AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i332_not_clear7_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI0588	99	N-carbamyl-L-amino acid amidohydrolase

Motif number 1

TTAGAAAAGGTTAATTTTCAACGAAAAATT	1	32	1	TTAATTTTCA	    0.957997	-68
CAAACAATTATAATTTTTCGTTGAAAATTA	1	43	0	TAATTTTTCG	    0.995772	-57
CGAAAAATTATAATTGTTTGACGAATATCA	1	53	1	TAATTGTTTG	    0.988583	-47
CTGATACGGTTTATTTTTTGATATTCGTCA	1	71	0	TTATTTTTTG	    0.993514	-29
          **********

Masking position 5
Map Score:   5.50641

Number of sites scoring better than the average of aligned sites = 210
Number in coding regions = 158
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 2

TTTCTAAGCGTAATATTGGTATTGCTAA  	1	9	0	TAATATTGGT	    0.991939	-91
AACGAAAAATTATAATTGTTTGACGAATAT	1	51	1	TATAATTGTT	    0.924968	-49
GTTTATTTTTTGATATTCGTCAAACAATTA	1	63	0	TGATATTCGT	     0.98613	-37
AGTTTTCTCCTGATACGGTTTATTTTTTGA	1	80	0	TGATACGGTT	    0.976959	-20
          **********

Masking position 5
Map Score:   1.16362

Number of sites scoring better than the average of aligned sites = 425
Number in coding regions = 374
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 3

          **********

No masking
Map Score:   1.66429e-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 4

          **********

No masking
Map Score:   1.66429e-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:   1.66429e-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