📄 meme.crp0.tcm
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********************************************************************************MEME - Motif discovery tool********************************************************************************MEME version 3.5.3 (Release date: 2006-03-08 09:30:25 +1000 (Wed, 08 Mar 2006))For further information on how to interpret these results or to geta copy of the MEME software please access http://meme.nbcr.net.This file may be used as input to the MAST algorithm for searchingsequence databases for matches to groups of motifs. MAST is availablefor interactive use and downloading at http://meme.nbcr.net.****************************************************************************************************************************************************************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 discovermotifs in biopolymers", Proceedings of the Second InternationalConference on Intelligent Systems for Molecular Biology, pp. 28-36,AAAI Press, Menlo Park, California, 1994.****************************************************************************************************************************************************************TRAINING SET********************************************************************************DATAFILE= /home/tbailey/tests/crp0.sALPHABET= ACGTSequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ ce1cg 1.0000 105 ara 1.0000 105 bglr1 1.0000 105 crp 1.0000 105 cya 1.0000 105 deop2 1.0000 105 gale 1.0000 105 ilv 1.0000 105 lac 1.0000 105 male 1.0000 105 malk 1.0000 105 malt 1.0000 105 ompa 1.0000 105 tnaa 1.0000 105 uxu1 1.0000 105 pbr322 1.0000 105 trn9cat 1.0000 105 tdc 1.0000 105 ****************************************************************************************************************************************************************COMMAND LINE SUMMARY********************************************************************************This information can also be useful in the event you wish to report aproblem with the MEME software.command: meme /home/tbailey/tests/crp0.s -mod tcm -dna -revcomp -nostatus -nmotifs 2 model: mod= tcm nmotifs= 2 evt= infobject function= E-value of product of p-valueswidth: minw= 8 maxw= 50 minic= 0.00width: wg= 11 ws= 1 endgaps= yesnsites: minsites= 2 maxsites= 50 wnsites= 0.8theta: prob= 1 spmap= uni spfuzz= 0.5em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05data: n= 1890 N= 18strands: + -sample: seed= 0 seqfrac= 1Letter frequencies in dataset:A 0.304 C 0.196 G 0.196 T 0.304 Background letter frequencies (from dataset with add-one prior applied):A 0.304 C 0.196 G 0.196 T 0.304 ****************************************************************************************************************************************************************MOTIF 1 width = 19 sites = 18 llr = 196 E-value = 2.8e-004********************************************************************************-------------------------------------------------------------------------------- Motif 1 Description--------------------------------------------------------------------------------Simplified A :::27222712:18:9333pos.