AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i065_bsub_mtub_100.orf -o065_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 =  	0.55
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	hutH	112	histidase

Motif number 1

CTGTTTTCACGCATAGCCCCCTATCGTCTAAG	1	25	0	GCAAGCCCCT	    0.999648	-88
GAAGTTCACAGCATAGCTCCTTTTTGTATGGG	1	56	1	GCAAGCCCTT	    0.999445	-57
CTTTACTTTGGTAAAGCGCCCATACAAAAAGG	1	74	0	GTAAGCCCCA	    0.996488	-39
        AAGCCCAACTCCTTTTTCTTTACT	1	99	0	GCCAACCCTT	    0.996335	-14
          *** *** ****

Masking position 5
Map Score:   7.71941

Number of sites scoring better than the average of aligned sites = 72
Number in coding regions = 64
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

CTATGCGTGAAAACAGAAGTTCACAGCATA	1	41	1	AAACAGAAGT	    0.994065	-72
GCGCCCATACAAAAAGGAGCTATGCTGTGA	1	61	0	AAAAAGGAGC	    0.997822	-52
CAAAGTAAAGAAAAAGGAGTTGGGCTT   	1	96	1	AAAAAGGAGT	    0.998159	-17
          **********

Masking position 5
Map Score:   5.26919

Number of sites scoring better than the average of aligned sites = 146
Number in coding regions = 102
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 3

       AACAGCCCATAGATCTTAGACGA	1	4	1	AGCCCATAGA	    0.997529	-109
CATAGATCTTAGACGATAGGGGGCTATGCG	1	18	1	AGACGATAGG	    0.969566	-95
CTTCTGTTTTCACGCATAGCCCCCTATCGT	1	30	0	CACGCATAGC	    0.980111	-83
TTTGGTAAAGCGCCCATACAAAAAGGAGCT	1	70	0	CGCCCATACA	    0.995724	-43
          **********

Masking position 6
Map Score:   2.05565

Number of sites scoring better than the average of aligned sites = 278
Number in coding regions = 235
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


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