AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00510_ctra_reg_100.orf -o00510_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	ubiA	111	4-hydroxybenzoate octaphenyltransferase
#2	mraY	145	Muramoyl-Pentapeptide Transferase

Motif number 1

AAAAGTACGTTGAAGTTCGTTTCAACGTAC	1	17	0	TGAAGTTCGT	     0.97072	-95
TCTTGCTGAAAAAAGTACGTTGAAGTTCGT	1	27	0	AAAAGTACGT	    0.917923	-85
TTTCAGCAAGAAAAGCTCCTTCTGATTACA	1	46	1	AAAAGCTCCT	     0.84551	-66
TTATAGGTGTAAAAGATCTTGTATTGTAAT	1	70	0	AAAAGATCTT	    0.941506	-42
GTAAAAGATCAGAATTTCTTTTTAGAATAG	2	11	1	AGAATTTCTT	    0.977319	-135
AGTCGCTGTAAGATGCTCTTTTTAACTTGC	2	57	1	AGATGCTCTT	    0.965423	-89
TTTAAGATAGAGAATTTCTTATAGGAGCTT	2	103	1	AGAATTTCTT	    0.977319	-43
TTTTATTATGGGAAGCTCCTATAAGAAATT	2	115	0	GGAAGCTCCT	    0.977382	-31
          **********

Masking position 3
Map Score:   11.3912

Number of sites scoring better than the average of aligned sites = 474
Number in coding regions = 470
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

TCTGTACGTTGAAACGAACTTCAACGTACT	1	14	1	GAAACGAACT	    0.973613	-98
ATTATAGGTGTAAAAGATCTTGTATTGTAA	1	71	0	TAAAAGATCT	    0.970016	-41
         GTAAAAGATCAGAATTTCTTT	2	2	1	TAAAAGATCA	    0.952756	-144
TTTCTATTCTAAAAAGAAATTCTGATCTTT	2	14	0	AAAAAGAAAT	    0.974396	-132
TTTCTTTTTAGAATAGAAATAGTTAACTTT	2	25	1	GAATAGAAAT	    0.880417	-121
AAGGCAAGTTAAAAAGAGCATCTTACAGCG	2	60	0	AAAAAGAGCA	     0.96894	-86
GGGAAGCTCCTATAAGAAATTCTCTATCTT	2	106	0	TATAAGAAAT	    0.872126	-40
TTCCCATAATAAAACGAGAAAACAG     	2	131	1	AAAACGAGAA	    0.917601	-15
          **********

Masking position 7
Map Score:   7.70139

Number of sites scoring better than the average of aligned sites = 637
Number in coding regions = 637
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

CACCTATAATCCCATAATATTCGAAGGGTT	1	91	1	CCCATAATAT	    0.991428	-21
ATGGGAAGCTCCTATAAGAAATTCTCTATC	2	108	0	CCTATAAGAA	    0.984337	-38
ATAGGAGCTTCCCATAATAAAACGAGAAAA	2	123	1	CCCATAATAA	    0.995118	-23
          **********

Masking position 6
Map Score:   2.60914

Number of sites scoring better than the average of aligned sites = 11
Number in coding regions = 11
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

AGTTCGTTTCAACGTACAGATAA       	1	4	0	AACGTACAGA	    0.891493	-108
ATGGGATTATAGGTGTAAAAGATCTTGTAT	1	76	0	AGGTGTAAAA	    0.906968	-36
AGAAATAGTTAACTTTCAAGTCGCTGTAAG	2	39	1	AACTTTCAAG	    0.948693	-107
TTCAAAAGGCAAGTTAAAAAGAGCATCTTA	2	65	0	AAGTTAAAAA	    0.945165	-81
CTTAAACTTAAGCTTTCAAAAGGCAAGTTA	2	79	0	AGCTTTCAAA	    0.976703	-67
TTGAAAGCTTAAGTTTAAGATAGAGAATTT	2	90	1	AAGTTTAAGA	     0.96385	-56
          **********

Masking position 8
Map Score:   1.21535

Number of sites scoring better than the average of aligned sites = 112
Number in coding regions = 112
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:   5.92755e-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:   5.92755e-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 7

          **********

No masking
Map Score:   5.92755e-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