AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00960_aquae_reg_300.orf -o00960_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -x5 -e 
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 =  	0.44
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	glgP	110	glycogen phosphorylase
#2	speC	35	ornithine decarboxylase

Motif number 1

GGGACAGAAGCCGCCTGTGTAAGCAGTTTT	1	39	0	CCGCCTGTGT	     0.99219	-72
CGGCTTCTGTCCCCGTATCATAGATACGCG	1	56	1	CCCCGTATCA	    0.993879	-55
CGGGCTAAAACCGCGTATCTATGATACGGG	1	67	0	CCGCGTATCT	    0.999092	-44
CGGTTTTAGCCCGCGGATTTACTATAAAAT	1	84	1	CCGCGGATTT	    0.995789	-27
          **********

Masking position 8
Map Score:   5.44361

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 45
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

CCTCACAAGATTCATTTTAAAAAACTGCTT	1	19	1	TTCATTTTAA	    0.898506	-92
CTGTCCCCGTATCATAGATACGCGGTTTTA	1	62	1	ATCATAGATA	    0.958831	-49
 TACTTGTATTTTATAGTAAATCCGCGGGC	1	92	0	TTTATAGTAA	    0.889725	-19
TATAAATACTTTTATAGATATTTGCT    	2	7	0	TTTATAGATA	    0.921272	-29
TATAAAAGTATTTATATTTATCGGA     	2	21	1	TTTATATTTA	     0.88288	-15
          **********

Masking position 5
Map Score:   5.11474

Number of sites scoring better than the average of aligned sites = 183
Number in coding regions = 156
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 3

TCATTTTAAAAAACTGCTTACACAGGCGGC	1	30	1	AAACTGCTTA	    0.977471	-81
ACGGGGACAGAAGCCGCCTGTGTAAGCAGT	1	42	0	AAGCCGCCTG	    0.989214	-69
CCGCGGGCTAAAACCGCGTATCTATGATAC	1	70	0	AAACCGCGTA	    0.995884	-41
ACGCGGTTTTAGCCCGCGGATTTACTATAA	1	81	1	AGCCCGCGGA	    0.992687	-30
          **********

Masking position 1
Map Score:   2.6055

Number of sites scoring better than the average of aligned sites = 93
Number in coding regions = 84
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

          **********

No masking
Map Score:   -9.70439e-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:   -9.70439e-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:   -9.70439e-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