AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i064_Histidine_Biosynthesis_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	hisG	145	ATP phosphoribosyltransferase

Motif number 1

         TCTTTCAGGCGATGTGTGCTG	1	2	1	CTTTCAGGCG	    0.994231	-144
ATCTGAATGTCTTCCAGCACACATCGCCTG	1	16	0	CTTCCAGCAC	    0.982078	-130
ACATTCAGATCTTCCAGTGGTGCATGAACG	1	36	1	CTTCCAGTGG	    0.993437	-110
GGAAGGTGATCTTCCGGGGGCTTTCTCATG	1	66	0	CTTCCGGGGG	    0.891918	-80
GGAAGATCACCTTCCGGGGGCTTTTTTATT	1	81	1	CTTCCGGGGG	    0.891918	-65
          **********

Masking position 3
Map Score:   14.0501

Number of sites scoring better than the average of aligned sites = 282
Number in coding regions = 260
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 2

ACGCATGAGAAAGCCCCCGGAAGATCACCT	1	63	1	AAGCCCCCGG	    0.999762	-83
CGCAATAAAAAAGCCCCCGGAAGGTGATCT	1	84	0	AAGCCCCCGG	    0.999762	-62
          **********

Masking position 2
Map Score:   5.11263

Number of sites scoring better than the average of aligned sites = 6
Number in coding regions = 4
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 3

CAGCACACATCGCCTGAAAGA         	1	2	0	CGCCTGAAAG	    0.966804	-144
GGTGCATGAACGCATGAGAAAGCCCCCGGA	1	54	1	CGCATGAGAA	    0.991662	-92
AGAAAGCCCCCGGAAGATCACCTTCCGGGG	1	70	1	CGGAAGATCA	    0.886895	-76
TTATCAACCGCGCAATAAAAAAGCCCCCGG	1	94	0	CGCAATAAAA	    0.941869	-52
TTTTATTGCGCGGTTGATAACGGTTCAGAC	1	104	1	CGGTTGATAA	    0.983215	-42
CGGTTGATAACGGTTCAGACAGGTTTAAAG	1	114	1	CGGTTCAGAC	    0.955216	-32
TTTGTTATTCCTCTTTAAACCTGTCTGAAC	1	126	0	CTCTTTAAAC	    0.800116	-20
          **********

Masking position 7
Map Score:   3.05214

Number of sites scoring better than the average of aligned sites = 3176
Number in coding regions = 2897
Number in noncoding regions = 279
Number of orfs with sites within 600 bp upstream = 286
Fraction of orfs with sites within 600 bp upstream = 0.0459364


Motif number 4

          **********

No masking
Map Score:   2.43208e-15

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:   2.43208e-15

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:   2.43208e-15

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