******************************************************************************** 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/SFPQ.fasta CONTROL SEQUENCES= --none-- ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr14:35024182-35024262 1.0000 80 chr14:35017150-35017230 1.0000 80 chr5:137806338-137806418 1.0000 80 chr9:126031175-126031255 1.0000 80 chr9:86536291-86536371 1.0000 80 chr10:97416497-97416577 1.0000 80 chr2:149402918-149402998 1.0000 80 chr11:65196058-65196138 1.0000 80 chr2:196521840-196521920 1.0000 80 chr11:65193728-65193808 1.0000 80 chr13:91101934-91102014 1.0000 80 chr11:65194952-65195032 1.0000 80 chr21:46494931-46495011 1.0000 80 chr9:103361119-103361199 1.0000 80 chr2:232574245-232574325 1.0000 80 chr22:38902488-38902568 1.0000 80 chr11:77532168-77532248 1.0000 80 chr5:137805122-137805202 1.0000 80 chr22:22427606-22427686 1.0000 80 chr3:119813411-119813491 1.0000 80 chr17:62501002-62501082 1.0000 80 chr17:7145823-7145903 1.0000 80 chr19:812997-813077 1.0000 80 chr9:139560677-139560757 1.0000 80 chr7:115383447-115383527 1.0000 80 chr7:111233350-111233430 1.0000 80 chr11:64053169-64053249 1.0000 80 chr9:130829561-130829641 1.0000 80 chr13:92325954-92326034 1.0000 80 chr5:137805363-137805443 1.0000 80 chr7:35840718-35840798 1.0000 80 chr2:85767407-85767487 1.0000 80 chr11:61447778-61447858 1.0000 80 chr16:89788369-89788449 1.0000 80 chr21:46494248-46494328 1.0000 80 chr10:17272498-17272578 1.0000 80 chr2:232575011-232575091 1.0000 80 chr21:11118100-11118180 1.0000 80 chr12:7053683-7053763 1.0000 80 chr12:7053883-7053963 1.0000 80 chr7:26240450-26240530 1.0000 80 chr1:148241926-148242006 1.0000 80 chr10:75210137-75210217 1.0000 80 chr13:81382341-81382421 1.0000 80 chr17:19015244-19015324 1.0000 80 chr2:232575210-232575290 1.0000 80 chr13:93271313-93271393 1.0000 80 chr19:13266125-13266205 1.0000 80 chr5:68664575-68664655 1.0000 80 chr20:60641447-60641527 1.0000 80 chr1:207377439-207377519 1.0000 80 chr11:10830631-10830711 1.0000 80 chr6:34360497-34360577 1.0000 80 chr8:15836596-15836676 1.0000 80 chr6:32941310-32941390 1.0000 80 chr6:41834609-41834689 1.0000 80 chr4:166248456-166248536 1.0000 80 chr19:813551-813631 1.0000 80 chr1:147736004-147736084 1.0000 80 chr5:176873788-176873868 1.0000 80 chr11:62608096-62608176 1.0000 80 chr17:56736208-56736288 1.0000 80 chr7:5569340-5569420 1.0000 80 chr17:56756749-56756829 1.0000 80 chr13:91800410-91800490 1.0000 80 chr1:194663313-194663393 1.0000 80 chr14:95623864-95623944 1.0000 80 chr1:27816797-27816877 1.0000 80 chr1:27561020-27561100 1.0000 80 chr1:73820317-73820397 1.0000 80 chr17:56708439-56708519 1.0000 80 chr2:149899741-149899821 1.0000 80 chr10:87203639-87203719 1.0000 80 chr17:62501307-62501387 1.0000 80 chr6:26232647-26232727 1.0000 80 chr1:16399853-16399933 1.0000 80 chr3:9438316-9438396 1.0000 80 chr1:146555881-146555961 1.0000 80 chr7:120736227-120736307 1.0000 80 chr5:29035797-29035877 1.0000 80 chr19:58908118-58908198 1.0000 80 chr17:56085033-56085113 1.0000 80 chr11:65666760-65666840 1.0000 80 chr6:26026717-26026797 1.0000 80 chr7:139096072-139096152 1.0000 80 chr16:53738011-53738091 1.0000 80 chr3:33065089-33065169 1.0000 80 chr21:40716954-40717034 1.0000 80 chr17:80055365-80055445 1.0000 80 chr3:167452542-167452622 1.0000 80 chr7:5569544-5569624 1.0000 80 chr1:147736209-147736289 1.0000 80 chr1:78470011-78470091 1.0000 80 chr1:11969039-11969119 1.0000 80 chr1:11968838-11968918 1.0000 80 chr6:41863164-41863244 1.0000 80 chr13:91303110-91303190 1.0000 80 chr22:21015779-21015859 1.0000 80 chr19:54713440-54713520 1.0000 80 