AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i210_trans4_ctra_reg_100.orf -o210_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	RCT00092	37	Chlamydia_trachomatis
#2	RCT00095	117	Chlamydia_trachomatis
#3	RCT00805	28	Chlamydia_trachomatis
#4	RCT00806	252	Chlamydia_trachomatis

Motif number 1

       CAAAAAGACAATCCTTCTGAACTCCA	1	4	1	AAAGAAACTT	    0.900417	-34
GCTCTTCACTAACGAAGATTATTAGTAAAGAGA	2	11	0	AACGAGATTT	    0.920412	-107
CCCTTACCCATAAGAGGAGTATTA         	2	104	1	TAAGAGATTT	     0.98585	-14
GTGTATAGAAAAAGATTTATTTTTC        	4	3	0	AAAGATTTTT	    0.943186	-250
ATTCTTAATTCAAGAAAACCTTTTTTATCGGGT	4	51	0	CAAGAAACTT	    0.837216	-202
TTTCTTGAATTAAGAATTAGTTTGATTTTTTCT	4	67	1	TAAGATTGTT	    0.939821	-186
CAGAGAAATATAAGATGTCGATTAGGTGCTTTG	4	127	0	TAAGAGTGTT	    0.985639	-126
TTTGCTAGAGTAAGAAGTTTTTTTTCTCTGTGC	4	159	0	TAAGAGTTTT	    0.988912	-94
TACTCTAGCAAAAGATGTACATTAACAAACCTC	4	180	1	AAAGAGTCTT	     0.98615	-73
CAATTATACCTAAGAGGTTTGTTAATGTACATC	4	193	0	TAAGAGTTTT	    0.990277	-60
          ***** ** * **

Masking position 5
Map Score:   14.328

Number of sites scoring better than the average of aligned sites = 188
Number in coding regions = 188
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

TCGTTAGTGAAGAGCAAACATAAGAGCAGA	2	29	1	AGAGCAAACA	     0.95971	-89
TAAGGGAAAAAAAGCAAAAAAAATAATGCT	2	80	0	AAAGCAAAAA	    0.975492	-38
TTTTATGTGTATAGAAAAAGATTTATTTTT	4	12	0	ATAGAAAAAG	    0.953187	-241
AGCTATAACCCGATAAAAAAGGTTTTCTTG	4	44	1	CGATAAAAAA	    0.897268	-209
GATTTTTTCTAAATCAAAAACCCCTCATAA	4	90	1	AAATCAAAAA	    0.915669	-163
TTCTCTGCACAGAGAAAAAAAACTTCTTAC	4	153	1	AGAGAAAAAA	    0.982621	-100
ACTTCTTACTCTAGCAAAAGATGTACATTA	4	174	1	CTAGCAAAAG	    0.948155	-79
GTCTCCTTAAATACAAAAAATGCCGTAATG	4	228	0	ATACAAAAAA	    0.891828	-25
          **********

Masking position 6
Map Score:   7.67381

Number of sites scoring better than the average of aligned sites = 417
Number in coding regions = 416
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 3

          TCTCTTTACTAATAATCTTC	2	1	1	TCTCTTTACT	    0.940103	-117
TCTTATGTTTGCTCTTCACTAACGAAGATT	2	24	0	GCTCTTCACT	     0.99461	-94
GAGCCCTAGAGCTCTGCTCTTATGTTTGCT	2	41	0	GCTCTGCTCT	    0.996566	-77
GAGCTCTAGGGCTCTGCTCCGTTAGCATTA	2	57	1	GCTCTGCTCC	    0.994159	-61
ATCTTATATTTCTCTGCACAGAGAAAAAAA	4	144	1	TCTCTGCACA	    0.986493	-109
          **********

Masking position 5
Map Score:   7.30227

Number of sites scoring better than the average of aligned sites = 73
Number in coding regions = 73
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

     TCTCTTTACTAATAATCTTCGTTAG	2	6	1	TTACTAATAA	    0.897274	-112
TTTTTTTCCCTTACCCATAAGAGGAGTATT	2	97	1	TTACCCATAA	    0.966841	-21
ATCTTTTTCTATACACATAAAATTAGCTAT	4	20	1	ATACACATAA	     0.92704	-233
ACACATAAAATTAGCTATAACCCGATAAAA	4	32	1	TTAGCTATAA	    0.935582	-221
GGTTTTTGATTTAGAAAAAATCAAACTAAT	4	82	0	TTAGAAAAAA	    0.900186	-171
AACAAACCTCTTAGGTATAATTGGTCATTA	4	203	1	TTAGGTATAA	    0.849728	-50
GTCTCCTTAAATACAAAAAATGCCGTAATG	4	228	0	ATACAAAAAA	    0.838304	-25
          **********

Masking position 7
Map Score:   2.74587

Number of sites scoring better than the average of aligned sites = 138
Number in coding regions = 138
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:   -2.03625e-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:   -2.03625e-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:   -2.03625e-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