AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i297_mixed12_ctra_reg_300.orf -o297_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	RCT00464	88	Chlamydia_trachomatis
#2	RCT00465	300	Chlamydia_trachomatis

Motif number 1

TCAACAGCTCGAAAAGAAAAATCCACTCT 	1	10	0	GAAAAGAAAA	    0.946706	-79
CTTTTCCCATAAAAAGAAATGATCCGCAGA	2	27	1	AAAAAGAAAT	    0.985771	-274
AGGCGAGTCAGAAAAGAGTTCTTATCTCTA	2	119	1	GAAAAGAGTT	    0.839506	-182
GTTTTTTGTCAAAATTAGATAATTTTTATT	2	165	1	AAAATTAGAT	    0.866166	-136
TAGATGTTTGAAAAATAAAAATTATCTAAT	2	178	0	AAAAATAAAA	    0.977806	-123
TCAAACATCTAAAAATAAAATCGATTTATT	2	197	1	AAAAATAAAA	    0.977806	-104
TTATTGCATGAATAATAAATCGATTTTATT	2	210	0	AATAATAAAT	    0.929634	-91
AATAATTTTAAAAAATAAATTATTAAAAAA	2	261	0	AAAAATAAAT	    0.988228	-40
CGCCACCATAAAAAATAATTTTAAAAAATA	2	274	0	AAAAATAATT	    0.963502	-27
          **********

Masking position 4
Map Score:   14.0599

Number of sites scoring better than the average of aligned sites = 248
Number in coding regions = 248
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

          AGAGTGGATTTTTCTTTTCGA	1	1	1	AGAGGGATTT	     0.97317	-88
GGCAAAATAAAGAGCTGATTCTTCTATCAAG	1	57	1	AGAGTGATTC	    0.993273	-32
TCTTTTTATGGGAAAAGATTCTTAGGAATTT	2	13	0	GGAAAGATTC	    0.977744	-288
TCCCATAAAAAGAAATGATCCGCAGAGGAGG	2	31	1	AGAATGATCC	    0.958871	-270
AATGATCCGCAGAGGAGGTTCAAGGTGAGGA	2	44	1	AGAGAGGTTC	    0.989104	-257
TACCTATCCAAGAGCAGATTCCTCACCTTGA	2	63	0	AGAGAGATTC	    0.996384	-238
TAGGCGAGTCAGAAAAGAGTTCTTATCTCTA	2	118	1	AGAAAGAGTT	    0.923058	-183
          **** ******

Masking position 3
Map Score:   9.29808

Number of sites scoring better than the average of aligned sites = 151
Number in coding regions = 149
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 3

CTTTTCGAGCTGTTGACAAAGGTAAAAGTG	1	24	1	TGTTGACAAA	    0.992601	-65
AGGTAAAAGTGGTTGGCAAAATAAAGAGCT	1	43	1	GGTTGGCAAA	    0.993777	-46
TCCACATCTTTGTTGGCATACCTATCCAAG	2	82	0	TGTTGGCATA	    0.978257	-219
AATTATCTAATTTTGACAAAAAACGGACCC	2	159	0	TTTTGACAAA	    0.981562	-142
ATTTTTAGATGTTTGAAAAATAAAAATTAT	2	183	0	GTTTGAAAAA	    0.924328	-118
          **********

Masking position 4
Map Score:   6.51357

Number of sites scoring better than the average of aligned sites = 23
Number in coding regions = 23
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

       AGAGTGGATTTTTCTTTTCGAGC	1	4	1	GTGGATTTTT	    0.895325	-85
AAAATAAAGAGCTGATTCTTCTATCAAGCA	1	60	1	GCTGATTCTT	    0.979027	-29
          GTAAATTCCTAAGAATCTTT	2	1	1	GTAAATTCCT	    0.924771	-300
TTTTATGGGAAAAGATTCTTAGGAATTTAC	2	11	0	AAAGATTCTT	    0.830267	-290
CTCCTCTGCGGATCATTTCTTTTTATGGGA	2	31	0	GATCATTTCT	    0.877781	-270
CTATCCAAGAGCAGATTCCTCACCTTGAAC	2	61	0	GCAGATTCCT	    0.982568	-240
GTCAAAATTAGATAATTTTTATTTTTCAAA	2	172	1	GATAATTTTT	    0.873019	-129
          **********

Masking position 5
Map Score:   2.10692

Number of sites scoring better than the average of aligned sites = 372
Number in coding regions = 372
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:   7.84029e-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:   7.84029e-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:   7.84029e-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