AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -icytR_bbur_opreg_100.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

ATAGTCAATGTAAAATAAGCTAAAAAC     	1	6	0	TAAAATAATA	    0.942419	-82
TTGACTATATTACAATATTTCAATAAAATAAA	1	30	1	TACAATATCA	    0.527874	-58
AATATTTCAATAAAATAAACCACAATGGCTAA	1	43	1	TAAAATAACA	    0.993883	-45
CAATGGCTAATAAAATATAACAGGTGGGAAAT	1	65	1	TAAAATATCA	    0.948645	-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

     GTTTTTAGCTTATTTTACATTGACT	1	6	1	TAGCTTATTT	    0.975055	-82
TATTGTAATATAGTCAATGTAAAATAAGCT	1	17	0	TAGTCAATGT	    0.994702	-71
TATATTTTATTAGCCATTGTGGTTTATTTT	1	54	0	TAGCCATTGT	    0.996578	-34
          **********

Masking position 2
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

          **********

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 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