AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i198_enolase_ctra_reg_100.orf -o198_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	RCT00560	161	Chlamydia_trachomatis

Motif number 1

AAAGGATCATAGCGAGGGATTCAATTCTGTG	1	20	0	AGCAGGGATT	    0.988286	-142
TTCCCTTAGTAGAAAAGGATCATAGCGAGGG	1	33	0	AGAAAGGATC	    0.998975	-129
CGCAATACAAAGAGAAGGCTCGGAGGGAGAT	1	63	0	AGAAAGGCTC	    0.998253	-99
TAACCGTTCTAGACAAGGATCTTGTT     	1	146	1	AGAAAGGATC	    0.998974	-16
          *** *******

Masking position 5
Map Score:   8.03021

Number of sites scoring better than the average of aligned sites = 24
Number in coding regions = 24
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

        AAAGGATACCACAGAATTGAAT	1	3	1	AGGATACCAC	    0.801733	-159
TTAGTAGAAAAGGATCATAGCGAGGGATTC	1	29	0	AGGATCATAG	    0.945391	-133
TACAAAGAGAAGGCTCGGAGGGAGATTCCC	1	59	0	AGGCTCGGAG	     0.98633	-103
TATGACCGCAATACAAAGAGAAGGCTCGGA	1	70	0	ATACAAAGAG	    0.919807	-92
GCGGTCATACATGCTCATCGGAGGAAATTA	1	91	1	ATGCTCATCG	    0.725953	-71
TGCTCATCGGAGGAAATTAGATAAAACGAG	1	102	1	AGGAAATTAG	    0.910933	-60
AGGAAATTAGATAAAACGAGCGAACTGCTT	1	112	1	ATAAAACGAG	    0.905819	-50
AGAACGGTTAATGAAAGCAGTTCGCTCGTT	1	126	0	ATGAAAGCAG	    0.956135	-36
TAACCGTTCTAGACAAGGATCTTGTT    	1	146	1	AGACAAGGAT	    0.797597	-16
          **********

Masking position 1
Map Score:   2.37303

Number of sites scoring better than the average of aligned sites = 1408
Number in coding regions = 1405
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

          **********

No masking
Map Score:   -2.10731e-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 4

          **********

No masking
Map Score:   -2.10731e-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:   -2.10731e-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