AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i114_Glutamine_Transport_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

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

Motif number 1

ACTGGCAGTTCCCTCTCCCCTATGGGGAGA	1	33	1	CCCTCTCCCC	    0.999694	-106
CTCACCCTAATCCTCTCCCCATAGGGGAGA	1	46	0	TCCTCTCCCC	    0.998788	-93
GGGTTTGCGCCCCTCACCCTAATCCTCTCC	1	58	0	CCCTCACCCT	    0.997899	-81
GGGGCGCAAACCCGCTCCGGGGCCATTAAT	1	75	1	CCCGCTCCGG	     0.99407	-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

        TAACGCTACACCTGTAAAACGC	1	3	1	ACGCTACACC	    0.990599	-136
CACTGGCAGTTCCCTCTCCCCTATGGGGAG	1	32	1	TCCCTCTCCC	    0.984756	-107
TGCGCCCCTCACCCTAATCCTCTCCCCATA	1	53	0	ACCCTAATCC	    0.992097	-86
AGGGTGAGGGGCGCAAACCCGCTCCGGGGC	1	68	1	GCGCAAACCC	    0.990964	-71
          **********

Masking position 4
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

AGGGAACTGCCAGTGCGTTTTACAGGTGTA	1	17	0	CAGTGCGTTT	    0.987082	-122
AAACCCGCTCCGGGGCCATTAATTACCCTG	1	82	1	CGGGGCCATT	    0.995374	-57
TAATCAAATTCAGGGTAATTAATGGCCCCG	1	92	0	CAGGGTAATT	    0.989603	-47
          **********

Masking position 9
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