AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i038_Galactose_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	HI0351	172	UDP-glucose 4-epimerase (galE)
#2	HI0819	37	galactokinase (galK)
#3	HI0820	207	galactose-1-phosphate uridylyltransferase (galT)

Motif number 1

AAGAATGGTGATTTTCAATAAAATAAAAAACC	1	95	0	ATTTTATAAA	    0.953174	-78
CTTGTTAATTATTGAGACTAAAAAATTATATC	1	142	0	ATTGACTAAA	    0.984847	-31
AATCTTATATTTTGATCATAAATAATTTACGA	3	36	1	TTTGAATAAA	    0.974515	-172
ATCATAAATAATTTACGATAAATTGAAAGCGG	3	50	1	ATTTAATAAA	    0.977579	-158
AACCGTGATCTTTGTCACAAAATAAGAAAATA	3	123	0	TTTGTCAAAA	    0.808451	-85
ATACTAAATTATTGTAAATAAACCGTGATCTT	3	143	0	ATTGTATAAA	    0.984495	-65
ATTTACAATAATTTAGTATAAATTAATGTAAT	3	156	1	ATTTAATAAA	    0.977579	-52
AATCGTTTACATTGATAAAAAACAGGAGTCAA	3	185	1	ATTGAAAAAA	    0.975867	-23
          *****  *****

Masking position 10
Map Score:   11.5004

Number of sites scoring better than the average of aligned sites = 291
Number in coding regions = 230
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 60
Fraction of orfs with sites within 600 bp upstream = 0.00963701


Motif number 2

TGATTTTCAATAAAATAAAAAACCTGTTGCTAA	1	86	0	TAAATAAAAC	    0.830456	-87
TCTCAATAATTAACAAGGAAATCATT       	1	157	1	TAAAAGAAAC	    0.990118	-16
TTATAGATTATAACAAGGAAAAAGTT       	3	4	0	TAAAAGAAAA	    0.917957	-204
AGTTCATACTTATGAAAGTAACCGCTTTCAATT	3	70	0	TATAAGTAAC	    0.990114	-138
CTTTCATAAGTATGAACTAAATCATAAAAAATT	3	85	1	TATAATAAAC	    0.939299	-123
TGTCACAAAATAAGAAAATAAGCAAAATTTTTT	3	110	0	TAAAAATAAC	    0.964704	-98
ATTTAGTATAAATTAATGTAATCGTTTACATTG	3	166	1	AATAAGTAAC	    0.946548	-42
TCCTGTTTTTTATCAATGTAAACGATTACATTA	3	179	0	TATAAGTAAC	    0.990114	-29
          *** ** **** *

Masking position 5
Map Score:   9.16777

Number of sites scoring better than the average of aligned sites = 123
Number in coding regions = 100
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

ACCTGTTGCTAAAAAGTATTGTTGTAGCGA	1	68	0	AAAAAGTATT	     0.73284	-105
ATTGAGACTAAAAAATTATATCACTATTTT	1	134	0	AAAAATTATA	    0.832282	-39
TGATTTCCTTGTTAATTATTGAGACTAAAA	1	151	0	GTTAATTATT	    0.809766	-22
TAATTAACAAGGAAATCATT          	1	163	1	GGAAATCATT	    0.875783	-10
GTTATAATCTATAAATCTTATATTTTGATC	3	23	1	ATAAATCTTA	    0.704074	-185
TCAATTTATCGTAAATTATTTATGATCAAA	3	46	0	GTAAATTATT	    0.966724	-162
TAAGTATGAACTAAATCATAAAAAATTTTG	3	91	1	CTAAATCATA	    0.912098	-117
AGAAAATAAGCAAAATTTTTTATGATTTAG	3	101	0	CAAAATTTTT	    0.724802	-107
TTAATTTATACTAAATTATTGTAAATAAAC	3	152	0	CTAAATTATT	    0.966724	-56
ATAATTTAGTATAAATTAATGTAATCGTTT	3	163	1	ATAAATTAAT	    0.702579	-45
          **********

Masking position 5
Map Score:   6.3255

Number of sites scoring better than the average of aligned sites = 1038
Number in coding regions = 846
Number in noncoding regions = 192
Number of orfs with sites within 600 bp upstream = 162
Fraction of orfs with sites within 600 bp upstream = 0.0260199


Motif number 4

    ATAACCTTATATCACACAACTAATGG	1	7	1	TTATATCACA	    0.975852	-166
ATATGAGAGGTTATCTCACTCGCTACAACA	1	49	1	TTATCTCACT	    0.979929	-124
ATCACCATTCTTACCACACAAAATAGTGAT	1	115	1	TTACCACACA	    0.920238	-58
GACTAAAAAATTATATCACTATTTTGTGTG	1	129	0	TTATATCACT	    0.975863	-44
GATTTATAGATTATAACAAGGAAAAAGTT 	3	10	0	TTATAACAAG	     0.89815	-198
ACCGTGATCTTTGTCACAAAATAAGAAAAT	3	124	0	TTGTCACAAA	    0.869077	-84
GACTCCTGTTTTTTATCAATGTAAACGATT	3	185	0	TTTTATCAAT	    0.828235	-23
          **********

Masking position 8
Map Score:   4.6689

Number of sites scoring better than the average of aligned sites = 149
Number in coding regions = 110
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 5

          **********

No masking
Map Score:   -7.8627e-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:   -7.8627e-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:   -7.8627e-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