AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i135_ecoli_mtub_100.orf -o135_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	tolB	132	periplasmic protein involved in the tonb-independent uptake of group A colicins
#2	pal	34	peptidoglycan-associated lipoprotein

Motif number 1

ACCGTCCGAACAGTCAACATCGCGA     	1	6	0	CAGTCAACAT	    0.994576	-127
ACTGTTCGGACGGTCAACATCAGGCACCGG	1	22	1	CGGTCAACAT	    0.996549	-111
GTATTTTAGTTTGTTAACATTCTGCTAAAT	1	78	1	TTGTTAACAT	    0.760641	-55
CGTGGGCCATCGGTCCAGATAAGGGAGATA	1	111	1	CGGTCCAGAT	    0.994749	-22
          **********

Masking position 4
Map Score:   5.42421

Number of sites scoring better than the average of aligned sites = 290
Number in coding regions = 270
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 2

         TCGCGATGTTGACTGTTCGGA	1	2	1	CGCGATGTTG	    0.991935	-131
GCAACCGGTGCCTGATGTTGACCGTCCGAA	1	26	0	CCTGATGTTG	    0.980236	-107
  CATATCTCCCTTATCTGGACCGATGGCC	1	115	0	CCTTATCTGG	    0.772807	-18
          **********

Masking position 5
Map Score:   0.871901

Number of sites scoring better than the average of aligned sites = 187
Number in coding regions = 166
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 3

ACGGGGTTCTGGTAGTTTTGTGTATTTTAG	1	57	1	GGTAGTTTTG	    0.991561	-76
GGTAGTTTTGTGTATTTTAGTTTGTTAACA	1	67	1	TGTATTTTAG	    0.980919	-66
GATGGCCCACGATAATTTAGCAGAATGTTA	1	92	0	GATAATTTAG	    0.980619	-41
          **********

Masking position 4
Map Score:   0.215971

Number of sites scoring better than the average of aligned sites = 83
Number in coding regions = 71
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 4

          **********

No masking
Map Score:   -2.10731e-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:   -2.10731e-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:   -2.10731e-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