AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i299_mixed14_ctra_reg_300.orf -o299_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	RCT00579	80	Chlamydia_trachomatis
#2	RCT00626	300	Chlamydia_trachomatis

Motif number 1

TGCATATACTCTATGCCTTAGATTAAGGAG	1	16	0	CTATGCCTTA	     0.98602	-65
CTGGAAGATACTATACCTTAGACTTCGATT	2	31	1	CTATACCTTA	    0.979462	-270
TCTGGAAGCACTCTTCCTTCTTCTATTCCT	2	62	1	CTCTTCCTTC	    0.979685	-239
CTTCCTTCTTCTATTCCTTGAGATGCTTGT	2	74	1	CTATTCCTTG	    0.997149	-227
GCTAATCCGCCGAATCCTTGCCCATAACCC	2	111	1	CGAATCCTTG	    0.975151	-190
TGCCCATAACCCATTCCTTGGATTCACTAT	2	129	1	CCATTCCTTG	     0.99373	-172
          **********

Masking position 8
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

TCGGGTTCGAAGAAAATTTTCGAGAATGCATATAC	1	37	0	AGATTTCAGA	    0.975107	-44
AGAAGAAGGAAGAGTGCTTCCAGAAAATCGAAGTC	2	51	0	AGACTTCGAA	    0.975494	-250
CTATTCCTTGAGATGCTTGTTCAAACTGCTAATCC	2	84	1	AGATTGTAAA	    0.984286	-217
AATCCTAGGAAGAAGGTTTTTTAAAGAGGAAATAG	2	155	0	AGATTTTAAA	    0.981086	-146
GATTGGTACGAGAAACCTTATAAAATCCTAGGAAG	2	178	0	AGACTTTAAA	    0.984286	-123
CTCAGCTGACAGAAATTTGACTATACACCATTTGC	2	217	0	AGATTGCATA	     0.96962	-84
AAGATCGTTAAGAACTCTGACTAAAGGCACAATTC	2	252	1	AGACTGCAAA	     0.99364	-49
          ***   *** * ***

Masking position 3
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

          ACACTCTCCTTAATCTAAGG	1	1	1	ACACTCTCCT	    0.861082	-80
TGCATTCTCGAAAATTTTCTTCGAACCCGA	1	42	1	AAAATTTTCT	    0.751751	-39
GCACTATGGAAGTGTTTCCTT         	2	2	0	AGTGTTTCCT	    0.942829	-299
TCTAAGGTATAGTATCTTCCAGCACTATGG	2	23	0	AGTATCTTCC	    0.839754	-278
ACCTTAGACTTCGATTTTCTGGAAGCACTC	2	45	1	TCGATTTTCT	    0.881718	-256
CCTTGGATTCACTATTTCCTCTTTAAAAAA	2	144	1	ACTATTTCCT	    0.966718	-157
CCTTCTTCCTAGGATTTTATAAGGTTTCTC	2	174	1	AGGATTTTAT	    0.816535	-127
AGAGTTCTTAACGATCTTCTCAGCTGACAG	2	240	0	ACGATCTTCT	    0.975094	-61
       AAAAGGGTATCCTTTTTTAGAGT	2	288	0	AGGGTATCCT	     0.67741	-13
          **********

Masking position 5
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	    0.986318	-31
GTGCTTCCAGAAAATCGAAGTCTAAGGTAT	2	43	0	AAAATCGAAG	    0.917079	-258
AGCATCTCAAGGAATAGAAGAAGGAAGAGT	2	71	0	GGAATAGAAG	     0.99027	-230
AGGATTCGGCGGATTAGCAGTTTGAACAAG	2	99	0	GGATTAGCAG	    0.969693	-202
GAGGAAATAGTGAATCCAAGGAATGGGTTA	2	135	0	TGAATCCAAG	    0.942502	-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