AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i017_Glycolysis___PPS_ctra_reg_100.orf -o017_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	RCT00177	116	Chlamydia_trachomatis
#2	RCT00178	24	Chlamydia_trachomatis
#3	RCT00359	112	Chlamydia_trachomatis

Motif number 1

AAAACATGGCTTTGCCATGAGGGATC        	1	3	0	TTTCGAGGGA	    0.982769	-114
GGCAAAGCCATGTTTTATGAGAGAGAAATCTTTT	1	21	1	TGTTGAGAGA	     0.96612	-96
AAAACGAATATGTGCCTAAAAAGATTTCTCTCTC	1	39	0	TGTCAAAAGA	    0.974813	-78
AGAGTGTTAATTTTTTAAGAGAGAGCCCACAATA	1	78	0	TTTTGAGAGA	    0.962221	-39
        TTTGTTTTGCAAGAGGTTGTATAC  	2	3	1	TGTTAAGAGG	    0.973431	-22
AGATAGTACAAGTAAAAAGAAAGAAGGTCTCTCG	3	63	1	AGTAGAAAGA	    0.868799	-50
TTTGAGGAAATGTGATACGAGAGACCTTCTTTCT	3	80	0	TGTTGAGAGA	     0.99728	-33
TCGTATCACATTTCCTCAAAAGGAGAATC     	3	94	1	TTTTAAAGGA	    0.928199	-19
          ***  *  ******

Masking position 10
Map Score:   10.9902

Number of sites scoring better than the average of aligned sites = 215
Number in coding regions = 215
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

CCTCATGGCAAAGCCATGTTTTATGAGAGAG	1	15	1	AAGCCATTTT	    0.977575	-102
TTAGGCACATATTCGTTTTTTTGGTATTGTG	1	54	1	ATTCGTTTTT	    0.979156	-63
TTTGTAGAACAATCGATCTTTTCATCTA   	3	8	0	AATCGATTTT	    0.985175	-105
ATCTTTCGCGATTCCATTTTTGTAGAACAAT	3	26	0	ATTCCATTTT	      0.9899	-87
GTGATACGAGAGACCTTCTTTCTTTTTACTT	3	72	0	AGACCTTTTT	    0.957672	-41
          ******* ***

Masking position 7
Map Score:   3.53022

Number of sites scoring better than the average of aligned sites = 81
Number in coding regions = 80
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

AAGCCATGTTTTATGAGAGAGAAATCTTTT	1	25	1	TTATGAGAGA	    0.982574	-92
TGTTAATTTTTTAAGAGAGAGCCCACAATA	1	78	0	TTAAGAGAGA	    0.990052	-39
AAAAATGGAATCGCGAAAGATCACGAAAGA	3	36	1	TCGCGAAAGA	    0.982289	-77
TCGCGAAAGATCACGAAAGATAGTACAAGT	3	46	1	TCACGAAAGA	    0.993286	-67
AGTACAAGTAAAAAGAAAGAAGGTCTCTCG	3	67	1	AAAAGAAAGA	    0.930691	-46
AGGAAATGTGATACGAGAGACCTTCTTTCT	3	80	0	ATACGAGAGA	    0.991748	-33
          **********

Masking position 6
Map Score:   10.0997

Number of sites scoring better than the average of aligned sites = 78
Number in coding regions = 78
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

          GATACAACCTAGTATAGAGT	1	107	0	GATACAACCT	    0.992881	-10
         GTATACAACCTCTTGCAAAAC	2	14	0	TATACAACCT	    0.994009	-11
TCTTTTTACTTGTACTATCTTTCGTGATCT	3	53	0	TGTACTATCT	    0.966662	-60
          **********

Masking position 4
Map Score:   0.775568

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 5

TTCGTTTTTTTGGTATTGTGGGCTCTCTCT	1	65	1	TGGTATTGTG	    0.991241	-52
TCTACAAAAATGGAATCGCGAAAGATCACG	3	31	1	TGGAATCGCG	    0.992351	-82
TCTCCTTTTGAGGAAATGTGATACGAGAGA	3	90	0	AGGAAATGTG	    0.984697	-23
          **********

Masking position 5
Map Score:   0.0330168

Number of sites scoring better than the average of aligned sites = 16
Number in coding regions = 16
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:   -2.46258e-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:   -2.46258e-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 8

          **********

No masking
Map Score:   -2.46258e-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