AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i348_weak9_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	csrA	234	carbon storage regulator; controls glycogen synthesis, gluconeogenesis, cell size and surface properties

Motif number 1

AGCGTCAGGCAATGCCGTGGACTCGCTTCA	1	15	1	AATGCCGTGG	    0.998784	-220
CGTTAATGCGAATGCCGTGAAGCGAGTCCA	1	32	0	AATGCCGTGA	    0.999286	-203
AACAGAATGTAATGCCATGACTGCTTAGAT	1	118	1	AATGCCATGA	     0.99717	-117
TATGATGGATAATGCCGGGATACAGAGAGA	1	183	1	AATGCCGGGA	    0.998784	-52
          **********

Masking position 3
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

TATCGACAACGATAAAGTCAGGTTGAAGTT	1	63	1	GATAAAGTCA	    0.956677	-172
AAGTTTAGCCGATATACACAACTTCAACCT	1	82	0	GATATACACA	    0.975386	-153
CTAAACTTAGGTTTAACAGAATGTAATGCC	1	104	1	GTTTAACAGA	    0.945175	-131
AGTAAGCAATGACAAACACATTACATCTAA	1	142	0	GACAAACACA	    0.979455	-93
ATAATGCCGGGATACAGAGAGACCCGACTC	1	191	1	GATACAGAGA	      0.9758	-44
CTCCTTGAAAGATTAAAAGAGTCGGGTCTC	1	209	0	GATTAAAAGA	    0.946202	-26
          **********

Masking position 6
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

ATCGTTGTCGATAGCGTTAATGCGAATGCC	1	46	0	ATAGCGTTAA	    0.655696	-189
AACGCTATCGACAACGATAAAGTCAGGTTG	1	58	1	ACAACGATAA	    0.969702	-177
GCCGATATACACAACTTCAACCTGACTTTA	1	75	0	ACAACTTCAA	    0.938196	-160
TTAACAGAATGTAATGCCATGACTGCTTAG	1	116	1	GTAATGCCAT	     0.86901	-119
CAAAAAGTAAGCAATGACAAACACATTACA	1	147	0	GCAATGACAA	    0.964919	-88
TATCCATCATATAACGCCAAAAAGTAAGCA	1	164	0	ATAACGCCAA	    0.983185	-71
          **********

Masking position 3
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