AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i205_dna_mismatch_repair_ctra_reg_300.orf -o205_ctra_300.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

ATCGTACAATATTTTTTTTACACGCGATGCCCGCTCTT	1	41	1	ATTTTTAGGT	    0.964316	-260
ATGGCGGATCCTTTATCGCCGAAGAGCGGGCATCGCGT	1	62	0	CTTTATAGGG	    0.967263	-239
CGCACTATAATTTTCTTGGGAATGTGTGCTTCTTTCTC	1	105	1	TTTTCTAGGG	    0.989845	-196
ATGTGTGCTTCTTTCTCCCTGATGGATTCCTTTTTCTC	1	126	1	CTTTCTAGAT	    0.978916	-175
TGATGGATTCCTTTTTCTCTTAAGAATTTTGCTTCCCA	1	145	1	CTTTTTAGAT	    0.969846	-156
ACGGTGTTGAATTTTTGGGGAATACAAGACTTTGGGAA	1	177	0	ATTTTTAAAG	    0.890426	-124
GTTTCGAAGGTTTTCTGATACATAAGAGCCTGTTCCCC	1	226	1	TTTTCTAAGG	    0.950363	-75
ATCGAAAAAATTTTTTATTCGTAGTAGGGGAACAGGCT	1	252	0	TTTTTTTGAG	    0.924027	-49
GAATAAAAAATTTTTTCGATCACGCAATACTAGATAAA	1	270	1	TTTTTTAGAT	    0.975192	-31
          ******     * * * *

Masking position 6
Map Score:   6.28938

Number of sites scoring better than the average of aligned sites = 332
Number in coding regions = 332
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

ATTTTTTTTACACGCGATGCCCGCTCTTCGGC	1	51	1	CCGCGATCCC	    0.996097	-250
AGAAAATTATAGTGCGTTACCATGGCGGATCC	1	89	0	ATGCGTTCCA	    0.973086	-212
GAGAAAGAAGCACACATTCCCAAGAAAATTAT	1	111	0	CCACATTCCA	    0.973256	-190
TTCCCAAAGTCTTGTATTCCCCAAAAATTCAA	1	177	1	CTGTATTCCC	    0.954832	-124
CCGTTGTACACTCGCGTTTCGAAGGTTTTCTG	1	211	1	CCGCGTTCGA	    0.991103	-90
GATACATAAGAGCCTGTTCCCCTACTACGAAT	1	242	1	ACCTGTTCCC	    0.909181	-59
TTTTTTCGATCACGCAATACTAGATAAAGCT 	1	280	1	CCGCAATCTA	    0.940587	-21
          * ****** ***

Masking position 8
Map Score:   3.66561

Number of sites scoring better than the average of aligned sites = 147
Number in coding regions = 147
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

GCGATAAAGGATCCGCCATGGTAACGCACTA	1	81	1	ATCGCCATGG	    0.966267	-220
AGAAAAAGGAATCCATCAGGGAGAAAGAAGC	1	132	0	ATCATCAGGG	    0.989323	-169
GGGAAGCAAAATTCTTAAGAGAAAAAGGAAT	1	151	0	ATCTTAAGAG	    0.978301	-150
AGGTTTTCTGATACATAAGAGCCTGTTCCCC	1	233	1	ATCATAAGAG	    0.987577	-68
AAAATTTTTTATTCGTAGTAGGGGAACAGGC	1	253	0	ATCGTAGTAG	    0.960737	-48
          ** ********

Masking position 2
Map Score:   0.8547

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 50
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