AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i176_cobalamin_biosynthesis_1_aful_reg_100.orf -o176_aful_100.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAG13740	100	Archaeoglobus_fulgidus

Motif number 1

        CACAACACCTCCAGATTTCTTGAGC	1	3	1	CACACTCAGA	    0.998825	-98
GTCAATCTGACACAAGCTCAAGAAATCTGGAGG	1	18	0	CAAACTCAGA	    0.998183	-83
ATAAATCTTACTGAAAATCCAAAAAATTTAAAT	1	54	0	CTAAATCAAA	    0.988936	-47
        TGCTGCAACTCTAAACTCAGTTAAA	1	86	0	CTCACTCAAA	    0.998167	-15
          ** ** *** ***

Masking position 8
Map Score:   5.25883

Number of sites scoring better than the average of aligned sites = 96
Number in coding regions = 85
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

GACACAAGCTCAAGAAATCTGGAGGTGTTG	1	13	0	CAAGAAATCT	    0.994451	-88
AATTTAAATAAAGTCAATCTGACACAAGCT	1	33	0	AAGTCAATCT	    0.978473	-68
ACTGAAAATCCAAAAAATTTAAATAAAGTC	1	48	0	CAAAAAATTT	    0.967491	-53
AAACTCAGTTAAATAAATCTTACTGAAAAT	1	69	0	AAATAAATCT	    0.976513	-32
          **********

Masking position 6
Map Score:   4.01642

Number of sites scoring better than the average of aligned sites = 76
Number in coding regions = 65
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

AATCCAAAAAATTTAAATAAAGTCAATCTG	1	42	0	ATTTAAATAA	    0.969042	-59
AGTTAAATAAATCTTACTGAAAATCCAAAA	1	63	0	ATCTTACTGA	    0.991107	-38
AGTAAGATTTATTTAACTGAGTTTAGAGTT	1	75	1	ATTTAACTGA	    0.995748	-26
          **********

Masking position 6
Map Score:   2.40182

Number of sites scoring better than the average of aligned sites = 9
Number in coding regions = 2
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

          **********

No masking
Map Score:   -1.04149e-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:   -1.04149e-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:   -1.04149e-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