chr1:73079255-73079335 1.0000 80 chr1:195928830-195928910 1.0000 80 chr4:187125405-187125485 1.0000 80 chr1:27816997-27817077 1.0000 80 chr7:110605476-110605556 1.0000 80 chr11:65197887-65197967 1.0000 80 chr12:69201608-69201688 1.0000 80 chr1:28837790-28837870 1.0000 80 chr1:144534213-144534293 1.0000 80 chr7:135284568-135284648 1.0000 80 chr6:27776881-27776961 1.0000 80 chr1:17231883-17231963 1.0000 80 chr11:65196298-65196378 1.0000 80 chr17:56708793-56708873 1.0000 80 chr1:145115653-145115733 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_SFPQ/ -dna -nmotifs 5 -w 8 -maxsize 250000 -nostatus ../result/final_prediction/K562/fasta/RankLinear0.6_40/SFPQ.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= 9120 N= 114 sample: seed= 0 hsfrac= 0 searchsize= 9120 norand= no csites= 1000 Letter frequencies in dataset: A 0.249 C 0.26 G 0.259 T 0.232 Background letter frequencies (from file dataset with add-one prior applied): A 0.249 C 0.26 G 0.259 T 0.232 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WTTTTAAW MEME-1 width = 8 sites = 19 llr = 167 E-value = 2.1e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif WTTTTAAW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 5::3:8a4 pos.-specific C :::::::: probability G 2::::::: matrix T 3aa7a2:6 bits 2.1 ** * * 1.9 ** * * 1.7 ** * * 1.5 ** *** Relative 1.3 ****** Entropy 1.1 ******* (12.7 bits) 0.8 ******* 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel ATTTTAAT consensus T A A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTTTTAAW MEME-1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr6:26026717-26026797 60 1.04e-05 CCTGACACCC ATTTTAAT CCACCTACTC chr1:207377439-207377519 41 1.04e-05 agccagaacc attttaat tcttgatcAT chr5:68664575-68664655 47 1.04e-05 GTTATGCAGC ATTTTAAT TCCCTTCACT chr7:110605476-110605556 60 2.15e-05 TAACTTTTTT ATTTTAAA ATGAAATTTG chr1:78470011-78470091 26 2.15e-05 TCCTTTACTT ATTTTAAA ATAACGCATT chr13:81382341-81382421 26 2.15e-05 ATGTGCACTT ATTTTAAA ACTCTTCGGA chr1:145115653-145115733 7 3.12e-05 TGGTTA TTTTTAAT GCCTTAATAC chr11:65196298-65196378 51 4.16e-05 AAGGAAATTT TTTTtaaa agtcctcagt chr7:115383447-115383527 50 4.16e-05 CATGAGTCTA TTTTTAAA TGGCCAAATT chr21:40716954-40717034 11 5.27e-05 TTTGTTCAAT ATTATAAT GAATACTGTT chr1:73820317-73820397 28 5.27e-05 tatctttcag attataat caaattggta chr6:32941310-32941390 47 6.35e-05 CCCATATGAT GTTTTAAT TCTTAGGTGG chr3:33065089-33065169 3 8.51e-05 GG ATTATAAA AGGGGAAAAC chr13:91800410-91800490 40 8.51e-05 tgcttatgga atttttat tcattatata chr10:87203639-87203719 68 1.07e-04 TGAAAACATG TTTATAAT CTTTT chr22:22427606-22427686 5 1.07e-04 GAAG GTTTTAAA CATTCTTAAT chr8:15836596-15836676 59 1.38e-04 AGTCCtttat ttttttat tgatgagtaa chr1:195928830-195928910 71 1.47e-04 cttcaagaag ttttttaa ct chr14:35017150-35017230 65 1.59e-04 CTTTCCTCCA GTTATAAT GTTGCCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTTTTAAW MEME-1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr6:26026717-26026797 1e-05 59_[+1]_13 chr1:207377439-207377519 1e-05 40_[+1]_32 chr5:68664575-68664655 1e-05 46_[+1]_26 chr7:110605476-110605556 2.2e-05 59_[+1]_13 chr1:78470011-78470091 2.2e-05 25_[+1]_47 chr13:81382341-81382421 2.2e-05 25_[+1]_47 chr1:145115653-145115733 3.1e-05 6_[+1]_66 chr11:65196298-65196378 4.2e-05 50_[+1]_22 chr7:115383447-115383527 4.2e-05 49_[+1]_23 chr21:40716954-40717034 5.3e-05 10_[+1]_62 chr1:73820317-73820397 5.3e-05 27_[+1]_45 chr6:32941310-32941390 6.3e-05 46_[+1]_26 chr3:33065089-33065169 8.5e-05 2_[+1]_70 chr13:91800410-91800490 8.5e-05 39_[+1]_33 chr10:87203639-87203719 0.00011 67_[+1]_5 chr22:22427606-22427686 