AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i038_Galactose_Metabolism__mtub_reg_100.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 =  	0.66
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	galT'	128	galT'

Motif number 1

GCGCCGCCGGGAGACGATGCACA       	1	4	0	GAGACGATGC	    0.980284	-125
GCGGCTCGCCGCGCCGCCGGGAGACGATGC	1	14	0	GCGCCGCCGG	    0.844763	-115
GCGGCGCGGCGAGCCGCCCCAAAACCAACG	1	27	1	GAGCCGCCCC	    0.888028	-102
CAACGATTGGGCCACGATGCGTAGGCATAG	1	52	1	GCCACGATGC	    0.980129	-77
GGTGAGGGCCGCGACGCCACCTCAGCTATG	1	77	0	GCGACGCCAC	    0.782997	-52
GCCCTCACCGGCGACACCACAGAGGATCTC	1	98	1	GCGACACCAC	    0.983496	-31
AGAGGATCTCGGGCCGATCCG         	1	118	1	GGGCCGATCC	    0.947624	-11
          **********

Masking position 5
Map Score:   18.6523

Number of sites scoring better than the average of aligned sites = 9801
Number in coding regions = 8999
Number in noncoding regions = 802
Number of orfs with sites within 600 bp upstream = 519
Fraction of orfs with sites within 600 bp upstream = 0.0833601


Motif number 2

CGCGCCGCCGGGAGACGATGCACA       	1	4	0	GGAGCGATGC	     0.95092	-125
ATCGTCTCCCGGCGGCGCGGCGAGCCGCCCC	1	16	1	GGCGCGCGGC	    0.687834	-113
CCCAATCGTTGGTTTTGGGGCGGCTCGCCGC	1	32	0	GGTTTGGGGC	      0.9928	-97
CCCCAAAACCAACGATTGGGCCACGATGCGT	1	43	1	AACGTTGGGC	    0.907164	-86
ATTGGGCCACGATGCGTAGGCATAGCTGAGG	1	57	1	GATGGTAGGC	    0.947115	-72
CGTAGGCATAGCTGAGGTGGCGTCGCGGCCC	1	71	1	GCTGGGTGGC	    0.953724	-58
CTGTGGTGTCGCCGGTGAGGGCCGCGACGCC	1	89	0	GCCGTGAGGG	     0.96376	-40
ACACCACAGAGGATCTCGGGCCGATCCG   	1	111	1	GGATTCGGGC	    0.955011	-18
          **** ******

Masking position 10
Map Score:   6.42523

Number of sites scoring better than the average of aligned sites = 24477
Number in coding regions = 22660
Number in noncoding regions = 1817
Number of orfs with sites within 600 bp upstream = 1006
Fraction of orfs with sites within 600 bp upstream = 0.16158


Motif number 3

          **********

No masking
Map Score:   -1.89414e-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 4

          **********

No masking
Map Score:   -1.89414e-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:   -1.89414e-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