AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i263_hypothetical_ctra_reg_100.orf -o263_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	RCT00738	300	Chlamydia_trachomatis

Motif number 1

TGTTCATGATGAGAACGATCGCAAAATGTT	1	17	1	GAGAACGATC	    0.938866	-284
AAAATGTTGCGAGAAAAGCCTTAGCTCTTT	1	39	1	GAGAAAAGCC	    0.991555	-262
CTAGGTTTTTGAGAAAGCTCTTCAAAGAGT	1	147	1	GAGAAAGCTC	    0.982933	-154
ATTCTTTACCAAAAATAGCCTCTTTCCTCT	1	190	0	AAAAATAGCC	    0.926569	-111
ATTTTTGGTAAAGAATATCCACGAGAGCTA	1	204	1	AAGAATATCC	    0.906435	-97
TTTTTCTAAAGAGAAAAATCCCTTTGAGCC	1	235	0	GAGAAAAATC	    0.963558	-66
TCTCTTTAGAAAAAAAGCTCGACCTTATCT	1	251	1	AAAAAAGCTC	    0.892089	-50
AAACTGGCCTGAGAATACCCGATTATCTAA	1	280	0	GAGAATACCC	    0.987751	-21
          GAAACTGGCCTGAGAATACC	1	291	0	GAAACTGGCC	    0.920515	-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

GCGAGAAAAGCCTTAGCTCTTTGAAATAAA	1	47	1	CCTTAGCTCT	    0.988674	-254
GATTAGGACTTCTCTGCTATCCTTATGGAC	1	82	0	TCTCTGCTAT	    0.886013	-219
AGAAGTCCTAATCTTGCTCTGGCATGGAAG	1	99	1	ATCTTGCTCT	    0.967037	-202
CTAGCGAGATCCCCTACTCTTTGAAGAGCT	1	162	0	CCCCTACTCT	    0.968987	-139
AAAAATAGCCTCTTTCCTCTAGCGAGATCC	1	180	0	TCTTTCCTCT	    0.961966	-121
TCCCTTTGAGCCCTAGCTCTCGTGGATATT	1	217	0	CCCTAGCTCT	    0.990602	-84
GCTCAAAGGGATTTTTCTCTTTAGAAAAAA	1	236	1	ATTTTTCTCT	    0.823172	-65
          **********

Masking position 8
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

GTTGCGAGAAAAGCCTTAGCTCTTTGAAAT	1	44	1	AAGCCTTAGC	    0.986152	-257
GATAGCAGAGAAGTCCTAATCTTGCTCTGG	1	91	1	AAGTCCTAAT	    0.944069	-210
AGCTTTCTCAAAAACCTAGTCACCGTACTC	1	136	0	AAAACCTAGT	    0.944066	-165
AAATCCCTTTGAGCCCTAGCTCTCGTGGAT	1	220	0	GAGCCCTAGC	    0.994011	-81
          **********

Masking position 7
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