AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i312_mixed26_ctra_reg_100.orf -o312_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	RCT00337	60	Chlamydia_trachomatis
#2	RCT00338	300	Chlamydia_trachomatis

Motif number 1

ATAGAACTCCGTGCCACCCTTCCCCGCCTTTT	1	11	0	GTCCCCCTTC	    0.991102	-50
TTTGCTCTTAGTTACCCCTCTTTTCGATATTT	2	15	1	GTACCCTCTT	    0.955501	-286
TGACGGCTGGGTCCCTCCTCCCCTATAGCTTT	2	124	1	GTCCCCTCCC	    0.999351	-177
TTCTAAAAAAGAACCTACCCTCGTCCTAGGTA	2	156	0	GACCACCCTC	    0.958546	-145
GTTTGGGTGTTTGCCACATCTCTAGGGAGGCG	2	201	1	TTCCCATCTC	    0.978336	-100
TCTTTGGATCTTACCGCCTCCCTAGAGATGTG	2	215	0	TTCCCCTCCC	    0.997627	-86
ATTTTGGGTTGTTCCTCCTCCCCTTTTTCTTT	2	242	0	GTCCCCTCCC	    0.999351	-59
          ** ** ******

Masking position 5
Map Score:   13.2163

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 50
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

   TGATCTCAGAAAAGAAGTTAACTGTTC	1	44	0	AGAAAAGAAG	    0.973607	-17
GGTAACTAAGAGCAAAACAC          	2	1	0	AGCAAAACAC	    0.947131	-300
AGCCAAAGGAAACAAAAATGTATTTTTCTG	2	61	0	AACAAAAATG	    0.951136	-240
GAACACTTTTAACAAAAAAGCGTTATATCC	2	94	0	AACAAAAAAG	    0.989447	-207
CTTATATTCTAAAAAAGAACCTACCCTCGT	2	164	0	AAAAAAGAAC	    0.958562	-137
CAAACACCCAAACAAAGCAGCTTATATTCT	2	184	0	AACAAAGCAG	    0.987045	-117
GGTAAGATCCAAAGAAAAAGGGGAGGAGGA	2	232	1	AAAGAAAAAG	    0.933192	-69
          **********

Masking position 5
Map Score:   7.87937

Number of sites scoring better than the average of aligned sites = 211
Number in coding regions = 211
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

         AAAAGGCGGGGAAGGGTGGCA	1	2	1	AAAGGCGGGG	    0.997568	-59
TTAAATATCGAAAAGAGGGGTAACTAAGAG	2	19	0	AAAAGAGGGG	    0.985848	-282
GGTAAAAGCTATAGGGGAGGAGGGACCCAG	2	130	0	ATAGGGGAGG	    0.994849	-171
ATCCAAAGAAAAAGGGGAGGAGGAACAACC	2	238	1	AAAGGGGAGG	    0.997955	-63
          **********

Masking position 3
Map Score:   6.31982

Number of sites scoring better than the average of aligned sites = 23
Number in coding regions = 23
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

        GTGTTTTGCTCTTAGTTACCCCT	2	3	1	GTTTTGCTTT	    0.889059	-298
GTTACCCCTCTTTTCGATATTTAAGTGAAAA	2	25	1	TTTTCGATTT	    0.830027	-276
TTTTTGTTTCCTTTGGCTTGAGGATATAACG	2	73	1	CTTTGGCTGA	    0.954245	-228
CCCTCCTCCCCTATAGCTTTTACCTAGGACG	2	136	1	CTATAGCTTT	    0.859296	-165
AAGCTGCTTTGTTTGGGTGTTTGCCACATCT	2	191	1	GTTTGGGTTT	    0.982121	-110
TCCCCTTTTTCTTTGGATCTTACCGCCTCCC	2	225	0	CTTTGGATTT	    0.972612	-76
ACCTTAAGAATTTTGGGTTGTTCCTCCTCCC	2	252	0	TTTTGGGTGT	    0.976729	-49
ACCCAAAATTCTTAAGGTTTTTCTACCTAAA	2	265	1	CTTAAGGTTT	    0.889155	-36
GATTTGTAGTTTTTAGGTAGAAAAACCTTAA	2	276	0	TTTTAGGTGA	    0.865263	-25
          ******** **

Masking position 8
Map Score:   5.00919

Number of sites scoring better than the average of aligned sites = 315
Number in coding regions = 314
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 5

          **********

No masking
Map Score:   2.36911e-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:   2.36911e-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:   2.36911e-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