AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00072_hinf_reg_300.orf -o00072_hinf_300.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -x5 -e 
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 = 	1

Input sequences:
#1	HI0774	205	acetate CoA-transferase, alpha subunit

Motif number 1

AGGCGGGTATAAGTTATTTTGATAGTGTTT	1	23	0	AAGTTATTTT	    0.932834	-183
AAGAAATACATCTTTCTTAGGCGGGTATAA	1	41	0	TCTTTCTTAG	    0.956095	-165
AAGAAAGATGTATTTCTTTTACGAAATTCT	1	53	1	TATTTCTTTT	    0.984105	-153
TTCTTTTACGAAATTCTTTTTGCTATTTTT	1	66	1	AAATTCTTTT	    0.899518	-140
AATATCAATCTAGTTCCTTTATTGCCTATC	1	96	1	TAGTTCCTTT	    0.962767	-110
AAATATAAGATACTTATTTGTTGATATTCT	1	156	1	TACTTATTTG	    0.932951	-50
TTGTTGATATTCTTTCTTTTAATCTCGTTA	1	173	1	TCTTTCTTTT	    0.983789	-33
TCTTTTAATCTCGTTATTAGGAGGTCTCT 	1	187	1	TCGTTATTAG	    0.930481	-19
          **********

Masking position 5
Map Score:   8.38781

Number of sites scoring better than the average of aligned sites = 697
Number in coding regions = 561
Number in noncoding regions = 136
Number of orfs with sites within 600 bp upstream = 113
Fraction of orfs with sites within 600 bp upstream = 0.0181497


Motif number 2

TGTTTAAAACACTATCAAAATAACTTATACC	1	17	1	ACTATCAAAT	    0.978417	-189
TGATATTAAAAATAGCAAAAAGAATTTCGTA	1	72	0	AATAGCAAAA	    0.988399	-134
TGCTATTTTTAATATCAATCTAGTTCCTTTA	1	86	1	AATATCAACT	    0.961259	-120
TCCTTTATTGCCTATCAAGGATCATCGCAAG	1	110	1	CCTATCAAGA	     0.96953	-96
TATCAAGGATCATCGCAAGAAACATATCCAT	1	122	1	CATCGCAAAA	    0.962725	-84
TAAAAGAAAGAATATCAACAAATAAGTATCT	1	163	0	AATATCAAAA	    0.990363	-43
          ******** **

Masking position 7
Map Score:   5.33865

Number of sites scoring better than the average of aligned sites = 295
Number in coding regions = 242
Number in noncoding regions = 53
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 3

TATTTTGATAGTGTTTTAAACAATCCTT  	1	9	0	GTGTTTTAAA	    0.878905	-197
GCGGGTATAAGTTATTTTGATAGTGTTTTA	1	21	0	GTTATTTTGA	    0.921134	-185
GAACTAGATTGATATTAAAAATAGCAAAAA	1	82	0	GATATTAAAA	    0.972666	-124
ATAAGTATCTTATATTTCAAATGGATATGT	1	143	0	TATATTTCAA	    0.763015	-63
TCCTAATAACGAGATTAAAAGAAAGAATAT	1	179	0	GAGATTAAAA	    0.967221	-27
TTTTAATCTCGTTATTAGGAGGTCTCT   	1	189	1	GTTATTAGGA	    0.945389	-17
          **********

Masking position 5
Map Score:   0.715286

Number of sites scoring better than the average of aligned sites = 678
Number in coding regions = 569
Number in noncoding regions = 109
Number of orfs with sites within 600 bp upstream = 91
Fraction of orfs with sites within 600 bp upstream = 0.0146161


Motif number 4

          **********

No masking
Map Score:   -2.46258e-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:   -2.46258e-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:   -2.46258e-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