AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i114_Glutamine_Transport_ecoli_reg_100.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -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 =  	0.5
 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	    0.999735	-106
CTCACCCTAATCCTCTCCCCATAGGGGAGA	1	46	0	TCCTCTCCCC	     0.99895	-93
GGGTTTGCGCCCCTCACCCTAATCCTCTCC	1	58	0	CCCTCACCCT	     0.99818	-81
GGGGCGCAAACCCGCTCCGGGGCCATTAAT	1	75	1	CCCGCTCCGG	    0.993894	-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

TGCGTTTTACAGGTGTAGCGTTA       	1	4	0	AGGTGTAGCG	    0.990025	-135
TCTCCCCATAGGGGAGAGGGAACTGCCAGT	1	33	0	GGGGAGAGGG	    0.989577	-106
CTATGGGGAGAGGATTAGGGTGAGGGGCGC	1	52	1	AGGATTAGGG	    0.992026	-87
GGCCCCGGAGCGGGTTTGCGCCCCTCACCC	1	69	0	CGGGTTTGCG	     0.99017	-70
          **********

Masking position 3
Map Score:   1.20247

Number of sites scoring better than the average of aligned sites = 338
Number in coding regions = 238
Number in noncoding regions = 100
Number of orfs with sites within 600 bp upstream = 67
Fraction of orfs with sites within 600 bp upstream = 0.0107613


Motif number 3

TACACCTGTAAAACGCACTGGCAGTTCCCT	1	17	1	AAACGCACTG	    0.986996	-122
CAGGGTAATTAATGGCCCCGGAGCGGGTTT	1	82	0	AATGGCCCCG	    0.995363	-57
CGGGGCCATTAATTACCCTGAATTTGATTA	1	92	1	AATTACCCTG	    0.989527	-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