AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i263_hypothetical_ctra_reg_300.orf -o263_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	RCT00738	300	Chlamydia_trachomatis

Motif number 1

TGTTCATGATGAGAACGATCGCAAAATGTT	1	17	1	GAGAACGATC	    0.931068	-284
AAAATGTTGCGAGAAAAGCCTTAGCTCTTT	1	39	1	GAGAAAAGCC	    0.990406	-262
CTAGGTTTTTGAGAAAGCTCTTCAAAGAGT	1	147	1	GAGAAAGCTC	     0.98171	-154
ATTCTTTACCAAAAATAGCCTCTTTCCTCT	1	190	0	AAAAATAGCC	    0.917305	-111
ATTTTTGGTAAAGAATATCCACGAGAGCTA	1	204	1	AAGAATATCC	    0.894924	-97
TTTTTCTAAAGAGAAAAATCCCTTTGAGCC	1	235	0	GAGAAAAATC	    0.958784	-66
TCTCTTTAGAAAAAAAGCTCGACCTTATCT	1	251	1	AAAAAAGCTC	    0.879046	-50
AAACTGGCCTGAGAATACCCGATTATCTAA	1	280	0	GAGAATACCC	    0.987063	-21
          GAAACTGGCCTGAGAATACC	1	291	0	GAAACTGGCC	     0.91056	-10
          **********

Masking position 4
Map Score:   11.2119

Number of sites scoring better than the average of aligned sites = 390
Number in coding regions = 389
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 2

TTTATTTCAAAGAGCTAAGGCTTTTCTCGC	1	47	0	AGAGCTAAGG	    0.988712	-254
GTCCATAAGGATAGCAGAGAAGTCCTAATC	1	82	1	ATAGCAGAGA	    0.886363	-219
CTTCCATGCCAGAGCAAGATTAGGACTTCT	1	99	0	AGAGCAAGAT	    0.967147	-202
AGCTCTTCAAAGAGTAGGGGATCTCGCTAG	1	162	1	AGAGTAGGGG	    0.969091	-139
GGATCTCGCTAGAGGAAAGAGGCTATTTTT	1	180	1	AGAGGAAAGA	    0.962093	-121
AATATCCACGAGAGCTAGGGCTCAAAGGGA	1	217	1	AGAGCTAGGG	    0.990635	-84
TTTTTTCTAAAGAGAAAAATCCCTTTGAGC	1	236	0	AGAGAAAAAT	    0.823677	-65
          **********

Masking position 3
Map Score:   5.56769

Number of sites scoring better than the average of aligned sites = 395
Number in coding regions = 394
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 3

ATTTCAAAGAGCTAAGGCTTTTCTCGCAAC	1	44	0	GCTAAGGCTT	    0.987491	-257
CCAGAGCAAGATTAGGACTTCTCTGCTATC	1	91	0	ATTAGGACTT	    0.949264	-210
GAGTACGGTGACTAGGTTTTTGAGAAAGCT	1	136	1	ACTAGGTTTT	    0.949261	-165
ATCCACGAGAGCTAGGGCTCAAAGGGATTT	1	220	1	GCTAGGGCTC	    0.994594	-81
          **********

Masking position 4
Map Score:   0.0598747

Number of sites scoring better than the average of aligned sites = 59
Number in coding regions = 59
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

          **********

No masking
Map Score:   7.91135e-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 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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