0.00011 4_[+1]_68 chr8:15836596-15836676 0.00014 58_[+1]_14 chr1:195928830-195928910 0.00015 70_[+1]_2 chr14:35017150-35017230 0.00016 64_[+1]_8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTTTTAAW MEME-1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF WTTTTAAW width=8 seqs=19 chr6:26026717-26026797 ( 60) ATTTTAAT 1 chr1:207377439-207377519 ( 41) ATTTTAAT 1 chr5:68664575-68664655 ( 47) ATTTTAAT 1 chr7:110605476-110605556 ( 60) ATTTTAAA 1 chr1:78470011-78470091 ( 26) ATTTTAAA 1 chr13:81382341-81382421 ( 26) ATTTTAAA 1 chr1:145115653-145115733 ( 7) TTTTTAAT 1 chr11:65196298-65196378 ( 51) TTTTTAAA 1 chr7:115383447-115383527 ( 50) TTTTTAAA 1 chr21:40716954-40717034 ( 11) ATTATAAT 1 chr1:73820317-73820397 ( 28) ATTATAAT 1 chr6:32941310-32941390 ( 47) GTTTTAAT 1 chr3:33065089-33065169 ( 3) ATTATAAA 1 chr13:91800410-91800490 ( 40) ATTTTTAT 1 chr10:87203639-87203719 ( 68) TTTATAAT 1 chr22:22427606-22427686 ( 5) GTTTTAAA 1 chr8:15836596-15836676 ( 59) TTTTTTAT 1 chr1:195928830-195928910 ( 71) TTTTTTAA 1 chr14:35017150-35017230 ( 65) GTTATAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTTTTAAW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 8322 bayes= 10.5888 E= 2.1e-002 108 -1089 -71 45 -1089 -1089 -1089 211 -1089 -1089 -1089 211 8 -1089 -1089 167 -1089 -1089 -1089 211 176 -1089 -1089 -55 201 -1089 -1089 -1089 76 -1089 -1089 132 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTTTTAAW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 19 E= 2.1e-002 0.526316 0.000000 0.157895 0.315789 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.263158 0.000000 0.000000 0.736842 0.000000 0.000000 0.000000 1.000000 0.842105 0.000000 0.000000 0.157895 1.000000 0.000000 0.000000 0.000000 0.421053 0.000000 0.000000 0.578947 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTTTTAAW MEME-1 regular expression -------------------------------------------------------------------------------- [AT]TT[TA]TAA[TA] -------------------------------------------------------------------------------- Time 1.39 secs. ******************************************************************************** ******************************************************************************** MOTIF AAAWAAKA MEME-2 width = 8 sites = 31 llr = 228 E-value = 2.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAWAAKA MEME-2 Description -------------------------------------------------------------------------------- Simplified A aa947a18 pos.-specific C :::13:1: probability G :::1::32 matrix T ::15::5: bits 2.1 ** * 1.9 ** * 1.7 ** * 1.5 *** * Relative 1.3 *** * * Entropy 1.1 *** ** * (10.6 bits) 0.8 *** ** * 0.6 *** ** * 0.4 ****** * 0.2 ******** 0.0 -------- Multilevel AAATAATA consensus AC G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAWAAKA MEME-2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr13:93271313-93271393 34 1.28e-05 TTTGTGTTTA AAATAATA AAGAAAATAC chr13:92325954-92326034 68 1.28e-05 GAACACCAGA AAATAATA GAAAA chr6:26232647-26232727 33 2.66e-05 CAAAACAAAC AAAAAATA ACCTCAGCCT chr7:115383447-115383527 13 2.66e-05 GTTTCCATAC AAAAAATA AAATTTACAT chr13:91800410-91800490 5 4.09e-05 agaa aaataaga atgtatgtac chr21:11118100-11118180 59 4.09e-05 atcatgactt aaataaga tggaagtttg chr7:139096072-139096152 33 6.97e-05 TAAAAGAAAA AAATCATA ATcatttact chr10:87203639-87203719 50 6.97e-05 GAAAAGAAGG AAAAAAGA TGAAAACATG chr22:21015779-21015859 30 8.41e-05 ctaacaggta aaaacata ctgttgccat chr11:65196058-65196138 5 8.41e-05 aaca aaAACATA CTGACACTGT chr17:56708793-56708873 19 1.12e-04 cccagctcaa aaataaaa aTGCACATAT chr17:56708439-56708519 