AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i033_Pyruvate_Synthase_1_synecho_reg_100.orf -o033_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	RCY19932	300	Synechocystis

Motif number 1

TAGAAAAAGTTAGGAAAAATTA        	1	3	0	TAGGAAAAAT	    0.983272	-298
ACCCGCAACTTAGAAAAAGTTAGGAAAAAT	1	13	0	TAGAAAAAGT	    0.960828	-288
ATCTAAACCATAGAAAAAAACCTGGGTGTG	1	79	0	TAGAAAAAAA	    0.987345	-222
GAATTTCCTTTCGGAAAAAACGCCATAACT	1	195	0	TCGGAAAAAA	    0.989121	-106
CTCCGTAAAGTCGAAAAAAATAATATTGTC	1	254	0	TCGAAAAAAA	    0.988266	-47
          **********

Masking position 5
Map Score:   8.26702

Number of sites scoring better than the average of aligned sites = 124
Number in coding regions = 88
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 2

CTAACTTTTTCTAAGTTGCGGGTAGGCCAGTGG	1	20	1	CTAGTTGGGT	    0.981359	-281
AGGTTTTTTTCTATGGTTTAGATTCGCTTTACC	1	86	1	CTAGGTTAGT	    0.835443	-215
GAGCTTAAAGCAAAGGTAAAGCGAATCTAAACC	1	100	0	CAAGGTAAGG	    0.947384	-201
TTGCTTTAAGCTCTGTTGAAGCGGTTTTTCTTG	1	120	1	CTCGTTGAGG	    0.977248	-181
TAACAGAATTTGAAGTTATGGCGTTTTTTCCGA	1	182	1	TGAGTTAGGG	    0.967033	-119
CGAAAGGAAATTCAGGTGTGGGGTAAACTAGCC	1	212	1	TTCGGTGGGG	    0.980613	-89
TTATTTTTTTCGACTTTACGGAGAACCCTCGGT	1	261	1	CGATTTAGGG	      0.8215	-40
ACGGAGAACCCTCGGTTAAGGAGCCGATAGTCA	1	278	1	CTCGTTAGGG	    0.967867	-23
          *** **** ** *

Masking position 7
Map Score:   5.52561

Number of sites scoring better than the average of aligned sites = 1594
Number in coding regions = 1411
Number in noncoding regions = 183
Number of orfs with sites within 600 bp upstream = 170
Fraction of orfs with sites within 600 bp upstream = 0.0273049


Motif number 3

ACAAAAGTTAGACTGGCGGCGATCGCCACT	1	48	0	GACTGGCGGC	    0.994591	-253
TCTTTAGAGTGACTTTGAGCTTGTAACCAA	1	150	0	GACTTTGAGC	    0.981708	-151
ATATTGTCAGGATTATGGGCTAGTTTACCC	1	232	0	GATTATGGGC	    0.987729	-69
         TGACTATCGGCTCCTTAACCG	1	290	0	GACTATCGGC	    0.989782	-11
          **********

Masking position 4
Map Score:   4.16292

Number of sites scoring better than the average of aligned sites = 97
Number in coding regions = 88
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 4

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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