AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -icspA_ctra_opreg_100.orf -g0.413 -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 =  	0.413
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	CT191	146	hypothetical protein

Motif number 1

GAAGGCTCAGGAAGAAGGCTCTTATACTTG	1	88	0	GAAGAAGGCT	    0.998232	-59
ACCTTCCTTCGCAGAAGGCTCAGGAAGAAG	1	101	0	GCAGAAGGCT	     0.99699	-46
AGCCTTCTGCGAAGGAAGGTGTGCTTGCGC	1	111	1	GAAGGAAGGT	    0.995472	-36
TGCGCATATCGAAGGAGCGTT         	1	136	1	GAAGGAGCGT	     0.99694	-11
          **********

Masking position 6
Map Score:   7.86631

Number of sites scoring better than the average of aligned sites = 36
Number in coding regions = 36
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 2

ATCCAAGGATTTACTAGAACTTAGCGCTAA	1	34	1	TTACTAGAAC	    0.913241	-113
AAAAGTCAAAGTATTAGCGCTAAGTTCTAG	1	47	0	GTATTAGCGC	    0.976183	-100
TTCGCAACAAGTATAAGAGCCTTCTTCCTG	1	81	1	GTATAAGAGC	     0.98721	-66
GAAGGAAGGTGTGCTTGCGCATATCGAAGG	1	121	1	GTGCTTGCGC	    0.589185	-26
          **********

Masking position 2
Map Score:   2.73658

Number of sites scoring better than the average of aligned sites = 64
Number in coding regions = 64
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 3

          **********

No masking
Map Score:   -1.17788e-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:   -1.17788e-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:   -1.17788e-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