AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i234_sensory_cassete_ctra_reg_300.orf -o234_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	RCT00600	178	Chlamydia_trachomatis

Motif number 1

          TTTCTCTCAAATTTTTCGATC	1	1	1	TTTCTTCAAA	    0.989791	-178
CTCTCAAATTTTTCGATCAAAAACTAGATAA	1	14	1	TTTCGTCAAA	    0.968591	-165
CTCATTCTCTGCTTTATCTAGTTTTTGATCG	1	27	0	GCTTTTCTAG	    0.915939	-152
GAGAATGAGCTGTTTATCACAGAACAAGTGT	1	49	1	TGTTTTCACA	    0.952825	-130
ATCTTCAGACTTTTTTTCAAGTTTAGACTAC	1	78	0	TTTTTTCAAG	    0.990244	-101
AGATATCGGTTTTTTTTCTGAGGCTCTTTGA	1	105	1	TTTTTTCTGA	    0.960094	-74
AACAAAAATAGTTTTTTCAAAGAGCCTCAGA	1	121	0	GTTTTTCAAA	    0.990244	-58
          ***** *****

Masking position 7
Map Score:   6.6427

Number of sites scoring better than the average of aligned sites = 236
Number in coding regions = 236
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

AAGCAGAGAATGAGCTGTTTATCACAGAACA	1	44	1	TGAGTGTTTA	    0.940143	-135
ACCGATATCTTCAGACTTTTTTTCAAGTTTA	1	84	0	TCAGCTTTTT	    0.988381	-95
TCTGAAGATATCGGTTTTTTTTCTGAGGCTC	1	100	1	TCGGTTTTTT	    0.988395	-79
GTTTTTTTTCTGAGGCTCTTTGAAAAAACTA	1	113	1	TGAGCTCTTT	    0.986417	-66
AATAGTTCAATGGGTTTATTTAT        	1	166	1	TGGGTTATTT	     0.98004	-13
          **** ******

Masking position 9
Map Score:   2.52012

Number of sites scoring better than the average of aligned sites = 114
Number in coding regions = 114
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

          **********

No masking
Map Score:   7.34864e-14

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 4

          **********

No masking
Map Score:   7.34864e-14

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 5

          **********

No masking
Map Score:   7.34864e-14

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