AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i174_Biotin_Biosynthesis_synecho_reg_100.orf -o174_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	RCY14039	107	Synechocystis
#2	RCY51943	111	Synechocystis

Motif number 1

TGATCAATTGGGTAGATGGATTTTAACCCG	1	24	1	GGTAGATGGA	    0.928448	-84
TTGTTGTATTGGGGGGTGGGTAATTC    	1	92	1	GGGGGGTGGG	    0.999443	-16
          TGGGAATGGGGACGCGGGGT	2	1	1	TGGGAATGGG	    0.966927	-111
GAATGGGGACGCGGGGTCAGTATATCGGCG	2	14	1	GCGGGGTCAG	    0.985298	-98
CAACGCTAGAGCTGGGTGGGCCA       	2	99	1	GCTGGGTGGG	    0.998174	-13
          **********

Masking position 7
Map Score:   5.09695

Number of sites scoring better than the average of aligned sites = 1546
Number in coding regions = 1406
Number in noncoding regions = 140
Number of orfs with sites within 600 bp upstream = 150
Fraction of orfs with sites within 600 bp upstream = 0.0240925


Motif number 2

CCCAATTGATCAAGTTAAGCACAGC     	1	6	0	CAAGTTAAGC	    0.981574	-102
GCTCATTGGTCAGCTCAAGCTTTACTAATC	1	57	1	CAGCTCAAGC	    0.998631	-51
 TGGCCCACCCAGCTCTAGCGTTGGAAAAC	2	93	0	CAGCTCTAGC	    0.997588	-19
          **********

Masking position 8
Map Score:   2.76012

Number of sites scoring better than the average of aligned sites = 51
Number in coding regions = 45
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

CTGTGCTTAACTTGATCAATTGGGTAGATGGAT	1	12	1	CTTGTCTTGG	    0.992484	-96
GTAGATGGATTTTAACCCGTAGGCTCATTGGTC	1	35	1	TTTACCTAGG	    0.979169	-73
CTAATCGTATTTTGTTGTATTGGGGGGTGGGTA	1	81	1	TTTGTGTTGG	    0.995895	-27
AATATCGGGTTTTGTTGACTAGGCGATCGCCGA	2	38	0	TTTGTGTAGG	    0.992965	-74
AAACGATGTGTTTAGTCTTTTAGTAGAATATCG	2	64	0	TTTATCTTAG	    0.966871	-48
          **** **  ****

Masking position 10
Map Score:   2.54906

Number of sites scoring better than the average of aligned sites = 347
Number in coding regions = 311
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 4

CTTTACTAATCGTATTTTGTTGTATTGGGG	1	76	1	CGTATTTTGT	    0.978668	-32
AATGGGGACGCGGGGTCAGTATATCGGCGA	2	15	1	CGGGGTCAGT	    0.989796	-97
AGTAGAATATCGGGTTTTGTTGACTAGGCG	2	46	0	CGGGTTTTGT	    0.996466	-66
TGGAAAACGATGTGTTTAGTCTTTTAGTAG	2	71	0	TGTGTTTAGT	    0.978667	-41
          **********

Masking position 6
Map Score:   3.1154

Number of sites scoring better than the average of aligned sites = 149
Number in coding regions = 136
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 5

ACGCGGGGTCAGTATATCGGCGATCGCCTA	2	22	1	AGTATATCGG	    0.996212	-90
GTCTTTTAGTAGAATATCGGGTTTTGTTGA	2	53	0	AGAATATCGG	    0.996212	-59
          **********

Masking position 5
Map Score:   1.28503

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 12
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 6

          **********

No masking
Map Score:   4.28758e-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:   4.28758e-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 8

          **********

No masking
Map Score:   4.28758e-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