AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i043_5_1_3_1_ctra_reg_100.orf -o043_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	RCT00118	300	Chlamydia_trachomatis

Motif number 1

ATGCAACATGTTCTACTCTGTCCTATATGC	1	29	0	TTCTACTCTG	    0.966623	-272
GACAAGAATTTTCTTGAATCCCTCCATAGC	1	81	0	TTCTTGAATC	    0.935264	-220
TTCAAGAAAATTCTTGTCTGCGCAGTGCAG	1	93	1	TTCTTGTCTG	    0.965503	-208
CCCAAAGCGATTCTGCACTGCGCAGACAAG	1	105	0	TTCTGCACTG	    0.951808	-196
CCCTCTATCCTCCTTTTCTCTTTACATACA	1	152	0	TCCTTTTCTC	    0.918534	-149
ACTAAGAGTTTCCCTCTATCCTCCTTTTCT	1	163	0	TCCCTCTATC	    0.869388	-138
ATAATTGCCATTGTACACTCTCCTTCTTAT	1	202	1	TTGTACACTC	    0.868891	-99
GACGCACATACACTTCAATCTTGTGGTCAA	1	250	0	CACTTCAATC	    0.805593	-51
       GGCCTCTTCTCTCATTTCCTTCT	1	288	0	CTCTTCTCTC	    0.986848	-13
          **********

Masking position 9
Map Score:   5.92743

Number of sites scoring better than the average of aligned sites = 771
Number in coding regions = 769
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	    0.950388	-248
AGCACTGATTGCTATGGAGGGATTCAAGAA	1	71	1	GCTATGGAGG	    0.969541	-230
TGCCTGTCGTGAAATGTATGTAAAGAGAAA	1	138	1	GAAATGTATG	    0.974774	-163
TATGTAAAGAGAAAAGGAGGATAGAGGGAA	1	154	1	GAAAAGGAGG	    0.986341	-147
AACCCTCTACGATAAGAAGGAGAGTGTACA	1	213	0	GATAAGAAGG	    0.980903	-88
CCACAAGATTGAAGTGTATGTGCGTCATCT	1	254	1	GAAGTGTATG	    0.922454	-47
TCTACAGAAGGAAATGAGAGAAGAGGCC  	1	283	1	GAAATGAGAG	    0.944584	-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

GCACTGCGCAGACAAGAATTTTCTTGAATCCC	1	89	0	GCAAAATTTT	    0.995867	-212
AGTGTACAATGGCAATTATTTTTGGGGAACTA	1	189	0	GCAATATTTT	    0.992743	-112
CAATCTTGTGGTCAAAAATTTTAACCCTCTAC	1	233	0	GCAAAATTTT	    0.995872	-68
          * *** ******

Masking position 5
Map Score:   1.82409

Number of sites scoring better than the average of aligned sites = 11
Number in coding regions = 11
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

CTGATTGCTATGGAGGGATTCAAGAAAATT	1	75	1	TGGAGGGATT	    0.953768	-226
AAAAGGAGGATAGAGGGAAACTCTTAGTTC	1	165	1	TAGAGGGAAA	    0.993407	-136
CCTCTACGATAAGAAGGAGAGTGTACAATG	1	210	0	AAGAAGGAGA	     0.95698	-91
CTTCTTATCGTAGAGGGTTAAAATTTTTGA	1	224	1	TAGAGGGTTA	    0.978629	-77
GTCATCTCTACAGAAGGAAATGAGAGAAGA	1	277	1	CAGAAGGAAA	     0.97514	-24
          **********

Masking position 4
Map Score:   3.08308

Number of sites scoring better than the average of aligned sites = 161
Number in coding regions = 161
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