AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i114_ecoli_mtub_100.orf -o114_ecoli_mtub_100.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 =  	0.58
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	glnP	138	glutamine high-affinity transport system; membrane component

Motif number 1

ACTGGCAGTTCCCTCTCCCCTATGGGGAGA	1	33	1	CCCTCTCCCC	    0.999721	-106
CTCACCCTAATCCTCTCCCCATAGGGGAGA	1	46	0	TCCTCTCCCC	    0.998895	-93
GGGTTTGCGCCCCTCACCCTAATCCTCTCC	1	58	0	CCCTCACCCT	    0.998084	-81
GGGGCGCAAACCCGCTCCGGGGCCATTAAT	1	75	1	CCCGCTCCGG	    0.993971	-64
          **********

Masking position 5
Map Score:   10.3094

Number of sites scoring better than the average of aligned sites = 108
Number in coding regions = 39
Number in noncoding regions = 69
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 2

GCGTTTTACAGGTGTAGCGTTA        	1	3	0	GGTGTAGCGT	     0.99045	-136
CTCCCCATAGGGGAGAGGGAACTGCCAGTG	1	32	0	GGGAGAGGGA	    0.984515	-107
TATGGGGAGAGGATTAGGGTGAGGGGCGCA	1	53	1	GGATTAGGGT	    0.991972	-86
GCCCCGGAGCGGGTTTGCGCCCCTCACCCT	1	68	0	GGGTTTGCGC	    0.990831	-71
          **********

Masking position 7
Map Score:   1.20247

Number of sites scoring better than the average of aligned sites = 367
Number in coding regions = 285
Number in noncoding regions = 82
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 3

TACACCTGTAAAACGCACTGGCAGTTCCCT	1	17	1	AAACGCACTG	    0.987412	-122
CAGGGTAATTAATGGCCCCGGAGCGGGTTT	1	82	0	AATGGCCCCG	    0.995412	-57
CGGGGCCATTAATTACCCTGAATTTGATTA	1	92	1	AATTACCCTG	    0.989897	-47
          **********

Masking position 2
Map Score:   0.3058

Number of sites scoring better than the average of aligned sites = 278
Number in coding regions = 254
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


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