AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i214_Ribosomal_Operon_1_synecho_reg_100.orf -o214_synecho_100.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 =  	0.48
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RCY42399	64	Synechocystis
#2	RCY23794	104	Synechocystis

Motif number 1

         CCAAGCCAAATTAGCAAGGCA	1	2	1	CAAGCCAAAT	    0.997161	-63
GCCAAATTAGCAAGGCAAATAATTATGTCC	1	15	1	CAAGGCAAAT	    0.997156	-50
          CAAGCTCAATGGGTTTGATT	2	1	1	CAAGCTCAAT	    0.992549	-104
ATCTGTGTCGCATGGTAACTGAACTCCTAA	2	71	0	CATGGTAACT	    0.981381	-34
          **********

Masking position 8
Map Score:   5.82148

Number of sites scoring better than the average of aligned sites = 130
Number in coding regions = 107
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 2

TTTCAAAAATACCCCCGCTTAATAACGGGA	1	42	0	ACCCCCGCTT	     0.99765	-23
GGGTTTGATTACTGCTGCTTGCCTTAGAGT	2	21	1	ACTGCTGCTT	    0.986354	-84
CCTTAGAGTAACCCCCTGTTGTTAATTTTT	2	42	1	ACCCCCTGTT	    0.993624	-63
          **********

Masking position 1
Map Score:   1.61618

Number of sites scoring better than the average of aligned sites = 364
Number in coding regions = 341
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 3

GCAAATAATTATGTCCCGTTATTAAGCGGG	1	29	1	ATGTCCCGTT	    0.992204	-36
CTCGACATCTGTGTCGCATGGTAACTGAAC	2	77	0	GTGTCGCATG	    0.994949	-28
TGCGACACAGATGTCGAGTGCCTCAG    	2	89	1	ATGTCGAGTG	     0.99524	-16
          **********

Masking position 4
Map Score:   1.2227

Number of sites scoring better than the average of aligned sites = 6
Number in coding regions = 5
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

ATAATTATGTCCCGTTATTAAGCGGGGGTA	1	33	1	CCCGTTATTA	    0.995329	-32
AGAGTAACCCCCTGTTGTTAATTTTTTAGG	2	46	1	CCTGTTGTTA	    0.995329	-59
          **********

Masking position 5
Map Score:   0.0547842

Number of sites scoring better than the average of aligned sites = 9
Number in coding regions = 7
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 5

          **********

No masking
Map Score:   -1.68098e-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:   -1.68098e-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:   -1.68098e-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