AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i257_hsp60_hsp10_ctra_reg_300.orf -o257_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	RCT00107	37	Chlamydia_trachomatis
#2	RCT00108	171	Chlamydia_trachomatis
#3	RCT00109	300	Chlamydia_trachomatis

Motif number 1

       TGATGCGCTCCTTAAATCTTCTTCAC	1	22	0	TCGCTCCTTA	    0.988549	-16
GATAGCAAAGTCCTCGCTTTTTTGCAACTGGTT	2	47	0	TCTCGCTTTT	    0.955185	-125
GCGAGGACTTTGCTATCGTTCTTCCTCTGAACG	2	63	1	TCTATCGTTT	    0.919383	-109
CCTCTGAACGTTCTATCGTTCAAATCCCTACGT	2	86	1	TCTATCGTTA	    0.870534	-86
       GTTTAAGCTCCTCGTATTTTTATATT	2	156	0	TAGCTCCTCA	    0.895102	-16
TTCTCAGAATTGATAGCCTTTGTAACAGGTGTG	3	22	0	TATAGCCTTT	    0.844991	-279
TCAAATGATCTTAGCTCTTTTATTGACTGTAAG	3	112	0	TAGCTCTTTT	    0.975114	-189
TGATCGAAACTACTCTCTTTGATCAAGAAACAG	3	188	1	TCTCTCTTTT	    0.982312	-113
GGGAAGAGAGTTAGCTGTTTCTTGATCAAAGAG	3	202	0	TAGCTGTTTT	    0.820656	-99
AGCTAAATCATCAGCTCCTTGGTTAGGATAGCC	3	241	0	TAGCTCCTTT	    0.987176	-60
        GAATCTCTCCTTAGAGGAAGCTGTT	3	286	0	ACTCTCCTTA	    0.890996	-15
          * ********  *

Masking position 9
Map Score:   8.79194

Number of sites scoring better than the average of aligned sites = 506
Number in coding regions = 506
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

   ATTTTTAAAAATAGCAGTTGATCATGCC	2	8	1	AAATAGCAGT	    0.927803	-164
TTTTGCAACTGGTTTAGCAGTTGGCATGATC	2	30	0	GGTTAGCAGT	    0.964119	-142
CACATCGATCAATAAAGCAGACCTCATATCC	3	66	1	AATAAGCAGA	    0.933888	-235
ACTGTAAGAGAATTAAGCTGTATGGATATGA	3	89	0	AATAAGCTGT	    0.976895	-212
AAGGGGAAGAGAGTTAGCTGTTTCTTGATCA	3	207	0	GAGTAGCTGT	    0.989503	-94
AGGAGCTGATGATTTAGCTGACACAAACATA	3	255	1	GATTAGCTGA	    0.980185	-46
TCTCTCCTTAGAGGAAGCTGTTTATGTTTGT	3	277	0	GAGAAGCTGT	    0.986375	-24
          *** *******

Masking position 6
Map Score:   7.72536

Number of sites scoring better than the average of aligned sites = 93
Number in coding regions = 93
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

GAAGATTTAAGGAGCGCATCA          	1	27	1	GAGCGCATCA	    0.954465	-11
TTTAAAAATAGCAGTTGATCATGCCAACTGC	2	14	1	GAGTTGATCA	    0.882711	-158
GATAGAACGTTCAGAGGAAGAACGATAGCAA	2	72	0	TAGAGGAAGA	     0.97578	-100
CCCTACGTTGGTAGCGGAACAAAGCCGGACC	2	111	1	GAGCGGAACA	    0.993042	-61
GGATAGCCAGTAAGGGGAAGAGAGTTAGCTG	3	218	0	TAGGGGAAGA	    0.971319	-83
TCCTAACCAAGGAGCTGATGATTTAGCTGAC	3	246	1	GAGCTGATGA	    0.974523	-55
GAATCTCTCCTTAGAGGAAGCTGTTTATGTT	3	280	0	TAGAGGAAGC	    0.925364	-21
          * *********

Masking position 8
Map Score:   3.4847

Number of sites scoring better than the average of aligned sites = 244
Number in coding regions = 244
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:   7.2008e-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 5

          **********

No masking
Map Score:   7.2008e-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:   7.2008e-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