AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -icytR_bbur_opreg_300.orf -g0.282 -x5 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.282
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	BB0618	87	cytidine deaminase (cdd)

Motif number 1

     GTTTTTAGCTTATTTTACATTGACTAT	1	6	1	TATTATTTTA	     0.94336	-82
TTTATTTTATTGAAATATTGTAATATAGTCAA	1	30	0	TGATATTGTA	    0.528579	-58
TTAGCCATTGTGGTTTATTTTATTGAAATATT	1	43	0	TGTTATTTTA	    0.993925	-45
ATTTCCCACCTGTTATATTTTATTAGCCATTG	1	65	0	TGATATTTTA	    0.949762	-23
          **  ********

Masking position 6
Map Score:   7.36366

Number of sites scoring better than the average of aligned sites = 64
Number in coding regions = 36
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 2

AGTCAATGTAAAATAAGCTAAAAAC     	1	6	0	AAATAAGCTA	    0.973868	-82
AGCTTATTTTACATTGACTATATTACAATA	1	17	1	ACATTGACTA	    0.994445	-71
AAAATAAACCACAATGGCTAATAAAATATA	1	54	1	ACAATGGCTA	    0.996411	-34
          **********

Masking position 3
Map Score:   2.13028

Number of sites scoring better than the average of aligned sites = 23
Number in coding regions = 12
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

TAATATAGTCAATGTAAAATAAGCTAAAAA	1	12	0	AATGTAAAAT	    0.768537	-76
TTATTGAAATATTGTAATATAGTCAATGTA	1	26	0	ATTGTAATAT	    0.843627	-62
ATTGTGGTTTATTTTATTGAAATATTGTAA	1	39	0	ATTTTATTGA	    0.946209	-49
CACCTGTTATATTTTATTAGCCATTGTGGT	1	61	0	ATTTTATTAG	    0.964385	-27
          **********

Masking position 5
Map Score:   0.937279

Number of sites scoring better than the average of aligned sites = 841
Number in coding regions = 506
Number in noncoding regions = 335
Number of orfs with sites within 600 bp upstream = 113
Fraction of orfs with sites within 600 bp upstream = 0.0181497


Motif number 4

          **********

No masking
Map Score:   5.21701e-14

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

          **********

No masking
Map Score:   5.21701e-14

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 6

          **********

No masking
Map Score:   5.21701e-14

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0