📄 meme.ino_up800.zoops
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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/INO_up800.sALPHABET= ACGTSequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ CHO1 1.0000 800 CHO2 1.0000 800 FAS1 1.0000 800 FAS2 1.0000 800 ACC1 1.0000 800 INO1 1.0000 800 OPI3 1.0000 800 ****************************************************************************************************************************************************************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/INO_up800.s -mod zoops -dna -revcomp -bfile /home/tbailey/tests/yeast.nc.6.freq -nostatus -nmotifs 2 model: mod= zoops 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= 7 wnsites= 0.8theta: prob= 1 spmap= uni spfuzz= 0.5em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05data: n= 5600 N= 7strands: + -sample: seed= 0 seqfrac= 1Letter frequencies in dataset:A 0.304 C 0.196 G 0.196 T 0.304 Background letter frequencies (from /home/tbailey/tests/yeast.nc.6.freq):A 0.324 C 0.176 G 0.176 T 0.324 ****************************************************************************************************************************************************************MOTIF 1 width = 16 sites = 7 llr = 113 E-value = 4.9e-002********************************************************************************-------------------------------------------------------------------------------- Motif 1 Description--------------------------------------------------------------------------------Simplified A 931::::9:a:::31:pos.-specific C 1413:1a:a:::7649probability G :3:::::::::a3:4:matrix T ::77a9:1::a::1:1 bits 2.5 * * * 2.3 * * * 2.0 * * * 1.8 * * ** *Information 1.5 * * ***** *content 1.3 * *** ***** *(23.2 bits) 1.0 * ********** ** 0.8 ** ************* 0.5 **************** 0.3 **************** 0.0 ----------------Multilevel ACTTTTCACATGCCCCconsensus A C GAG sequence G ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value--------------------------------------------------------------------------------Sequence name Strand Start P-value Site ------------- ------ ----- --------- ----------------INO1 - 620 2.22e-10 AATAGACAAT ACTTTTCACATGCCGC ATTTAGCCGCCHO2 + 350 4.67e-09 CAATTGCCAC ACTTTTCTCATGCCGC ATTCATTATTACC1 + 79 9.66e-09 CGCCCGTTAA AATCTTCACATGGCCC GGCCGCGCGCFAS1 + 91 2.21e-08 CGACGGCCAA AAACTTCACATGCCGC CCAGCCAAGCCHO1 + 636 3.90e-08 CACGCCTTTG AGCTTTCACATGGACC CATCTAAAGAOPI3 - 585 1.08e-07 AACCGGTGCA ACTTTCCACATGCACT CTCATTGACAFAS2 + 563 1.49e-07 TTATCTCCCG CGTTTTCACATGCTAC CTCATTCGCC---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 block diagrams--------------------------------------------------------------------------------SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM------------- ---------------- -------------INO1 2.2e-10 619_[-1]_165CHO2 4.7e-09 349_[+1]_435ACC1 9.7e-09 78_[+1]_706FAS1 2.2e-08 90_[+1]_694CHO1 3.9e-08 635_[+1]_149OPI3 1.1e-07 584_[-1]_200FAS2 1.5e-07 562_[+1]_222---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 in BLOCKS format--------------------------------------------------------------------------------BL MOTIF 1 width=16 seqs=7INO1 ( 620) ACTTTTCACATGCCGC 1 CHO2 ( 350) ACTTTTCTCATGCCGC 1 ACC1 ( 79) AATCTTCACATGGCCC 1 FAS1 ( 91) AAACTTCACATGCCGC 1 CHO1 ( 636) AGCTTTCACATGGACC 1 OPI3 ( 585) ACTTTCCACATGCACT 1 FAS2 ( 563) CGTTTTCACATGCTAC 1 //---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix--------------------------------------------------------------------------------log-odds matrix: alength= 4 w= 16 n= 5495 bayes= 10.2211 E= 4.9e-002 140 -30 -945 -945 -18 129 70 -945 -118 -30 -945 114 -945 70 -945 114 -945 -945 -945 162 -945 -30 -945 140 -945 251 -945 -945 140 -945 -945 -118 -945 251 -945 -945 162 -945 -945 -945 -945 -945 -945 162 -945 -945 251 -945 -945 202 70 -945 -18 170 -945 -118 -118 129 129 -945 -945 229 -945 -118 ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Motif 1 position-specific probability matrix--------------------------------------------------------------------------------letter-probability matrix: alength= 4 w= 16 nsites= 7 E= 4.9e-002 0.857143 0.142857 0.000000 0.000000 0.285714 0.428571 0.285714 0.000000 0.142857 0.142857 0.000000 0.714286 0.000000 0.285714 0.000000 0.714286 0.000000 0.000000 0.000000 1.000000 0.000000 0.142857 0.000000 0.857143 0.000000 1.000000 0.000000 0.000000 0.857143 0.000000 0.000000 0.142857 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.714286 0.285714 0.000000 0.285714 0.571429 0.000000 0.142857 0.142857 0.428571 0.428571 0.000000 0.000000 0.857143 0.000000 0.142857 --------------------------------------------------------------------------------⌨️ 快捷键说明
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