AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i136_ecoli_bsub_100.orf -o136_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	yfiB	105	similar to ABC transporter (ATP-binding protein)

Motif number 1

CTCCCGAAAAGGAGGGCAGTCT        	1	3	0	GGAGGGCAGT	    0.996846	-103
CTCCTTTTCGGGAGGGTTTTCGTTTGCCGT	1	19	1	GGAGGGTTTT	     0.99886	-87
ACTTTACTATGGCGGTCTTTTTGACGGCAA	1	42	0	GGCGGTCTTT	      0.9966	-64
AAAGGGGTTTGGAGGCTTTTAC        	1	94	1	GGAGGCTTTT	    0.997473	-12
          **********

Masking position 10
Map Score:   8.47404

Number of sites scoring better than the average of aligned sites = 84
Number in coding regions = 62
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 2

       AGACTGCCCTCCTTTTCGGGAGG	1	4	1	CTGCCCTCCT	    0.988969	-102
CGGCAAACGAAAACCCTCCCGAAAAGGAGG	1	18	0	AAACCCTCCC	    0.997344	-88
TGCCGTCAAAAAGACCGCCATAGTAAAGTA	1	43	1	AAGACCGCCA	    0.993006	-63
       GTAAAAGCCTCCAAACCCCTTTT	1	93	0	AAAGCCTCCA	    0.995902	-13
          **********

Masking position 5
Map Score:   4.09748

Number of sites scoring better than the average of aligned sites = 228
Number in coding regions = 201
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 3

  AGACTGCCCTCCTTTTCGGGAGGGTTTT	1	9	1	CTCCTTTTCG	    0.991948	-97
TACTATGGCGGTCTTTTTGACGGCAAACGA	1	38	0	GTCTTTTTGA	    0.972487	-68
ACTCGATTGTCTCTTTCTTTACTTTACTAT	1	62	0	CTCTTTCTTT	    0.974026	-44
AGCCTCCAAACCCCTTTTTACTCGATTGTC	1	81	0	CCCCTTTTTA	    0.990318	-25
          **********

Masking position 5
Map Score:   0.686787

Number of sites scoring better than the average of aligned sites = 418
Number in coding regions = 290
Number in noncoding regions = 128
Number of orfs with sites within 600 bp upstream = 139
Fraction of orfs with sites within 600 bp upstream = 0.0223257


Motif number 4

          **********

No masking
Map Score:   -1.9652e-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:   -1.9652e-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:   -1.9652e-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