AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i209_rpod_synecho_reg_100.orf -o209_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	RCY17385	152	Synechocystis

Motif number 1

CCGGTGAAGGAGAGTGCAATTTGCAGATTATTC	1	32	0	AGAGGAATTG	    0.997641	-121
CCTTCACCGGGGGGTGCTTTTTGCTGGTTGACC	1	55	1	GGGGGTTTTG	    0.985366	-98
ATGCTTGAGTAGAGCTTAAGTTGACAAGTATCT	1	88	1	AGAGTAATTG	    0.984973	-65
GTGACGATGGGGAGAGATACTTGTCAACTTAAG	1	102	0	GGAGGTATTG	    0.997837	-51
TCTCCTTCTAAGAGTGACGATGGGGAGAGATAC	1	115	0	AGAGGCGTGG	    0.989877	-38
ACTCTTAGAAGGAGAGTAGGTTGATTTATC   	1	133	1	GGAGGAGTTG	     0.99861	-20
          **** * ** ***

Masking position 11
Map Score:   9.46319

Number of sites scoring better than the average of aligned sites = 264
Number in coding regions = 230
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 2

ATCTGCAAATTGCACTCTCCTTCACCGGGG	1	37	1	TGCACTCTCC	    0.987563	-116
ACCAGCAAAAAGCACCCCCCGGTGAAGGAG	1	53	0	AGCACCCCCC	    0.996275	-100
TGTCAACTTAAGCTCTACTCAAGCATGGTC	1	84	0	AGCTCTACTC	    0.986365	-69
GTTGACAAGTATCTCTCCCCATCGTCACTC	1	107	1	ATCTCTCCCC	    0.995352	-46
TAAATCAACCTACTCTCCTTCTAAGAGTGA	1	131	0	TACTCTCCTT	    0.927061	-22
          **********

Masking position 5
Map Score:   5.54584

Number of sites scoring better than the average of aligned sites = 934
Number in coding regions = 828
Number in noncoding regions = 106
Number of orfs with sites within 600 bp upstream = 109
Fraction of orfs with sites within 600 bp upstream = 0.0175072


Motif number 3

          **********

No masking
Map Score:   6.63809e-14

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 4

          **********

No masking
Map Score:   6.63809e-14

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:   6.63809e-14

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