AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i004_4_1_1_21_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	purE	117	phosphoribosylaminoimidazole carboxylase = AIR carboxylase, catalytic subunit

Motif number 1

AGGAAAACGGTTGCGTGGCTGTGAAATCAGCA	1	25	0	TTGCGGGCTT	    0.991318	-93
ACGCAACCGTTTTCCTTGCTCTCTTTCCGTGC	1	41	1	TTTCCTGCTT	    0.997691	-77
CCTTGCTCTCTTTCCGTGCTATTCTCTGTGCC	1	54	1	TTTCCTGCTT	    0.997686	-64
TCCGTGCTATTCTCTGTGCCCTCTAAAGCCGA	1	66	1	TCTCTTGCCT	    0.992694	-52
GTGGTGCACAACTCTCGGCTTTAGAGGGCACA	1	80	0	ACTCTGGCTT	    0.989993	-38
          ***** **** *

Masking position 12
Map Score:   6.39089

Number of sites scoring better than the average of aligned sites = 272
Number in coding regions = 239
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 2

AATCAGCAAAGTTGCGGGTTTT        	1	3	0	GTTGCGGGTT	    0.988938	-115
AACCCGCAACTTTGCTGATTTCACAGCCAC	1	13	1	TTTGCTGATT	    0.848798	-105
AAGGAAAACGGTTGCGTGGCTGTGAAATCA	1	28	0	GTTGCGTGGC	    0.989834	-90
ACGCAACCGTTTTCCTTGCTCTCTTTCCGT	1	41	1	TTTCCTTGCT	    0.982435	-77
CCTTGCTCTCTTTCCGTGCTATTCTCTGTG	1	54	1	TTTCCGTGCT	    0.995145	-64
TCCGTGCTATTCTCTGTGCCCTCTAAAGCC	1	66	1	TCTCTGTGCC	    0.954087	-52
AAAGCCGAGAGTTGTGCACCACAGGAGTTT	1	90	1	GTTGTGCACC	    0.925777	-28
          **********

Masking position 3
Map Score:   5.88932

Number of sites scoring better than the average of aligned sites = 5227
Number in coding regions = 4835
Number in noncoding regions = 392
Number of orfs with sites within 600 bp upstream = 402
Fraction of orfs with sites within 600 bp upstream = 0.0645679


Motif number 3

          **********

No masking
Map Score:   -2.59896e-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 4

          **********

No masking
Map Score:   -2.59896e-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:   -2.59896e-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