AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i295_mixed10_ctra_reg_300.orf -o295_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	RCT00096	300	Chlamydia_trachomatis
#2	RCT00430	300	Chlamydia_trachomatis

Motif number 1

AAGGAACTATAACCAACCCGACTTTTTCCGCA	1	23	1	AACAACCCGC	    0.928238	-278
CGCAAACGACATTCATCCCCCTCCGATATCCT	1	51	1	ATCATCCCCT	      0.9905	-250
TATTCCATCTAAACATCCCCATGGAAAGGACT	1	103	0	AACATCCCCT	    0.994054	-198
AAGTAATAAGATGCATCTCTTTATTAAAAAAA	1	193	0	ATCATCTCTT	    0.905871	-108
TATCTATGGGTACCATCCCTGCTCTGAGTTCT	2	142	1	TACATCCCTC	    0.966345	-159
CTCTGAGTTCTAAGAACCCTCTACCAGAGTCG	2	163	1	TAGAACCCTT	    0.867855	-138
ATTTCTAAGAAACCATCCCCATATCGCTAGTA	2	206	0	AACATCCCCT	    0.994055	-95
TGAGGGGGATATGGATCCCTATAATTCTCAGA	2	237	1	ATGATCCCTT	    0.968132	-64
          ** ******* *

Masking position 5
Map Score:   8.29686

Number of sites scoring better than the average of aligned sites = 119
Number in coding regions = 118
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

GATATCCTTGAAAATCTCAAGGATTGACAG	1	75	1	AAAATCTCAA	    0.964818	-226
TTCGACACACAAAATCTAAAACTAAAATTA	1	145	1	AAAATCTAAA	     0.97605	-156
ATGTTCTCCTAAAAACTACAAAGTCAAAAA	1	275	0	AAAAACTACA	    0.922662	-26
CCGCAACCATCAAAACAAAACTTCAAATAT	2	29	1	CAAAACAAAA	    0.903043	-272
AACAAAACTTCAAATATAAAAATTTTTATT	2	42	1	CAAATATAAA	    0.930678	-259
AAGCATCAGCAAAATAAAAATTTTTATATT	2	54	0	AAAATAAAAA	    0.828663	-247
AGAGAACAGCCAAATCTCCAGCCACTATAG	2	266	1	CAAATCTCCA	    0.957053	-35
          **********

Masking position 4
Map Score:   4.6436

Number of sites scoring better than the average of aligned sites = 153
Number in coding regions = 153
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

          CTTTTACAAAAAAAGGAACTATAACCAA	1	1	1	CTTTAAAGGA	    0.978208	-300
ACCAACCCGACTTTTTCCGCAAACGACATTCATCCCCC	1	34	1	CTTTGAAGAA	    0.978215	-267
ACTAGTGAAACTTTTTTTAATAAAGAGATGCATCTTAT	1	182	1	CTTTATAGAA	    0.988617	-119
CATCTTATTACTTGTAGTGCAAGGGAAATCTTGCCTTT	1	212	1	CTTTGAAGAA	    0.978212	-89
ATTATCAAGTCTCCTCTGAATAGAGAAACCAGTTCTTC	2	98	0	CTCTATAGAA	    0.990287	-203
GAGTCGCCACCTCTTCCTACTAGCGATATGGGGATGGT	2	189	1	CTCTATAGAA	    0.990559	-112
TTTGGCTGTTCTCTGAGAATTATAGGGATCCATATCCC	2	242	0	CTCGATAGGA	    0.955994	-59
          *** *   * **  ** *

Masking position 12
Map Score:   4.18556

Number of sites scoring better than the average of aligned sites = 55
Number in coding regions = 55
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

CATGGGGATGTTTAGATGGAATATTTATAA	1	112	1	TTTAGATGGA	    0.817566	-189
GTTTCACTAGTTTCTGTGTAATTTTAGTTT	1	163	0	TTTCTGTGTA	      0.8276	-138
CTTGCCTTTTTTAAGGTGAATATTTACACT	1	241	1	TTAAGGTGAA	    0.805555	-60
CTTTGTAGTTTTTAGGAGAACATCATTAA 	1	282	1	TTTAGGAGAA	    0.973747	-19
AAAATAGATTTTTAGAAGAACTGGTTTCTC	2	84	1	TTTAGAAGAA	    0.958949	-217
CCTGCTCTGAGTTCTAAGAACCCTCTACCA	2	159	1	GTTCTAAGAA	    0.861334	-142
ATCCCCCTCATTTCTAAGAAACCATCCCCA	2	217	0	TTTCTAAGAA	    0.958936	-84
ATTTGGCTGTTCTCTGAGAATTATAGGGAT	2	251	0	TCTCTGAGAA	    0.907855	-50
          **********

Masking position 10
Map Score:   3.3791

Number of sites scoring better than the average of aligned sites = 386
Number in coding regions = 386
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

TTCAAGGATATCGGAGGGGGATGAATGTCG	1	57	0	TCGGAGGGGG	    0.996713	-244
GTTTCTCTATTCAGAGGAGACTTGATAATA	2	107	1	TCAGAGGAGA	    0.972021	-194
TTCTTAGAACTCAGAGCAGGGATGGTACCC	2	149	0	TCAGAGCAGG	    0.980885	-152
ATATCGCTAGTAGGAAGAGGTGGCGACTCT	2	188	0	TAGGAAGAGG	    0.959829	-113
GTTTCTTAGAAATGAGGGGGATATGGATCC	2	225	1	AATGAGGGGG	    0.937498	-76
          **********

Masking position 5
Map Score:   1.24111

Number of sites scoring better than the average of aligned sites = 91
Number in coding regions = 91
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:   1.30983e-12

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:   1.30983e-12

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:   1.30983e-12

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