AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i064_Histidine_Biosynthesis_ecoli_reg_300.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	hisL	255	his operon leader peptide
#2	hisG	145	ATP phosphoribosyltransferase

Motif number 1

         TCTTTCAGGCGATGTGTGCTG	2	2	1	CTTTCAGGCG	    0.989216	-144
ACATTCAGATCTTCCAGTGGTGCATGAACG	2	36	1	CTTCCAGTGG	    0.994715	-110
GGAAGGTGATCTTCCGGGGGCTTTCTCATG	2	66	0	CTTCCGGGGG	    0.972951	-80
GGAAGATCACCTTCCGGGGGCTTTTTTATT	2	81	1	CTTCCGGGGG	    0.972951	-65
          **********

Masking position 3
Map Score:   9.14103

Number of sites scoring better than the average of aligned sites = 65
Number in coding regions = 59
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 2

TATTTTATGGCAATGGATTTGTTTAATGAA	1	155	0	CAATGGATTT	     0.92469	-101
CGTTAGAAAGCAAGGGCTTTTTTATATATT	1	181	0	CAAGGGCTTT	    0.995191	-75
TAAACATTCACAGAGACTTTT         	1	245	1	CAGAGACTTT	    0.965131	-11
GGTGATCTTCCGGGGGCTTTCTCATGCGTT	2	62	0	CGGGGGCTTT	    0.998385	-84
GATCACCTTCCGGGGGCTTTTTTATTGCGC	2	85	1	CGGGGGCTTT	    0.998385	-61
          **********

Masking position 8
Map Score:   8.37114

Number of sites scoring better than the average of aligned sites = 260
Number in coding regions = 232
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 3

GGTGCCATCAGCTAAGAGGACAGTCCTCTTA	1	103	1	GCTAGAGGAC	    0.993181	-153
AAAGGAGGGGGCTAAGAGGACTGTCCTCTTA	1	115	0	GCTAGAGGAC	    0.993181	-141
ATGAATGAGCGGGGAAAGGAGGGGGCTAAGA	1	129	0	GGGAAAGGAG	    0.983814	-127
AAGTGGTTTAGGTTAAAAGACATCAGTTGAA	1	214	1	GGTAAAAGAC	    0.988664	-42
GGTTCAGACAGGTTTAAAGAGGAATAACAAA	2	125	1	GGTTAAAGAG	    0.947918	-21
          *** *******

Masking position 7
Map Score:   3.13497

Number of sites scoring better than the average of aligned sites = 51
Number in coding regions = 40
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 4

TAATAAATAGTTAATTAACGCTCATCATTG	1	15	0	TTAATTAACG	    0.963129	-241
TACAAACTAATTAATAAATAGTTAATTAAC	1	26	0	TTAATAAATA	    0.900728	-230
ATGGATTTGTTTAATGAATGAGCGGGGAAA	1	143	0	TTAATGAATG	    0.969346	-113
AGACATCAGTTGAATAAACATTCACAGAGA	1	231	1	TGAATAAACA	     0.95635	-25
CTTCCAGTGGTGCATGAACGCATGAGAAAG	2	46	1	TGCATGAACG	    0.971947	-100
          **********

Masking position 5
Map Score:   1.21866

Number of sites scoring better than the average of aligned sites = 265
Number in coding regions = 221
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 60
Fraction of orfs with sites within 600 bp upstream = 0.00963701


Motif number 5

          **********

No masking
Map Score:   -8.2833e-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:   -8.2833e-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 7

          **********

No masking
Map Score:   -8.2833e-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