AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i244_regulatory1_synecho_reg_100.orf -o244_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	RCY47541	210	Synechocystis

Motif number 1

CGCCCACCATCCATGCAGTAGCTGGAAATG	1	88	0	CCATGCAGTA	     0.96964	-123
AACAGATTAGCCGCCCACCATCCATGCAGT	1	99	0	CCGCCCACCA	    0.995684	-112
TAGGGCATGGCCGTCCCTTAGTTGAACAGA	1	123	0	CCGTCCCTTA	    0.990293	-88
TAAGGGACGGCCATGCCCTAGAATTTGATG	1	133	1	CCATGCCCTA	    0.989255	-78
GACATCTTTTCAGCCCAACACCGCTATTTT	1	163	1	CAGCCCAACA	     0.95847	-48
CGCTATTTTTCCACCCCATAACTAGTTAAT	1	184	1	CCACCCCATA	    0.994474	-27
          **********

Masking position 10
Map Score:   7.02478

Number of sites scoring better than the average of aligned sites = 1056
Number in coding regions = 948
Number in noncoding regions = 108
Number of orfs with sites within 600 bp upstream = 118
Fraction of orfs with sites within 600 bp upstream = 0.0189528


Motif number 2

CGTAAACCCATTTCCAGCTACTGCATGGAT	1	80	1	TTTCCAGCTA	    0.923801	-131
TTGAACAGATTAGCCGCCCACCATCCATGC	1	102	0	TAGCCGCCCA	    0.724251	-109
TTCTAGGGCATGGCCGTCCCTTAGTTGAAC	1	126	0	TGGCCGTCCC	    0.876174	-85
GCTGAAAAGATGTCCATCAAATTCTAGGGC	1	147	0	TGTCCATCAA	    0.942441	-64
ATGGACATCTTTTCAGCCCAACACCGCTAT	1	160	1	TTTCAGCCCA	    0.977633	-51
CACCGCTATTTTTCCACCCCATAACTAGTT	1	181	1	TTTCCACCCC	    0.993615	-30
          **********

Masking position 1
Map Score:   5.1136

Number of sites scoring better than the average of aligned sites = 1983
Number in coding regions = 1783
Number in noncoding regions = 200
Number of orfs with sites within 600 bp upstream = 202
Fraction of orfs with sites within 600 bp upstream = 0.0324446


Motif number 3

AATGTTGCCAATGGGAAAGAGATAAAGACA	1	42	1	ATGGGAAAGA	    0.920024	-169
CTGCATGGATGGTGGGCGGCTAATCTGTTC	1	100	1	GGTGGGCGGC	    0.981399	-111
CCGTCCCTTAGTTGAACAGATTAGCCGCCC	1	113	0	GTTGAACAGA	    0.886186	-98
CTGTTCAACTAAGGGACGGCCATGCCCTAG	1	124	1	AAGGGACGGC	    0.967207	-87
ATGCCCTAGAATTTGATGGACATCTTTTCA	1	145	1	ATTTGATGGA	     0.86574	-66
AAATAGCGGTGTTGGGCTGAAAAGATGTCC	1	162	0	GTTGGGCTGA	    0.976253	-49
TTAACTAGTTATGGGGTGGAAAAATAGCGG	1	183	0	ATGGGGTGGA	    0.986394	-28
          **********

Masking position 9
Map Score:   3.08826

Number of sites scoring better than the average of aligned sites = 3001
Number in coding regions = 2700
Number in noncoding regions = 301
Number of orfs with sites within 600 bp upstream = 305
Fraction of orfs with sites within 600 bp upstream = 0.0489881


Motif number 4

          **********

No masking
Map Score:   3.71914e-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 5

          **********

No masking
Map Score:   3.71914e-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:   3.71914e-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