AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i071_Tryptophan_Biosynthesis_ctra_reg_300.orf -o071_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	RCT00164	300	Chlamydia_trachomatis
#2	RCT00312	295	Chlamydia_trachomatis

Motif number 1

GAATTTTTGAATATCTTGGAAGCAATCAGC	1	93	0	ATATCTTGGA	     0.90256	-208
TTAAGAAGCCTTTTATTTGATTAAGAGATG	1	189	1	TTTTATTTGA	    0.934495	-112
GTCGCCAGTTTTTTCTATGATTTTAACACT	1	262	1	TTTTCTATGA	     0.96796	-39
CCGAAAACAAATTGCTTTGATGGCTCAGAG	2	21	1	ATTGCTTTGA	    0.972591	-275
TTGGAAATGGTTTTCTGTGAGTTTCTTTGT	2	70	1	TTTTCTGTGA	    0.979049	-226
GTAATACTCGATTTCTTGCAAGGAAGGCTT	2	159	1	ATTTCTTGCA	    0.883836	-137
GAAGGCTTATTTTTATATGATTTATTTTCT	2	181	1	TTTTATATGA	    0.839278	-115
TTTATTTTCTATTGCTTTGATATAAATCTC	2	201	1	ATTGCTTTGA	    0.972591	-95
TTTGATATAAATCTCTTGGATATGCTAATC	2	216	1	ATCTCTTGGA	    0.932104	-80
TGTCTTACTTTTTTCTGTGAATTTGCTTAA	2	250	1	TTTTCTGTGA	    0.979049	-46
          **********

Masking position 6
Map Score:   13.0961

Number of sites scoring better than the average of aligned sites = 332
Number in coding regions = 332
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

AAGCTGATTTGCATGGCATGCTGCAGCTATACT	1	55	0	GCGGCAGCTG	    0.999289	-246
GAAGCAATCAGCTTGAAAAGCTGATTTGCATGG	1	72	0	GCGAAAGCTG	    0.995648	-229
TCAAAAGAAAGCCAGGCACGCTGTAAGAGGATG	1	122	0	GCGGCAGCTG	    0.999289	-179
TCGATTTCTTGCAAGGAAGGCTTATTTTTATAT	2	166	1	GCGGAAGCTT	    0.995648	-130
          **  **** ****

Masking position 8
Map Score:   5.21794

Number of sites scoring better than the average of aligned sites = 7
Number in coding regions = 7
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

AGCTTGAAAAGCTGATTTGCATGGCATGCTGCAG	1	62	0	GCTATTCTGG	    0.996737	-239
GAAAGCTGGCGCTTATCTACTTGGCGATAGGCCT	1	153	1	GCTATTCTGG	    0.996736	-148
CATGAGATTTGCTGAATAACCTGTGCATGTATTT	2	107	1	GCTAAACTGT	    0.962523	-189
TGCAAGGAAGGCTTATTTTTATATGATTTATTTT	2	175	1	GCTATTTTAT	     0.85204	-121
TCTTGGATATGCTAATCTTCTTGTCTTACTTTTT	2	229	1	GCTATTCTGT	    0.994878	-67
CTGTGAATTTGCTTAAATAGTTGGTTTTAGCCCC	2	264	1	GCTAATGTGG	    0.978933	-32
          *** ** * * ***

Masking position 5
Map Score:   4.47298

Number of sites scoring better than the average of aligned sites = 31
Number in coding regions = 31
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

CGCTGTAAGAGGATGAATTTTTGAATATCTTG	1	105	0	GTGAATTTTT	    0.935314	-196
CAGCGTGCCTGGCTTTCTTTTGAAAGCTGGCG	1	132	1	GTTTCTTTTG	    0.976795	-169
ATAGAAGTAAGAGCGTCTTTTTTGCGCAGGAT	1	224	1	GCGTCTTTTT	     0.96688	-77
GGTTTTCTGTGAGTTTCTTTGTCTGTAAACAT	2	78	1	GTTTCTTTGT	     0.94889	-218
AATAACCTGTGCATGTATTTTGTAAGATAGAT	2	121	1	GTGTATTTTG	    0.957203	-175
TAATCTTCTTGTCTTACTTTTTTCTGTGAATT	2	241	1	GTTACTTTTT	    0.964556	-55
          *  *********

Masking position 8
Map Score:   0.677286

Number of sites scoring better than the average of aligned sites = 112
Number in coding regions = 112
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:   -2.67574e-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:   -2.67574e-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:   -2.67574e-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