2 1.12e-04 T AAATAAAA AAGGAAAATA chr5:137806338-137806418 57 1.27e-04 CTGACCCCTA AAATCAGA GGAACAATGA chr7:135284568-135284648 56 1.70e-04 GGATTGAGAT AAATAACA GCGTGTTAGA chr1:28837790-28837870 63 1.70e-04 ATCACTTATT AAATAACA TTCTTTTGTG chr7:120736227-120736307 72 1.70e-04 ACACTGTGCT AAATAATG A chr6:26026717-26026797 42 1.86e-04 TACGCCTGGG AAAACAGA CCTGACACCC chr17:62501002-62501082 54 1.86e-04 AAAACCACTG AAAACAGA CTTCGAGAGG chr1:195928830-195928910 43 2.31e-04 tccttctttc aaagaaga ggaattgaaa chr21:40716954-40717034 38 2.31e-04 TATCTGCTAC AAAAAATG TACAATTTAG chr17:56756749-56756829 19 2.31e-04 TGTGTGGAGA AAAAAATG ACCATTAGAA chr8:15836596-15836676 5 2.31e-04 AAGC AAAGAAGA CCAATATCTT chr7:111233350-111233430 60 3.02e-04 aatatgtgca aattaata gatcctatag chr1:78470011-78470091 2 3.62e-04 A AAATCATG TTTAAGTCCT chr3:33065089-33065169 39 3.62e-04 ACAGATGGTC AAAACAAA TTGACTTTGG chr2:149899741-149899821 63 3.94e-04 TCCTGAATTC AAAGAAAA CTAACTTCTT chr14:35017150-35017230 11 3.94e-04 CCCCAGGAGG AAACAAGA GACTCTGATG chr1:73820317-73820397 7 5.00e-04 aggcag aaagaaca agttatcttt chr13:91303110-91303190 44 6.29e-04 gtcacttcca aattcata caccttcagt chr12:69201608-69201688 71 7.26e-04 GTGTAAACAC AAGAAATA CA chr6:32941310-32941390 24 7.70e-04 TCTGCGATGT AAACAATG AGATTCCCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAWAAKA MEME-2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr13:93271313-93271393 1.3e-05 33_[+2]_39 chr13:92325954-92326034 1.3e-05 67_[+2]_5 chr6:26232647-26232727 2.7e-05 32_[+2]_40 chr7:115383447-115383527 2.7e-05 12_[+2]_60 chr13:91800410-91800490 4.1e-05 4_[+2]_68 chr21:11118100-11118180 4.1e-05 58_[+2]_14 chr7:139096072-139096152 7e-05 32_[+2]_40 chr10:87203639-87203719 7e-05 49_[+2]_23 chr22:21015779-21015859 8.4e-05 29_[+2]_43 chr11:65196058-65196138 8.4e-05 4_[+2]_68 chr17:56708793-56708873 0.00011 18_[+2]_54 chr17:56708439-56708519 0.00011 1_[+2]_71 chr5:137806338-137806418 0.00013 56_[+2]_16 chr7:135284568-135284648 0.00017 55_[+2]_17 chr1:28837790-28837870 0.00017 62_[+2]_10 chr7:120736227-120736307 0.00017 71_[+2]_1 chr6:26026717-26026797 0.00019 41_[+2]_31 chr17:62501002-62501082 0.00019 53_[+2]_19 chr1:195928830-195928910 0.00023 42_[+2]_30 chr21:40716954-40717034 0.00023 37_[+2]_35 chr17:56756749-56756829 0.00023 18_[+2]_54 chr8:15836596-15836676 0.00023 4_[+2]_68 chr7:111233350-111233430 0.0003 59_[+2]_13 chr1:78470011-78470091 0.00036 1_[+2]_71 chr3:33065089-33065169 0.00036 38_[+2]_34 chr2:149899741-149899821 0.00039 62_[+2]_10 chr14:35017150-35017230 0.00039 10_[+2]_62 chr1:73820317-73820397 0.0005 6_[+2]_66 chr13:91303110-91303190 0.00063 43_[+2]_29 chr12:69201608-69201688 0.00073 70_[+2]_2 chr6:32941310-32941390 0.00077 23_[+2]_49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAWAAKA MEME-2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF AAAWAAKA width=8 seqs=31 chr13:93271313-93271393 ( 34) AAATAATA 1 chr13:92325954-92326034 ( 68) AAATAATA 1 chr6:26232647-26232727 ( 33) AAAAAATA 1 chr7:115383447-115383527 ( 13) AAAAAATA 1 chr13:91800410-91800490 ( 5) AAATAAGA 1 chr21:11118100-11118180 ( 59) AAATAAGA 1 chr7:139096072-139096152 ( 33) AAATCATA 1 chr10:87203639-87203719 ( 50) AAAAAAGA 1 chr22:21015779-21015859 ( 30) AAAACATA 1 chr11:65196058-65196138 ( 5) AAAACATA 1 chr17:56708793-56708873 ( 19) AAATAAAA 1 chr17:56708439-56708519 ( 2) AAATAAAA 1 chr5:137806338-137806418 ( 57) AAATCAGA 1 chr7:135284568-135284648 ( 56) AAATAACA 1 chr1:28837790-28837870 ( 63) AAATAACA 1 chr7:120736227-120736307 ( 72) AAATAATG 1 chr6:26026717-26026797 ( 42) AAAACAGA 1 chr17:62501002-62501082 ( 54) AAAACAGA 1 