-specific C 212:2262:3119:9:41:probability G :5:8:324234::1:1::1matrix T 848:13122339:111266 bits 2.4 2.1 * * 1.9 * * 1.6 * * Information 1.4 * * * content 1.2 * ** ** ** (15.7 bits) 0.9 * ** ***** 0.7 ***** ***** 0.5 ***** * * ******** 0.2 ***** ************* 0.0 -------------------Multilevel TGTGATCGAGGTCACACTTconsensus CTCACG A TT AAAsequence A C CA T ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value--------------------------------------------------------------------------------Sequence name Strand Start P-value Site ------------- ------ ----- --------- -------------------ara + 58 2.02e-08 ACATTGATTA TTTGCACGGCGTCACACTT TGCTATGCCAce1cg + 64 5.44e-07 AGACTGTTTT TTTGATCGTTTTCACAAAA ATGGAAGTCCmalt - 41 6.87e-07 TGTGTCTGAA TTTGCACTGTGTCACAATT CCAAATCTTTgale + 45 6.87e-07 ATTCCACTAA TTTATTCCATGTCACACTT TTCGCATCTTompa + 51 8.61e-07 TTTTCATATG CCTGACGGAGTTCACACTT GTAAGTTTTCdeop2 - 60 1.19e-06 CGCAACACAC TTCGATACACATCACAATT AAGGAAATCTmale + 17 1.47e-06 CCGCCAATTC TGTAACAGAGATCACACAA AGCGACGGTGdeop2 + 10 2.00e-06 AGTGAATTA TTTGAACCAGATCGCATTA CAGTGATGCAcrp + 66 2.43e-06 ACTGCATGTA TGCAAAGGACGTCACATTA CCGTGCAGTAbglr1 + 79 3.88e-06 AGTTAATAAC TGTGAGCATGGTCATATTT TTATCAAT ce1cg - 17 5.52e-06 ACGCGCTATT CTCGCCCGATGCCACAAAA ACCAGCACAAtdc + 79 6.54e-06 TGAAAGTTAA TTTGTGAGTGGTCGCACAT ATCCTGTT pbr322 - 53 6.54e-06 CTTACGCATC TGTGCGGTATTTCACACCG CATATGGTGClac + 12 9.07e-06 ACGCAATTAA TGTGAGTTAGCTCACTCAT TAGGCACCCCcya - 50 9.07e-06 TGGTCTAAAA CGTGATCAATTTAACACCT TGCTGATTGAtnaa + 74 1.06e-05 CCCGAACGAT TGTGATTCGATTCACATTT AAACAATTTCilv + 42 1.92e-05 CAGTACAAAA CGTGATCAACCCCTCAATT TTCCCTTTGCmalk - 61 2.06e-05 CCACGATTTT TGCAAGCAACATCACGAAA TTCCTTACAT---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 block diagrams--------------------------------------------------------------------------------SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM------------- ---------------- -------------ara 2e-08 57_[+1]_29ce1cg 5.5e-06 16_[-1]_28_[+1]_23malt 6.9e-07 40_[-1]_46gale 6.9e-07 44_[+1]_42ompa 8.6e-07 50_[+1]_36deop2 1.2e-06 9_[+1]_31_[-1]_27male 1.5e-06 16_[+1]_70crp 2.4e-06 65_[+1]_21bglr1 3.9e-06 78_[+1]_8tdc 6.5e-06 78_[+1]_8pbr322 6.5e-06 52_[-1]_34lac 9.1e-06 11_[+1]_75cya 9.1e-06 49_[-1]_37tnaa 1.1e-05 73_[+1]_13ilv 1.9e-05 41_[+1]_45malk 2.1e-05 60_[-1]_26---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 in BLOCKS format--------------------------------------------------------------------------------BL MOTIF 1 width=19 seqs=18ara ( 58) TTTGCACGGCGTCACACTT 1 ce1cg ( 64) TTTGATCGTTTTCACAAAA 1 malt ( 41) TTTGCACTGTGTCACAATT 1 gale ( 45) TTTATTCCATGTCACACTT 1 ompa ( 51) CCTGACGGAGTTCACACTT 1 deop2 ( 60) TTCGATACACATCACAATT 1 male ( 17) TGTAACAGAGATCACACAA 1 deop2 ( 10) TTTGAACCAGATCGCATTA 1 crp ( 66) TGCAAAGGACGTCACATTA 1 bglr1 ( 79) TGTGAGCATGGTCATATTT 1 ce1cg ( 17) CTCGCCCGATGCCACAAAA 1 tdc ( 79) TTTGTGAGTGGTCGCACAT 1 pbr322 ( 53) TGTGCGGTATTTCACACCG 1 lac ( 12) TGTGAGTTAGCTCACTCAT 1 cya ( 50) CGTGATCAATTTAACACCT 1 tnaa ( 74) TGTGATTCGATTCACATTT 1 ilv ( 42) CGTGATCAACCCCTCAATT 1 malk ( 61) TGCAAGCAACATCACGAAA 1 //---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix--------------------------------------------------------------------------------log-odds matrix: alength= 4 w= 19 n= 1566 bayes= 7.84106 E= 2.8e-004 -1081 18 -1081 135 -1081 -182 135 55 -1081 18 -1081 135 -45 -1081 199 -1081 113 18 -1081 -145 -45 -23 50 13 -87 150 -23 -145 -45 18 99 -87 113 -1081 -23 -87 -245 50 77 13 -45 -82 99 -13 -1081 -82 -1081 155 -245 227 -1081 -1081 145 -1081 -82 -245 -1081 227 -1081 -245 155 -1081 -182 -245 13 118 -1081 -45 13 -82 -1081 87 ⌨️ 快捷键说明
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