AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i009_synecho_ctra_300.orf -o009_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RCT00585	18	Chlamydia_trachomatis
#2	RCT00586	154	Chlamydia_trachomatis
#3	RCT00587	300	Chlamydia_trachomatis

Motif number 1

     TCTTGCTGCCTACAAGGA       	1	6	1	CTGCCTACAA	    0.984842	-13
GATCAGATTTAGGCCTAGAAAAACCCCTCC	2	29	0	AGGCCTAGAA	    0.990282	-126
TTATCTAAAAATCCCTAGATTTCTTGTTTT	2	72	1	ATCCCTAGAT	    0.946828	-83
AAGGAAAAATCGGCCTAGAAAGTGACAGTT	2	112	0	CGGCCTAGAA	    0.988242	-43
CCCAAACTATATCCCTACAAATCGCGAATT	3	93	0	ATCCCTACAA	    0.970899	-208
CACATACTGCATGCCTGCAGTGCATCCCCA	3	119	0	ATGCCTGCAG	    0.951818	-182
ATAAGCGAAGAGTTCTAGAGAAATGTAGGA	3	186	1	AGTTCTAGAG	    0.766963	-115
TTTGTTTGGCAGTCCTACATTTCTCTAGAA	3	198	0	AGTCCTACAT	    0.937106	-103
GGCGATTCTCCTGCCTATAGGGAGTTGGCC	3	277	1	CTGCCTATAG	    0.937879	-24
          **********

Masking position 6
Map Score:   11.1382

Number of sites scoring better than the average of aligned sites = 332
Number in coding regions = 294
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 2

AAGACGGGAGGGGTTTTTCTAGGCCTAAAT	2	23	1	GGGTTTTTCT	     0.99022	-132
CTGATCAACAGGCTTTTTTTTATCTAAAAA	2	53	1	GGCTTTTTTT	    0.941582	-102
CCTAGATTTCTTGTTTTTCTTAAGATAAAC	2	85	1	TTGTTTTTCT	    0.975958	-70
GGATTGATCATTGTTTTTTTGAATTTTGGA	3	60	0	TTGTTTTTTT	    0.971111	-241
GTATGACAAGGGGTTTTTTGAATAAGCGAA	3	165	1	GGGTTTTTTG	    0.982584	-136
AAATACAATAGTGTATTTTTTGTTTGGCAG	3	216	0	GTGTATTTTT	    0.967952	-85
AAATACACTATTGTATTTCGCGATACTTTC	3	228	1	TTGTATTTCG	    0.922379	-73
          **********

Masking position 6
Map Score:   8.89291

Number of sites scoring better than the average of aligned sites = 363
Number in coding regions = 290
Number in noncoding regions = 73
Number of orfs with sites within 600 bp upstream = 79
Fraction of orfs with sites within 600 bp upstream = 0.0126887


Motif number 3

TTATCTAAAAATCCCTAGATTTCTTGTTTT	2	72	1	ATCCCTAGAT	    0.888654	-83
ATCATAGTAGATTCTAAAACAGTTGATATT	3	31	1	ATTCTAAAAC	    0.763833	-270
AACAGTTGATATTCCAAAATTCAAAAAAAC	3	48	1	ATTCCAAAAT	    0.963775	-253
ACAATGATCAATCCCAAAATTCGCGATTTG	3	76	1	ATCCCAAAAT	    0.984403	-225
CCCAAACTATATCCCTACAAATCGCGAATT	3	93	0	ATCCCTACAA	    0.860301	-208
CCTGCAGTGCATCCCCAAACTATATCCCTA	3	106	0	ATCCCCAAAC	    0.989403	-195
CTCTTCGCTTATTCAAAAAACCCCTTGTCA	3	168	0	ATTCAAAAAA	    0.672906	-133
GAAATGTAGGACTGCCAAACAAAAAATACA	3	205	1	ACTGCCAAAC	    0.786657	-96
TAATGAAAGTATCGCGAAATACAATAGTGT	3	232	0	ATCGCGAAAT	    0.925419	-69
AGGCAGGAGAATCGCCAAAACGGGTGGGAG	3	263	0	ATCGCCAAAA	    0.963433	-38
          **********

Masking position 7
Map Score:   6.99058

Number of sites scoring better than the average of aligned sites = 1934
Number in coding regions = 1696
Number in noncoding regions = 238
Number of orfs with sites within 600 bp upstream = 258
Fraction of orfs with sites within 600 bp upstream = 0.0414391


Motif number 4

GGCCTAGAAAAACCCCTCCCGTCTTTTCTA	2	18	0	AACCCCTCCC	    0.970765	-137
AAAAAACAATGATCAATCCCAAAATTCGCG	3	71	1	GATCAATCCC	    0.928487	-230
GCATCCCCAAACTATATCCCTACAAATCGC	3	98	0	ACTATATCCC	    0.914991	-203
GCATGCCTGCAGTGCATCCCCAAACTATAT	3	111	0	AGTGCATCCC	    0.980976	-190
CCCATCACATACTGCATGCCTGCAGTGCAT	3	124	0	ACTGCATGCC	    0.925548	-177
TCATACTATTGGTCCTTCCCATCACATACT	3	141	0	GGTCCTTCCC	    0.957181	-160
CGATACTTTCATTACCTCCCACCCGTTTTG	3	248	1	ATTACCTCCC	     0.95485	-53
     AAAAGGCCAACTCCCTATAGGCAGG	3	286	0	GCCAACTCCC	    0.927035	-15
          **********

Masking position 7
Map Score:   3.01683

Number of sites scoring better than the average of aligned sites = 1550
Number in coding regions = 1382
Number in noncoding regions = 168
Number of orfs with sites within 600 bp upstream = 190
Fraction of orfs with sites within 600 bp upstream = 0.0305172


Motif number 5

          **********

No masking
Map Score:   -4.16788e-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:   -4.16788e-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:   -4.16788e-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