chr1:195928830-195928910 ( 43) AAAGAAGA 1 chr21:40716954-40717034 ( 38) AAAAAATG 1 chr17:56756749-56756829 ( 19) AAAAAATG 1 chr8:15836596-15836676 ( 5) AAAGAAGA 1 chr7:111233350-111233430 ( 60) AATTAATA 1 chr1:78470011-78470091 ( 2) AAATCATG 1 chr3:33065089-33065169 ( 39) AAAACAAA 1 chr2:149899741-149899821 ( 63) AAAGAAAA 1 chr14:35017150-35017230 ( 11) AAACAAGA 1 chr1:73820317-73820397 ( 7) AAAGAACA 1 chr13:91303110-91303190 ( 44) AATTCATA 1 chr12:69201608-69201688 ( 71) AAGAAATA 1 chr6:32941310-32941390 ( 24) AAACAATG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAWAAKA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 8322 bayes= 8.02624 E= 2.2e+002 201 -1160 -1160 -1160 201 -1160 -1160 -1160 186 -1160 -300 -184 51 -201 -100 96 151 16 -1160 -1160 201 -1160 -1160 -1160 -95 -143 17 106 175 -1160 -68 -1160 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAWAAKA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 31 E= 2.2e+002 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.903226 0.000000 0.032258 0.064516 0.354839 0.064516 0.129032 0.451613 0.709677 0.290323 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.129032 0.096774 0.290323 0.483871 0.838710 0.000000 0.161290 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAWAAKA MEME-2 regular expression -------------------------------------------------------------------------------- AAA[TA][AC]A[TG]A -------------------------------------------------------------------------------- Time 2.56 secs. ******************************************************************************** ******************************************************************************** MOTIF ATTTATTT MEME-3 width = 8 sites = 8 llr = 79 E-value = 2.2e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATTTATTT MEME-3 Description -------------------------------------------------------------------------------- Simplified A a:::8:1: pos.-specific C ::::::1: probability G :::1:::: matrix T :aa93a8a bits 2.1 *** * * 1.9 *** * * 1.7 *** * * 1.5 **** * * Relative 1.3 ****** * Entropy 1.1 ******** (14.2 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel ATTTATTT consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTATTT MEME-3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr7:110605476-110605556 10 9.67e-06 GCTAGTTGC ATTTATTT GTAACAATTA chr13:91303110-91303190 20 9.67e-06 AATAAAACCA ATTTATTT Aataatgtca chr11:62608096-62608176 55 9.67e-06 GCGAAGAttt atttattt tttgagatgg chr22:22427606-22427686 70 9.67e-06 TGTGGTGGAA ATTTATTT CTA chr8:15836596-15836676 27 1.87e-05 TATCTTCAAT ATTTTTTT CATGTACCGA chr7:115383447-115383527 65 2.91e-05 AAATGGCCAA ATTTATAT CAGGGGCA chr2:149899741-149899821 46 3.99e-05 CTTGTATGAA ATTTATCT CCTGAATTCA chr6:41834609-41834689 17 8.05e-05 cctttaagaC ATTGTTTT GAAAGATATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTATTT MEME-3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr7:110605476-110605556 9.7e-06 9_[+3]_63 chr13:91303110-91303190 9.7e-06 19_[+3]_53 chr11:62608096-62608176 9.7e-06 54_[+3]_18 chr22:22427606-22427686 9.7e-06 69_[+3]_3 chr8:15836596-15836676 1.9e-05 26_[+3]_46 chr7:115383447-115383527 2.9e-05 64_[+3]_8 chr2:149899741-149899821 4e-05 45_[+3]_27 chr6:41834609-41834689 8e-05 16_[+3]_56 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTATTT MEME-3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF ATTTATTT width=8 seqs=8 chr7:110605476-110605556 ( 10) ATTTATTT 1 chr13:91303110-91303190 ( 20) ATTTATTT 1 chr11:62608096-62608176 ( 55) ATTTATTT 1 chr22:22427606-22427686 ( 70) ATTTATTT 1 chr8:15836596-15836676 ( 27) ATTTTTTT 1 