AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i348_weak9_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	csrA	234	carbon storage regulator; controls glycogen synthesis, gluconeogenesis, cell size and surface properties
#2	HI0813	77	carbon storage regulator (csrA)
#3	HI0814	187	alanyl-tRNA synthetase (alaS)

Motif number 1

       TATAAGCGTCAGGCAATGCCGTG	1	4	1	AAGCGTCAGG	    0.937059	-231
AAGCGTCAGGCAATGCCGTGGACTCGCTTC	1	14	1	CAATGCCGTG	    0.975108	-221
GCGTTAATGCGAATGCCGTGAAGCGAGTCC	1	33	0	GAATGCCGTG	    0.975242	-202
TCGACAACGATAAAGTCAGGTTGAAGTTGT	1	65	1	TAAAGTCAGG	    0.948244	-170
TAACAGAATGTAATGCCATGACTGCTTAGA	1	117	1	TAATGCCATG	    0.971575	-118
ATATGATGGATAATGCCGGGATACAGAGAG	1	182	1	TAATGCCGGG	    0.992842	-53
GAAAGATTAAAAGAGTCGGGTCTCTCTGTA	1	203	0	AAGAGTCGGG	    0.960973	-32
ACTTCTCAAATAGCGTCGTGAAGTGCGGTT	3	63	1	TAGCGTCGTG	    0.978167	-125
          **********

Masking position 2
Map Score:   10.0424

Number of sites scoring better than the average of aligned sites = 987
Number in coding regions = 920
Number in noncoding regions = 67
Number of orfs with sites within 600 bp upstream = 55
Fraction of orfs with sites within 600 bp upstream = 0.00883392


Motif number 2

AACGATAAAGTCAGGTTGAAGTTGTGTATATCG	1	70	1	TGGTTGAGTT	    0.985221	-165
TTAGATGTAATGTGTTTGTCATTGCTTACTTTT	1	142	1	TGTTTGCATT	    0.982208	-93
GTCATTGCTTACTTTTTGGCGTTATATGATGGA	1	159	1	ATTTTGCGTT	    0.873484	-76
TCAATCAAGGAACGGTTGGCATTCCACCAACCA	2	18	0	AGGTTGCATT	      0.9349	-60
TTTTATCTCCTTAGTTTGCATTTATTAGATATC	2	54	0	TGTTTGATTT	    0.972878	-24
ATTTGAGAAGTGCGGTTAAAATTTAAGTTATTT	3	41	0	TGGTTAAATT	    0.860403	-147
AAGTGCGGTTTTATTTTGGAGTTTTGGCAAAAA	3	83	1	TTTTTGAGTT	    0.963621	-105
TATTTTTGCATATTTTTGAAATTTATAAAAAGG	3	117	0	TTTTTGAATT	    0.956371	-71
ATAGGGCGACTTAGTTTTTATTTTTATTATGGG	3	147	1	TGTTTTATTT	    0.800228	-41
          *  ***** ****

Masking position 7
Map Score:   6.7609

Number of sites scoring better than the average of aligned sites = 449
Number in coding regions = 390
Number in noncoding regions = 59
Number of orfs with sites within 600 bp upstream = 71
Fraction of orfs with sites within 600 bp upstream = 0.0114038


Motif number 3

GCGTCAGGCAATGCCGTGGACTCGCTTCAC	1	16	1	ATGCCGTGGA	    0.994539	-219
GTTAATGCGAATGCCGTGAAGCGAGTCCAC	1	31	0	ATGCCGTGAA	    0.996123	-204
ACAGAATGTAATGCCATGACTGCTTAGATG	1	119	1	ATGCCATGAC	    0.985108	-116
ATGATGGATAATGCCGGGATACAGAGAGAC	1	184	1	ATGCCGGGAT	    0.842112	-51
          **********

Masking position 2
Map Score:   4.79208

Number of sites scoring better than the average of aligned sites = 101
Number in coding regions = 95
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

TGCGAATGCCGTGAAGCGAGTCCACGGCAT	1	26	0	GTGAAGCGAG	    0.993263	-209
GACGCTATTTGAGAAGTGCGGTTAAAATTT	3	50	0	GAGAAGTGCG	    0.996328	-138
AAATAGCGTCGTGAAGTGCGGTTTTATTTT	3	70	1	GTGAAGTGCG	    0.997913	-118
          **********

Masking position 5
Map Score:   2.9966

Number of sites scoring better than the average of aligned sites = 59
Number in coding regions = 55
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

TCCCGGCATTATCCATCATATAACGCCAAAAAGT	1	169	0	ATCTCATAAC	    0.949476	-66
GACTCTTTTAATCTTTCAAGGAGCAAAGA     	1	216	1	ATCTCAAAGC	    0.994679	-19
ACGGTTGGCATTCCACCAACCAGCTTGTA     	2	6	0	TTCCCAAAGC	    0.967467	-72
TAGATATCCTATCAATCAAGGAACGGTTGGCATT	2	28	0	ATCTCAAAAC	     0.98907	-50
GTTATTTCAGATTATTCAAAAAACAATTTCTTGT	3	14	0	ATTTCAAAAC	    0.977619	-174
TTTTAACCGCACTTCTCAAATAGCGTCGTGAAGT	3	53	1	ACTTCAAAGC	    0.965295	-135
TATTTTGGAGTTTTGGCAAAAAGCCTTTTTATAA	3	94	1	TTTGCAAAGC	    0.935059	-94
          ***  ****  ***

Masking position 8
Map Score:   5.42973

Number of sites scoring better than the average of aligned sites = 129
Number in coding regions = 108
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 6

          **********

No masking
Map Score:   3.15071e-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 7

          **********

No masking
Map Score:   3.15071e-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 8

          **********

No masking
Map Score:   3.15071e-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