AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00900_hpyl_reg_300.orf -o00900_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	HP0925	155	recombinational DNA repair protein (recR)

Motif number 1

CACTTCCATTTAAACGCTTCATTAAGCGCT	1	44	1	TAAACGCTTC	    0.901219	-112
AACGCTTCATTAAGCGCTTTTTCATATTAT	1	56	1	TAAGCGCTTT	    0.517447	-100
TGTTTTTTAAAAGGGGGTTTAATTAAATAA	1	82	0	AAGGGGGTTT	    0.966059	-74
AAAGCCACTAAAAGGGCTTTTATTGTTTTT	1	105	0	AAAGGGCTTT	    0.533981	-51
AAAGCCCTTTTAGTGGCTTTCAAGTCAAGT	1	115	1	TAGTGGCTTT	    0.989077	-41
          **********

Masking position 8
Map Score:   7.17845

Number of sites scoring better than the average of aligned sites = 665
Number in coding regions = 606
Number in noncoding regions = 59
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 2

ATGTGCTATCTCAATTTTAAGGAATAAC  	1	9	0	TCAATTTTAA	    0.981791	-147
TTATAACACTTCCATTTAAACGCTTCATTA	1	38	1	TCCATTTAAA	    0.988651	-118
TTAATTAAACCCCCTTTTAAAAAACAATAA	1	86	1	CCCCTTTTAA	     0.98751	-70
AACAATAAAAGCCCTTTTAGTGGCTTTCAA	1	108	1	GCCCTTTTAG	    0.988422	-48
GGCTTTCAAGTCAAGTTAAGTTTGATATAC	1	129	1	TCAAGTTAAG	    0.949489	-27
          **********

Masking position 6
Map Score:   4.13955

Number of sites scoring better than the average of aligned sites = 563
Number in coding regions = 483
Number in noncoding regions = 80
Number of orfs with sites within 600 bp upstream = 70
Fraction of orfs with sites within 600 bp upstream = 0.0112432


Motif number 3

        GTTATTCCTTAAAATTGAGATA	1	3	1	TATTCCTTAA	    0.984156	-153
CGCTTTTTCATATTATTTAATTAAACCCCC	1	70	1	TATTATTTAA	    0.980294	-86
GGGCTTTTATTGTTTTTTAAAAGGGGGTTT	1	92	0	TGTTTTTTAA	    0.976691	-64
          **********

Masking position 9
Map Score:   0.651067

Number of sites scoring better than the average of aligned sites = 217
Number in coding regions = 156
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 4

          **********

No masking
Map Score:   -3.30951e-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:   -3.30951e-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:   -3.30951e-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