402827 1.0000 80 chr1:65991396-65991476 1.0000 80 chr19:10613928-10614008 1.0000 80 chr19:5623406-5623486 1.0000 80 chr22:19750694-19750774 1.0000 80 chr1:975747-975827 1.0000 80 chr17:46702389-46702469 1.0000 80 chr6:43478132-43478212 1.0000 80 chr22:21212844-21212924 1.0000 80 chr16:67876970-67877050 1.0000 80 chr11:118965319-11896539 1.0000 80 chr1:3663539-3663619 1.0000 80 chr17:7476401-7476481 1.0000 80 chr10:88854415-88854495 1.0000 80 chr17:79829734-79829814 1.0000 80 chr7:149570478-149570558 1.0000 80 chr15:29130833-29130913 1.0000 80 chr22:19771893-19771973 1.0000 80 chr9:97021802-97021882 1.0000 80 chr12:120972608-12097268 1.0000 80 chr9:139835240-139835320 1.0000 80 chr11:65625054-65625134 1.0000 80 chr11:316258-316338 1.0000 80 chr14:88237680-88237760 1.0000 80 chr16:88878018-88878098 1.0000 80 chr9:130830701-130830781 1.0000 80 chr19:798119-798199 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_RBM14/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/K562/fasta/RankLinear0.6_40/RBM14.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 0.151 C 0.346 G 0.353 T 0.15 Background letter frequencies (from file dataset with add-one prior applied): A 0.151 C 0.346 G 0.353 T 0.15 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTGTKTTG MEME-1 width = 8 sites = 9 llr = 95 E-value = 2.9e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTGTKTTG MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :::::2:: probability G :1813::a matrix T a92978a: bits 2.7 * * 2.5 * * 2.2 ** * * 1.9 ** * * Relative 1.6 ** * ** Entropy 1.4 ** ***** (15.3 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel TTGTTTTG consensus T GC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGTKTTG MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr20:52209758-52209838 57 1.42e-06 TCCGGACGCA TTGTTTTG GCCGCTTCCA chr7:100027425-100027505 32 1.42e-06 CGCGGGCCTC TTGTTTTG GTCTCGCGGG chr8:145597883-145597963 27 2.02e-06 tttccctctt tttttttg aggcagggtc chr4:1004450-1004530 3 5.36e-06 GT TTGTGTTG CAAGACTGGG chr7:5467147-5467227 1 6.78e-06 . TTTTGTTG GCGCAGGCTC chr1:120255071-120255151 56 1.01e-05 TAGCGCGCAA TTGTTCTG GCAGCCTCGC chr1:2205519-2205599 71 1.81e-05 TCAATGGCAC TGGTTTTG CT chr7:157261240-157261320 25 1.81e-05 TCCCTCACCT TTGGTTTG CCCGCGTTCT chr22:19593511-19593591 37 2.87e-05 GGGGCTCCTC TTGTGCTG CCAGAGCTGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGTKTTG MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr20:52209758-52209838 1.4e-06 56_[+1]_16 chr7:100027425-100027505 1.4e-06 31_[+1]_41 chr8:145597883-145597963 2e-06 26_[+1]_46 chr4:1004450-1004530 5.4e-06 2_[+1]_70 chr7:5467147-5467227 6.8e-06 [+1]_72 chr1:120255071-120255151 1e-05 55_[+1]_17 chr1:2205519-2205599 1.8e-05 70_[+1]_2 chr7:157261240-157261320 1.8e-05 24_[+1]_48 chr22:19593511-19593591 2.9e-05 36_[+1]_36 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGTKTTG MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TTGTKTTG width=8 seqs=9 chr20:52209758-52209838 ( 57) TTGTTTTG 1 chr7:100027425-100027505 ( 32) TTGTTTTG 1 chr8:145597883-145597963 ( 27) TTTTTTTG 1 chr4:1004450-1004530 ( 3) TTGTGTTG 1 chr7:5467147-5467227 ( 1) TTTTGTTG 1 chr1:120255071-120255151 ( 56) TTGTTCTG 1 chr1:2205519-2205599 ( 71) TGGTTTTG 1 chr7:157261240-157261320 ( 25) TTGGTTTG 1 chr22:19593511-19593591 ( 37) TTGTGCTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGTKTTG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 11.8333 E= 2.9e+003 -982 -982 -982 274 -982 -982 -166 257 -982 -982 114 57 -982 -982 -166 257 -982 -982 -8 215 -982 -64 -982 237 -982 -982 -982 274 -982 -982 150 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGTKTTG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9 E= 2.9e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.111111 0.888889 0.000000 0.000000 0.777778 0.222222 0.000000 0.000000 0.111111 0.888889 0.000000 0.000000 0.333333 0.666667 0.000000 0.222222 0.000000 0.777778 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTGTKTTG MEME-1 regular expression -------------------------------------------------------------------------------- TT[GT]T[TG][TC]TG -------------------------------------------------------------------------------- Time 4.82 secs. ******************************************************************************** ******************************************************************************** MOTIF CWTTTAGT MEME-2 width = 8 sites = 6 llr = 67 E-value = 3.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif CWTTTAGT MEME-2 Description -------------------------------------------------------------------------------- Simplified A :3:::8:2 pos.-specific C a:::2::: probability G :::::2a: matrix T :7aa8::8 bits 2.7 ** 2.5 ** 2.2 ** * 1.9 ***** * Relative 1.6 ****** * Entropy 1.4 ******** (16.2 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel CTTTTAGT consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWTTTAGT MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr17:29815492-29815572 3 1.40e-06 TG CTTTTAGT GGACTAGGAA chr19:1081185-1081265 33 1.40e-06 GGGGTGGGCT CTTTTAGT TCTGGGGAGC chr22:21798856-21798936 14 2.81e-06 GGGTTGACTT CATTTAGT GTAGAGACAG chr6:168226721-168226801 26 5.64e-06 CAGCGCCGCC CATTTAGA CCCAGCACCG chr16:1662917-1662997 39 1.21e-05 GGCGTCGGTC CTTTCAGT GGCGAAAAGC chr22:19644166-19644246 16 1.21e-05 AGCACTCTCA CTTTTGGT CACCGGTCCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWTTTAGT MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr17:29815492-29815572 1.4e-06 2_[+2]_70 chr19:1081185-1081265 1.4e-06 32_[+2]_40 chr22:21798856-21798936 2.8e-06 13_[+2]_59 chr6:168226721-168226801 5.6e-06 25_[+2]_47 chr16:1662917-1662997 1.2e-05 38_[+2]_34 chr22:19644166-19644246 1.2e-05 15_[+2]_57 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWTTTAGT MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF CWTTTAGT width=8 seqs=6 chr17:29815492-29815572 ( 3) CTTTTAGT 1 chr19:1081185-1081265 ( 33) CTTTTAGT 1 chr22:21798856-21798936 ( 14) CATTTAGT 1 chr6:168226721-168226801 ( 26) CATTTAGA 1 chr16:1662917-1662997 ( 39) CTTTCAGT 1 chr22:19644166-19644246 ( 16) CTTTTGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWTTTAGT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 12.0178 E= 3.3e+003 -923 153 -923 -923 114 -923 -923 215 -923 -923 -923 274 -923 -923 -923 274 -923 -105 -923 247 246 -923 -108 -923 -923 -923 150 -923 14 -923 -923 247 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWTTTAGT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6 E= 3.3e+003 0.000000 1.000000 0.000000 0.