AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i265_hypothetical10_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	ybgC	149	orf, hypothetical protein

Motif number 1

GCCTGGAGCGGCCCATAATTTTTTAAAGAGA	1	19	0	GCCCATAATT	    0.997247	-131
GCCGCTCCAGGCCCATAAATTTTTACGCTCC	1	38	1	GCCCATAATT	    0.997246	-112
ATTTTTACGCTCCCTTAACTTGCCCTCATTC	1	56	1	TCCCTTAATT	    0.991165	-94
TTGCCCTCATTCCCAAACCTCAATCGCGCGC	1	75	1	TCCCAAACTC	    0.982001	-75
GCGTTTAAAAGCTCTAACTTTTGTTGCATTA	1	117	1	GCTCTAACTT	    0.973326	-33
          ******** **

Masking position 7
Map Score:   7.20434

Number of sites scoring better than the average of aligned sites = 150
Number in coding regions = 124
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 2

AGCGTAAAAATTTATGGGCCTGGAGCGGCC	1	37	0	TTTATGGGCC	    0.977953	-113
CCCATAAATTTTTACGCTCCCTTAACTTGC	1	49	1	TTTACGCTCC	    0.996378	-101
TTACGCTCCCTTAACTTGCCCTCATTCCCA	1	60	1	TTAACTTGCC	    0.954307	-90
ACGCTGCTACTATACGCGCGCGATTGAGGT	1	91	0	TATACGCGCG	    0.991934	-59
TTAGAGCTTTTAAACGCTGCTACTATACGC	1	104	0	TAAACGCTGC	    0.974391	-46
          **********

Masking position 4
Map Score:   3.45379

Number of sites scoring better than the average of aligned sites = 1812
Number in coding regions = 1679
Number in noncoding regions = 133
Number of orfs with sites within 600 bp upstream = 149
Fraction of orfs with sites within 600 bp upstream = 0.0239319


Motif number 3

ATTGAGGTTTGGGAATGAGGGCAAGTTAAG	1	69	0	GGGAATGAGG	    0.998212	-81
CTATACGCGCGCGATTGAGGTTTGGGAATG	1	82	0	GCGATTGAGG	    0.998184	-68
          **********

Masking position 6
Map Score:   0.988104

Number of sites scoring better than the average of aligned sites = 27
Number in coding regions = 19
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

          **********

No masking
Map Score:   -6.86222e-14

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:   -6.86222e-14

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:   -6.86222e-14

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