AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i063_Glycine_Catabolism_ctra_reg_100.orf -o063_ctra_100.ace -a/home/amcguire/alignace/lib/ORF_ctra.txt -z/skink1/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	RCT00269	19	Chlamydia_trachomatis
#2	RCT00270	194	Chlamydia_trachomatis

Motif number 1

TCTAATAGGGAGGGAGGATCTGTACAGATCCT	2	15	1	AGGGGGTCTG	     0.99884	-180
CAAAGACCGAAGGGAGGATCTGTACAGATCCT	2	29	0	AGGGGGTCTG	     0.99884	-166
TGAGATATTCTAGAGGGATCTCTTTCTCTCTT	2	101	1	TAGAGGTCTC	    0.990072	-94
TTTTCTTAAAAGGATTGTTCTCAAAAAAGAAG	2	167	1	AGGATGTCTC	    0.995362	-28
GTTCTCAAAAAAGAAGGGTCTC          	2	183	1	AAGAGGTCTC	    0.994412	-12
          **** ** ****

Masking position 9
Map Score:   10.4427

Number of sites scoring better than the average of aligned sites = 26
Number in coding regions = 26
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

  AATAGTCCTACTCAATCCT         	1	2	0	TACTCAATCC	    0.971172	-18
TCTGTACAGATCCTCCCTCCCTATTAGAAG	2	13	0	TCCTCCCTCC	    0.998997	-182
TCTGTACAGATCCTCCCTTCGGTCTTTGTC	2	33	1	TCCTCCCTTC	    0.998449	-162
AGGGATCTCTTTCTCTCTTCGTAAAGGAAT	2	114	1	TTCTCTCTTC	    0.988576	-81
          **********

Masking position 4
Map Score:   5.74741

Number of sites scoring better than the average of aligned sites = 35
Number in coding regions = 35
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

      CTCTTCTAATAGGGAGGGAGGATCT	2	5	1	TCAATAGGGA	    0.987016	-190
CCATGAGATATTCTAGAGGGATCTCTTTCTC	2	98	1	TTTAGAGGGA	    0.955152	-97
CTTTCTCTCTTCGTAAAGGAATTCTGTAGAA	2	122	1	TCTAAAGGAA	    0.993756	-73
CCTTTTAAGAAAAAAAAGGAAAACTACTTCT	2	149	0	AAAAAAGGAA	    0.883254	-46
TCCTTTTTTTTCTTAAAAGGATTGTTCTCAA	2	160	1	TCTAAAAGGA	    0.986491	-35
AGGATTGTTCTCAAAAAAGAAGGGTCTC   	2	177	1	TCAAAAAGAA	    0.981795	-18
          ** ********

Masking position 5
Map Score:   5.45665

Number of sites scoring better than the average of aligned sites = 183
Number in coding regions = 183
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

ATTATTATCAAGTTTTCATGGACAAAGACC	2	53	0	AGTTTTCATG	    0.982603	-142
CTACTTCTACAGAATTCCTTTACGAAGAGA	2	127	0	AGAATTCCTT	     0.98332	-68
CTGTAGAAGTAGTTTTCCTTTTTTTTCTTA	2	145	1	AGTTTTCCTT	    0.994571	-50
          **********

Masking position 1
Map Score:   1.22282

Number of sites scoring better than the average of aligned sites = 29
Number in coding regions = 29
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:   -1.82309e-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:   -1.82309e-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:   -1.82309e-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