AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00410_hinf_reg_300.orf -o00410_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	HI0675	110	aminoacyl-histidine dipeptidase (pepD)

Motif number 1

AATTTAAACTAAGGTGCAATT         	1	2	0	AAGGTGCAAT	    0.989305	-109
GTTTAAATTTATCGAGAAATAAAAAATTGC	1	23	1	ATCGAGAAAT	    0.986756	-88
GCGTAAGGATAACCCGAAATGGCGTTTTAT	1	51	1	AACCCGAAAT	     0.98566	-60
ACTGAAAATATTGACGAAATAATAGCATAA	1	77	0	TTGACGAAAT	    0.935478	-34
TTTCAGTAAAAAGGAGCAATT         	1	100	1	AAGGAGCAAT	    0.993256	-11
          **********

Masking position 8
Map Score:   5.33813

Number of sites scoring better than the average of aligned sites = 389
Number in coding regions = 341
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 2

      AATTGCACCTTAGTTTAAATTTAT	1	5	1	GCACCTTAGT	    0.963301	-106
TTATCCTTACGCAATTTTTTATTTCTCGAT	1	33	0	GCAATTTTTT	    0.993765	-78
GGCGTTTTATGCTATTATTTCGTCAATATT	1	71	1	GCTATTATTT	    0.972185	-40
TATTATTTCGTCAATATTTTCAGTAAAAAG	1	83	1	TCAATATTTT	    0.903679	-28
      AATTGCTCCTTTTTACTGAAAATA	1	97	0	GCTCCTTTTT	    0.992593	-14
          **********

Masking position 10
Map Score:   4.60684

Number of sites scoring better than the average of aligned sites = 909
Number in coding regions = 714
Number in noncoding regions = 195
Number of orfs with sites within 600 bp upstream = 165
Fraction of orfs with sites within 600 bp upstream = 0.0265018


Motif number 3

          AATTGCACCTTAGTTTAAAT	1	1	1	AATTGCACCT	    0.970919	-110
AGAAATAAAAAATTGCGTAAGGATAACCCG	1	37	1	AATTGCGTAA	    0.992424	-74
TTGACGAAATAATAGCATAAAACGCCATTT	1	67	0	AATAGCATAA	    0.988897	-44
          **********

Masking position 2
Map Score:   0.922957

Number of sites scoring better than the average of aligned sites = 136
Number in coding regions = 125
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 4

          **********

No masking
Map Score:   -1.46782e-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:   -1.46782e-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:   -1.46782e-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