chr7:115383447-115383527 ( 65) ATTTATAT 1 chr2:149899741-149899821 ( 46) ATTTATCT 1 chr6:41834609-41834689 ( 17) ATTGTTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTATTT MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 8322 bayes= 10.7588 E= 2.2e+003 200 -965 -965 -965 -965 -965 -965 211 -965 -965 -965 211 -965 -965 -105 192 159 -965 -965 11 -965 -965 -965 211 -99 -106 -965 169 -965 -965 -965 211 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTATTT MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8 E= 2.2e+003 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.125000 0.875000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 0.000000 1.000000 0.125000 0.125000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTATTT MEME-3 regular expression -------------------------------------------------------------------------------- ATTT[AT]TTT -------------------------------------------------------------------------------- Time 3.69 secs. ******************************************************************************** ******************************************************************************** MOTIF TCTGTTWT MEME-4 width = 8 sites = 5 llr = 54 E-value = 6.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCTGTTWT MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::::::4: pos.-specific C :a:::::: probability G :::a:::: matrix T a:a:aa6a bits 2.1 * * ** * 1.9 ****** * 1.7 ****** * 1.5 ****** * Relative 1.3 ****** * Entropy 1.1 ******** (15.5 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TCTGTTTT consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGTTWT MEME-4 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr1:194663313-194663393 66 1.05e-05 ATGTTTCCAA TCTGTTTT GAAATAT chr1:148241926-148242006 59 1.05e-05 CCTCTTAGCC TCTGTTTT TTTGTTGTTG chr22:22427606-22427686 27 1.05e-05 CTTAATATAC TCTGTTTT TGATATTACG chr1:17231883-17231963 62 2.18e-05 ctcttaacag tctgttat ccctaggaag chr13:91101934-91102014 41 2.18e-05 CTCAGACTTG TCTGTTAT TCTGTCCTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGTTWT MEME-4 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr1:194663313-194663393 1.1e-05 65_[+4]_7 chr1:148241926-148242006 1.1e-05 58_[+4]_14 chr22:22427606-22427686 1.1e-05 26_[+4]_46 chr1:17231883-17231963 2.2e-05 61_[+4]_11 chr13:91101934-91102014 2.2e-05 40_[+4]_32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGTTWT MEME-4 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF TCTGTTWT width=8 seqs=5 chr1:194663313-194663393 ( 66) TCTGTTTT 1 chr1:148241926-148242006 ( 59) TCTGTTTT 1 chr22:22427606-22427686 ( 27) TCTGTTTT 1 chr1:17231883-17231963 ( 62) TCTGTTAT 1 chr13:91101934-91102014 ( 41) TCTGTTAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGTTWT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 8322 bayes= 11.6438 E= 6.3e+003 -897 -897 -897 211 -897 194 -897 -897 -897 -897 -897 211 -897 -897 195 -897 -897 -897 -897 211 -897 -897 -897 211 68 -897 -897 137 -897 -897 -897 211 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGTTWT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5 E= 6.3e+003 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.400000 0.000000 0.000000 0.600000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTGTTWT MEME-4 regular expression -------------------------------------------------------------------------------- TCTGTT[TA]T -------------------------------------------------------------------------------- Time 4.82 secs. ******************************************************************************** ******************************************************************************** MOTIF GTTGTTTT MEME-5 width = 8 sites = 2 llr = 23 E-value = 1.4e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTTGTTTT MEME-5 Description -------------------------------------------------------------------------------- Simplified A :::::::: pos.