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.000000 0.833333 0.833333 0.000000 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.166667 0.000000 0.000000 0.833333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWTTTAGT MEME-2 regular expression -------------------------------------------------------------------------------- C[TA]TTTAGT -------------------------------------------------------------------------------- Time 8.44 secs. ******************************************************************************** ******************************************************************************** MOTIF AATRAGAA MEME-3 width = 8 sites = 5 llr = 58 E-value = 7.4e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif AATRAGAA MEME-3 Description -------------------------------------------------------------------------------- Simplified A a8:68:8a pos.-specific C :::::::: probability G :::42a:: matrix T :2a:::2: bits 2.7 * * * 2.5 * * * 2.2 * * * 1.9 *** ** Relative 1.6 *** * ** Entropy 1.4 ******** (16.7 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AATAAGAA consensus T GG T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATRAGAA MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr7:150652288-150652368 28 2.09e-06 CCTGGGAGGG AATGAGAA CAGGAGCCAG chr7:158824561-158824641 4 2.09e-06 TGC AATGAGAA GAGATGGTCA chr6:32940644-32940724 56 3.34e-06 GACTCCCCAC AATAAGTA CGTTTCCGCG chr5:71403670-71403750 26 3.34e-06 TTCTGGGCTA ATTAAGAA TAATCCGAAT chr19:798323-798403 50 4.81e-06 CCTCCCTGGG AATAGGAA GCGGGAGAGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATRAGAA MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:150652288-150652368 2.1e-06 27_[+3]_45 chr7:158824561-158824641 2.1e-06 3_[+3]_69 chr6:32940644-32940724 3.3e-06 55_[+3]_17 chr5:71403670-71403750 3.3e-06 25_[+3]_47 chr19:798323-798403 4.8e-06 49_[+3]_23 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATRAGAA MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AATRAGAA width=8 seqs=5 chr7:150652288-150652368 ( 28) AATGAGAA 1 chr7:158824561-158824641 ( 4) AATGAGAA 1 chr6:32940644-32940724 ( 56) AATAAGTA 1 chr5:71403670-71403750 ( 26) ATTAAGAA 1 chr19:798323-798403 ( 50) AATAGGAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATRAGAA MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 12.7769 E= 7.4e+003 273 -897 -897 -897 241 -897 -897 42 -897 -897 -897 274 199 -897 18 -897 241 -897 -82 -897 -897 -897 150 -897 241 -897 -897 42 273 -897 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATRAGAA MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 7.4e+003 1.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 0.600000 0.000000 0.400000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.000000 0.200000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATRAGAA MEME-3 regular expression -------------------------------------------------------------------------------- A[AT]T[AG][AG]G[AT]A -------------------------------------------------------------------------------- Time 12.13 secs. ******************************************************************************** ******************************************************************************** MOTIF MATTATTA MEME-4 width = 8 sites = 2 llr = 28 E-value = 3.7e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif MATTATTA MEME-4 Description -------------------------------------------------------------------------------- Simplified A 5a::a::a pos.