AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i299_mixed14_ctra_reg_100.orf -o299_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	RCT00579	80	Chlamydia_trachomatis
#2	RCT00626	300	Chlamydia_trachomatis

Motif number 1

CTCCTTAATCTAAGGCATAGAGTATATGCA	1	16	1	TAAGGCATAG	    0.986861	-65
AATCGAAGTCTAAGGTATAGTATCTTCCAG	2	31	0	TAAGGTATAG	    0.980696	-270
AGGAATAGAAGAAGGAAGAGTGCTTCCAGA	2	62	0	GAAGGAAGAG	    0.980906	-239
ACAAGCATCTCAAGGAATAGAAGAAGGAAG	2	74	0	CAAGGAATAG	    0.997319	-227
GGGTTATGGGCAAGGATTCGGCGGATTAGC	2	111	0	CAAGGATTCG	    0.976634	-190
ATAGTGAATCCAAGGAATGGGTTATGGGCA	2	129	0	CAAGGAATGG	    0.994108	-172
          **********

Masking position 3
Map Score:   9.17922

Number of sites scoring better than the average of aligned sites = 45
Number in coding regions = 45
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

GTATATGCATTCTCGAAAATTTTCTTCGAACCCGA	1	37	1	TCTGAAATCT	    0.973125	-44
GACTTCGATTTTCTGGAAGCACTCTTCCTTCTTCT	2	51	1	TTCGAAGTCT	    0.973542	-250
GGATTAGCAGTTTGAACAAGCATCTCAAGGAATAG	2	84	0	TTTACAATCT	    0.983022	-217
CTATTTCCTCTTTAAAAAACCTTCTTCCTAGGATT	2	155	1	TTTAAAATCT	     0.97957	-146
CTTCCTAGGATTTTATAAGGTTTCTCGTACCAATC	2	178	1	TTTAAAGTCT	    0.983022	-123
GCAAATGGTGTATAGTCAAATTTCTGTCAGCTGAG	2	217	1	TATGCAATCT	    0.967215	-84
GAATTGTGCCTTTAGTCAGAGTTCTTAACGATCTT	2	252	0	TTTGCAGTCT	    0.993123	-49
          *** * ***   ***

Masking position 8
Map Score:   6.4599

Number of sites scoring better than the average of aligned sites = 55
Number in coding regions = 55
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

CCTTAGATTAAGGAGAGTGT          	1	1	0	AGGAGAGTGT	    0.866563	-80
TCGGGTTCGAAGAAAATTTTCGAGAATGCA	1	42	0	AGAAAATTTT	    0.760191	-39
         AAGGAAACACTTCCATAGTGC	2	2	1	AGGAAACACT	    0.945235	-299
CCATAGTGCTGGAAGATACTATACCTTAGA	2	23	1	GGAAGATACT	    0.845931	-278
GAGTGCTTCCAGAAAATCGAAGTCTAAGGT	2	45	0	AGAAAATCGA	      0.8865	-256
TTTTTTAAAGAGGAAATAGTGAATCCAAGG	2	144	0	AGGAAATAGT	    0.968144	-157
GAGAAACCTTATAAAATCCTAGGAAGAAGG	2	174	0	ATAAAATCCT	    0.822911	-127
CTGTCAGCTGAGAAGATCGTTAAGAACTCT	2	240	1	AGAAGATCGT	    0.975854	-61
ACTCTAAAAAAGGATACCCTTTT       	2	288	1	AGGATACCCT	    0.675422	-13
          **********

Masking position 6
Map Score:   3.38932

Number of sites scoring better than the average of aligned sites = 768
Number in coding regions = 765
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

ATATATTTTCGGGTTCGAAGAAAATTTTCG	1	50	0	GGGTTCGAAG	    0.987197	-31
GTGCTTCCAGAAAATCGAAGTCTAAGGTAT	2	43	0	AAAATCGAAG	     0.92205	-258
AGCATCTCAAGGAATAGAAGAAGGAAGAGT	2	71	0	GGAATAGAAG	    0.990897	-230
AGGATTCGGCGGATTAGCAGTTTGAACAAG	2	99	0	GGATTAGCAG	    0.971608	-202
GAGGAAATAGTGAATCCAAGGAATGGGTTA	2	135	0	TGAATCCAAG	    0.946038	-166
          **********

Masking position 5
Map Score:   1.24507

Number of sites scoring better than the average of aligned sites = 155
Number in coding regions = 155
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:   -6.79689e-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:   -6.79689e-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:   -6.79689e-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