AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00120_hinf_reg_300.orf -o00120_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	HI0185	122	alcohol dehydrogenase, class III (adhC)
#2	HI1062	85	(3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ)
#3	HI1064	56	conserved hypothetical protein

Motif number 1

TTTTGTTTAAAGGGAATAAAAA         	1	2	0	AGGGATAAAA	    0.943203	-121
CTTTAAACAAAAATGATAAAAAAACACTTGC	1	21	1	AAATATAAAA	    0.803241	-102
AGTGAACTCTAAAGTGTAAACTGTTGCTATC	1	57	1	AAAGGTAAAC	    0.972673	-66
TTACGTAAGCAAGATAGCAACAGTTTACACT	1	69	0	AAGAAGCAAC	    0.923393	-54
CAATGAATTAAGAGGAAAAACA         	1	111	1	AGAGAAAAAC	    0.976095	-12
ATTTATAGCTAAAAATAAAACGCACTCAATA	2	15	0	AAAATAAAAC	    0.854051	-71
GATACCTTACAAAAAATAAACAAATAAAATC	2	62	0	AAAAATAAAC	    0.981268	-24
TATTTTTTGTAAGGTATCAAC          	2	75	1	AAGGATCAAC	    0.988281	-11
TTTAAGCCAGAAGGAAAAAACA         	3	2	0	AAGGAAAAAC	    0.990787	-55
          **** ******

Masking position 9
Map Score:   8.9959

Number of sites scoring better than the average of aligned sites = 681
Number in coding regions = 525
Number in noncoding regions = 156
Number of orfs with sites within 600 bp upstream = 131
Fraction of orfs with sites within 600 bp upstream = 0.0210408


Motif number 2

    TTTTTATTCCCTTTAAACAAAAATGAT	1	7	1	TTCCTTTAAA	    0.991511	-116
CACTTTAGAGTTCACTCTAAAGCAAGTGTTT	1	42	0	TTCCTCTAAA	    0.993904	-81
AGCAACAGTTTACACTTTAGAGTTCACTCTA	1	54	0	TACCTTTAGA	    0.958281	-69
      TGTTTTTCCTCTTAATTCATTGACA	1	108	0	TTTCTCTTAA	    0.951765	-15
CGTTTTATTTTTAGCTATAAATATCGTATAA	2	24	1	TTACTATAAA	    0.967093	-62
AAAATTGGCTTATTCTATAAAATAACCGCTC	3	32	1	TATCTATAAA	    0.965348	-25
          *** *******

Masking position 6
Map Score:   5.62795

Number of sites scoring better than the average of aligned sites = 158
Number in coding regions = 110
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 3

TTATTCCCTTTAAACAAAAATGATAAAAAAAC	1	14	1	TAAACAAAAG	    0.965859	-109
GAGTTCACTCTAAAGCAAGTGTTTTTTTATCA	1	34	0	TAAAGCAATT	    0.953308	-89
TTGCCTTACGTAAGCAAGATAGCAACAGTTTA	1	73	0	TAAGCAAGTG	    0.980838	-50
CTTGCTTACGTAAGGCAACTTTGTCAATGAAT	1	87	1	TAAGGCAATT	    0.976828	-36
TTACAAAAAATAAACAAATAAAATCTATCGGA	2	55	0	TAAACAAAAA	    0.876855	-31
GCCAATTTTTTAAGCCAGAAGGAAAAAACA  	3	9	0	TAAGCCAGAG	    0.987835	-48
TTTTATAGAATAAGCCAATTTTTTAAGCCAGA	3	22	0	TAAGCCAATT	    0.990054	-35
          ******** * *

Masking position 7
Map Score:   5.82751

Number of sites scoring better than the average of aligned sites = 470
Number in coding regions = 403
Number in noncoding regions = 67
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 4

AAACAAAAATGATAAAAAAACACTTGCTTT	1	25	1	GATAAAAAAA	    0.934017	-98
TTGCTATCTTGCTTACGTAAGGCAACTTTG	1	80	1	GCTTACGTAA	    0.939925	-43
GATATTTATAGCTAAAAATAAAACGCACTC	2	19	0	GCTAAAAATA	     0.95736	-67
   GTTGATACCTTACAAAAAATAAACAAA	2	69	0	CCTTACAAAA	    0.970103	-17
TTTCCTTCTGGCTTAAAAAATTGGCTTATT	3	16	1	GCTTAAAAAA	    0.990636	-41
          **********

Masking position 5
Map Score:   2.80816

Number of sites scoring better than the average of aligned sites = 427
Number in coding regions = 356
Number in noncoding regions = 71
Number of orfs with sites within 600 bp upstream = 63
Fraction of orfs with sites within 600 bp upstream = 0.0101189


Motif number 5

          **********

No masking
Map Score:   -2.39152e-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:   -2.39152e-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 7

          **********

No masking
Map Score:   -2.39152e-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