AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i043_5_1_3_1_ctra_reg_300.orf -o043_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	RCT00118	300	Chlamydia_trachomatis

Motif number 1

TCTGCATATAGGACAGAGTAGAACATGTTGCAT	1	26	1	GAAGAGAGAA	    0.993511	-275
ATTCTTGTCTGCGCAGTGCAGAATCGCTTTGGG	1	102	1	GGAGTGAGAA	    0.961902	-199
TGAAATGTATGTAAAGAGAAAAGGAGGATAGAG	1	147	1	GAAGAGAAAG	    0.992017	-154
GAGAAAAGGAGGATAGAGGGAAACTCTTAGTTC	1	162	1	GAAGAGGAAA	    0.993511	-139
ACGATAAGAAGGAGAGTGTACAATGGCAATTAT	1	202	0	GAAGTGACAA	    0.978064	-99
CCTTCTTATCGTAGAGGGTTAAAATTTTTGACC	1	223	1	GAAGGGTAAA	    0.961956	-78
TCTACAGAAGGAAATGAGAGAAGAGGCC     	1	283	1	GATGAGGAAG	    0.955334	-18
          * * **** ****

Masking position 12
Map Score:   5.96139

Number of sites scoring better than the average of aligned sites = 151
Number in coding regions = 151
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

TTTCGTATCGCCAATGCAACATGTTCTACT	1	42	0	CCAATGCAAC	    0.974764	-259
ATTGGCGATACGAAAGCACTGATTGCTATG	1	57	1	CGAAAGCACT	    0.973267	-244
TTGAATCCCTCCATAGCAATCAGTGCTTTC	1	68	0	CCATAGCAAT	     0.99343	-233
CAGGCACACCCCAAAGCGATTCTGCACTGC	1	114	0	CCAAAGCGAT	    0.989858	-187
GGAGAGTGTACAATGGCAATTATTTTTGGG	1	195	0	CAATGGCAAT	    0.957123	-106
          **********

Masking position 3
Map Score:   3.6503

Number of sites scoring better than the average of aligned sites = 72
Number in coding regions = 72
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

TTCTGCATATAGGACAGAGTAGAACATGTTG	1	25	1	AGGAAGAGTA	    0.992969	-276
GTGAAATGTATGTAAAGAGAAAAGGAGGATA	1	146	1	TGTAAGAGAA	    0.935506	-155
AGAGAAAAGGAGGATAGAGGGAAACTCTTAG	1	161	1	AGGAAGAGGG	    0.991479	-140
TACGATAAGAAGGAGAGTGTACAATGGCAAT	1	205	0	AGGAAGTGTA	    0.972101	-96
CATTTCCTTCTGTAGAGATGACGCACATACA	1	268	0	TGTAAGATGA	    0.916968	-33
ACAGAAGGAAATGAGAGAAGAGGCC      	1	286	1	ATGAAGAAGA	    0.904156	-15
          **** ******

Masking position 6
Map Score:   2.80573

Number of sites scoring better than the average of aligned sites = 265
Number in coding regions = 265
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

TGTCCTATATGCAGAAATTGATCGTTAATC	1	11	0	GCAGAAATTG	    0.925045	-290
CGATACGAAAGCACTGATTGCTATGGAGGG	1	62	1	GCACTGATTG	    0.959706	-239
TGCCTGTCGTGAAATGTATGTAAAGAGAAA	1	138	1	GAAATGTATG	    0.948196	-163
TAGTTCCCCAAAAATAATTGCCATTGTACA	1	189	1	AAAATAATTG	    0.769444	-112
CCACAAGATTGAAGTGTATGTGCGTCATCT	1	254	1	GAAGTGTATG	     0.97634	-47
CATCTCTACAGAAGGAAATGAGAGAAGAGG	1	279	1	GAAGGAAATG	    0.956641	-22
          **********

Masking position 3
Map Score:   0.538995

Number of sites scoring better than the average of aligned sites = 331
Number in coding regions = 331
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


Motif number 7

          **********

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