AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i307_mixed21_ctra_reg_100.orf -o307_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	RCT00577	197	Chlamydia_trachomatis

Motif number 1

          AATCTCCTTTGGATCTCTCT	1	1	1	AATCTCCTTT	    0.979257	-197
ATCTCCTTTGGATCTCTCTTTGACAAGGGA	1	12	1	GATCTCTCTT	    0.963755	-186
AGGAAGATAAGGTTTCCCTTGTCAAAGAGA	1	26	0	GGTTTCCCTT	    0.927976	-172
AGGGAAACCTTATCTTCCTGATTTTTGTTT	1	37	1	TATCTTCCTG	    0.972027	-161
TCCTGATTTTTGTTTTTTTGATCTACAGCA	1	52	1	TGTTTTTTTG	    0.859376	-146
TTCTTTCACTAAGCTTTTTTATTTTAAGAG	1	96	0	AAGCTTTTTT	    0.794714	-102
CGGCGATAAGAATTTTCTTTCACTAAGCTT	1	110	0	AATTTTCTTT	    0.926652	-88
TTATCGCCGCTATCATCCTGCCCATACTCT	1	131	1	TATCATCCTG	    0.845626	-67
ACAGAGGTGCTGTTTCTTTTTTTTGTCATC	1	165	1	TGTTTCTTTT	    0.899952	-33
       AAAAATCCCTTTGGATGACAAAA	1	185	0	AATCCCTTTG	    0.882266	-13
          **********

Masking position 9
Map Score:   6.74059

Number of sites scoring better than the average of aligned sites = 1384
Number in coding regions = 1381
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 2

TCCCTTGTCAAAGAGAGATCCAAAGGAGATT	1	11	0	AAAGAGATCC	    0.987375	-187
AATCAGGAAGATAAGGTTTCCCTTGTCAAAG	1	29	0	ATAGGTTTCC	    0.983622	-169
AGAGGTTTCCAACAGGGTTGCTGTAGATCAA	1	69	0	AAAGGGTTGC	    0.996739	-129
TTTTTATTTTAAGAGGTTTCCAACAGGGTTG	1	80	0	AAAGGTTTCC	    0.994965	-118
ATACTCTCTATACAGAGGTGCTGTTTCTTTT	1	154	1	TAAGAGGTGC	    0.960296	-44
          ** ********

Masking position 4
Map Score:   4.57307

Number of sites scoring better than the average of aligned sites = 68
Number in coding regions = 67
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 3

TTTTTGATCTACAGCAACCCTGTTGGAAAC	1	66	1	ACAGCAACCC	    0.997658	-132
AAAAAAAGAAACAGCACCTCTGTATAGAGA	1	158	0	ACAGCACCTC	    0.997646	-40
          **********

Masking position 6
Map Score:   0.36658

Number of sites scoring better than the average of aligned sites = 5
Number in coding regions = 5
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:   8.05918e-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:   8.05918e-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 6

          **********

No masking
Map Score:   8.05918e-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