AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i113_synecho_ctra_100.orf -o113_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	RCT00704	104	Chlamydia_trachomatis

Motif number 1

TCTAAAGGCCCCCTTTCCCCGGATAGGAGA	1	18	1	CCCTTTCCCC	    0.998683	-87
TACAAAAGCCCCCTTTCTCCTATCCGGGGA	1	33	0	CCCTTTCTCC	    0.994789	-72
GGGGCTTTTGTATTTTCCGCTTATTTGCCT	1	51	1	TATTTTCCGC	    0.986878	-54
ATTTTCCGCTTATTTGCCTCCGAAGCGGGT	1	62	1	TATTTGCCTC	    0.958088	-43
ACTACTCTTATGCTTTCACCCGCTTCGGAG	1	79	0	TGCTTTCACC	    0.989701	-26
          **********

Masking position 5
Map Score:   6.41243

Number of sites scoring better than the average of aligned sites = 1743
Number in coding regions = 1516
Number in noncoding regions = 227
Number of orfs with sites within 600 bp upstream = 249
Fraction of orfs with sites within 600 bp upstream = 0.0399936


Motif number 2

TCCGGGGAAAGGGGGCCTTTAGAATGGCCT	1	11	0	GGGGGCCTTT	    0.996412	-94
ATAGGAGAAAGGGGGCTTTTGTATTTTCCG	1	40	1	GGGGGCTTTT	    0.998685	-65
CACCCGCTTCGGAGGCAAATAAGCGGAAAA	1	63	0	GGAGGCAAAT	    0.990062	-42
          **********

Masking position 10
Map Score:   4.57365

Number of sites scoring better than the average of aligned sites = 242
Number in coding regions = 179
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 3

GGCCATTCTAAAGGCCCCCTTTCCCCGGAT	1	12	1	AAGGCCCCCT	    0.858788	-93
GGAAAATACAAAAGCCCCCTTTCTCCTATC	1	39	0	AAAGCCCCCT	    0.982899	-66
          **********

Masking position 2
Map Score:   3.65893

Number of sites scoring better than the average of aligned sites = 5
Number in coding regions = 5
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

CCCCTTTCCCCGGATAGGAGAAAGGGGGCT	1	27	1	CGGATAGGAG	    0.986752	-78
TTGTATTTTCCGCTTATTTGCCTCCGAAGC	1	58	1	CGCTTATTTG	    0.903867	-47
TGCTTTCACCCGCTTCGGAGGCAAATAAGC	1	69	0	CGCTTCGGAG	    0.985891	-36
AGCGGGTGAAAGCATAAGAGTAGTAGGACA	1	85	1	AGCATAAGAG	    0.935669	-20
          **********

Masking position 5
Map Score:   3.31472

Number of sites scoring better than the average of aligned sites = 178
Number in coding regions = 165
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


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


Motif number 7

          **********

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