AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i297_mixed12_ctra_reg_100.orf -o297_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	RCT00464	88	Chlamydia_trachomatis
#2	RCT00465	300	Chlamydia_trachomatis

Motif number 1

 AGAGTGGATTTTTCTTTTCGAGCTGTTGA	1	10	1	TTTTCTTTTC	    0.942659	-79
TCTGCGGATCATTTCTTTTTATGGGAAAAG	2	27	0	ATTTCTTTTT	    0.984642	-274
TAGAGATAAGAACTCTTTTCTGACTCGCCT	2	119	0	AACTCTTTTC	    0.828792	-182
AATAAAAATTATCTAATTTTGACAAAAAAC	2	165	0	ATCTAATTTT	    0.856929	-136
ATTAGATAATTTTTATTTTTCAAACATCTA	2	178	1	TTTTATTTTT	    0.976062	-123
AATAAATCGATTTTATTTTTAGATGTTTGA	2	197	0	TTTTATTTTT	    0.976062	-104
AATAAAATCGATTTATTATTCATGCAATAA	2	210	1	ATTTATTATT	    0.924416	-91
TTTTTTAATAATTTATTTTTTAAAATTATT	2	261	1	ATTTATTTTT	    0.987292	-40
TATTTTTTAAAATTATTTTTTATGGTGGCG	2	274	1	AATTATTTTT	    0.960706	-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

CACTTTTACCTTTGTCAACAGCTCGAAAAG	1	24	0	TTTGTCAACA	    0.988821	-65
AGCTCTTTATTTTGCCAACCACTTTTACCT	1	43	0	TTTGCCAACC	    0.981354	-46
CCTAAGAATCTTTTCCCATAAAAAGAAATG	2	18	1	TTTTCCCATA	    0.857439	-283
CTTGGATAGGTATGCCAACAAAGATGTGGA	2	82	1	TATGCCAACA	    0.942939	-219
GGGTCCGTTTTTTGTCAAAATTAGATAATT	2	159	1	TTTGTCAAAA	    0.966513	-142
ATAATTTTTATTTTTCAAACATCTAAAAAT	2	183	1	TTTTTCAAAC	    0.953258	-118
TTTGTCTGGCTTTTTTAATAATTTATTTTT	2	251	1	TTTTTTAATA	    0.848488	-50
TAATAATTTATTTTTTAAAATTATTTTTTA	2	266	1	TTTTTTAAAA	    0.843518	-35
          **********

Masking position 8
Map Score:   8.02215

Number of sites scoring better than the average of aligned sites = 213
Number in coding regions = 213
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

TCGAAAAGAAAAATCCACTCT          	1	1	0	AAATCACTCT	    0.966318	-88
CTTGATAGAAGAATCAGCTCTTTATTTTGCC	1	57	0	GAATCGCTCT	    0.997527	-32
TCCTCACCTTGAACCTCCTCTGCGGATCATT	2	44	0	GAACCCCTCT	    0.994596	-257
TCAAGGTGAGGAATCTGCTCTTGGATAGGTA	2	63	1	GAATCGCTCT	    0.997527	-238
ACTCTTTTCTGACTCGCCTATGCTATTCCAC	2	107	0	GACTCCCTAT	    0.972431	-194
          ***** *****

Masking position 9
Map Score:   6.38573

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 31
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

       AGAGTGGATTTTTCTTTTCGAGC	1	4	1	GTGGATTTTT	    0.910403	-85
AAAATAAAGAGCTGATTCTTCTATCAAGCA	1	60	1	GCTGATTCTT	     0.98233	-29
          GTAAATTCCTAAGAATCTTT	2	1	1	GTAAATTCCT	    0.934981	-300
TTTTATGGGAAAAGATTCTTAGGAATTTAC	2	11	0	AAAGATTCTT	     0.86647	-290
CTATCCAAGAGCAGATTCCTCACCTTGAAC	2	61	0	GCAGATTCCT	    0.985082	-240
GTCAAAATTAGATAATTTTTATTTTTCAAA	2	172	1	GATAATTTTT	    0.799404	-129
          **********

Masking position 5
Map Score:   1.40393

Number of sites scoring better than the average of aligned sites = 254
Number in coding regions = 254
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