AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i312_mixed26_synecho_reg_300.orf -o312_synecho_300.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	RCY33042	153	Synechocystis
#2	RCY51152	40	Synechocystis

Motif number 1

GAAGATTTTTCCTGGACGGGTAGAGAAAGG	1	24	1	CCTGGACGGG	    0.647123	-130
ACGGGTAGAGAAAGGATTGACGGAGTTAAG	1	39	1	AAAGGATTGA	    0.903604	-115
TTAGTTGAAACAAGGATGGGGGATAGGACA	1	69	1	CAAGGATGGG	    0.986885	-85
CCTGCCGGGGCAATGCCAGAAGCCCATTGT	1	105	0	CAATGCCAGA	    0.940555	-49
TGGTTTACTACCCTGCCGGGGCAATGCCAG	1	116	0	CCCTGCCGGG	    0.522297	-38
AAATTCTAATCAATGCTTGGTTTACTACCC	1	133	0	CAATGCTTGG	    0.974818	-21
CTCCCCTTAAACCTGATTGAGC        	2	29	1	ACCTGATTGA	    0.885974	-12
          **********

Masking position 5
Map Score:   5.93427

Number of sites scoring better than the average of aligned sites = 3618
Number in coding regions = 3339
Number in noncoding regions = 279
Number of orfs with sites within 600 bp upstream = 289
Fraction of orfs with sites within 600 bp upstream = 0.0464182


Motif number 2

CCGTCAATCCTTTCTCTACCCGTCCAGGAAA	1	31	0	TTCTCTACCC	    0.982596	-123
TGTACAATTTGTCCTATCCCCCATCCTTGTT	1	77	0	GTCTATCCCC	    0.994024	-77
ATGGGCTTCTGGCATTGCCCCGGCAGGGTAG	1	108	1	GGATTGCCCC	    0.981146	-46
TCAATGCTTGGTTTACTACCCTGCCGGGGCA	1	123	0	GTTACTACCC	    0.967713	-31
TTATCCCATAGGAATCTCCCCTTAAACCTGA	2	14	1	GGATCTCCCC	     0.99767	-27
          ** ********

Masking position 9
Map Score:   2.93086

Number of sites scoring better than the average of aligned sites = 776
Number in coding regions = 694
Number in noncoding regions = 82
Number of orfs with sites within 600 bp upstream = 97
Fraction of orfs with sites within 600 bp upstream = 0.0155798


Motif number 3

          **********

No masking
Map Score:   2.227e-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 4

          **********

No masking
Map Score:   2.227e-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:   2.227e-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