AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i179_folate_biosynthesis_ctra_reg_300.orf -o179_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	RCT00289	300	Chlamydia_trachomatis

Motif number 1

AACGATTACCAAGATCGGCAAGGTATCATTTCTTAT	1	50	1	AAGTGAGTAT	    0.973149	-251
TTTGTCAAAGAAACTTTATAAGAAATGATACCTTGC	1	67	0	AAATTAGAAT	    0.980276	-234
TCTTTGACAAAAGATGGTAAAGAAATTTTAAGTCGG	1	92	1	AAGTGAGAAT	    0.994304	-209
TCGGAGCCATCACTTATGGATGGAAGTAATTTCATT	1	124	1	CACTTAGAAG	    0.965607	-177
AACTGACTAAAAGCTTTTAATGAAATTACTTCCATC	1	142	0	AAGTTAGAAT	    0.996159	-159
GATCATAATCAAGCTCTAAAGGCAATATGTTCTCCG	1	199	1	AAGTTAGAAT	    0.996159	-102
GAATAGTCACAACATATGGAAGTAAGGC        	1	283	1	AACTTAGAAG	    0.989159	-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	    0.969435	-235
ATTTCTTTACCATCTTTTGTCAAAGAAACT	1	88	0	CATCTTTTGT	    0.963362	-213
AAGTCGGAGCCATCACTTATGGATGGAAGT	1	121	1	CATCACTTAT	    0.980612	-180
TGTCTTAGGGCACCTCTTGCTTGATCATAA	1	177	1	CACCTCTTGC	    0.991512	-124
CCGTTAAAGTCACCTCGTACTTATAGCTCA	1	232	1	CACCTCGTAC	    0.980961	-69
ACTATTCTCGCATCTCTAATTAACCGATTG	1	260	0	CATCTCTAAT	    0.980612	-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

    CAACATCTTTCAGGCTATCAGGTATATA	1	7	1	CTTTAGGCAT	    0.982648	-294
TAATCGTTCTCTTTGAGGGTATATACCTGATA	1	26	0	CTTTAGGGAT	    0.982649	-275
GGTAAAGAAATTTTAAGTCGGAGCCATCACTT	1	107	1	TTTTAGTCGA	    0.942394	-194
TGACTAAAAGCTTTTAATGAAATTACTTCCAT	1	143	0	CTTTAATGAA	    0.904279	-158
TCATTAAAAGCTTTTAGTCAGTTGTCTTAGGG	1	155	1	CTTTAGTCGT	    0.989781	-146
TACGAGGTGACTTTAACGGAGAACATATTGCC	1	219	0	CTTTACGGGA	    0.972161	-82
ACCGATTGAGCTATAAGTACGAGGTGACTTTA	1	236	0	CTATAGTAGA	    0.868254	-65
          **** **** **

Masking position 6
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

AAACTTTATAAGAAATGATACCTTGCCGAT	1	63	0	AGAAATGATA	    0.952145	-238
CTTTTGTCAAAGAAACTTTATAAGAAATGA	1	75	0	AGAAACTTTA	    0.979795	-226
AAGATGGTAAAGAAATTTTAAGTCGGAGCC	1	102	1	AGAAATTTTA	     0.97708	-199
TATGGATGGAAGTAATTTCATTAAAAGCTT	1	138	1	AGTAATTTCA	    0.871036	-163
          **********

Masking position 5
Map Score:   1.72768

Number of sites scoring better than the average of aligned sites = 51
Number in coding regions = 51
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


Motif number 7

          **********

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