AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i348_ecoli_mtub_100.orf -o348_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	csrA	234	carbon storage regulator; controls glycogen synthesis, gluconeogenesis, cell size and surface properties

Motif number 1

TGAAGCGAGTCCACGGCATTGCCTGACGCT	1	15	0	CCACGGCATT	     0.99889	-220
TGGACTCGCTTCACGGCATTCGCATTAACG	1	32	1	TCACGGCATT	    0.999348	-203
ATCTAAGCAGTCATGGCATTACATTCTGTT	1	118	0	TCATGGCATT	    0.997416	-117
TCTCTCTGTATCCCGGCATTATCCATCATA	1	183	0	TCCCGGCATT	     0.99889	-52
          **********

Masking position 8
Map Score:   12.2049

Number of sites scoring better than the average of aligned sites = 57
Number in coding regions = 50
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

AACTTCAACCTGACTTTATCGTTGTCGATA	1	63	0	TGACTTTATC	      0.9521	-172
AGGTTGAAGTTGTGTATATCGGCTAAACTT	1	82	1	TGTGTATATC	     0.97273	-153
GGCATTACATTCTGTTAAACCTAAGTTTAG	1	104	0	TCTGTTAAAC	    0.939459	-131
TTAGATGTAATGTGTTTGTCATTGCTTACT	1	142	1	TGTGTTTGTC	    0.977227	-93
GAGTCGGGTCTCTCTGTATCCCGGCATTAT	1	191	0	TCTCTGTATC	    0.973187	-44
GAGACCCGACTCTTTTAATCTTTCAAGGAG	1	209	1	TCTTTTAATC	    0.940587	-26
          **********

Masking position 5
Map Score:   3.96441

Number of sites scoring better than the average of aligned sites = 381
Number in coding regions = 306
Number in noncoding regions = 75
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 3

GGCATTCGCATTAACGCTATCGACAACGAT	1	46	1	TTAACGCTAT	    0.657121	-189
CAACCTGACTTTATCGTTGTCGATAGCGTT	1	58	0	TTATCGTTGT	    0.968515	-177
TAAAGTCAGGTTGAAGTTGTGTATATCGGC	1	75	1	TTGAAGTTGT	     0.93569	-160
CTAAGCAGTCATGGCATTACATTCTGTTAA	1	116	0	ATGGCATTAC	    0.864154	-119
TGTAATGTGTTTGTCATTGCTTACTTTTTG	1	147	1	TTGTCATTGC	    0.963453	-88
TGCTTACTTTTTGGCGTTATATGATGGATA	1	164	1	TTGGCGTTAT	    0.983018	-71
          **********

Masking position 8
Map Score:   1.63874

Number of sites scoring better than the average of aligned sites = 2921
Number in coding regions = 2712
Number in noncoding regions = 209
Number of orfs with sites within 600 bp upstream = 229
Fraction of orfs with sites within 600 bp upstream = 0.0367812


Motif number 4

          **********

No masking
Map Score:   -2.46258e-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:   -2.46258e-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:   -2.46258e-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