AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i194_dna_replication_ctra_reg_100.orf -o194_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	RCT00229	119	Chlamydia_trachomatis
#2	RCT00319	292	Chlamydia_trachomatis

Motif number 1

TAAACCTCCCTAGCAGTATACTCGGTTTTTTC	1	24	0	TAGCAGTTCT	     0.98233	-96
CATAATCGATTATCTAGGTGCTAGACCTAAAT	1	85	1	TATCTAGTCT	    0.980852	-35
TTCCTTGGATTAGCTAGATGCTGTTAAATTAT	2	49	1	TAGCTAGTCT	    0.992427	-244
ATATTTTTTATAGCTGTCTCATAATTTAACAG	2	69	0	TAGCTGTTAT	    0.861269	-224
TTTTCCCCTGTATTAATCTACTCTAACTTCGT	2	113	0	TATTAATTCT	    0.880761	-180
AAGAATAGTATAGCACGATTCTTTAGTTATGA	2	200	1	TAGCACGTCT	    0.979557	-93
CACGATTCTTTAGTTATGACCTCTTATCAAGT	2	213	1	TAGTTATACT	    0.772024	-80
TATGACCTCTTATCAAGTTTCTTCAAGAAGGT	2	227	1	TATCAAGTCT	    0.980852	-66
          ******* * **

Masking position 2
Map Score:   7.02443

Number of sites scoring better than the average of aligned sites = 186
Number in coding regions = 186
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

ACAAAAAGAAAAAACCGAGTATACTGCTAGGGA	1	17	1	AAACGGTATA	    0.904536	-103
TGCAAAATAAAGGTTAGGGTATAAACCTCCCTA	1	44	0	AGGAGGTATA	    0.995729	-76
TCCAAGGAATAGGCAAGCGTATCTCAAATTTTA	2	25	0	AGGAGGTATC	    0.993666	-268
AACTTCGTAAAAGAGAGAGTATATTTTTTATAG	2	88	0	AAGAGGTATA	    0.991219	-205
CTCTTTTACGAAGTTAGAGTAGATTAATACAGG	2	106	1	AAGAGGTAGA	    0.987006	-187
TTCTTCATCAAGAATAGTATAGCACGATTCTTT	2	191	1	AGAAGATAGC	    0.887086	-102
CCGAGATTCTTGGCCAGGATATAGTC       	2	277	1	TGGAGATATA	    0.929597	-16
          ***  ** *****

Masking position 11
Map Score:   5.71146

Number of sites scoring better than the average of aligned sites = 90
Number in coding regions = 90
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

AAAAAGATTAATGAAACCCATTCATAGTTT	2	162	1	ATGAAACCCA	    0.889894	-131
ATTCTTGATGAAGAAAACTATGAATGGGTT	2	176	0	AAGAAAACTA	    0.930308	-117
TTTCTTCATCAAGAATAGTATAGCACGATT	2	190	1	AAGAATAGTA	    0.930315	-103
GTCATAACTAAAGAATCGTGCTATACTATT	2	203	0	AAGAATCGTG	    0.984149	-90
TACCTTCTTGAAGAAACTTGATAAGAGGTC	2	230	0	AAGAAACTTG	     0.97571	-63
TATCCTGGCCAAGAATCTCGGAAAAATTGT	2	268	0	AAGAATCTCG	    0.970847	-25
          **********

Masking position 5
Map Score:   3.08991

Number of sites scoring better than the average of aligned sites = 136
Number in coding regions = 135
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 4

GGAGGTTTATACCCTAACCTTTATTTTGCA	1	47	1	ACCCTAACCT	    0.989459	-73
          AGCCTCACTTTAAATAAAAT	2	1	1	AGCCTCACTT	    0.963946	-292
TAAAAAATATACTCTCTCTTTTACGAAGTT	2	91	1	ACTCTCTCTT	    0.983834	-202
GTATTAATCTACTCTAACTTCGTAAAAGAG	2	106	0	ACTCTAACTT	    0.987769	-187
         GACTATATCCTGGCCAAGAAT	2	282	0	ACTATATCCT	    0.920124	-11
          **********

Masking position 5
Map Score:   3.49213

Number of sites scoring better than the average of aligned sites = 51
Number in coding regions = 51
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

AACCTTTATTTTGCATCTATCCTCATAATC	1	62	1	TTGCATCTAT	    0.771603	-58
TATTTAGGTCTAGCACCTAGATAATCGATT	1	88	0	TAGCACCTAG	     0.93857	-32
CATAATTTAACAGCATCTAGCTAATCCAAG	2	52	0	CAGCATCTAG	    0.991444	-241
GTAAACTAATCAGCAAAAAGATTAATGAAA	2	148	1	CAGCAAAAAG	    0.945304	-145
TCATAGTTTTCTTCATCAAGAATAGTATAG	2	183	1	CTTCATCAAG	    0.631241	-110
TATCAAGTTTCTTCAAGAAGGTACCGCCCG	2	237	1	CTTCAAGAAG	    0.636591	-56
GATTCTTGGCCAGGATATAGTC        	2	281	1	CAGGATATAG	    0.889534	-12
          **********

Masking position 5
Map Score:   1.35941

Number of sites scoring better than the average of aligned sites = 462
Number in coding regions = 457
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 6

          **********

No masking
Map Score:   4.78496e-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:   4.78496e-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:   4.78496e-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