-specific C 5::::::: probability G :::::::: matrix T ::aa:aa: bits 2.7 ******* 2.5 ******* 2.2 ******* 1.9 ******* Relative 1.6 ******* Entropy 1.4 ******* (20.3 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AATTATTA consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MATTATTA MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr5:71403670-71403750 41 2.63e-07 GAATAATCCG AATTATTA GATATGAGAC chr2:60777005-60777085 63 8.66e-07 TGCGGTTATT CATTATTA ATGACGCTGC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MATTATTA MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr5:71403670-71403750 2.6e-07 40_[+4]_32 chr2:60777005-60777085 8.7e-07 62_[+4]_10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MATTATTA MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF MATTATTA width=8 seqs=2 chr5:71403670-71403750 ( 41) AATTATTA 1 chr2:60777005-60777085 ( 63) CATTATTA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MATTATTA MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 13.1555 E= 3.7e+003 172 53 -765 -765 272 -765 -765 -765 -765 -765 -765 273 -765 -765 -765 273 272 -765 -765 -765 -765 -765 -765 273 -765 -765 -765 273 272 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MATTATTA MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 3.7e+003 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MATTATTA MEME-4 regular expression -------------------------------------------------------------------------------- [AC]ATTATTA -------------------------------------------------------------------------------- Time 15.73 secs. ******************************************************************************** ******************************************************************************** MOTIF AGRAAAAA MEME-5 width = 8 sites = 2 llr = 26 E-value = 6.8e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGRAAAAA MEME-5 Description -------------------------------------------------------------------------------- Simplified A a:5aaaaa pos.-specific C :::::::: probability G :a5::::: matrix T :::::::: bits 2.7 * ***** 2.5 * ***** 2.2 * ***** 1.9 * ***** Relative 1.6 * ***** Entropy 1.4 ** ***** (19.0 bits) 1.1 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel AGAAAAAA consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGRAAAAA MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr21:18984591-18984671 64 6.32e-07 GCGGAGCTCC AGAAAAAA CACCGACGC chr9:136242350-136242430 47 2.11e-06 CCCCAGTGAG AGGAAAAA CGTGCGGGGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGRAAAAA MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr21:18984591-18984671 6.3e-07 63_[+5]_9 chr9:136242350-136242430 2.1e-06 46_[+5]_26 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGRAAAAA MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AGRAAAAA width=8 seqs=2 chr21:18984591-18984671 ( 64) AGAAAAAA 1 chr9:136242350-136242430 ( 47) AGGAAAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGRAAAAA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 18250 bayes= 12.3073 E= 6.8e+004 272 -765 -765 -765 -765 -765 150 -765 172 -765 50 -765 272 -765 -765 -765 272 -765 -765 -765 272 -765 -765 -765 272 -765 -765 -765 272 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGRAAAAA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 6.8e+004 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGRAAAAA