AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i013_Glycolysis___PPS_ctra_reg_100.orf -o013_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

        GATCCCTCATGGCAAAGCCATGTTTT	1	3	1	TCCCTCGAAA	    0.984318	-114
AAAAGATTTCTCTCTCATAAAACATGGCTTTGCC	1	21	0	TCTCTCAACA	    0.963417	-96
GAGAGAGAAATCTTTTTAGGCACATATTCGTTTT	1	39	1	TCTTTTGACA	    0.976981	-78
TATTGTGGGCTCTCTCTTAAAAAATTAACACTCT	1	78	1	TCTCTCAAAA	    0.959884	-39
  GTATACAACCTCTTGCAAAACAAA        	2	3	0	CCTCTTAACA	    0.975414	-22
CGAGAGACCTTCTTTCTTTTTACTTGTACTATCT	3	63	0	TCTTTCTACT	     0.87935	-50
AGAAAGAAGGTCTCTCGTATCACATTTCCTCAAA	3	80	1	TCTCTCAACA	    0.997506	-33
     GATTCTCCTTTTGAGGAAATGTGATACGA	3	94	0	TCCTTTAAAA	    0.934303	-19
          ******  *  ***

Masking position 12
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

GCCATGTTTTATGAGAGAGAAATCTTTTTA	1	27	1	ATGAGAGAGA	    0.988218	-90
TGTTAATTTTTTAAGAGAGAGCCCACAATA	1	78	0	TTAAGAGAGA	    0.990211	-39
AAAAATGGAATCGCGAAAGATCACGAAAGA	3	36	1	TCGCGAAAGA	    0.989022	-77
TCGCGAAAGATCACGAAAGATAGTACAAGT	3	46	1	TCACGAAAGA	    0.990873	-67
AGTACAAGTAAAAAGAAAGAAGGTCTCTCG	3	67	1	AAAAGAAAGA	    0.962213	-46
AGGAAATGTGATACGAGAGACCTTCTTTCT	3	80	0	ATACGAGAGA	    0.993752	-33
          **********

Masking position 6
Map Score:   10.951

Number of sites scoring better than the average of aligned sites = 82
Number in coding regions = 82
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

ATGAGAGAGAAATCTTTTTAGGCACATATTCG	1	37	1	AATCTTTTGG	    0.852054	-80
TTAGGCACATATTCGTTTTTTTGGTATTGTGG	1	54	1	ATTCTTTTTT	    0.965902	-63
         GATACAACCTAGTATAGAGTGTT	1	104	0	ATACACCTGT	    0.922445	-13
        GTATACAACCTCTTGCAAAACAAA	2	11	0	ATACACCTTT	    0.954555	-14
TTTGTAGAACAATCGATCTTTTCATCTA    	3	7	0	AATCATCTTT	     0.94902	-106
ATCTTTCGCGATTCCATTTTTGTAGAACAATC	3	25	0	ATTCATTTTG	    0.973096	-88
TACGAGAGACCTTCTTTCTTTTTACTTGTACT	3	67	0	CTTCTTCTTT	    0.922725	-46
         GATTCTCCTTTTGAGGAAATGTG	3	100	0	ATTCCCTTTG	    0.941084	-13
          **** **** **

Masking position 9
Map Score:   3.28135

Number of sites scoring better than the average of aligned sites = 329
Number in coding regions = 329
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:   -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 5

          **********

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 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