AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -icoldbox_hinf_opreg_100.orf -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	HI0231	120	ATP-dependent RNA helicase (deaD)

Motif number 1

AATTTTTCTATTCGTTCTACTGCAAAGAGCG	1	30	0	TTCGTTCTCT	    0.995382	-91
GCAGAGCGAATGAATTTTTCTATTCGTTCTA	1	42	0	TGAATTTTCT	    0.948232	-79
GAAAAATTCATTCGCTCTGCTCAACTTAATA	1	53	1	TTCGCTCTCT	    0.997008	-68
CAAAGAGGCCTTCGGTTTATTAAGTTGAGCA	1	70	0	TTCGGTTTTT	    0.969845	-51
AAGGCCTCTTTGAGCTTTCCTTATTTATATT	1	89	1	TGAGCTTTCT	    0.993288	-32
          ******** **

Masking position 6
Map Score:   5.03562

Number of sites scoring better than the average of aligned sites = 176
Number in coding regions = 147
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 2

CGAATGAATTTTTCTATTCGTTCTACTGCA	1	37	0	TTTCTATTCG	    0.996905	-84
GCTTTCCTTATTTATATTCGAGTATTTTA 	1	102	1	TTTATATTCG	    0.994986	-19
          **********

Masking position 5
Map Score:   1.74632

Number of sites scoring better than the average of aligned sites = 4
Number in coding regions = 3
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 3

          **********

No masking
Map Score:   -7.57276e-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:   -7.57276e-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:   -7.57276e-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