MEME-5 regular expression -------------------------------------------------------------------------------- AG[AG]AAAAA -------------------------------------------------------------------------------- Time 19.29 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr19:2049084-2049164 7.76e-01 80 chr22:19593511-19593591 1.09e-01 36_[+1(2.87e-05)]_36 chr22:21800828-21800908 2.79e-01 80 chr22:19675965-19676045 1.00e+00 80 chr22:21385686-21385766 7.39e-02 80 chr22:20130332-20130412 7.33e-01 80 chr22:22068482-22068562 1.08e-01 80 chr1:17051668-17051748 3.39e-01 80 chr7:128482599-128482679 8.45e-01 80 chr22:19644166-19644246 4.38e-02 15_[+2(1.21e-05)]_57 chr22:20133466-20133546 3.99e-01 80 chr15:79104236-79104316 9.90e-01 80 chr22:19763401-19763481 1.58e-01 80 chr1:12123750-12123830 9.28e-01 80 chr7:129419039-129419119 7.46e-01 80 chr22:50920615-50920695 5.75e-01 80 chr22:20784952-20785032 5.45e-01 80 chr22:19787240-19787320 1.88e-01 80 chr2:172967037-172967117 3.25e-01 80 chr21:18984591-18984671 3.07e-03 63_[+5(6.32e-07)]_9 chr22:19951066-19951146 5.25e-02 80 chr18:2846667-2846747 7.78e-01 80 chr1:68151469-68151549 7.53e-01 80 chr17:73839692-73839772 9.96e-01 80 chr22:20130672-20130752 9.98e-01 80 chr1:47902877-47902957 9.94e-01 80 chr22:20130974-20131054 4.44e-01 80 chr18:3452167-3452247 1.00e+00 80 chr2:32582747-32582827 6.52e-02 1_[+5(7.92e-05)]_71 chr6:139695295-139695375 1.47e-01 80 chr17:72984183-72984263 8.91e-01 80 chr9:86536255-86536335 9.96e-01 80 chr19:10613016-10613096 9.21e-01 80 chr21:46273915-46273995 6.71e-01 80 chr7:158824345-158824425 2.84e-01 80 chr7:158824561-158824641 7.64e-04 3_[+3(2.09e-06)]_69 chr22:21435053-21435133 7.47e-01 80 chr17:27620207-27620287 8.38e-02 1_[+2(7.40e-05)]_71 chr16:578398-578478 2.61e-01 80 chr7:150652073-150652153 1.78e-01 80 chr2:60777005-60777085 3.48e-04 62_[+4(8.66e-07)]_10 chr1:245027423-245027503 9.98e-01 80 chr6:64282694-64282774 6.13e-01 80 chr6:31649140-31649220 2.95e-01 80 chr8:124408058-124408138 8.12e-01 80 chr1:205498267-205498347 1.00e+00 80 chr13:91827491-91827571 3.31e-01 80 chr17:79075976-79076056 4.31e-02 56_[+1(8.42e-05)]_16 chr1:28586675-28586755 7.69e-01 80 chr20:62497027-62497107 3.70e-01 80 chr7:99156746-99156826 9.41e-01 80 chr19:41770727-41770807 7.15e-01 80 chr16:30569362-30569442 5.50e-01 80 chr18:2847352-2847432 9.86e-01 80 chr4:83294730-83294810 1.00e+00 80 chr16:578598-578678 1.06e-01 80 chr5:34930058-34930138 9.45e-01 80 chr1:145075707-145075787 6.36e-01 80 chr22:22315576-22315656 7.09e-01 80 chr22:21327610-21327690 2.38e-02 80 chr11:44749274-44749354 9.00e-01 80 chr11:44749514-44749594 9.54e-01 80 chr7:128482398-128482478 9.98e-01 80 chr9:136150126-136150206 9.33e-01 80 chr2:133016812-133016892 1.34e-02 80 chr20:57581581-57581661 8.32e-01 80 chr22:19951272-19951352 3.43e-02 38_[+5(7.92e-05)]_34 chr1:16399671-16399751 9.51e-01 80 chr1:1242866-1242946 9.93e-01 80 chr7:148480128-148480208 2.98e-02 80 chr13:50699143-50699223 2.36e-01 80 chr22:21327934-21328014 7.46e-01 80 chr5:137802049-137802129 6.53e-02 80 chr7:100492532-100492612 2.97e-01 80 chr19:662649-662729 4.47e-01 80 chr19:1080977-1081057 5.24e-01 80 chr19:1081185-1081265 1.38e-03 32_[+2(1.40e-06)]_40 chr6:151712320-151712400 1.00e+00 80 chr22:19892139-19892219 1.31e-01 80 chr7:25019559-25019639 9.68e-01 80 chr17:49244448-49244528 