-specific C :::::::: probability G a::a:::: matrix T :aa:aaaa bits 2.1 ** **** 1.9 ******** 1.7 ******** 1.5 ******** Relative 1.3 ******** Entropy 1.1 ******** (16.6 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GTTGTTTT consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTGTTTT MEME-5 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------- chr22:21015779-21015859 65 1.05e-05 ttgttttcta gttgtttt gctactct chr1:148241926-148242006 73 1.05e-05 TTTTTTTGTT GTTGTTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTGTTTT MEME-5 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr22:21015779-21015859 1e-05 64_[+5]_8 chr1:148241926-148242006 1e-05 72_[+5] -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTGTTTT MEME-5 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF GTTGTTTT width=8 seqs=2 chr22:21015779-21015859 ( 65) GTTGTTTT 1 chr1:148241926-148242006 ( 73) GTTGTTTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTGTTTT MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 8322 bayes= 12.0224 E= 1.4e+004 -765 -765 194 -765 -765 -765 -765 210 -765 -765 -765 210 -765 -765 194 -765 -765 -765 -765 210 -765 -765 -765 210 -765 -765 -765 210 -765 -765 -765 210 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTGTTTT MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.4e+004 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 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 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTTGTTTT MEME-5 regular expression -------------------------------------------------------------------------------- GTTGTTTT -------------------------------------------------------------------------------- Time 5.95 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr14:35024182-35024262 5.78e-01 80 chr14:35017150-35017230 9.22e-03 80 chr5:137806338-137806418 1.43e-01 80 chr9:126031175-126031255 1.00e+00 80 chr9:86536291-86536371 1.00e+00 80 chr10:97416497-97416577 9.98e-01 80 chr2:149402918-149402998 6.17e-01 80 chr11:65196058-65196138 9.69e-02 4_[+2(8.41e-05)]_68 chr2:196521840-196521920 1.00e+00 80 chr11:65193728-65193808 2.55e-01 80 chr13:91101934-91102014 2.26e-03 40_[+4(2.18e-05)]_32 chr11:65194952-65195032 8.68e-01 80 chr21:46494931-46495011 1.00e+00 80 chr9:103361119-103361199 9.10e-01 80 chr2:232574245-232574325 1.00e+00 80 chr22:38902488-38902568 9.95e-01 80 chr11:77532168-77532248 1.00e+00 80 chr5:137805122-137805202 1.08e-01 80 chr22:22427606-22427686 4.73e-06 26_[+4(1.05e-05)]_16_[+3(7.04e-05)]_\ 11_[+3(9.67e-06)]_3 chr3:119813411-119813491 1.00e+00 80 chr17:62501002-62501082 3.51e-02 80 chr17:7145823-7145903 1.00e+00 80 chr19:812997-813077 1.00e+00 80 chr9:139560677-139560757 1.00e+00 80 chr7:115383447-115383527 4.98e-07 12_[+2(2.66e-05)]_29_[+1(4.16e-05)]_\ 7_[+3(2.91e-05)]_8 chr7:111233350-111233430 2.92e-01 80 chr11:64053169-64053249 9.99e-01 80 chr9:130829561-130829641 1.00e+00 80 chr13:92325954-92326034 3.51e-03 67_[+2(1.28e-05)]_5 chr5:137805363-137805443 3.15e-01 80 chr7:35840718-35840798 1.00e+00 80 chr2:85767407-85767487 1.30e-01 80 chr11:61447778-61447858 9.99e-01 80 chr16:89788369-89788449 3.96e-01 80 chr21:46494248-46494328 1.00e+00 80 chr10:17272498-17272578 9.90e-01 80 chr2:232575011-232575091 1.00e+00 80 chr21:11118100-11118180 4.16e-03 