AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i113_Amino_Acid_Transport_4_ctra_reg_300.orf -o113_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	RCT00703	300	Chlamydia_trachomatis
#2	RCT00704	104	Chlamydia_trachomatis

Motif number 1

TACACTCTATGCAACGCCCTTTTTATAGGCTTG	1	35	0	GCAGCCCTTT	    0.991519	-266
TTTGCTTCTTGAATACACTCTATGCAACGCCCT	1	48	0	GAACACTCTT	    0.972266	-253
TATTCAAGAAGCAAACACCCTGTAGTTCTCTGG	1	66	1	GCACACCCTT	     0.99482	-235
CAAGGTTCTTGCAAAGATCTTTTCATTCCTACC	1	151	1	GCAGATCTTT	    0.926297	-150
TAAAATCTTAACAATCCCTCTCTATCCTCTCTG	1	184	0	ACACCCTCTT	    0.977906	-117
TTGGGATGTTGAAGCGCCTTTATAAACTATTTA	1	223	1	GAAGCCTTTT	    0.955542	-78
TAGTATTATAGCACAAATCTTATTAACTAAATA	1	250	0	GCAAATCTTT	    0.765181	-51
AGGCCATTCTAAAGGCCCCCTTTCCCCGGATAG	2	11	1	AAACCCCCTT	    0.948396	-94
CGGAAAATACAAAAGCCCCCTTTCTCCTATCCG	2	37	0	AAACCCCCTT	     0.96597	-68
          ***  ****** *

Masking position 3
Map Score:   10.2801

Number of sites scoring better than the average of aligned sites = 213
Number in coding regions = 211
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

CTTTTTATAGGCTTGCCAGCGGCTATTGATA	1	19	0	GCTTGCCAGG	    0.982056	-282
TAGTTCTCTGGATTCCCCGAGAGATTCTACC	1	88	1	GATTCCCCGG	    0.963005	-213
TTTGCAAGAACCTTGCCCCTAACAAAAAATC	1	135	0	CCTTGCCCCA	    0.989522	-166
TCTTTTCATTCCTACCCAGAGAGGATAGAGA	1	168	1	CCTACCCAGG	    0.937218	-133
CTAAAGGCCCCCTTTCCCCGGATAGGAGAAA	2	19	1	CCTTTCCCCG	    0.996855	-86
ACAAAAGCCCCCTTTCTCCTATCCGGGGAAA	2	31	0	CCTTTCTCCA	    0.931202	-74
CTACTCTTATGCTTTCACCCGCTTCGGAGGC	2	77	0	GCTTTCACCG	     0.97421	-28
          ********* *

Masking position 3
Map Score:   5.53466

Number of sites scoring better than the average of aligned sites = 159
Number in coding regions = 158
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

GCAACGCCCTTTTTATAGGCTTGCCAGCGG	1	28	0	TTTTATAGGC	    0.977028	-273
AACATGATTTTTTGTTAGGGGCAAGGTTCT	1	130	1	TTTGTTAGGG	    0.949328	-171
AAGATTTTAATTTGATTGGGATGTTGAAGC	1	208	1	TTTGATTGGG	    0.972188	-93
ACTAAATAGTTTATAAAGGCGCTTCAACAT	1	228	0	TTATAAAGGC	    0.957975	-73
AATTTATTTTTAATTTTGGCAGGTTT    	1	285	1	TAATTTTGGC	    0.849029	-16
AAGGGGGCCTTTAGAATGGCCT        	2	3	0	TTAGAATGGC	    0.972859	-102
          **********

Masking position 1
Map Score:   3.16752

Number of sites scoring better than the average of aligned sites = 151
Number in coding regions = 151
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

GCCGGTAGAATCTCTCGGGGAATCCAGAGA	1	92	0	TCTCTCGGGG	      0.9947	-209
CCCTCTCTATCCTCTCTGGGTAGGAATGAA	1	172	0	CCTCTCTGGG	    0.990303	-129
CCCCCTTTCTCCTATCCGGGGAAAGGGGGC	2	25	0	CCTATCCGGG	    0.994721	-80
          **********

Masking position 5
Map Score:   2.55794

Number of sites scoring better than the average of aligned sites = 4
Number in coding regions = 4
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:   3.08538e-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:   3.08538e-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 7

          **********

No masking
Map Score:   3.08538e-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