AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00960_aquae_reg_100.orf -o00960_aquae_100.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

AAAACTGCTTACACAGGCGGCTTCTGTCCC	1	39	1	ACACAGGCGG	    0.992629	-72
CGCGTATCTATGATACGGGGACAGAAGCCG	1	56	0	TGATACGGGG	    0.994245	-55
CCCGTATCATAGATACGCGGTTTTAGCCCG	1	67	1	AGATACGCGG	    0.999146	-44
ATTTTATAGTAAATCCGCGGGCTAAAACCG	1	84	0	AAATCCGCGG	    0.996041	-27
          **********

Masking position 3
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	    0.895869	-92
CTGTCCCCGTATCATAGATACGCGGTTTTA	1	62	1	ATCATAGATA	    0.957265	-49
 TACTTGTATTTTATAGTAAATCCGCGGGC	1	92	0	TTTATAGTAA	    0.892299	-19
TATAAATACTTTTATAGATATTTGCT    	2	7	0	TTTATAGATA	    0.922983	-29
TATAAAAGTATTTATATTTATCGGA     	2	21	1	TTTATATTTA	    0.885154	-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

GCCGCCTGTGTAAGCAGTTTTTTAAAATGA	1	30	0	TAAGCAGTTT	    0.978437	-81
ACTGCTTACACAGGCGGCTTCTGTCCCCGT	1	42	1	CAGGCGGCTT	    0.989421	-69
GTATCATAGATACGCGGTTTTAGCCCGCGG	1	70	1	TACGCGGTTT	    0.995884	-41
TTATAGTAAATCCGCGGGCTAAAACCGCGT	1	81	0	TCCGCGGGCT	    0.993004	-30
          **********

Masking position 10
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