AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i046_synecho_ctra_100.orf -o046_synecho_ctra_100.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RCT00325	34	Chlamydia_trachomatis
#2	RCT00326	28	Chlamydia_trachomatis
#3	RCT00843	196	Chlamydia_trachomatis

Motif number 1

          AAAAAATCTTTGTTAGTGGTG	2	1	1	AAAAATCTTT	    0.875442	-28
     GACGAAACACCACTAACAAAGATTTT	2	13	0	AAACCACTAA	    0.953477	-16
TCCTTTTGGGACAACAACTTTTCAAGAGTTT	3	18	1	ACACAACTTT	    0.963964	-179
CAAACAAGTAAACAAAACTCTTGAAAAGTTG	3	32	0	AAAAAACTCT	    0.923743	-165
TTCTTTGAATTATAAAAATTACCAAACAAGT	3	54	0	TAAAAAATTA	    0.767248	-143
CAAAGAAGGTTATACAACTTAAGTATCTCTT	3	78	1	TAACAACTTA	    0.973594	-119
CGGGGATTGTAACACCACTTTTATTTAGGCT	3	111	0	AAACCACTTT	    0.989971	-86
GTTATTAAATAAAACCAATTACGTATTAAGG	3	170	1	AAACCAATTA	    0.957586	-27
          ** ********

Masking position 4
Map Score:   6.44541

Number of sites scoring better than the average of aligned sites = 589
Number in coding regions = 462
Number in noncoding regions = 127
Number of orfs with sites within 600 bp upstream = 137
Fraction of orfs with sites within 600 bp upstream = 0.0220045


Motif number 2

        AAAGAAGGATCTTTTTAGCTGA	1	3	1	AGAAGGATCT	    0.980249	-32
TTTTTAGCTGAGAGGGAGCTGCT       	1	22	1	AGAGGGAGCT	     0.97244	-13
TATAATTCAAAGAAGGTTATACAACTTAAG	3	71	1	AGAAGGTTAT	    0.907222	-126
GTTATACAACTTAAGTATCTCTTGAAGCCT	3	86	1	TTAAGTATCT	     0.91165	-111
CAATTACGTATTAAGGTTATTC        	3	185	1	TTAAGGTTAT	    0.941479	-12
          **********

Masking position 3
Map Score:   2.79268

Number of sites scoring better than the average of aligned sites = 207
Number in coding regions = 182
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 3

TCCCTCTCAGCTAAAAAGATCCTTCTTT  	1	9	0	CTAAAAAGAT	    0.959027	-26
GAAACACCACTAACAAAGATTTTTT     	2	6	0	TAACAAAGAT	    0.872069	-23
ACAACAACTTTTCAAGAGTTTTGTTTACTT	3	28	1	TTCAAGAGTT	    0.970971	-169
TTATTTAGGCTTCAAGAGATACTTAAGTTG	3	92	0	TTCAAGAGAT	    0.990986	-105
AGCTCGAACGCACAAGAGACCGGGGATTGT	3	132	0	CACAAGAGAC	    0.973926	-65
          **********

Masking position 5
Map Score:   1.90385

Number of sites scoring better than the average of aligned sites = 143
Number in coding regions = 122
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 4

          **********

No masking
Map Score:   -3.95472e-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:   -3.95472e-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:   -3.95472e-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