AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00900_hpyl_reg_100.orf -o00900_hpyl_100.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

GTTTAAATGGAAGTGTTATAATGTGCTATCTCA	1	26	0	AAGGATAATG	     0.97382	-130
GCGCTTAATGAAGCGTTTAAATGGAAGTGTTAT	1	40	0	AAGGTAAATG	    0.991438	-116
ATAATATGAAAAAGCGCTTAATGAAGCGTTTAA	1	53	0	AAACTTAATG	    0.981828	-103
TGTTTTTTAAAAGGGGGTTTAATTAAATAATAT	1	79	0	AAGGTTTAAT	    0.917212	-77
CCCCTTTTAAAAAACAATAAAAGCCCTTTTAGT	1	96	1	AAACTAAAAG	    0.981827	-60
CTTGACTTGAAAGCCACTAAAAGGGCTTTTATT	1	111	0	AAGCTAAAAG	    0.994976	-45
AGTGGCTTTCAAGTCAAGTTAAGTTTGATATAC	1	126	1	AAGCGTTAAG	    0.976202	-30
          *** *  ******

Masking position 11
Map Score:   6.70475

Number of sites scoring better than the average of aligned sites = 872
Number in coding regions = 797
Number in noncoding regions = 75
Number of orfs with sites within 600 bp upstream = 57
Fraction of orfs with sites within 600 bp upstream = 0.00915516


Motif number 2

CACTTCCATTTAAACGCTTCATTAAGCGCT	1	44	1	TAAACGCTTC	    0.903472	-112
AACGCTTCATTAAGCGCTTTTTCATATTAT	1	56	1	TAAGCGCTTT	    0.519103	-100
TGTTTTTTAAAAGGGGGTTTAATTAAATAA	1	82	0	AAGGGGGTTT	    0.966766	-74
AAAGCCACTAAAAGGGCTTTTATTGTTTTT	1	105	0	AAAGGGCTTT	    0.537085	-51
AAAGCCCTTTTAGTGGCTTTCAAGTCAAGT	1	115	1	TAGTGGCTTT	    0.988232	-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 3

        GTTATTCCTTAAAATTGAGATA	1	3	1	TATTCCTTAA	    0.983937	-153
CGCTTTTTCATATTATTTAATTAAACCCCC	1	70	1	TATTATTTAA	    0.980023	-86
GGGCTTTTATTGTTTTTTAAAAGGGGGTTT	1	92	0	TGTTTTTTAA	    0.976371	-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