AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i179_folate_biosynthesis_ctra_reg_100.orf -o179_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	RCT00289	300	Chlamydia_trachomatis

Motif number 1

AACGATTACCAAGATCGGCAAGGTATCATTTCTTAT	1	50	1	AAGTGAGTAT	    0.969882	-251
TTTGTCAAAGAAACTTTATAAGAAATGATACCTTGC	1	67	0	AAATTAGAAT	    0.977858	-234
TCTTTGACAAAAGATGGTAAAGAAATTTTAAGTCGG	1	92	1	AAGTGAGAAT	    0.993594	-209
TCGGAGCCATCACTTATGGATGGAAGTAATTTCATT	1	124	1	CACTTAGAAG	    0.961458	-177
AACTGACTAAAAGCTTTTAATGAAATTACTTCCATC	1	142	0	AAGTTAGAAT	    0.995679	-159
GATCATAATCAAGCTCTAAAGGCAATATGTTCTCCG	1	199	1	AAGTTAGAAT	    0.995679	-102
GAATAGTCACAACATATGGAAGTAAGGC        	1	283	1	AACTTAGAAG	    0.987815	-18
          *** * *  * * ***

Masking position 10
Map Score:   8.73372

Number of sites scoring better than the average of aligned sites = 41
Number in coding regions = 41
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

GGCAAGGTATCATTTCTTATAAAGTTTCTT	1	66	1	CATTTCTTAT	    0.967509	-235
ATTTCTTTACCATCTTTTGTCAAAGAAACT	1	88	0	CATCTTTTGT	     0.96107	-213
AAGTCGGAGCCATCACTTATGGATGGAAGT	1	121	1	CATCACTTAT	    0.979376	-180
TGTCTTAGGGCACCTCTTGCTTGATCATAA	1	177	1	CACCTCTTGC	    0.990965	-124
CCGTTAAAGTCACCTCGTACTTATAGCTCA	1	232	1	CACCTCGTAC	    0.979746	-69
ACTATTCTCGCATCTCTAATTAACCGATTG	1	260	0	CATCTCTAAT	    0.979376	-41
          **********

Masking position 2
Map Score:   6.6709

Number of sites scoring better than the average of aligned sites = 168
Number in coding regions = 168
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

TATATACCTGATAGCCTGAAAGATGTTG    	1	7	0	ATGCCTAAAG	    0.980213	-294
TATCAGGTATATACCCTCAAAGAGAACGATTA	1	26	1	ATCCCTAAAG	    0.980213	-275
AAGTGATGGCTCCGACTTAAAATTTCTTTACC	1	107	0	TCGACTAAAA	    0.934682	-194
ATGGAAGTAATTTCATTAAAAGCTTTTAGTCA	1	143	1	TTCATTAAAG	    0.892049	-158
CCCTAAGACAACTGACTAAAAGCTTTTAATGA	1	155	0	ACGACTAAAG	    0.988335	-146
GGCAATATGTTCTCCGTTAAAGTCACCTCGTA	1	219	1	TCCCGTAAAG	    0.968301	-82
TAAAGTCACCTCGTACTTATAGCTCAATCGGT	1	236	1	TCTACTATAG	    0.852173	-65
          ** **** ****

Masking position 9
Map Score:   2.91789

Number of sites scoring better than the average of aligned sites = 134
Number in coding regions = 134
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