AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i203_dna_repair_hpyl_reg_100.orf -o203_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	RHP00783	187	AE000511

Motif number 1

     GTGTGATTCCTTAAAAATAATTTTTT	1	6	1	ATTCCTAAAA	    0.968458	-182
ATTCTTTTCAAGTAACAAAAAATTATTTTTA	1	22	0	AGTAACAAAA	    0.980613	-166
ACTTGAAAAGAATACCCAAAAAATAATTAAA	1	40	1	AATACCAAAA	     0.97187	-148
ATACCCAAAAAATAATTAAAAACGATTAAAT	1	51	1	AATAATAAAA	    0.992051	-137
AAAACGATTAAATAATGAAACATTAATAAAA	1	69	1	AATAATAAAC	    0.966846	-119
ATAATGAAACATTAATAAAAATAAAAACTTT	1	80	1	ATTAATAAAA	    0.989668	-108
CTTATGTAAAATTCATGAAAAGTTTTTATTT	1	98	0	ATTCATAAAA	    0.981891	-90
ATGATAAAAAAGCAATTAAAACCCCCTTTTT	1	129	1	AGCAATAAAA	    0.960281	-59
CTTGAAACAAAATTTTAAAAAAGGGGGTTTT	1	146	0	AATTTTAAAA	    0.843247	-42
          ****** ****

Masking position 8
Map Score:   14.6586

Number of sites scoring better than the average of aligned sites = 355
Number in coding regions = 274
Number in noncoding regions = 81
Number of orfs with sites within 600 bp upstream = 75
Fraction of orfs with sites within 600 bp upstream = 0.0120463


Motif number 2

GTGATTCCTTAAAAATAATTTTTTGTTACT	1	13	1	AAAAATAATT	    0.942748	-175
AGAATACCCAAAAAATAATTAAAAACGATT	1	48	1	AAAAATAATT	    0.942748	-140
TTAAAAACGATTAAATAATGAAACATTAAT	1	66	1	TTAAATAATG	    0.914793	-122
TTAATAAAAATAAAAACTTTTCATGAATTT	1	91	1	TAAAAACTTT	    0.852637	-97
CATCTTATGTAAAATTCATGAAAAGTTTTT	1	102	0	AAAATTCATG	    0.915547	-86
TAAGATGATAAAAAAGCAATTAAAACCCCC	1	125	1	AAAAAGCAAT	    0.821516	-63
CCCCCTTTTTTAAAATTTTGTTTCAAGCTT	1	150	1	TAAAATTTTG	    0.858838	-38
CTATTGTAGCTTAAAGCTTGAAACAAAATT	1	163	0	TTAAAGCTTG	    0.902923	-25
          **********

Masking position 4
Map Score:   3.76142

Number of sites scoring better than the average of aligned sites = 2965
Number in coding regions = 2621
Number in noncoding regions = 344
Number of orfs with sites within 600 bp upstream = 233
Fraction of orfs with sites within 600 bp upstream = 0.0374237


Motif number 3

          **********

No masking
Map Score:   3.50598e-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 4

          **********

No masking
Map Score:   3.50598e-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:   3.50598e-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