AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i028_Glyoxylate_Metabolism_hinf_reg_300.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	HI0050	74	conserved hypothetical transmembrane protein
#2	HI0051	38	conserved hypothetical transmembrane protein
#3	HI0052	26	conserved hypothetical protein
#4	HI0053	109	zinc-type alcohol dehydrogenase

Motif number 1

AAATAATAGTAACATTATAAGCTC      	1	5	0	AACATTATAA	    0.973521	-70
TAAACTACACAAAATAATAGTAACATTATA	1	16	0	AAAATAATAG	    0.936969	-59
GGTACACCAAGAAATAACAATAAGAATAAA	1	42	0	GAAATAACAA	    0.964223	-33
        AAAACATAATCAATAAGGAGAA	3	3	1	AACATAATCA	    0.981979	-24
ATGATTATGAAACATAAAAACTCTTTTTGG	4	31	0	AACATAAAAA	    0.981761	-79
ATCATAGTTAAACATAACAAGTAATTTTAT	4	61	1	AACATAACAA	    0.993235	-49
ATATGCCATTGACAGAATAAAATTACTTGT	4	77	0	GACAGAATAA	    0.973453	-33
          **********

Masking position 4
Map Score:   10.2847

Number of sites scoring better than the average of aligned sites = 160
Number in coding regions = 121
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

          GAGCTTATAATGTTACTATT	1	1	1	GAGCTTATAA	    0.971578	-74
TTATTTTGTGTAGTTTATTCTTATTGTTAT	1	29	1	TAGTTTATTC	    0.946513	-46
GAACATAGGGGATCTTATTAA         	2	2	0	GATCTTATTA	     0.97842	-37
CCCTATGTTCAATTTTATAAATTGCTC   	2	22	1	AATTTTATAA	     0.94991	-17
CATAACAAGTAATTTTATTCTGTCAATGGC	4	73	1	AATTTTATTC	    0.966964	-37
          **********

Masking position 5
Map Score:   2.48136

Number of sites scoring better than the average of aligned sites = 241
Number in coding regions = 197
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 3

AAACTACACAAAATAATAGTAACATTATAA	1	15	0	AAATAATAGT	    0.869845	-60
CAAGAAATAACAATAAGAATAAACTACACA	1	35	0	CAATAAGAAT	    0.986449	-40
AAAACATAATCAATAAGGAGAAAGTT    	3	11	1	CAATAAGGAG	    0.988349	-16
TTTGGTATTCCAAAAAGAGTTTTTATGTTT	4	22	1	CAAAAAGAGT	    0.959814	-88
TGTCAATGGCATATAAGGAGTCTAAAA   	4	93	1	ATATAAGGAG	    0.919634	-17
          **********

Masking position 5
Map Score:   1.87097

Number of sites scoring better than the average of aligned sites = 285
Number in coding regions = 208
Number in noncoding regions = 77
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


Motif number 4

          **********

No masking
Map Score:   2.72438e-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:   2.72438e-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:   2.72438e-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