AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i203_dna_repair_hpyl_reg_300.orf -o203_hpyl_300.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	    0.965503	-182
ATTCTTTTCAAGTAACAAAAAATTATTTTTA	1	22	0	AGTAACAAAA	    0.978768	-166
ACTTGAAAAGAATACCCAAAAAATAATTAAA	1	40	1	AATACCAAAA	    0.969219	-148
ATACCCAAAAAATAATTAAAAACGATTAAAT	1	51	1	AATAATAAAA	    0.991285	-137
AAAACGATTAAATAATGAAACATTAATAAAA	1	69	1	AATAATAAAC	     0.96374	-119
ATAATGAAACATTAATAAAAATAAAAACTTT	1	80	1	ATTAATAAAA	    0.988677	-108
CTTATGTAAAATTCATGAAAAGTTTTTATTT	1	98	0	ATTCATAAAA	    0.980169	-90
ATGATAAAAAAGCAATTAAAACCCCCTTTTT	1	129	1	AGCAATAAAA	    0.956588	-59
CTTGAAACAAAATTTTAAAAAAGGGGGTTTT	1	146	0	AATTTTAAAA	     0.83059	-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

GATTCCTTAAAAATAATTTTTTGTTACTTG	1	15	1	AAATAATTTT	    0.932075	-173
AATCGTTTTTAATTATTTTTTGGGTATTCT	1	48	0	AATTATTTTT	    0.852763	-140
TTCATTATTTAATCGTTTTTAATTATTTTT	1	58	0	AATCGTTTTT	    0.708902	-130
TAATAAAAATAAAAACTTTTCATGAATTTT	1	92	1	AAAAACTTTT	    0.514012	-96
AGGGGGTTTTAATTGCTTTTTTATCATCTT	1	126	0	AATTGCTTTT	     0.82612	-62
AAAGCTTGAAACAAAATTTTAAAAAAGGGG	1	151	0	ACAAAATTTT	     0.88213	-37
          ACATACTATTGTAGCTTAAA	1	178	0	ACATACTATT	    0.891767	-10
          **********

Masking position 1
Map Score:   6.64948

Number of sites scoring better than the average of aligned sites = 964
Number in coding regions = 815
Number in noncoding regions = 149
Number of orfs with sites within 600 bp upstream = 104
Fraction of orfs with sites within 600 bp upstream = 0.0167041


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