AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00480_ctra_reg_100.orf -o00480_ctra_100.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -x5 -e 
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 =  	0.41
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	zwf	300	Glucose-6-P Dehyrogenase

Motif number 1

AAGAGAGAGCCCACAATACCAAAAAAACGA	1	46	0	CCACAATACC	    0.997406	-255
TTAATTTCTTCCAAGATACAACCTAGTATA	1	91	0	CCAAGATACA	    0.989774	-210
GACTTTGGCCCCACATTACCAGCCTGTCCT	1	122	1	CCACATTACC	    0.993473	-179
CCAAAAATAACCACGATACAGGGAGGACAG	1	145	0	CCACGATACA	    0.997406	-156
          **********

Masking position 7
Map Score:   7.14259

Number of sites scoring better than the average of aligned sites = 7
Number in coding regions = 7
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 2

     TGTTTTATGAGAGAGAAATCTTTTT	1	6	1	TATGAGAGAG	    0.965728	-295
GTTAATTTTTTAAGAGAGAGCCCACAATAC	1	57	0	TAAGAGAGAG	    0.941106	-244
AGATACAACCTAGTATAGAGTGTTAATTTT	1	78	0	TAGTATAGAG	    0.938551	-223
TCTTGGAAGAAATTAAAGACTTTGGCCCCA	1	105	1	AATTAAAGAC	     0.80645	-196
AACCACGATACAGGGAGGACAGGCTGGTAA	1	137	0	CAGGGAGGAC	    0.939525	-164
TTGTATAAAGCAGGAAAGAGCTTCCTAGAG	1	193	0	CAGGAAAGAG	    0.990412	-108
CAATTTAACAAAGGAAGGACGTCTATCCGA	1	220	1	AAGGAAGGAC	    0.974236	-81
AACAAAGTTTTCGGATAGACGTCCTTCCTT	1	230	0	TCGGATAGAC	    0.946629	-71
          **********

Masking position 9
Map Score:   4.8915

Number of sites scoring better than the average of aligned sites = 482
Number in coding regions = 482
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 3

AAGATTTCTCTCTCATAAAACA          	1	1	0	TCTCTAAACA	    0.968354	-300
GAGAGAGAAATCTTTTTAGGCACATATTCGTT	1	19	1	TCTTTTAGCA	    0.950435	-282
TTGTGGGCTCTCTCTTAAAAAATTAACACTCT	1	60	1	TCTCTAAAAA	    0.908706	-241
CTAGGTTGTATCTTGGAAGAAATTAAAGACTT	1	95	1	TCTTGAAGAA	    0.918362	-206
AGAGGTCAAGTCTCCTGTAGCACCAAAAATAA	1	165	0	TCTCTGTACA	    0.960807	-136
GCGACCTAAGTCTCATGAGCAATTTCGCGAAG	1	277	1	TCTCTGAGAA	    0.989855	-24
          **** **** **

Masking position 3
Map Score:   2.97749

Number of sites scoring better than the average of aligned sites = 149
Number in coding regions = 148
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

TAGGCACATATTCGTTTTTTTGGTATTGTG	1	35	1	TTCGTTTTTT	    0.968556	-266
GTATAGAGTGTTAATTTTTTAAGAGAGAGC	1	66	0	TTAATTTTTT	    0.948577	-235
GCCAAAGTCTTTAATTTCTTCCAAGATACA	1	101	0	TTAATTTCTT	      0.9154	-200
CTGTATCGTGGTTATTTTTGGTGCTACAGG	1	154	1	GTTATTTTTG	    0.848296	-147
ATAGACGTCCTTCCTTTGTTAAATTGTATA	1	216	0	TTCCTTTGTT	    0.947556	-85
ATCCGAAAACTTTGTTTGTGTTGGGTTTGC	1	244	1	TTTGTTTGTG	    0.946869	-57
          **********

Masking position 5
Map Score:   1.02666

Number of sites scoring better than the average of aligned sites = 314
Number in coding regions = 314
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:   7.91135e-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:   7.91135e-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:   7.91135e-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