AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i291_hish_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	HI1647	300	conserved hypothetical protein
#2	HI1648	51	conserved hypothetical protein

Motif number 1

TTTTAAAAACCTTTTTCTATGTGGTTAGAT	1	19	0	CTTTTTCTAT	    0.969896	-282
TAGAAAAAGGTTTTTAAAAACATTTCAAGG	1	30	1	TTTTTAAAAA	    0.464601	-271
TTTCAAGGTTTTTTTAATAACTATTGTGGC	1	52	1	TTTTTAATAA	    0.714224	-249
AAAGTAGCTCTTTTTTCTATTATTAAATTG	1	107	1	TTTTTTCTAT	     0.97827	-194
TTAATTTCAGTTTTTTGTATAAACGAAGTG	1	158	0	TTTTTTGTAT	     0.97178	-143
GACATTATGCCTTTTAATATATACACATTT	1	196	1	CTTTTAATAT	    0.875167	-105
TATATACACATTTTTTCAAACTTGTTCTAA	1	213	1	TTTTTTCAAA	    0.909114	-88
TTTTTTCAAACTTGTTCTAAAGACTTTTCT	1	223	1	CTTGTTCTAA	    0.882466	-78
AGCTACGTTTTTTATTGTAATGTAGAAAAG	1	246	0	TTTATTGTAA	    0.844493	-55
CATTATTTGATTATTTGTATTGATAGCTAC	1	270	0	TTATTTGTAT	    0.828963	-31
          **********

Masking position 5
Map Score:   10.646

Number of sites scoring better than the average of aligned sites = 408
Number in coding regions = 234
Number in noncoding regions = 174
Number of orfs with sites within 600 bp upstream = 181
Fraction of orfs with sites within 600 bp upstream = 0.0290716


Motif number 2

TTCGTCCTTAAGTGCCACAATAGTTATTAAA	1	64	0	AGTGCCACAT	    0.977483	-237
AATAGAAAAAAGAGCTACTTTAGCTGAAAGA	1	97	0	AGAGCTACTT	     0.99023	-204
GTATATATTAAAAGGCATAATGTCTAGCGTG	1	189	0	AAAGGCATAT	    0.887216	-112
ATTTGTATTGATAGCTACGTTTTTTATTGTA	1	257	0	ATAGCTACTT	    0.965327	-44
GGCACCTTGTAGAGCTAATATTCCGATTTTC	2	13	0	AGAGCTAAAT	    0.955686	-39
CATGTTCCGCAAAGGCACCTTGTAGAGCTAA	2	26	0	AAAGGCACTT	    0.975636	-26
          ******** **

Masking position 7
Map Score:   2.39937

Number of sites scoring better than the average of aligned sites = 364
Number in coding regions = 327
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 3

AACTATTGTGGCACTTAAGGACGAAATTCTTTC	1	70	1	GATTAAGACG	    0.994723	-231
TTGTATAAACGAAGTGTAGAACGTCAGAAGGAT	1	141	0	GATGTAGACG	    0.996582	-160
ACAAAAAACTGAAATTAAGCACGCTAGACATTA	1	170	1	GATTAAGACG	    0.994723	-131
GTTTTTTATTGTAATGTAGAAAAGTCTTTAGAA	1	237	0	GATGTAGAAA	    0.948644	-64
          * * ***** ***

Masking position 8
Map Score:   0.710772

Number of sites scoring better than the average of aligned sites = 34
Number in coding regions = 31
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

CACATAGAAAAAGGTTTTTAAAAACATTTC	1	26	1	AAGGTTTTTA	    0.933882	-275
AAGGTTTTTAAAAACATTTCAAGGTTTTTT	1	36	1	AAAACATTTC	     0.86991	-265
AAAACATTTCAAGGTTTTTTTAATAACTAT	1	46	1	AAGGTTTTTT	    0.931688	-255
ACTTTAGCTGAAAGAATTTCGTCCTTAAGT	1	82	0	AAAGAATTTC	    0.926829	-219
AGAACGTCAGAAGGATTGTCCAATTTAATA	1	127	0	AAGGATTGTC	    0.964258	-174
ACTTGTTCTAAAGACTTTTCTACATTACAA	1	232	1	AAGACTTTTC	    0.974421	-69
          **********

Masking position 7
Map Score:   2.1243

Number of sites scoring better than the average of aligned sites = 602
Number in coding regions = 489
Number in noncoding regions = 113
Number of orfs with sites within 600 bp upstream = 133
Fraction of orfs with sites within 600 bp upstream = 0.021362


Motif number 5

          **********

No masking
Map Score:   4.78496e-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:   4.78496e-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:   4.78496e-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