AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i205_dna_mismatch_repair_ctra_reg_100.orf -o205_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	RCT00758	300	Chlamydia_trachomatis

Motif number 1

ATCGTACAATATTTTTTTTACACGCGATGCCCGCTC	1	41	1	ATTTTTTCGG	    0.925242	-260
CCATGGCGGATCCTTTATCGCCGAAGAGCGGGCATC	1	66	0	TCTTTTCCAG	    0.994034	-235
AACGCACTATAATTTTCTTGGGAATGTGTGCTTCTT	1	103	1	ATTTTTTGAG	    0.910597	-198
GAATGTGTGCTTCTTTCTCCCTGATGGATTCCTTTT	1	124	1	TCTTTTCCAG	    0.994034	-177
CCTGATGGATTCCTTTTTCTCTTAAGAATTTTGCTT	1	143	1	TCTTTTCCAG	    0.994034	-158
TCTCTTAAGAATTTTGCTTCCCAAAGTCTTGTATTC	1	160	1	ATTTGTTCAG	    0.962796	-141
GATACATAAGAGCCTGTTCCCCTACTACGAATAAAA	1	242	1	ACCTGTCCAT	    0.877184	-59
ACGAATAAAAAATTTTTTCGATCACGCAATACTAGA	1	268	1	ATTTTTCAAG	    0.973666	-33
          AGCTTTATCTAGTATTGCGTGATCGA	1	285	0	ACTTTTCAAT	    0.934658	-16
          * **** ** *  * *

Masking position 8
Map Score:   6.5918

Number of sites scoring better than the average of aligned sites = 306
Number in coding regions = 306
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

         TCTTATGATCCACTATTCGTG	1	2	1	CTTATGATCC	    0.892173	-299
ATTTTTTTTACACGCGATGCCCGCTCTTCG	1	51	1	CACGCGATGC	    0.987655	-250
GAGAAAGAAGCACACATTCCCAAGAAAATT	1	113	0	CACACATTCC	    0.978761	-188
TTCCCAAAGTCTTGTATTCCCCAAAAATTC	1	177	1	CTTGTATTCC	    0.939659	-124
CCGTTGTACACTCGCGTTTCGAAGGTTTTC	1	211	1	CTCGCGTTTC	    0.981808	-90
TTTTTTCGATCACGCAATACTAGATAAAGC	1	280	1	CACGCAATAC	    0.971694	-21
          **********

Masking position 8
Map Score:   2.90849

Number of sites scoring better than the average of aligned sites = 180
Number in coding regions = 180
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

ATATAAGCATCGTACAATATTTTTTTTACACGCG	1	33	1	CGAAATTTTT	    0.984232	-268
GCCATGGTAACGCACTATAATTTTCTTGGGAATG	1	95	1	CGTAAATTTT	    0.993068	-206
ATTCCTTTTTCTCTTAAGAATTTTGCTTCCCAAA	1	151	1	CTAAAATTTT	    0.975219	-150
GAGTGTACAACGGTGTTGAATTTTTGGGGAATAC	1	190	0	CGTTAATTTT	    0.977559	-111
TCCCCTACTACGAATAAAAAATTTTTTCGATCAC	1	259	1	CGAAAAATTT	    0.984218	-42
          **   ** ******

Masking position 9
Map Score:   1.85086

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 44
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:   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 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