AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00072_hinf_reg_100.orf -o00072_hinf_100.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

AAACACTATCAAAATAACTTATACCCGCCT	1	23	1	AAAATAACTT	    0.934623	-183
TTATACCCGCCTAAGAAAGATGTATTTCTT	1	41	1	CTAAGAAAGA	    0.957299	-165
AGAATTTCGTAAAAGAAATACATCTTTCTT	1	53	0	AAAAGAAATA	    0.984553	-153
AAAAATAGCAAAAAGAATTTCGTAAAAGAA	1	66	0	AAAAGAATTT	    0.902106	-140
GATAGGCAATAAAGGAACTAGATTGATATT	1	96	0	AAAGGAACTA	    0.963796	-110
AGAATATCAACAAATAAGTATCTTATATTT	1	156	0	CAAATAAGTA	    0.934747	-50
TAACGAGATTAAAAGAAAGAATATCAACAA	1	173	0	AAAAGAAAGA	    0.984246	-33
 AGAGACCTCCTAATAACGAGATTAAAAGA	1	187	0	CTAATAACGA	    0.932339	-19
          **********

Masking position 6
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	     0.97746	-189
TGATATTAAAAATAGCAAAAAGAATTTCGTA	1	72	0	AATAGCAAAA	    0.987872	-134
TGCTATTTTTAATATCAATCTAGTTCCTTTA	1	86	1	AATATCAACT	    0.959549	-120
TCCTTTATTGCCTATCAAGGATCATCGCAAG	1	110	1	CCTATCAAGA	    0.968173	-96
TATCAAGGATCATCGCAAGAAACATATCCAT	1	122	1	CATCGCAAAA	    0.961077	-84
TAAAAGAAAGAATATCAACAAATAAGTATCT	1	163	0	AATATCAAAA	    0.989925	-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

  AAGGATTGTTTAAAACACTATCAAAATA	1	9	1	TTTAAAACAC	    0.878905	-197
TAAAACACTATCAAAATAACTTATACCCGC	1	21	1	TCAAAATAAC	    0.921134	-185
TTTTTGCTATTTTTAATATCAATCTAGTTC	1	82	1	TTTTAATATC	    0.972666	-124
ACATATCCATTTGAAATATAAGATACTTAT	1	143	1	TTGAAATATA	    0.763015	-63
ATATTCTTTCTTTTAATCTCGTTATTAGGA	1	179	1	TTTTAATCTC	    0.967221	-27
   AGAGACCTCCTAATAACGAGATTAAAA	1	189	0	TCCTAATAAC	    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