AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i071_Tryptophan_Biosynthesis_ctra_reg_100.orf -o071_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	RCT00164	300	Chlamydia_trachomatis
#2	RCT00312	295	Chlamydia_trachomatis

Motif number 1

GAATTTTTGAATATCTTGGAAGCAATCAGC	1	93	0	ATATCTTGGA	    0.893217	-208
TTAAGAAGCCTTTTATTTGATTAAGAGATG	1	189	1	TTTTATTTGA	     0.92797	-112
GTCGCCAGTTTTTTCTATGATTTTAACACT	1	262	1	TTTTCTATGA	    0.964642	-39
CCGAAAACAAATTGCTTTGATGGCTCAGAG	2	21	1	ATTGCTTTGA	    0.969738	-275
TTGGAAATGGTTTTCTGTGAGTTTCTTTGT	2	70	1	TTTTCTGTGA	    0.976853	-226
GTAATACTCGATTTCTTGCAAGGAAGGCTT	2	159	1	ATTTCTTGCA	     0.87295	-137
GAAGGCTTATTTTTATATGATTTATTTTCT	2	181	1	TTTTATATGA	    0.825047	-115
TTTATTTTCTATTGCTTTGATATAAATCTC	2	201	1	ATTGCTTTGA	    0.969738	-95
TTTGATATAAATCTCTTGGATATGCTAATC	2	216	1	ATCTCTTGGA	     0.92536	-80
TGTCTTACTTTTTTCTGTGAATTTGCTTAA	2	250	1	TTTTCTGTGA	    0.976853	-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	    0.999346	-246
GAAGCAATCAGCTTGAAAAGCTGATTTGCATGG	1	72	0	GCGAAAGCTG	    0.995996	-229
TCAAAAGAAAGCCAGGCACGCTGTAAGAGGATG	1	122	0	GCGGCAGCTG	    0.999346	-179
TCGATTTCTTGCAAGGAAGGCTTATTTTTATAT	2	166	1	GCGGAAGCTT	    0.995996	-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

CTGCAGCATGCCATGCAAATCAGCTTTTCAAGCT	1	62	1	CCAGAATAGC	    0.996426	-239
AGGCCTATCGCCAAGTAGATAAGCGCCAGCTTTC	1	153	0	CCAGAATAGC	    0.996425	-148
AAATACATGCACAGGTTATTCAGCAAATCTCATG	2	107	0	ACAGTTTAGC	    0.959087	-189
AAAATAAATCATATAAAAATAAGCCTTCCTTGCA	2	175	0	ATAAAATAGC	    0.840153	-121
AAAAAGTAAGACAAGAAGATTAGCATATCCAAGA	2	229	0	ACAGAATAGC	    0.994391	-67
GGGGCTAAAACCAACTATTTAAGCAAATTCACAG	2	264	0	CCACATTAGC	    0.976967	-32
          *** * * ** ***

Masking position 10
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

CAAGATATTCAAAAATTCATCCTCTTACAGCG	1	105	1	AAAAATTCAC	    0.931313	-196
CGCCAGCTTTCAAAAGAAAGCCAGGCACGCTG	1	132	0	CAAAAGAAAC	    0.975292	-169
ATCCTGCGCAAAAAAGACGCTCTTACTTCTAT	1	224	0	AAAAAGACGC	    0.964758	-77
ATGTTTACAGACAAAGAAACTCACAGAAAACC	2	78	0	ACAAAGAAAC	     0.94568	-218
ATCTATCTTACAAAATACATGCACAGGTTATT	2	121	0	CAAAATACAC	    0.954489	-175
AATTCACAGAAAAAAGTAAGACAAGAAGATTA	2	241	0	AAAAAGTAAC	    0.962291	-55
          *********  *

Masking position 5
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