AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i028_Glyoxylate_Metabolism_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	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

      GAGCTTATAATGTTACTATTATTT	1	5	1	TTATAATGTT	    0.975043	-70
TATAATGTTACTATTATTTTGTGTAGTTTA	1	16	1	CTATTATTTT	    0.940462	-59
TTTATTCTTATTGTTATTTCTTGGTGTACC	1	42	1	TTGTTATTTC	    0.966261	-33
TTCTCCTTATTGATTATGTTTT        	3	3	0	TGATTATGTT	    0.983024	-24
CCAAAAAGAGTTTTTATGTTTCATAATCAT	4	31	1	TTTTTATGTT	    0.982817	-79
ATAAAATTACTTGTTATGTTTAACTATGAT	4	61	0	TTGTTATGTT	    0.993631	-49
ACAAGTAATTTTATTCTGTCAATGGCATAT	4	77	1	TTATTCTGTC	    0.974978	-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

TAAGATCCCCTATGTTCAATTTTATAAATT	2	15	1	TATGTTCAAT	    0.989959	-24
AAAGAGTTTTTATGTTTCATAATCATATCA	4	35	1	TATGTTTCAT	    0.989982	-75
AATTACTTGTTATGTTTAACTATGATATGA	4	57	0	TATGTTTAAC	    0.974003	-53
TTAGACTCCTTATATGCCATTGACAGAATA	4	88	0	TATATGCCAT	    0.957568	-22
          **********

Masking position 5
Map Score:   2.25932

Number of sites scoring better than the average of aligned sites = 67
Number in coding regions = 59
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

TTATAATGTTACTATTATTTTGTGTAGTTT	1	15	1	ACTATTATTT	    0.874202	-60
TGTGTAGTTTATTCTTATTGTTATTTCTTG	1	35	1	ATTCTTATTG	    0.986961	-40
    AACTTTCTCCTTATTGATTATGTTTT	3	11	0	CTCCTTATTG	     0.98879	-16
AAACATAAAAACTCTTTTTGGAATACCAAA	4	22	0	ACTCTTTTTG	    0.961293	-88
   TTTTAGACTCCTTATATGCCATTGACA	4	93	0	CTCCTTATAT	    0.922473	-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

AGAATAAACTACACAAAATAATAGTAACAT	1	20	0	ACACAAAATA	    0.960254	-55
CCAAGAAATAACAATAAGAATAAACTACAC	1	36	0	ACAATAAGAA	    0.944011	-39
TGCTACAGGTACACCAAGAAATAACAATAA	1	49	0	ACACCAAGAA	    0.993418	-26
TCTTTTTGGAATACCAAATATCTATTTTT 	4	10	0	ATACCAAATA	    0.977065	-100
ATAGTTAAACATAACAAGTAATTTTATTCT	4	64	1	ATAACAAGTA	    0.977065	-46
          **********

Masking position 6
Map Score:   4.79339

Number of sites scoring better than the average of aligned sites = 226
Number in coding regions = 209
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


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


Motif number 7

          **********

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