4.46e-01 80 chr17:80054362-80054442 8.28e-01 80 chr11:64036935-64037015 9.29e-01 80 chr8:144465929-144466009 5.11e-01 80 chr1:228270813-228270893 9.09e-01 80 chr7:5468964-5469044 8.78e-03 [+2(2.52e-05)]_72 chr11:118927597-11892767 9.84e-01 80 chr7:157261240-157261320 3.82e-03 24_[+1(1.81e-05)]_48 chr4:153857080-153857160 3.53e-01 80 chr4:153857279-153857359 5.03e-01 80 chr2:32582538-32582618 3.07e-01 80 chr22:22318508-22318588 6.03e-01 80 chr17:46100954-46101034 2.01e-01 72_[+1(7.63e-05)] chr5:172754382-172754462 9.81e-02 80 chr17:19015253-19015333 3.26e-04 35_[+5(3.27e-06)]_37 chr5:172754789-172754869 5.89e-02 80 chr7:150652288-150652368 7.23e-03 27_[+3(2.09e-06)]_45 chr6:86352253-86352333 7.51e-01 80 chr1:28586421-28586501 9.26e-01 80 chr1:840520-840600 9.06e-01 80 chr6:154831092-154831172 9.84e-01 80 chr22:19738706-19738786 9.63e-01 80 chr1:36274133-36274213 8.21e-01 80 chr16:1662917-1662997 1.78e-02 38_[+2(1.21e-05)]_34 chr1:36274333-36274413 8.53e-01 80 chr15:20545559-20545639 9.88e-01 80 chr8:127570265-127570345 4.24e-01 80 chr1:68151691-68151771 5.46e-01 80 chr22:20081936-20082016 9.06e-01 80 chr7:100027425-100027505 9.31e-04 31_[+1(1.42e-06)]_41 chr15:79104436-79104516 1.00e+00 80 chr17:29815492-29815572 3.94e-04 2_[+2(1.40e-06)]_70 chr17:79894760-79894840 8.96e-01 80 chr2:60776714-60776794 9.91e-01 80 chr7:66309574-66309654 2.12e-02 67_[+3(8.68e-05)]_5 chr19:798323-798403 3.01e-02 49_[+3(4.81e-06)]_23 chr5:72794702-72794782 5.83e-01 80 chr16:83987319-83987399 4.39e-01 80 chr17:79479410-79479490 9.98e-01 80 chr5:71403670-71403750 1.58e-07 25_[+3(3.34e-06)]_7_[+4(2.63e-07)]_\ 32 chr19:2050426-2050506 3.18e-01 80 chr7:150652487-150652567 8.74e-01 80 chr16:30621399-30621479 9.27e-01 80 chr1:1225870-1225950 9.92e-01 80 chr20:32699692-32699772 6.62e-01 80 chr17:3867865-3867945 9.93e-02 80 chr2:112813397-112813477 1.04e-01 72_[+1(7.63e-05)] chr6:43739133-43739213 9.20e-01 80 chr6:64283024-64283104 1.04e-01 80 chr3:171758463-171758543 8.10e-01 80 chr1:46767457-46767537 9.92e-01 80 chr16:88947777-88947857 9.09e-01 80 chr6:34664188-34664268 4.30e-03 49_[+5(7.92e-05)]_23 chr1:28199126-28199206 9.71e-01 80 chr5:172754588-172754668 2.65e-01 80 chr4:123300576-123300656 2.72e-01 80 chr1:150551587-150551667 9.61e-01 80 chr7:1498032-1498112 1.51e-01 80 chr21:46238461-46238541 8.76e-01 80 chr9:140173274-140173354 1.00e+00 80 chr22:20050870-20050950 3.10e-01 80 chr6:32134970-32135050 7.19e-01 80 chr11:2720573-2720653 7.30e-01 80 chr19:1605082-1605162 3.03e-01 80 chr8:145597883-145597963 6.82e-03 26_[+1(2.02e-06)]_46 chr16:28834908-28834988 9.43e-01 80 chr22:19629728-19629808 7.13e-01 80 chr13:81281623-81281703 6.76e-01 80 chr16:22309209-22309289 1.12e-01 80 chr5:36877321-36877401 9.80e-01 80 chr22:21385960-21386040 9.19e-01 80 chr5:36877522-36877602 1.01e-01 80 chr9:19230903-19230983 6.32e-01 80 chr9:131465835-131465915 5.65e-01 80 chr12:98909758-98909838 8.83e-01 80 chr11:189786-189866 3.56e-01 80 chr1:36772151-36772231 3.75e-01 80 chr7:5467147-5467227 2.40e-02 [+1(6.78e-06)]_72 chr6:136871023-136871103 7.41e-01 80 chr1:36786617-36786697 8.59e-01 80 chr6:168226721-168226801 1.28e-02 25_[+2(5.64e-06)]_47 chr18:3262436-3262516 8.39e-01 80 chr20:52209758-52209838 7.56e-04 56_[+1(1.42e-06)]_16 chr19:12902844-12902924 1.50e-01 80 chr20:60794551-60794631 8.49e-01 80 chr5:41925754-41925834 