AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i113_Amino_Acid_Transport_4_ctra_reg_100.orf -o113_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	RCT00704	104	Chlamydia_trachomatis

Motif number 1

TCTAAAGGCCCCCTTTCCCCGGATAGGAGA	1	18	1	CCCTTTCCCC	    0.998664	-87
TACAAAAGCCCCCTTTCTCCTATCCGGGGA	1	33	0	CCCTTTCTCC	    0.994714	-72
GGGGCTTTTGTATTTTCCGCTTATTTGCCT	1	51	1	TATTTTCCGC	     0.98669	-54
ATTTTCCGCTTATTTGCCTCCGAAGCGGGT	1	62	1	TATTTGCCTC	    0.957505	-43
ACTACTCTTATGCTTTCACCCGCTTCGGAG	1	79	0	TGCTTTCACC	    0.989553	-26
          **********

Masking position 5
Map Score:   6.41243

Number of sites scoring better than the average of aligned sites = 175
Number in coding regions = 175
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

GGCCATTCTAAAGGCCCCCTTTCCCCGGAT	1	12	1	AAGGCCCCCT	     0.85482	-93
GGAAAATACAAAAGCCCCCTTTCTCCTATC	1	39	0	AAAGCCCCCT	    0.982291	-66
          **********

Masking position 2
Map Score:   3.65893

Number of sites scoring better than the average of aligned sites = 1
Number in coding regions = 1
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

AGCCCCCTTTCTCCTATCCGGGGAAAGGGG	1	27	0	CTCCTATCCG	    0.986962	-78
GCTTCGGAGGCAAATAAGCGGAAAATACAA	1	58	0	CAAATAAGCG	    0.904695	-47
GCTTATTTGCCTCCGAAGCGGGTGAAAGCA	1	69	1	CTCCGAAGCG	    0.986203	-36
TGTCCTACTACTCTTATGCTTTCACCCGCT	1	85	0	CTCTTATGCT	    0.936755	-20
          **********

Masking position 6
Map Score:   3.31472

Number of sites scoring better than the average of aligned sites = 84
Number in coding regions = 84
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:   -1.17788e-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 5

          **********

No masking
Map Score:   -1.17788e-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:   -1.17788e-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