AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i312_mixed26_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 
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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	yabF	144	similar to hypothetical proteins

Motif number 1

TTTTGCGCCCTCTGTTTTTTTCGTTATAAT	1	34	1	TCTGTTTTTT	    0.984909	-111
GAAAATGCACTTTGTCTATTATAACGAAAA	1	51	0	TTTGTCTATT	    0.991855	-94
AAGTGCATTTTCTGCTTATTAGACGCTCGA	1	69	1	TCTGCTTATT	    0.959782	-76
TTCATGAAACTTTTTCTTATATCGAGCGTC	1	90	0	TTTTTCTTAT	    0.910324	-55
AATAAAAACTTTTGTATATTCATGAAACTT	1	108	0	TTTGTATATT	     0.98745	-37
TATACAAAAGTTTTTATTTTGTCTTGGAGG	1	120	1	TTTTTATTTT	     0.96377	-25
          **********

Masking position 7
Map Score:   7.88367

Number of sites scoring better than the average of aligned sites = 955
Number in coding regions = 758
Number in noncoding regions = 197
Number of orfs with sites within 600 bp upstream = 201
Fraction of orfs with sites within 600 bp upstream = 0.032284


Motif number 2

CCCTCTGAATACATAAGTATATA       	1	4	0	ACATAAGTAT	    0.981769	-141
CTCGATATAAGAAAAAGTTTCATGAATATA	1	94	1	GAAAAAGTTT	    0.980731	-51
TCATGAATATACAAAAGTTTTTATTTTGTC	1	113	1	ACAAAAGTTT	     0.99353	-32
          **********

Masking position 5
Map Score:   1.55695

Number of sites scoring better than the average of aligned sites = 65
Number in coding regions = 43
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 3

ACTTATGTATTCAGAGGGTTTTGCGCCCTC	1	16	1	TCAGAGGGTT	     0.98852	-129
AACGAAAAAAACAGAGGGCGCAAAACCCTC	1	29	0	ACAGAGGGCG	    0.998374	-116
GTTATAATAGACAAAGTGCATTTTCTGCTT	1	56	1	ACAAAGTGCA	    0.982349	-89
          **********

Masking position 5
Map Score:   0.553614

Number of sites scoring better than the average of aligned sites = 152
Number in coding regions = 130
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

          **********

No masking
Map Score:   -1.53887e-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:   -1.53887e-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:   -1.53887e-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