AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i174_Biotin_Biosynthesis_ctra_reg_300.orf -o174_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

GCATATAGGACAGAGTAGAACATGTTGCAT	1	29	1	CAGAGTAGAA	    0.979971	-272
GCTATGGAGGGATTCAAGAAAATTCTTGTC	1	81	1	GATTCAAGAA	    0.947292	-220
CTGCACTGCGCAGACAAGAATTTTCTTGAA	1	93	0	CAGACAAGAA	    0.974697	-208
CTTGTCTGCGCAGTGCAGAATCGCTTTGGG	1	105	1	CAGTGCAGAA	    0.981537	-196
ATAAGAAGGAGAGTGTACAATGGCAATTAT	1	202	0	GAGTGTACAA	    0.941466	-99
TTGACCACAAGATTGAAGTGTATGTGCGTC	1	250	1	GATTGAAGTG	    0.856095	-51
AGAAGGAAATGAGAGAAGAGGCC       	1	288	1	GAGAGAAGAG	    0.987758	-13
          **********

Masking position 7
Map Score:   5.55769

Number of sites scoring better than the average of aligned sites = 354
Number in coding regions = 352
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

TTGCATTGGCGATACGAAAGCACTGATTGC	1	53	1	GATACGAAAG	    0.948327	-248
AGCACTGATTGCTATGGAGGGATTCAAGAA	1	71	1	GCTATGGAGG	    0.968248	-230
TGCCTGTCGTGAAATGTATGTAAAGAGAAA	1	138	1	GAAATGTATG	    0.973698	-163
TATGTAAAGAGAAAAGGAGGATAGAGGGAA	1	154	1	GAAAAGGAGG	    0.985751	-147
AACCCTCTACGATAAGAAGGAGAGTGTACA	1	213	0	GATAAGAAGG	    0.980083	-88
CCACAAGATTGAAGTGTATGTGCGTCATCT	1	254	1	GAAGTGTATG	    0.919328	-47
TCTACAGAAGGAAATGAGAGAAGAGGCC  	1	283	1	GAAATGAGAG	    0.942295	-18
          **********

Masking position 6
Map Score:   5.5444

Number of sites scoring better than the average of aligned sites = 215
Number in coding regions = 215
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

AATTTTCTTGAATCCCTCCATAGCAATCAG	1	75	0	AATCCCTCCA	    0.937841	-226
CTATCCTCCTTTTCTCTTTACATACATTTC	1	148	0	TTTCTCTTTA	    0.851541	-153
GAACTAAGAGTTTCCCTCTATCCTCCTTTT	1	165	0	TTTCCCTCTA	    0.995845	-136
CATTGTACACTCTCCTTCTTATCGTAGAGG	1	210	1	TCTCCTTCTT	    0.935226	-91
TCAAAAATTTTAACCCTCTACGATAAGAAG	1	224	0	TAACCCTCTA	    0.976335	-77
TCTTCTCTCATTTCCTTCTGTAGAGATGAC	1	277	0	TTTCCTTCTG	     0.97332	-24
          **********

Masking position 7
Map Score:   2.96343

Number of sites scoring better than the average of aligned sites = 329
Number in coding regions = 329
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