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Дата изменения: Wed May 30 16:50:48 2012
Дата индексирования: Tue Oct 2 14:26:32 2012
Кодировка:

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/tmp/gibbs9188/Gibbs9188 /tmp/gibbs9188/data.txt 16 20 -n -r -W 0.8 -w 0.1 -p 200 -j 5 -i 2000 -S 40 -C 0.5 -P /tmp/gibbs9188/prior.txt -R 1,1,8 -U /tmp/gibbs9188/spacing.txt -M 1,24 -B /tmp/gibbs9188/data.txt_info-det -y -nopt -o /tmp/gibbs9188/outfile.txt

Gibbs 3.10.001 Sep 8 2009
Data file: /tmp/gibbs9188/data.txt
Output file: /tmp/gibbs9188/outfile.txt
Priors file: /tmp/gibbs9188/prior.txt
Background Composition Model file: /tmp/gibbs9188/data.txt_info-det
Spacing Model file: /tmp/gibbs9188/spacing.txt
Current directory: /tmp/gibbs9188
The following options are set:
Concentrated Region False Sequence type False
Collapsed Alphabet False Pseudocount weight True
Use Expectation/Maximization False Don't Xnu sequence False
Help flag False Near optimal cutoff True
Number of iterations True Don't fragment False
Don't use map maximization False Repeat regions False
Output file True Informed priors file True
Plateau periods True palindromic sequence True
Don't Reverse complement True Number of seeds True
Seed Value False Pseudosite weight True
Suboptimal sampler output False Overlap False
Allow width to vary False Wilcoxon signed rank False
Sample along length False Output Scan File False
Output prior file False Modular Sampler False
Ignore Spacing Model False Sample Background False
Bkgnd Comp Model True Init from prior False
Homologous Seq pairs False Parallel Tempering False
Group Sampler False No progress info False
Fragment from middle False Verify Mode False
Alternate sample on k False No freq. soln. True
Calc. def. pseudo wt. False Motif/Recur smpl False
Phylogenetic Sampling False Supress Near Opt. True
Nearopt display cutoff False Sample model False
Hierarchical Model False Centroid model False
Print Bayesian Counts False Align Centroid False
Calculate Credibility Limits False Frequency Bkgnd. False

site_samp = 0
nMotifLen = 16
nAlphaLen = 4
nNumMotifs = 20
dPseudoCntWt = 0.1
dPseudoSiteWt = 0.8
nMaxIterations = 2000
lSeedVal = 1338376669
nPlateauPeriods = 200
nSeeds = 40
nNumMotifTypes = 1
dCutoff = 0.5
dNearOptDispCutoff = 0.5
RevComplement = 0
glOverlapParam = 0
Rcutoff factor = 0
Post Plateau Samples = 0
Frag/Shft Per. = 5
Frag width = 24

Sequences to be Searched:
_________________________
#1 pheA
#2 aroH2
#3 tyrB
#4 aroKB2
#5 aroKB1
#6 aroF+tyrA
#7 aroA
#8 aroL
#9 aroC
#10 aroG
#11 aroD+ydiB
Processed Sequence Length: 2750 Total sequence length: 2750

======================================================================
======================== MAP MAXIMIZATION RESULTS ====================
======================================================================

-------------------------------------------------------------------------
MOTIF a

Motif model (residue frequency x 100)
____________________________________________
Pos. # a t c g Info
_____________________________
1 | 63 . . 36 0.6
2 | 63 18 . 18 0.4
3 | 9 9 18 63 0.4
4 | 9 90 . . 0.9
5 | 72 . 27 . 0.7
6 | 45 45 . 9 0.3
7 | . 81 9 9 0.7
8 | . 9 . 90 1.1
9 | 9 18 72 . 0.7
10 | 81 . . 18 0.8
11 | 63 36 . . 0.5
12 | . 81 9 9 0.7
13 | 81 . 18 . 0.8
14 | 27 45 18 9 0.1
15 | . 54 45 . 0.6
16 | . 63 18 18 0.4

nonsite 27 29 20 22
site 32 34 14 17

Motif probability model
____________________________________________
Pos. # a t c g
____________________________________________
1 | 0.581 0.045 0.032 0.342
2 | 0.581 0.199 0.032 0.189
3 | 0.119 0.122 0.186 0.573
4 | 0.119 0.814 0.032 0.035
5 | 0.658 0.045 0.263 0.035
6 | 0.427 0.430 0.032 0.112
7 | 0.042 0.737 0.109 0.112
8 | 0.042 0.122 0.032 0.804
9 | 0.119 0.199 0.647 0.035
10 | 0.734 0.045 0.032 0.189
11 | 0.581 0.353 0.032 0.035
12 | 0.042 0.737 0.109 0.112
13 | 0.734 0.045 0.186 0.035
14 | 0.273 0.430 0.186 0.112
15 | 0.042 0.507 0.416 0.035
16 | 0.042 0.584 0.186 0.189

Background probability model
0.270 0.290 0.211 0.229

16 columns
Num Motifs: 11
2, 1 48 tagag AACTAGTGCATTAGCT tattt 63 0.90 F aroH2
5, 1 129 cgctg GAGTATTGAGATAATT ttcag 144 0.77 F aroKB1
5, 2 153 agtct GACTCTCGCAATATCT tatga 168 0.94 F aroKB1
7, 1 139 cacag GAATAATGTATTACCT gtggt 154 0.91 F aroA
8, 1 94 gctaa ATGTAATTTATTATTT acact 109 0.00 F aroL
9, 1 120 gccga AATTATTGCGATCATG ccctg 135 0.56 F aroC
10, 1 148 attgg AAGTATTGCATTCACT aagat 163 0.96 F aroG
10, 2 169 aagat AAGTATGGCAACACTG gaaca 184 0.54 F aroG
11, 1 22 cgggt GGGTAATGCAATATTC ttttc 37 0.98 F aroD+ydiB
11, 2 43 ttttc AGGTCATGCAAGATCT tacgg 58 0.94 F aroD+ydiB
11, 3 116 aaact ATGACATGCAATATTC ctgga 131 0.55 F aroD+ydiB
****************

Column 1 : Sequence Number, Site Number
Column 2 : Left End Location
Column 4 : Motif Element
Column 6 : Right End Location
Column 7 : Probability of Element
Column 8 : Forward Motif (F) or Reverse Complement (R)
Column 9 : Sequence Description from Fast A input

Log Motif portion of MAP for motif a = -174.63130
Log Fragmentation portion of MAP for motif a = -0.00000

Log Background portion of Map = -3557.52488
Log Alignment portion of Map = -73.11557
Log Site/seq portion of Map = 0.00000
Log Null Map = -3798.83776
Non Palindromic Map = -12.93336
Log Map = -6.43399

log MAP = sum of motif and fragmentation parts of MAP + background + alignment + sites/seq - Null

Frequency Map = -7.165969
Nearopt Map = -7.165969
Maximal Map = -6.433989
Elapsed time: 23.500000 secs