AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i135_Transmembrane_Transport_9_ecoli_reg_100.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	tolB	132	periplasmic protein involved in the tonb-independent uptake of group A colicins
#2	pal	34	peptidoglycan-associated lipoprotein

Motif number 1

     TCGCGATGTTGACTGTTCGGACGGT	1	6	1	ATGTTGACTG	    0.994504	-127
CCGGTGCCTGATGTTGACCGTCCGAACAGT	1	22	0	ATGTTGACCG	    0.996622	-111
ATTTAGCAGAATGTTAACAAACTAAAATAC	1	78	0	ATGTTAACAA	    0.766076	-55
TATCTCCCTTATCTGGACCGATGGCCCACG	1	111	0	ATCTGGACCG	    0.994367	-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

GTCAACATCAGGCACCGGTTGCCACGGGGT	1	34	1	GGCACCGGTT	    0.997994	-99
GGCACCGGTTGCCACGGGGTTCTGGTAGTT	1	44	1	GCCACGGGGT	    0.897209	-89
ATTATCGTGGGCCATCGGTCCAGATAAGGG	1	106	1	GCCATCGGTC	    0.994206	-27
          **********

Masking position 4
Map Score:   2.53125

Number of sites scoring better than the average of aligned sites = 247
Number in coding regions = 239
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

CTAAAATACACAAAACTACCAGAACCCCGT	1	57	0	CAAAACTACC	    0.991561	-76
TGTTAACAAACTAAAATACACAAAACTACC	1	67	0	CTAAAATACA	    0.980919	-66
TAACATTCTGCTAAATTATCGTGGGCCATC	1	92	1	CTAAATTATC	    0.980619	-41
          **********

Masking position 5
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