AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i166_Nitrate_Transport_ctra_reg_100.orf -o166_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	RCT00172	300	Chlamydia_trachomatis
#2	RCT00816	52	Chlamydia_trachomatis

Motif number 1

          TCTTTCGCACAGAAAAAATCCATT	1	1	1	TCTTGCAGAA	    0.981463	-300
GATAATCTTTTCTTGTGCTTAAAATCGCTCTTGG	1	38	1	TCTTGCAAAA	    0.846472	-263
CAAAGCGCCATCTTAATCCAAGAGCGATTTTAAG	1	55	0	TCTTTCAGAG	    0.949008	-246
CCGAAGATTCTCAGTAACAAAGCGCCATCTTAAT	1	72	0	TCAGACAGCG	    0.940763	-229
TGATTTGCATTCAGAAGGTCAGGAGTTCGAATCT	1	150	1	TCAGGGAGGA	    0.973401	-151
CGGTTATAGCTCAGTTGGTTAGAGCGCGACACTG	1	201	1	TCAGGGAGAG	    0.994742	-100
GAAGGAAGAATCATAGGGGAAGAGAGCAT     	2	6	0	TCATGGAGAG	    0.994844	-47
AAAAACGACTTCATGAAGGAAGAATCATAGGGGA	2	20	0	TCATAGAGAA	    0.970757	-33
          ****  **  ****

Masking position 11
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

AATCCATTTTTGATAATCTTTTCTTGTGCT	1	27	1	TGATAATCTT	    0.919532	-274
GCTTTGTTACTGAGAATCTTCGGTAACAGC	1	83	1	TGAGAATCTT	    0.971279	-218
TGAATGCAAATCAGATGCTCTACCAACTAA	1	133	0	TCAGATGCTC	    0.978173	-168
TGATTTGCATTCAGAAGGTCAGGAGTTCGA	1	150	1	TCAGAAGGTC	    0.988182	-151
CGGTTATAGCTCAGTTGGTTAGAGCGCGAC	1	201	1	TCAGTTGGTT	    0.875487	-100
AGCGCGACACTGATAATGTCGAGGTCCCAA	1	223	1	TGATAATGTC	    0.947281	-78
          **********

Masking position 3
Map Score:   3.03189

Number of sites scoring better than the average of aligned sites = 150
Number in coding regions = 150
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

AAAAGATTATCAAAAATGGATTTTTTCTGT	1	19	0	CAAAAATGGA	    0.923171	-282
ATTTTAAGCACAAGAAAAGATTATCAAAAA	1	33	0	CAAGAAAAGA	     0.95741	-268
ATGGAGACTAGGAGATTCGAACTCCTGACC	1	166	0	GGAGATTCGA	    0.932919	-135
TTGCGGTTACCAAGACTTGAACTTGGGACC	1	245	0	CAAGACTTGA	     0.91356	-56
AAAACACGAACGAAATAAGAAATATTTCTG	1	278	0	CGAAATAAGA	    0.897351	-23
        GGGAAAACACGAACGAAATAAG	1	289	0	GAAAACACGA	    0.971808	-12
   AAAAATAGAAAAAACGACTTCATGAAG	2	36	0	GAAAAAACGA	    0.969635	-17
          **********

Masking position 5
Map Score:   2.68318

Number of sites scoring better than the average of aligned sites = 208
Number in coding regions = 207
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

CTTGAGAGCGGCTGTTACCGAAGATTCTCA	1	93	0	GCTGTTACCG	    0.996677	-208
AACCAACTGAGCTATAACCGCAGGGATGGA	1	191	0	GCTATAACCG	    0.990987	-110
TCAGTGTCGCGCTCTAACCAACTGAGCTAT	1	206	0	GCTCTAACCA	    0.990597	-95
TTCTGGACTTGCGGTTACCAAGACTTGAAC	1	253	0	GCGGTTACCA	    0.991283	-48
          **********

Masking position 5
Map Score:   5.02004

Number of sites scoring better than the average of aligned sites = 19
Number in coding regions = 19
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