AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i223_Pseudouridylate_Synthase_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -x5 
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 = 	0

Input sequences:
#1	HI1198	120	conserved hypothetical protein
#2	HI1199	47	conserved hypothetical protein

Motif number 1

          CCGCACTTTAGTTTTCTAAA	1	1	1	CCGCACTTTA	    0.986648	-120
GAAAGCCAATCTACGCTTTAGAAAACTAAA	1	17	0	CTACGCTTTA	    0.970877	-104
GATTGGCTTTCTACGCCTTTATTTTTATAT	1	36	1	CTACGCCTTT	    0.965081	-85
ATTTTTATATGCTCGCCATTATAAAGTGAG	1	56	1	GCTCGCCATT	    0.969658	-65
GCAATTTTGTGCTCACTTTATAATGGCGAG	1	67	0	GCTCACTTTA	       0.989	-54
GCTATAATCAGCGCACATTTTTTAAGGAAG	1	95	1	GCGCACATTT	    0.967214	-26
ATAATGGAAAGGTCGCTTTCACAAGCGTCT	2	16	0	GGTCGCTTTC	    0.968632	-32
          **********

Masking position 9
Map Score:   6.51324

Number of sites scoring better than the average of aligned sites = 1439
Number in coding regions = 974
Number in noncoding regions = 465
Number of orfs with sites within 600 bp upstream = 291
Fraction of orfs with sites within 600 bp upstream = 0.0467395


Motif number 2

CGTAGAAAGCCAATCTACGCTTTAGAAAAC	1	21	0	CAATCTACGC	     0.98576	-100
CGTAGATTGGCTTTCTACGCCTTTATTTTT	1	32	1	CTTTCTACGC	    0.985763	-89
GCCTTTATTTTTATATGCTCGCCATTATAA	1	50	1	TTATATGCTC	    0.973508	-71
ATTATAGCAATTTTGTGCTCACTTTATAAT	1	73	0	TTTTGTGCTC	    0.943033	-48
AAAATTGCTATAATCAGCGCACATTTTTTA	1	89	1	TAATCAGCGC	     0.97556	-32
         CTTATAGACGCTTGTGAAAGC	2	2	1	TTATAGACGC	    0.968899	-46
          **********

Masking position 4
Map Score:   5.65191

Number of sites scoring better than the average of aligned sites = 307
Number in coding regions = 268
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 3

TTTTTATATGCTCGCCATTATAAAGTGAGC	1	57	1	CTCGCCATTA	    0.972305	-64
     GTGTTTCTTCCTTAAAAAATGTGCG	1	106	0	TCTTCCTTAA	    0.956345	-15
TGAAAGCGACCTTTCCATTATTCAAGGAAA	2	25	1	CTTTCCATTA	    0.990291	-23
        TGTTTTCCTTGAATAATGGAAA	2	36	0	TTTTCCTTGA	    0.982255	-12
          **********

Masking position 8
Map Score:   0.686336

Number of sites scoring better than the average of aligned sites = 203
Number in coding regions = 164
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 4

          **********

No masking
Map Score:   1.72962e-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:   1.72962e-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 6

          **********

No masking
Map Score:   1.72962e-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