AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i262_3_5_1_28_synecho_reg_100.orf -o262_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	RCY35276	173	Synechocystis

Motif number 1

GATGAACGCCTGGACTGGATCTGTCAAAAAAT	1	30	1	TGGACGGTCT	     0.93534	-144
TGTCAAAAAATGTTACAGATTGGCTCTAATTA	1	51	1	TGTTAAGTTG	    0.926791	-123
TACCAAAATTTGTTAAGCTTTGTATCTAATTA	1	77	0	TGTTAGCTTG	    0.981375	-97
TAACAAATTTTGGTAGGCCTAGGGGTCAGCAT	1	94	1	TGGTAGCTAG	    0.979519	-80
GTAGGCCTAGGGGTCAGCATTGCCAAGGCGGC	1	106	1	GGGTCGCTTG	     0.99519	-68
TTATGGGGATGGGGCCGCCTTGGCAATGCTGA	1	119	0	GGGGCGCTTG	    0.994204	-55
TAAGAATATTTGGACGAGTTTTATGGGGATGG	1	139	0	TGGACAGTTT	    0.948433	-35
         ATGGGAAACGTTTTAAGAATATT	1	161	0	TGGGAACTTT	    0.966867	-13
          ***** ** ***

Masking position 10
Map Score:   8.40535

Number of sites scoring better than the average of aligned sites = 2281
Number in coding regions = 2087
Number in noncoding regions = 194
Number of orfs with sites within 600 bp upstream = 223
Fraction of orfs with sites within 600 bp upstream = 0.0358175


Motif number 2

AATGGCGGAGTAGGGAAAGGATGAACGCCT	1	11	1	TAGGGAAAGG	    0.977694	-163
CCTACCAAAATTTGTTAAGCTTTGTATCTA	1	81	0	TTTGTTAAGC	    0.841149	-93
CTTAACAAATTTTGGTAGGCCTAGGGGTCA	1	92	1	TTTGGTAGGC	    0.980119	-82
TGGTAGGCCTAGGGGTCAGCATTGCCAAGG	1	104	1	AGGGGTCAGC	    0.961847	-70
ACGAGTTTTATGGGGATGGGGCCGCCTTGG	1	128	0	TGGGGATGGG	    0.977719	-46
TTTAAGAATATTTGGACGAGTTTTATGGGG	1	143	0	TTTGGACGAG	    0.915334	-31
          ATGGGAAACGTTTTAAGAAT	1	164	0	ATGGGAAACG	    0.934997	-10
          **********

Masking position 4
Map Score:   1.65887

Number of sites scoring better than the average of aligned sites = 6163
Number in coding regions = 5492
Number in noncoding regions = 671
Number of orfs with sites within 600 bp upstream = 603
Fraction of orfs with sites within 600 bp upstream = 0.0968519


Motif number 3

          **********

No masking
Map Score:   -2.03625e-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:   -2.03625e-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:   -2.03625e-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