AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i327_not_clear2_ctra_reg_100.orf -o327_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	RCT00063	185	Chlamydia_trachomatis

Motif number 1

TTTTAGAGAATTTTTAGAAAGTCTTA    	1	7	0	TTTTTAGAAA	    0.512792	-179
ACGGGGCTTCTTTTTAGAGAATTTTTAGAA	1	18	0	TTTTTAGAGA	    0.646591	-168
GGCGAGGGGATTTTTAAAGACAAAAGAAAA	1	65	0	TTTTTAAAGA	    0.574906	-121
CCCCTCGCCTTTTTTATAAACTCTTCTAGA	1	86	1	TTTTTATAAA	    0.568978	-100
GTGAGTTGTCTATCTAGAGAAAAGTAATCT	1	119	0	TATCTAGAGA	    0.706657	-67
          **********

Masking position 5
Map Score:   9.49622

Number of sites scoring better than the average of aligned sites = 83
Number in coding regions = 83
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

GCTTCTTTTTAGAGAATTTTTAGAAAGTCT	1	13	0	AGAGAATTTT	    0.931967	-173
CCGAGATAGAACGGGGCTTCTTTTTAGAGA	1	28	0	ACGGGGCTTC	    0.990334	-158
TCTATCTCGGACGGGGCTTTTCTTTTGTCT	1	48	1	ACGGGGCTTT	    0.996292	-138
AAAAAAGGCGAGGGGATTTTTAAAGACAAA	1	71	0	AGGGGATTTT	    0.991184	-115
GGACATGTTAACGGAATTGTGAGTTGTCTA	1	137	0	ACGGAATTGT	    0.980298	-49
  TGTTTTTAACCGAGTTTTTGCTTCGAAA	1	168	0	ACCGAGTTTT	    0.983891	-18
          **********

Masking position 8
Map Score:   8.4516

Number of sites scoring better than the average of aligned sites = 102
Number in coding regions = 102
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

CGTCCGAGATAGAACGGGGCTTCTTTTTAG	1	31	0	AGAACGGGGC	    0.997881	-155
CGTTCTATCTCGGACGGGGCTTTTCTTTTG	1	45	1	CGGACGGGGC	    0.999074	-141
GTTTTTGCTTCGAAAAGGACATGTTAACGG	1	153	0	CGAAAAGGAC	    0.984455	-33
          **********

Masking position 4
Map Score:   2.37633

Number of sites scoring better than the average of aligned sites = 7
Number in coding regions = 7
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:   2.37484e-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 5

          **********

No masking
Map Score:   2.37484e-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:   2.37484e-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