AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i033_Pyruvate_Synthase_1_synecho_reg_300.orf -o033_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	RCY19932	300	Synechocystis

Motif number 1

        TAATTTTTCCTAACTTTTTCTA	1	3	1	ATTTTTCCTA	    0.985437	-298
ATTTTTCCTAACTTTTTCTAAGTTGCGGGT	1	13	1	ACTTTTTCTA	    0.965797	-288
CACACCCAGGTTTTTTTCTATGGTTTAGAT	1	79	1	TTTTTTTCTA	    0.988989	-222
AGTTATGGCGTTTTTTCCGAAAGGAAATTC	1	195	1	TTTTTTCCGA	    0.990536	-106
GACAATATTATTTTTTTCGACTTTACGGAG	1	254	1	TTTTTTTCGA	    0.989791	-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

CCACTGGCCTACCCGCAACTTAGAAAAAGTTAG	1	20	0	ACCCAACTAG	     0.98393	-281
GGTAAAGCGAATCTAAACCATAGAAAAAAACCT	1	86	0	ACTAACCTAG	    0.855172	-215
GGTTTAGATTCGCTTTACCTTTGCTTTAAGCTC	1	100	1	CCTTACCTTG	    0.954415	-201
CAAGAAAAACCGCTTCAACAGAGCTTAAAGCAA	1	120	0	CCTCAACGAG	    0.976953	-181
TCGGAAAAAACGCCATAACTTCAAATTCTGTTA	1	182	0	CCCTAACTCA	    0.971522	-119
GGCTAGTTTACCCCACACCTGAATTTCCTTTCG	1	212	0	CCCCACCGAA	    0.983285	-89
ACCGAGGGTTCTCCGTAAAGTCGAAAAAAATAA	1	261	0	CCCTAAATCG	    0.815503	-40
TGACTATCGGCTCCTTAACCGAGGGTTCTCCGT	1	278	0	CCCTAACGAG	    0.964488	-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

AGTGGCGATCGCCGCCAGTCTAACTTTTGT	1	48	1	GCCGCCAGTC	    0.994857	-253
TTGGTTACAAGCTCAAAGTCACTCTAAAGA	1	150	1	GCTCAAAGTC	     0.98261	-151
GGGTAAACTAGCCCATAATCCTGACAATAT	1	232	1	GCCCATAATC	     0.98815	-69
CGGTTAAGGAGCCGATAGTCA         	1	290	1	GCCGATAGTC	    0.989512	-11
          **********

Masking position 7
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