AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i258_ecoli_mtub_100.orf -o258_ecoli_mtub_100.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 =  	0.58
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	b2748	193	orf, hypothetical protein

Motif number 1

TTGTACTTTCCCGTCTCCTCTGTTCATAAT	1	12	1	CCGTCTCCTC	    0.990397	-182
AGATTATGTTCTGCACGCCCTGGGTATACG	1	62	1	CTGCACGCCC	    0.984456	-132
CGCGTTGTCGCGGTATCCCCAACAGAGGAT	1	121	1	CGGTATCCCC	    0.988315	-73
GAAGACGACTCTACATCCTCTGTTGGGGAT	1	135	0	CTACATCCTC	    0.989799	-59
CCCTGAAAAACGGCATCATCATCCCATGCA	1	168	0	CGGCATCATC	    0.990424	-26
         CCTGCCCCCTGAAAAACGGCA	1	183	0	CTGCCCCCTG	    0.989943	-11
          **********

Masking position 1
Map Score:   7.102

Number of sites scoring better than the average of aligned sites = 864
Number in coding regions = 775
Number in noncoding regions = 89
Number of orfs with sites within 600 bp upstream = 84
Fraction of orfs with sites within 600 bp upstream = 0.0134918


Motif number 2

TGTACTTTCCCGTCTCCTCTGTTCATAATTCA	1	13	1	CGTCCCCTGT	    0.972918	-181
GCGTGCAGAACATAATCTCATTATTAGTTACG	1	48	0	CATATCCATT	    0.942098	-146
TCCATTGTTACGTATACCCAGGGCGTGCAGAA	1	70	0	CGTAACCAGG	    0.987612	-124
GGGGATACCGCGACAACGCGGGCAAATGTACC	1	109	0	CGACACCGGG	    0.964714	-85
GACGACTCTACATCCTCTGTTGGGGATACCGC	1	130	0	CATCTCGTTG	    0.946936	-64
GATGTAGAGTCGTCTTCGGATGCATGGGATGA	1	148	1	CGTCTCGATG	    0.982541	-46
AAAACGGCATCATCATCCCATGCATCCGAAGA	1	160	0	CATCTCCATG	    0.989138	-34
          **** ** ****

Masking position 7
Map Score:   5.63767

Number of sites scoring better than the average of aligned sites = 1498
Number in coding regions = 1415
Number in noncoding regions = 83
Number of orfs with sites within 600 bp upstream = 92
Fraction of orfs with sites within 600 bp upstream = 0.0147767


Motif number 3

TGCACGCCCTGGGTATACGTAACAATGGAC	1	73	1	GGGTATACGT	    0.986325	-121
ACGTAACAATGGACAAATGTGGTACATTTG	1	89	1	GGACAAATGT	    0.994199	-105
GCGACAACGCGGGCAAATGTACCACATTTG	1	102	0	GGGCAAATGT	    0.997862	-92
          **********

Masking position 5
Map Score:   2.62825

Number of sites scoring better than the average of aligned sites = 26
Number in coding regions = 24
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 4

          **********

No masking
Map Score:   -4.73059e-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:   -4.73059e-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:   -4.73059e-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