AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i274_hypothetical19_hpyl_reg_100.orf -o274_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 =  	0.39
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RHP00723	124	AE000511

Motif number 1

TATTACTATGGTTTTATCGTGTTATTTTAT	1	22	1	GTTTTATCGT	    0.970531	-103
TTTTATCTAAGTTTTGGCATGCGCCAAAAC	1	46	1	GTTTTGGCAT	    0.992392	-79
AATTTTGCGTGTTTTGGCGCATGCCAAAAC	1	56	0	GTTTTGGCGC	     0.99931	-69
TAAAATAAGCGTTTTGATGCCATTTTTGGA	1	99	1	GTTTTGATGC	    0.989151	-26
TTTGATGCCATTTTTGGAGCGATC      	1	111	1	TTTTTGGAGC	    0.986675	-14
          **********

Masking position 5
Map Score:   8.80633

Number of sites scoring better than the average of aligned sites = 295
Number in coding regions = 281
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 2

CATAGTAATAAAGATAACCCC         	1	2	0	AAGATAACCC	    0.993784	-123
AAACTTAGATAAAATAACACGATAAAACCA	1	30	0	AAAATAACAC	    0.985675	-95
CAAAACACGCAAAATTATCGCTTTTAAGAT	1	70	1	AAAATTATCG	    0.975423	-55
CTTTTAAGATAAAATAAGCGTTTTGATGCC	1	90	1	AAAATAAGCG	    0.993316	-35
          **********

Masking position 5
Map Score:   3.78197

Number of sites scoring better than the average of aligned sites = 212
Number in coding regions = 182
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 3

GATAAAATAACACGATAAAACCATAGTAAT	1	23	0	CACGATAAAA	    0.992595	-102
ATGCCAAAACTTAGATAAAATAACACGATA	1	36	0	TTAGATAAAA	    0.983445	-89
TTATCGCTTTTAAGATAAAATAAGCGTTTT	1	84	1	TAAGATAAAA	    0.994096	-41
          **********

Masking position 5
Map Score:   3.68776

Number of sites scoring better than the average of aligned sites = 64
Number in coding regions = 43
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 4

          **********

No masking
Map Score:   -6.15168e-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:   -6.15168e-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 6

          **********

No masking
Map Score:   -6.15168e-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