AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i164_NIF1_ctra_reg_300.orf -o164_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	RCT00653	300	Chlamydia_trachomatis

Motif number 1

ATAAAAAATCAAAAAATCGCTAGA      	1	5	0	AAAAAATCGC	    0.873851	-296
ACACAAACAAATAAAAAATCAAAAAATCGC	1	15	0	ATAAAAAATC	    0.963125	-286
TTTGTGTTGTAGAAAAATTCCATTTTTTTT	1	38	1	AGAAAAATTC	    0.948971	-263
TACGAATCGTAAAAAAAATGGAATTTTTCT	1	48	0	AAAAAAAATG	    0.969922	-253
ACAGCCCTTAAGAAAAAAACTTGTTGGCTA	1	76	0	AGAAAAAAAC	    0.978329	-225
CACCTTCTTGAAAAAAAAAGAAAGACAGCC	1	153	0	AAAAAAAAAG	    0.933459	-148
AGGTGTTCGAAAAAAATATCTCGAATTGCA	1	178	1	AAAAAATATC	    0.974847	-123
CAAAAAAGGCAAAACAAATCCTGAACTGCA	1	204	0	AAAACAAATC	    0.961144	-97
GGAGCTCGTGAGAAAAGAGCCTATTATCTC	1	242	0	AGAAAAGAGC	    0.955529	-59
          **********

Masking position 6
Map Score:   11.5486

Number of sites scoring better than the average of aligned sites = 461
Number in coding regions = 461
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

TCAAACAGCCCTTAAGAAAAAAACTTGTTGG	1	79	0	CTAAGAAAAA	    0.927083	-222
CTCCCTAGACCCAAGGAAAGGACTGTCAAAC	1	104	0	CCAGGAAAGG	    0.956694	-197
TTCCTTGGGTCTAGGGAGAGACATCCTCTTT	1	117	1	CTGGGAGAGA	     0.99652	-184
GAAAGACAGCCTAGGGAAAGAGGATGTCTCT	1	133	0	CTGGGAAAGA	      0.9958	-168
TTTTTTGAGACAGAGGAGATAATAGGCTCTT	1	227	1	CAAGGAGATA	    0.918099	-74
TGGAGTGGAGCTCGTGAGAAAAGAGCCTATT	1	247	0	CTGTGAGAAA	    0.970321	-54
GAGTGGCATCCTGATGAAAGAGGAGGATC  	1	282	1	CTATGAAAGA	    0.985152	-19
          ** ********

Masking position 7
Map Score:   7.72699

Number of sites scoring better than the average of aligned sites = 207
Number in coding regions = 207
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

TTTTTCTTAAGGGCTGTTTGACAGTCCTTT	1	89	1	GGGCTGTTTG	    0.950856	-212
CTAGGGAAAGAGGATGTCTCTCCCTAGACC	1	124	0	AGGATGTCTC	    0.992697	-177
CTCTTTCCCTAGGCTGTCTTTCTTTTTTTT	1	142	1	AGGCTGTCTT	    0.995074	-159
ATTGCAGTTCAGGATTTGTTTTGCCTTTTT	1	202	1	AGGATTTGTT	     0.90233	-99
AGGAGATAATAGGCTCTTTTCTCACGAGCT	1	240	1	AGGCTCTTTT	    0.962434	-61
CTCTTTCATCAGGATGCCACTCTATTTGGA	1	274	0	AGGATGCCAC	    0.926385	-27
          **********

Masking position 5
Map Score:   2.66137

Number of sites scoring better than the average of aligned sites = 156
Number in coding regions = 156
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