AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i309_synecho_ctra_300.orf -o309_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RCY27002	202	Synechocystis
#2	RCY07501	62	Synechocystis

Motif number 1

         ATCTAGCCCACAATTGATCGA	1	2	1	TCTAGCCCAC	    0.941124	-201
ATCGAAGCTCGTCGGACCAGTACTGGGCTC	1	35	1	GTCGGACCAG	    0.981715	-168
CACCCCTGGATTGAGCCCAGTACTGGTCCG	1	47	0	TTGAGCCCAG	    0.951205	-156
GCCGGCCCGGGCCAGCCTGTCCCCATATCC	1	115	0	GCCAGCCTGT	     0.97595	-88
AAAAAATTGCGCCGGCCCGGGCCAGCCTGT	1	125	0	GCCGGCCCGG	    0.872643	-78
GCTTGAGTTTGCCGGCCCATCGCCTCTAAC	2	19	1	GCCGGCCCAT	    0.946838	-44
          **********

Masking position 5
Map Score:   6.90059

Number of sites scoring better than the average of aligned sites = 1414
Number in coding regions = 1324
Number in noncoding regions = 90
Number of orfs with sites within 600 bp upstream = 97
Fraction of orfs with sites within 600 bp upstream = 0.0155798


Motif number 2

CGATCATTCGATCAATTGTGGGCTAGAT   	1	8	0	ACAATTGTGG	    0.995152	-195
AGCTCGTCGGACCAGTACTGGGCTCAATCCA	1	40	1	ACAGTACTGG	    0.996861	-163
GGGAATCTGAAGGAATTCTGGAAATTTACCT	1	78	0	AGAATTCTGG	     0.98711	-125
TCTAAGCAACAACAGTAGTGGCATTGTCCGT	1	168	1	ACAGTAGTGG	    0.996861	-35
          * *********

Masking position 6
Map Score:   4.21719

Number of sites scoring better than the average of aligned sites = 85
Number in coding regions = 78
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

TCTAGCCCACAATTGATCGAATGATCGAAG	1	12	1	AATTGATCGA	    0.915018	-191
GAATTCTGGAAATTTACCTTCACCCCTGGA	1	67	0	AATTTACCTT	    0.950367	-136
GAATTCCTTCAGATTCCCTAATATGGATAT	1	91	1	AGATTCCCTA	    0.942701	-112
        ATAATTCACCTATAACGGACAA	1	191	0	AATTCACCTA	    0.978549	-12
CATCGCCTCTAACTTCCCTATTTTATCGGT	2	36	1	AACTTCCCTA	    0.974234	-27
        AGAAATGACCGATAAAATAGGG	2	51	0	AAATGACCGA	    0.979827	-12
          **********

Masking position 4
Map Score:   2.88277

Number of sites scoring better than the average of aligned sites = 661
Number in coding regions = 564
Number in noncoding regions = 97
Number of orfs with sites within 600 bp upstream = 97
Fraction of orfs with sites within 600 bp upstream = 0.0155798


Motif number 4

          **********

No masking
Map Score:   -2.59896e-14

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:   -2.59896e-14

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:   -2.59896e-14

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