AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i065_ecoli_bsub_100.orf -o065_ecoli_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -x5 -e 
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 =  	0.47
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	hutH	112	histidase

Motif number 1

CTGTTTTCACGCATAGCCCCCTATCGTCTAAG	1	25	0	GCAAGCCCCT	    0.999666	-88
GAAGTTCACAGCATAGCTCCTTTTTGTATGGG	1	56	1	GCAAGCCCTT	    0.999473	-57
CTTTACTTTGGTAAAGCGCCCATACAAAAAGG	1	74	0	GTAAGCCCCA	     0.99667	-39
        AAGCCCAACTCCTTTTTCTTTACT	1	99	0	GCCAACCCTT	    0.996525	-14
          *** *** ****

Masking position 5
Map Score:   7.71941

Number of sites scoring better than the average of aligned sites = 75
Number in coding regions = 72
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

TATGCTGTGAACTTCTGTTTTCACGCATAG	1	41	0	ACTTCTGTTT	    0.993749	-72
TCACAGCATAGCTCCTTTTTGTATGGGCGC	1	61	1	GCTCCTTTTT	    0.997705	-52
   AAGCCCAACTCCTTTTTCTTTACTTTG	1	96	0	ACTCCTTTTT	    0.998061	-17
          **********

Masking position 6
Map Score:   5.26919

Number of sites scoring better than the average of aligned sites = 33
Number in coding regions = 15
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 3

TCGTCTAAGATCTATGGGCTGTT       	1	4	0	TCTATGGGCT	    0.997649	-109
CGCATAGCCCCCTATCGTCTAAGATCTATG	1	18	0	CCTATCGTCT	    0.971001	-95
ACGATAGGGGGCTATGCGTGAAAACAGAAG	1	30	1	GCTATGCGTG	    0.981058	-83
AGCTCCTTTTTGTATGGGCGCTTTACCAAA	1	70	1	TGTATGGGCG	    0.995931	-43
          **********

Masking position 5
Map Score:   2.05565

Number of sites scoring better than the average of aligned sites = 578
Number in coding regions = 550
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 4

          **********

No masking
Map Score:   1.3033e-13

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:   1.3033e-13

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:   1.3033e-13

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