58_[+2(4.09e-05)]_14 chr12:7053683-7053763 1.00e+00 80 chr12:7053883-7053963 9.96e-01 80 chr7:26240450-26240530 1.00e+00 80 chr1:148241926-148242006 2.06e-05 58_[+4(1.05e-05)]_6_[+5(1.05e-05)] chr10:75210137-75210217 2.00e-01 80 chr13:81382341-81382421 6.66e-04 25_[+1(2.15e-05)]_47 chr17:19015244-19015324 5.10e-01 80 chr2:232575210-232575290 1.00e+00 80 chr13:93271313-93271393 2.57e-04 33_[+2(1.28e-05)]_39 chr19:13266125-13266205 7.01e-01 80 chr5:68664575-68664655 4.52e-03 46_[+1(1.04e-05)]_26 chr20:60641447-60641527 1.00e+00 80 chr1:207377439-207377519 6.06e-05 40_[+1(1.04e-05)]_32 chr11:10830631-10830711 9.39e-01 80 chr6:34360497-34360577 9.50e-01 80 chr8:15836596-15836676 5.12e-06 26_[+3(1.87e-05)]_22_[+3(1.87e-05)]_\ 16 chr6:32941310-32941390 4.71e-04 46_[+1(6.35e-05)]_26 chr6:41834609-41834689 3.81e-04 16_[+5(7.03e-05)]_56 chr4:166248456-166248536 1.00e+00 80 chr19:813551-813631 9.77e-01 80 chr1:147736004-147736084 2.96e-01 80 chr5:176873788-176873868 9.98e-01 80 chr11:62608096-62608176 1.93e-04 50_[+3(9.67e-06)]_22 chr17:56736208-56736288 4.38e-01 80 chr7:5569340-5569420 1.00e+00 80 chr17:56756749-56756829 1.98e-01 80 chr13:91800410-91800490 8.12e-05 4_[+2(4.09e-05)]_27_[+3(6.03e-05)]_\ 33 chr1:194663313-194663393 3.21e-04 65_[+4(1.05e-05)]_7 chr14:95623864-95623944 9.94e-01 80 chr1:27816797-27816877 9.34e-01 80 chr1:27561020-27561100 1.00e+00 80 chr1:73820317-73820397 1.34e-03 27_[+1(5.27e-05)]_45 chr17:56708439-56708519 1.38e-01 80 chr2:149899741-149899821 3.53e-03 45_[+3(3.99e-05)]_27 chr10:87203639-87203719 1.57e-03 49_[+2(6.97e-05)]_23 chr17:62501307-62501387 2.80e-01 80 chr6:26232647-26232727 1.91e-02 32_[+2(2.66e-05)]_40 chr1:16399853-16399933 1.00e+00 80 chr3:9438316-9438396 1.00e+00 80 chr1:146555881-146555961 8.36e-01 80 chr7:120736227-120736307 2.17e-02 80 chr5:29035797-29035877 5.85e-02 80 chr19:58908118-58908198 9.40e-01 80 chr17:56085033-56085113 8.68e-01 80 chr11:65666760-65666840 1.00e+00 80 chr6:26026717-26026797 1.57e-03 59_[+1(1.04e-05)]_13 chr7:139096072-139096152 6.52e-03 32_[+2(6.97e-05)]_40 chr16:53738011-53738091 9.89e-01 80 chr3:33065089-33065169 8.36e-03 2_[+1(8.51e-05)]_70 chr21:40716954-40717034 7.46e-04 10_[+1(5.27e-05)]_62 chr17:80055365-80055445 9.90e-01 80 chr3:167452542-167452622 9.51e-01 80 chr7:5569544-5569624 1.00e+00 80 chr1:147736209-147736289 1.79e-01 80 chr1:78470011-78470091 3.84e-05 25_[+1(2.15e-05)]_47 chr1:11969039-11969119 8.12e-01 80 chr1:11968838-11968918 9.99e-01 80 chr6:41863164-41863244 1.00e+00 80 chr13:91303110-91303190 9.51e-04 19_[+3(9.67e-06)]_53 chr22:21015779-21015859 9.77e-06 29_[+2(8.41e-05)]_16_[+5(7.03e-05)]_\ 3_[+5(1.05e-05)]_8 chr19:54713440-54713520 1.00e+00 80 chr1:73079255-73079335 1.65e-01 80 chr1:195928830-195928910 1.31e-04 80 chr4:187125405-187125485 1.00e+00 80 chr1:27816997-27817077 4.70e-01 80 chr7:110605476-110605556 6.07e-06 9_[+3(9.67e-06)]_42_[+1(2.15e-05)]_\ 13 chr11:65197887-65197967 2.22e-01 80 chr12:69201608-69201688 4.15e-01 80 chr1:28837790-28837870 1.50e-04 80 chr1:144534213-144534293 8.15e-03 63_[+4(7.51e-05)]_9 chr7:135284568-135284648 1.81e-02 80 chr6:27776881-27776961 4.69e-02 80 chr1:17231883-17231963 1.91e-02 61_[+4(2.18e-05)]_11 chr11:65196298-65196378 1.48e-06 46_[+3(1.87e-05)]_26 chr17:56708793-56708873 2.93e-01 80 chr1:145115653-145115733 5.15e-05 6_[+1(3.12e-05)]_66 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (5) found. ******************************************************************************** CPU: c17n10.farnam.hpc.yale.internal ********************************************************************************