AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i166_Nitrate_Transport_ctra_reg_300.orf -o166_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	RCT00172	300	Chlamydia_trachomatis
#2	RCT00816	52	Chlamydia_trachomatis

Motif number 1

AATGGATTTTTTCTGTGCGAAAGA          	1	1	0	TTCTGCAAGA	    0.981978	-300
CCAAGAGCGATTTTAAGCACAAGAAAAGATTATC	1	38	0	TTTTGCAAGA	    0.849762	-263
CTTAAAATCGCTCTTGGATTAAGATGGCGCTTTG	1	55	1	CTCTGAAAGA	    0.952652	-246
ATTAAGATGGCGCTTTGTTACTGAGAATCTTCGG	1	72	1	CGCTGTCTGA	    0.944963	-229
AGATTCGAACTCCTGACCTTCTGAATGCAAATCA	1	150	0	TCCTCCCTGA	    0.975335	-151
CAGTGTCGCGCTCTAACCAACTGAGCTATAACCG	1	201	0	CTCTCCCTGA	    0.995135	-100
     ATGCTCTCTTCCCCTATGATTCTTCCTTC	2	6	1	CTCTCCATGA	    0.995229	-47
TCCCCTATGATTCTTCCTTCATGAAGTCGTTTTT	2	20	1	TTCTCTATGA	    0.972891	-33
          ****  **  ****

Masking position 14
Map Score:   6.17476

Number of sites scoring better than the average of aligned sites = 152
Number in coding regions = 152
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

CTTGAGAGCGGCTGTTACCGAAGATTCTCA	1	93	0	GCTGTTACCG	    0.994463	-208
CAAATCAGATGCTCTACCAACTAAGCTAAG	1	127	0	GCTCTACCAA	    0.953658	-174
AACCAACTGAGCTATAACCGCAGGGATGGA	1	191	0	GCTATAACCG	    0.989512	-110
TCAGTGTCGCGCTCTAACCAACTGAGCTAT	1	206	0	GCTCTAACCA	    0.995823	-95
TTCTGGACTTGCGGTTACCAAGACTTGAAC	1	253	0	GCGGTTACCA	    0.986832	-48
          **********

Masking position 5
Map Score:   5.44868

Number of sites scoring better than the average of aligned sites = 52
Number in coding regions = 52
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

AAGATTATCAAAAATGGATTTTTTCTGTGCGA	1	15	0	AAATGGATTT	    0.662773	-286
ATCTTAATCCAAGAGCGATTTTAAGCACAAGA	1	48	0	AAGGCGATTT	    0.935456	-253
AGAAGGTCAGGAGTTCGAATCTCCTAGTCTCC	1	162	1	GAGTCGATCT	    0.987122	-139
TATAACCGCAGGGATGGAGACTAGGAGATTCG	1	177	0	GGGTGGAACT	     0.92759	-124
CAGTTGGTTAGAGCGCGACACTGATAATGTCG	1	212	1	GAGGCGAACT	    0.987172	-89
TTGAACTTGGGACCTCGACATTATCAGTGTCG	1	227	0	GACTCGAATT	    0.947679	-74
TCGAGGTCCCAAGTTCAAGTCTTGGTAACCGC	1	241	1	AAGTCAATCT	    0.898988	-60
CTTCCTTCATGAAGTCGTTTTTTCTATTTTT 	2	32	1	GAATCGTTTT	    0.848685	-21
          *** **** ***

Masking position 12
Map Score:   2.882

Number of sites scoring better than the average of aligned sites = 263
Number in coding regions = 261
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

ATCTTAATCCAAGAGCGATTTTAAGCACAA	1	50	0	AAGAGCGATT	    0.909397	-251
AAGTCCCCTTGAGAGCGGCTGTTACCGAAG	1	100	0	GAGAGCGGCT	    0.989599	-201
AGAAGGTCAGGAGTTCGAATCTCCTAGTCT	1	162	1	GAGTTCGAAT	    0.930861	-139
CAGTTGGTTAGAGCGCGACACTGATAATGT	1	212	1	GAGCGCGACA	    0.995594	-89
TTGAACTTGGGACCTCGACATTATCAGTGT	1	229	0	GACCTCGACA	    0.966562	-72
          **********

Masking position 2
Map Score:   0.859526

Number of sites scoring better than the average of aligned sites = 87
Number in coding regions = 87
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:   -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