AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i198_synecho_ctra_100.orf -o198_synecho_ctra_100.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	RCY30474	106	Synechocystis
#2	RCT00560	161	Chlamydia_trachomatis

Motif number 1

ACCGGAGAGGGGAAGGGGATGCCCCTATAA	1	68	1	GGAAGGGGAT	    0.990784	-39
AAAGGATCATAGCGAGGGATTCAATTCTGT	2	21	0	AGCGAGGGAT	    0.992216	-141
TTCCCTTAGTAGAAAAGGATCATAGCGAGG	2	34	0	AGAAAAGGAT	    0.990045	-128
GAGAAGGCTCGGAGGGAGATTCCCTTAGTA	2	53	0	GGAGGGAGAT	    0.974008	-109
CGCAATACAAAGAGAAGGCTCGGAGGGAGA	2	64	0	AGAGAAGGCT	    0.987861	-98
TAACCGTTCTAGACAAGGATCTTGTT    	2	146	1	AGACAAGGAT	    0.988111	-16
          **********

Masking position 10
Map Score:   8.292

Number of sites scoring better than the average of aligned sites = 361
Number in coding regions = 313
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 55
Fraction of orfs with sites within 600 bp upstream = 0.00883392


Motif number 2

GGGGGAAAGTTGTCGCTCTGTGACCTCCGT	1	20	0	TGTCGCTCTG	    0.975524	-87
GAGCGACAACTTTCCCCCCGTATCCAGGGC	1	32	1	TTTCCCCCCG	    0.987574	-75
TCTCCGGTATTTCTGCCCTGGATACGGGGG	1	46	0	TTCTGCCCTG	    0.866482	-61
GCATCCCCTTCCCCTCTCCGGTATTTCTGC	1	60	0	CCCCTCTCCG	     0.98093	-47
GAATTGAATCCCTCGCTATGATCCTTTTCT	2	24	1	CCTCGCTATG	    0.943519	-138
ACTAAGGGAATCTCCCTCCGAGCCTTCTCT	2	54	1	TCTCCCTCCG	    0.994134	-108
CCCTCCGAGCCTTCTCTTTGTATTGCGGTC	2	67	1	CTTCTCTTTG	    0.860166	-95
GTTTTATCTAATTTCCTCCGATGAGCATGT	2	99	0	ATTTCCTCCG	    0.907037	-63
          **********

Masking position 6
Map Score:   6.44282

Number of sites scoring better than the average of aligned sites = 2403
Number in coding regions = 2171
Number in noncoding regions = 232
Number of orfs with sites within 600 bp upstream = 254
Fraction of orfs with sites within 600 bp upstream = 0.0407967


Motif number 3

TGTCGCTCTGTGACCTCCGTTGGCAAAAG 	1	10	0	TGACCTCCGT	    0.992406	-97
   ACACAGTTGACAGCCATAATTATAGGG	1	90	0	TGACAGCCAT	    0.995413	-17
TGAGCATGTATGACCGCAATACAAAGAGAA	2	78	0	TGACCGCAAT	    0.995413	-84
GAACGGTTAATGAAAGCAGTTCGCTCGTTT	2	125	0	TGAAAGCAGT	    0.982019	-37
          **********

Masking position 3
Map Score:   4.79193

Number of sites scoring better than the average of aligned sites = 131
Number in coding regions = 121
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 4

AAAAGGATCATAGCGAGGGATTCAATTCTG	2	22	0	TAGCGAGGGA	    0.989366	-140
ATTCCCTTAGTAGAAAAGGATCATAGCGAG	2	35	0	TAGAAAAGGA	    0.990017	-127
CCGCAATACAAAGAGAAGGCTCGGAGGGAG	2	65	0	AAGAGAAGGC	    0.984325	-97
TTAACCGTTCTAGACAAGGATCTTGTT   	2	145	1	TAGACAAGGA	    0.993242	-17
          **********

Masking position 6
Map Score:   3.32115

Number of sites scoring better than the average of aligned sites = 60
Number in coding regions = 51
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 5

          **********

No masking
Map Score:   3.15071e-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:   3.15071e-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:   3.15071e-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