AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i021_Succinyl-CoA_Synthetase_synecho_reg_100.orf -o021_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	RCY10148	16	Synechocystis
#2	RCY23515	146	Synechocystis
#3	RCY51144	104	Synechocystis

Motif number 1

        CGGGGATCAACGGCGATCGCTA	2	3	1	GGGATCAACG	    0.992249	-144
TTTGGTGATGGGGGTCTACCCCCCTATCAG	2	33	0	GGGGTCTACC	    0.996288	-114
TATCTCTGCAGGCCTCCACCTTCCCCT   	2	130	1	GGCCTCCACC	    0.994897	-17
GCTTCACTGTATCGTCAACCAGAGCAAAAT	3	16	0	ATCGTCAACC	    0.967866	-89
CGCAGCTATCGGGGTCAACCAGTCCAAGCT	3	43	0	GGGGTCAACC	    0.999057	-62
TGCGGAGTAGGGCATCAAGCCACAGTTTTC	3	69	1	GGCATCAAGC	    0.992249	-36
          **********

Masking position 5
Map Score:   11.36

Number of sites scoring better than the average of aligned sites = 366
Number in coding regions = 323
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 2

GGGGTCTACCCCCCTATCAGTAGCGATCGCC	2	22	0	CCCCTTCAGT	    0.956637	-125
GGGGGGTAGACCCCCATCACCAAAGCCCCCA	2	39	1	CCCCCTCACC	    0.995599	-108
TCCAGTCATACCATCTTCCCTCATTATTGGG	2	66	0	CCATCTCCCT	    0.980906	-81
CCGGAAAAACCAGGACTCAGCAAGGTTTAGT	2	97	0	CAGGATCAGC	    0.899822	-50
CTGCAGGCCTCCACCTTCCCCT         	2	135	1	CCACCTCCCC	    0.994583	-12
TCAACCAGTCCAAGCTTCACTGTATCGTCAA	3	28	0	CAAGCTCACT	    0.978796	-77
TGGCTTGATGCCCTACTCCGCAGCTATCGGG	3	60	0	CCCTATCCGC	    0.964053	-45
AGTAGGGCATCAAGCCACAGTTTTCCTTTAA	3	74	1	CAAGCACAGT	    0.892151	-31
          ***** *****

Masking position 8
Map Score:   6.41117

Number of sites scoring better than the average of aligned sites = 3443
Number in coding regions = 3214
Number in noncoding regions = 229
Number of orfs with sites within 600 bp upstream = 224
Fraction of orfs with sites within 600 bp upstream = 0.0359782


Motif number 3

       ATTTTAGAGATCACTT       	1	4	1	TTAGAGATCA	    0.942135	-13
CCCCCTATCAGTAGCGATCGCCGTTGATCC	2	14	0	GTAGCGATCG	    0.997365	-133
GTGGAGGCCTGCAGAGATAGACCGGAAAAA	2	119	0	GCAGAGATAG	    0.990155	-28
GCCCTACTCCGCAGCTATCGGGGTCAACCA	3	52	0	GCAGCTATCG	    0.993634	-53
          **********

Masking position 7
Map Score:   3.14447

Number of sites scoring better than the average of aligned sites = 711
Number in coding regions = 674
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 4

TAGACCGGAAAAACCAGGACTCAGCAAGGT	2	102	0	AAACCAGGAC	    0.990524	-45
ACTGTATCGTCAACCAGAGCAAAATGTCCC	3	11	0	CAACCAGAGC	    0.996498	-94
CTATCGGGGTCAACCAGTCCAAGCTTCACT	3	38	0	CAACCAGTCC	    0.996386	-67
          **********

Masking position 6
Map Score:   1.37304

Number of sites scoring better than the average of aligned sites = 95
Number in coding regions = 84
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 5

          **********

No masking
Map Score:   -4.23894e-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:   -4.23894e-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:   -4.23894e-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