AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -igcvA_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	CT283	170	hypothetical protein

Motif number 1

AATAGGGAGGGAGGATCTGTACAGATCCTC	1	18	1	GAGGATCTGT	    0.994427	-153
AGACCGAAGGGAGGATCTGTACAGATCCTC	1	28	0	GAGGATCTGT	    0.994427	-143
GAGATCCCTCTAGAATATCTCATGGTACTT	1	93	0	TAGAATATCT	    0.897018	-78
GATATTCTAGAGGGATCTCTTTCTCTCTTC	1	104	1	AGGGATCTCT	    0.845071	-67
TCTCTTCGTAAAGGAATTCTGTAGAAGTAG	1	127	1	AAGGAATTCT	    0.977327	-44
TAAGAAAAAAAAGGAAAACTACTTCTACAG	1	145	0	AAGGAAAACT	    0.949509	-26
          **********

Masking position 5
Map Score:   7.26211

Number of sites scoring better than the average of aligned sites = 328
Number in coding regions = 328
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

CTGTACAGATCCTCCCTCCCTATTAGAAGA	1	12	0	CCTCCCTCCC	    0.998322	-159
CTGTACAGATCCTCCCTTCGGTCTTTGTCC	1	34	1	CCTCCCTTCG	    0.999231	-137
GGGATCTCTTTCTCTCTTCGTAAAGGAATT	1	115	1	TCTCTCTTCG	    0.994322	-56
          **********

Masking position 7
Map Score:   4.27257

Number of sites scoring better than the average of aligned sites = 10
Number in coding regions = 10
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:   -4.02577e-13

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:   -4.02577e-13

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:   -4.02577e-13

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