AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icarP_ecoli_hinf_100.orf -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	carA	300	carbamoyl-phosphate synthetase, glutamine (small) subunit

Motif number 1

AATAAAAACGAGCAGAAAAAAGTGGACCAA	1	27	0	AGCAGAAAAA	    0.909342	-274
GCAAGAAGATTGCATGAAATAAAAACGAGC	1	44	0	TGCATGAAAT	    0.928208	-257
ACGCTTGCGCAGCAAGAAGATTGCATGAAA	1	55	0	AGCAAGAAGA	     0.95568	-246
ACAGGCATTAAGCGACAAAAAGATCATCTA	1	99	0	AGCGACAAAA	    0.950286	-202
TGTCGCTTAATGCCTGTAAAACATGCATGA	1	112	1	TGCCTGTAAA	    0.939807	-189
AACATGCATGAGCCACAAAATAATATAAAA	1	131	1	AGCCACAAAA	    0.980858	-170
TGCCGCCGTTTGCCAGAAATTCGTCGGTAA	1	204	1	TGCCAGAAAT	    0.972893	-97
TGAATTAATATGCAAATAAAGTGAGTGAAT	1	264	1	TGCAAATAAA	    0.909441	-37
          **********

Masking position 8
Map Score:   6.57931

Number of sites scoring better than the average of aligned sites = 1625
Number in coding regions = 1414
Number in noncoding regions = 211
Number of orfs with sites within 600 bp upstream = 239
Fraction of orfs with sites within 600 bp upstream = 0.0383874


Motif number 2

GCTGCGCAAGCGTTTTCCAGAACAGGTTAGATGATCT	1	72	1	CGTTCCAGAT	    0.981745	-229
AGGCATTAAGCGACAAAAAGATCATCTAACCTGTTCT	1	90	0	CGCAAAAGAT	     0.95641	-211
TAAAAAATCCCGCCATTAAGTTGACTTTTAGCGCCCA	1	156	1	CGCTTAAGAT	    0.995571	-145
TGGCAAACGGCGGCATTCTGGAGATATGGGCGCTAAA	1	182	0	CGCTTCTGAT	    0.991525	-119
GCCAGAAATTCGTCGGTAAGCAGATTTGCATTGATTT	1	215	1	CGCGTAAGAT	    0.987981	-86
CATTGATTTACGTCATCATTGTGAATTAATATGCAAA	1	243	1	CGCTCATTAT	    0.952258	-58
        AACACCCTCCAGAGAATATTCACTCACTT	1	282	0	CACTCCAGAT	    0.982261	-19
          ** * *****   *  *

Masking position 14
Map Score:   3.9737

Number of sites scoring better than the average of aligned sites = 607
Number in coding regions = 577
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 3

CTTTTTGTCGCTTAATGCCTGTAAAACATG	1	107	1	CTTAATGCCT	    0.990316	-194
TAAAAGTCAACTTAATGGCGGGATTTTTTA	1	156	0	CTTAATGGCG	    0.993337	-145
CCCATATCTCCAGAATGCCGCCGTTTGCCA	1	189	1	CAGAATGCCG	    0.982358	-112
          **********

Masking position 5
Map Score:   1.20078

Number of sites scoring better than the average of aligned sites = 156
Number in coding regions = 140
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 4

CGTTTTTATTTCATGCAATCTTCTTGCTGC	1	47	1	TCATGCAATC	     0.92597	-254
TCTAACCTGTTCTGGAAAACGCTTGCGCAG	1	73	0	TCTGGAAAAC	    0.995129	-228
TCGCTTAATGCCTGTAAAACATGCATGAGC	1	114	1	CCTGTAAAAC	     0.96806	-187
CCGACGAATTTCTGGCAAACGGCGGCATTC	1	201	0	TCTGGCAAAC	    0.996759	-100
          **********

Masking position 7
Map Score:   2.12745

Number of sites scoring better than the average of aligned sites = 531
Number in coding regions = 491
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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