AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icarP_ecoli_hinf_300.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	    0.911632	-274
GCAAGAAGATTGCATGAAATAAAAACGAGC	1	44	0	TGCATGAAAT	    0.930059	-257
ACGCTTGCGCAGCAAGAAGATTGCATGAAA	1	55	0	AGCAAGAAGA	    0.956855	-246
ACAGGCATTAAGCGACAAAAAGATCATCTA	1	99	0	AGCGACAAAA	    0.951597	-202
TGTCGCTTAATGCCTGTAAAACATGCATGA	1	112	1	TGCCTGTAAA	    0.941377	-189
AACATGCATGAGCCACAAAATAATATAAAA	1	131	1	AGCCACAAAA	    0.981379	-170
TGCCGCCGTTTGCCAGAAATTCGTCGGTAA	1	204	1	TGCCAGAAAT	    0.973624	-97
TGAATTAATATGCAAATAAAGTGAGTGAAT	1	264	1	TGCAAATAAA	    0.911729	-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

AGATCATCTAACCTGTTCTGGAAAACGCTTGCGCAGC	1	72	0	ATCTGGAACG	    0.981862	-229
AGAACAGGTTAGATGATCTTTTTGTCGCTTAATGCCT	1	90	1	ATCTTTTGCG	    0.956699	-211
TGGGCGCTAAAAGTCAACTTAATGGCGGGATTTTTTA	1	156	0	ATCTTAAGCG	    0.995601	-145
TTTAGCGCCCATATCTCCAGAATGCCGCCGTTTGCCA	1	182	1	ATCAGAAGCG	    0.991582	-119
AAATCAATGCAAATCTGCTTACCGACGAATTTCTGGC	1	215	0	ATCTTACGCG	    0.988063	-86
TTTGCATATTAATTCACAATGATGACGTAAATCAATG	1	243	0	ATAATGAGCG	    0.952572	-58
AAGTGAGTGAATATTCTCTGGAGGGTGTT        	1	282	1	ATCTGGAGTG	    0.982382	-19
          *  *   ***** * **

Masking position 1
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

TTGCTGCGCAAGCGTTTTCCAGAACAGGTTAGA	1	70	1	ACGTTCCAGA	    0.987106	-231
AAAAAATCCCGCCATTAAGTTGACTTTTAGCGC	1	157	1	GCATTGTTGA	    0.951824	-144
GGCAAACGGCGGCATTCTGGAGATATGGGCGCT	1	185	0	GCATTGGAGA	    0.989727	-116
CCAGAATGCCGCCGTTTGCCAGAAATTCGTCGG	1	198	1	GCGTTCCAGA	    0.997497	-103
CCAGAAATTCGTCGGTAAGCAGATTTGCATTGA	1	216	1	GCGGTGCAGA	    0.996193	-85
          * ****  *****

Masking position 6
Map Score:   1.63049

Number of sites scoring better than the average of aligned sites = 500
Number in coding regions = 470
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 4

          **********

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 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