AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i109_Sulfate_trans-Cys_Synthase_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	subI	124	subI

Motif number 1

GCGCACGGGTGGGGAGTCAGCGACAACA  	1	9	0	GGGGAGTCAG	    0.960928	-116
GCGGTCTGATGTGGAGTTCGTGAGTCCTGC	1	37	1	GTGGAGTTCG	    0.986526	-88
AAGGCGATCGCTGAACATTGCAGGACTCAC	1	56	0	CTGAACATTG	    0.952491	-69
CCCGTAGCGGCGGAAAGGCGATCGCTGAAC	1	70	0	CGGAAAGGCG	    0.976383	-55
CCGCCGCTACGGGAACGTTGTCCAAAGTCC	1	87	1	GGGAACGTTG	    0.995522	-38
CCTTCCGGTGCGGGACTTTGGACAACGTTC	1	99	0	CGGGACTTTG	    0.995537	-26
AGTCCCGCACCGGAAGGTCGCCA       	1	112	1	CGGAAGGTCG	    0.997316	-13
          **********

Masking position 5
Map Score:   10.9968

Number of sites scoring better than the average of aligned sites = 3136
Number in coding regions = 2891
Number in noncoding regions = 245
Number of orfs with sites within 600 bp upstream = 249
Fraction of orfs with sites within 600 bp upstream = 0.0399936


Motif number 2

TGACTCCCCACCCGTGCGCGGTCTGATGTG	1	20	1	CCCGTGCGCG	    0.541532	-105
CGCCTTTCCGCCGCTACGGGAACGTTGTCC	1	80	1	CCGCTACGGG	    0.562291	-45
TGGCGACCTTCCGGTGCGGGACTTTGGACA	1	105	0	CCGGTGCGGG	    0.541692	-20
          **********

Masking position 5
Map Score:   6.57193

Number of sites scoring better than the average of aligned sites = 347
Number in coding regions = 317
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 3

GGTGGGGAGTCAGCGACAACA         	1	2	0	CAGCGACAAC	    0.982579	-123
AACTCCACATCAGACCGCGCACGGGTGGGG	1	25	0	CAGACCGCGC	    0.990029	-100
CTGAACATTGCAGGACTCACGAACTCCACA	1	46	0	CAGGACTCAC	    0.987768	-79
CTGCAATGTTCAGCGATCGCCTTTCCGCCG	1	63	1	CAGCGATCGC	    0.997365	-62
          **********

Masking position 2
Map Score:   1.07013

Number of sites scoring better than the average of aligned sites = 3159
Number in coding regions = 2924
Number in noncoding regions = 235
Number of orfs with sites within 600 bp upstream = 203
Fraction of orfs with sites within 600 bp upstream = 0.0326052


Motif number 4

          **********

No masking
Map Score:   -6.15168e-14

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:   -6.15168e-14

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:   -6.15168e-14

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