AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i060_Diaminopimelate_Pathway_ctra_reg_100.orf -o060_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	RCT00346	236	Chlamydia_trachomatis

Motif number 1

TAATTTATTTAGAGAAAGAACTTTAGATGT	1	28	0	AGAGAAAGAA	    0.973268	-209
ATAAATTAGGAAAAAGAGCAAGTTTGCGAA	1	50	1	AAAAAGAGCA	    0.986568	-187
TAGCTCCAACAGGAAAAGCAAAGCAAATTC	1	77	0	AGGAAAAGCA	    0.987545	-160
AAAATGGCTAAAAGAAACCACTGCAGCAGT	1	125	0	AAAGAAACCA	    0.980387	-112
TAGTATTATGAAAAAAAGCATAGGCCTTGT	1	201	1	AAAAAAAGCA	    0.993904	-36
          **********

Masking position 5
Map Score:   6.03567

Number of sites scoring better than the average of aligned sites = 166
Number in coding regions = 166
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

AGTGAGTAAATAGCTCCAACAGGAAAAGCA	1	87	0	TAGCTCCAAC	    0.987396	-150
GTGGAACCTATAGGATCCTCTTAGAAAATG	1	149	0	TAGGATCCTC	    0.926219	-88
GAGGATCCTATAGGTTCCACAATGGTGGAT	1	159	1	TAGGTTCCAC	    0.988263	-78
TATCAGCAACTCTCATCCACCATTGTGGAA	1	173	0	TCTCATCCAC	    0.974368	-64
TTCATAATACTATCAGCAACTCTCATCCAC	1	183	0	TATCAGCAAC	    0.964376	-54
  CCTCCCAGTATCTCCGACAAGGCCTATG	1	219	0	TATCTCCGAC	    0.976677	-18
          **********

Masking position 1
Map Score:   4.48805

Number of sites scoring better than the average of aligned sites = 151
Number in coding regions = 151
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

CTTTGCTTTTCCTGTTGGAGCTATTTACTC	1	84	1	CCTGTTGGAG	    0.997857	-153
CTTATACTATACTGCTGCAGTGGTTTCTTT	1	115	1	ACTGCTGCAG	    0.987387	-122
AAGCATAGGCCTTGTCGGAGATACTGGGAG	1	216	1	CTTGTCGGAG	    0.993019	-21
          **********

Masking position 9
Map Score:   0.35619

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 47
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

TTCTCTAAATAAATTAGGAAAAAGAGCAAGT	1	42	1	AAATTGGAAA	    0.983897	-195
AAAGCAAAGCAAATTCGCAAACTTGCTCTTT	1	62	0	AAATTGCAAA	    0.983897	-175
AGTATAGTATAAGTGAGTAAATAGCTCCAAC	1	97	0	AAGTGGTAAA	    0.985065	-140
TCCTCTTAGAAAATGGCTAAAAGAAACCACT	1	133	0	AAATGCTAAA	    0.976715	-104
          ***** *****

Masking position 4
Map Score:   0.309707

Number of sites scoring better than the average of aligned sites = 42
Number in coding regions = 42
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:   -2.17836e-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:   -2.17836e-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:   -2.17836e-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