AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i262_3_5_1_28_synecho_reg_300.orf -o262_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	RCY35276	173	Synechocystis

Motif number 1

GATGAACGCCTGGACTGGATCTGTCAAAAAAT	1	30	1	TGGACGGTCT	    0.940949	-144
TGTCAAAAAATGTTACAGATTGGCTCTAATTA	1	51	1	TGTTAAGTTG	      0.9331	-123
TACCAAAATTTGTTAAGCTTTGTATCTAATTA	1	77	0	TGTTAGCTTG	    0.983066	-97
TAACAAATTTTGGTAGGCCTAGGGGTCAGCAT	1	94	1	TGGTAGCTAG	    0.981376	-80
GTAGGCCTAGGGGTCAGCATTGCCAAGGCGGC	1	106	1	GGGTCGCTTG	    0.995633	-68
TTATGGGGATGGGGCCGCCTTGGCAATGCTGA	1	119	0	GGGGCGCTTG	    0.994737	-55
TAAGAATATTTGGACGAGTTTTATGGGGATGG	1	139	0	TGGACAGTTT	    0.952972	-35
         ATGGGAAACGTTTTAAGAATATT	1	161	0	TGGGAACTTT	    0.969835	-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

AGGCGTTCATCCTTTCCCTACTCCGCCATT	1	11	0	CCTTTCCCTA	    0.975813	-163
TAGATACAAAGCTTAACAAATTTTGGTAGG	1	81	1	GCTTAACAAA	    0.829759	-93
TGACCCCTAGGCCTACCAAAATTTGTTAAG	1	92	0	GCCTACCAAA	    0.978438	-82
CCTTGGCAATGCTGACCCCTAGGCCTACCA	1	104	0	GCTGACCCCT	    0.958686	-70
CCAAGGCGGCCCCATCCCCATAAAACTCGT	1	128	1	CCCATCCCCA	     0.97584	-46
CCCCATAAAACTCGTCCAAATATTCTTAAA	1	143	1	CTCGTCCAAA	    0.908689	-31
ATTCTTAAAACGTTTCCCAT          	1	164	1	CGTTTCCCAT	    0.929774	-10
          **********

Masking position 7
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