AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i288_tpal_bbur_300.orf -o288_tpal_bbur_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 =  	0.4
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RBB00563	35	3615
#2	RBB00560	83	3615

Motif number 1

GAACTTAAACGATAATAATA          	1	1	0	GATAATAATA	    0.874476	-35
TTTAAGTTCAGTTTATATTTTAGA      	1	22	1	GTTTATATTT	    0.976974	-14
GTTTATAATAGCTTATAATTAATTTCATAA	2	13	0	GCTTATAATT	    0.963705	-71
TTGTAAATATGTTTATAATAGCTTATAATT	2	23	0	GTTTATAATA	    0.893532	-61
TTTTTTATTGTGTTATAATACATTAAAGT 	2	65	1	TGTTATAATA	     0.61941	-19
          **********

Masking position 5
Map Score:   7.50434

Number of sites scoring better than the average of aligned sites = 41
Number in coding regions = 10
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 2

       TCTAAAATATAAACTGAACTTAA	1	23	0	AAAATATAAA	    0.890398	-13
   TTTTATGAAATTAATTATAAGCTATTA	2	8	1	AAATTAATTA	    0.801172	-76
AGCTATTATAAACATATTTACAAATCAATT	2	30	1	AACATATTTA	     0.95128	-54
ACATATTTACAAATCAATTTTGTCTTTTTT	2	41	1	AAATCAATTT	    0.744587	-43
AATGTATTATAACACAATAAAAAAGACAAA	2	59	0	AACACAATAA	    0.983693	-25
ATTGTGTTATAATACATTAAAGT       	2	71	1	AATACATTAA	    0.956576	-13
          **********

Masking position 6
Map Score:   4.80079

Number of sites scoring better than the average of aligned sites = 721
Number in coding regions = 191
Number in noncoding regions = 530
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 3

          **********

No masking
Map Score:   1.16119e-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:   1.16119e-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:   1.16119e-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