1.80e-01 80 chr22:20227686-20227766 9.90e-01 80 chr6:32940644-32940724 1.55e-04 55_[+3(3.34e-06)]_17 chr5:180673941-180674021 7.77e-01 80 chr15:51200515-51200595 1.32e-01 80 chr4:1004450-1004530 1.54e-02 2_[+1(5.36e-06)]_70 chr22:20939348-20939428 8.16e-01 80 chr4:1004065-1004145 1.00e+00 80 chr5:10565062-10565142 8.03e-01 80 chr5:10565536-10565616 7.42e-01 80 chr9:136242350-136242430 6.55e-03 46_[+5(2.11e-06)]_26 chr5:71403465-71403545 6.70e-01 80 chr16:2285864-2285944 7.87e-02 80 chr2:111877944-111878024 8.30e-01 80 chr22:20308058-20308138 5.38e-01 80 chr4:24585825-24585905 7.17e-02 7_[+5(2.94e-05)]_65 chr2:178128888-178128968 9.61e-01 80 chr1:120255071-120255151 5.29e-03 55_[+1(1.01e-05)]_17 chr11:63581564-63581644 9.66e-01 80 chr5:137803178-137803258 5.97e-01 80 chr1:1208420-1208500 9.72e-02 80 chr17:41399889-41399969 1.15e-01 80 chr1:71512686-71512766 7.84e-01 80 chr19:46404640-46404720 2.33e-01 80 chr12:54412226-54412306 2.22e-01 80 chr8:145133758-145133838 4.31e-01 80 chr8:144466135-144466215 1.39e-01 80 chr17:73774856-73774936 6.24e-01 80 chr1:6479157-6479237 9.99e-01 80 chr11:65729497-65729577 9.76e-01 80 chr1:220101490-220101570 3.88e-01 80 chr1:840791-840871 8.31e-01 80 chr17:40828648-40828728 2.31e-01 80 chr1:2205519-2205599 1.70e-03 70_[+1(1.81e-05)]_2 chr17:79827485-79827565 8.45e-01 80 chr1:228328341-228328421 6.23e-01 80 chr5:141016881-141016961 1.00e+00 80 chr17:80055195-80055275 7.07e-01 80 chr17:79825066-79825146 9.95e-01 80 chr11:34937685-34937765 9.53e-01 80 chr9:139562795-139562875 9.24e-01 80 chr11:34937897-34937977 9.05e-01 80 chr1:236558955-236559035 5.72e-01 80 chr6:42016279-42016359 4.99e-01 80 chr2:26101031-26101111 8.80e-01 80 chr10:62703595-62703675 9.86e-01 80 chr22:19810152-19810232 9.95e-01 80 chr6:137114038-137114118 8.58e-01 80 chr11:506488-506568 8.12e-01 80 chr5:137802906-137802986 5.82e-01 80 chr2:232573486-232573566 7.43e-01 80 chr1:178995615-178995695 3.33e-01 80 chr22:21798856-21798936 4.14e-04 13_[+2(2.81e-06)]_59 chr22:19809948-19810028 6.37e-01 80 chr13:81278635-81278715 7.60e-01 80 chr7:25019758-25019838 5.49e-01 80 chr15:50646666-50646746 1.89e-01 80 chr1:44440911-44440991 3.72e-01 80 chr6:20402747-20402827 9.99e-01 80 chr1:65991396-65991476 1.00e+00 80 chr19:10613928-10614008 6.76e-01 80 chr19:5623406-5623486 3.33e-01 80 chr22:19750694-19750774 7.97e-01 80 chr1:975747-975827 7.82e-01 80 chr17:46702389-46702469 1.14e-01 80 chr6:43478132-43478212 6.01e-01 80 chr22:21212844-21212924 7.64e-01 80 chr16:67876970-67877050 4.57e-01 80 chr11:118965319-11896539 1.00e+00 80 chr1:3663539-3663619 7.62e-01 80 chr17:7476401-7476481 9.86e-01 80 chr10:88854415-88854495 1.00e+00 80 chr17:79829734-79829814 1.14e-01 80 chr7:149570478-149570558 7.92e-01 80 chr15:29130833-29130913 9.20e-01 80 chr22:19771893-19771973 9.67e-01 80 chr9:97021802-97021882 5.75e-01 80 chr12:120972608-12097268 4.12e-01 80 chr9:139835240-139835320 1.73e-02 71_[+5(7.92e-05)]_1 chr11:65625054-65625134 1.00e+00 80 chr11:316258-316338 5.50e-01 80 chr14:88237680-88237760 2.61e-02 80 chr16:88878018-88878098 8.26e-01 80 chr9:130830701-130830781 9.62e-02 55_[+2(2.52e-05)]_17 chr19:798119-798199 2.67e-01 80 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c22n10.farnam.hpc.yale.internal ********************************************************************************