AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i122_Arsenical_Resistance_Pump_mtub_reg_100.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 =  	0.66
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	Rv2642	135	hypothetical protein Rv2642

Motif number 1

GCTTGGAGACGCACCCCGGGGTCAGGCCTA	1	14	0	GCACCCCGGG	    0.999629	-122
CCCGGGGTGGGCTCCGCGGCTTGGAGACGC	1	32	0	GCTCCGCGGC	     0.98927	-104
GCCGCGGAGCCCACCCCGGGCCACTCAATG	1	42	1	CCACCCCGGG	    0.998891	-94
GGTGAACGGCGCTACGCGGGTTAGGGGGCA	1	70	0	GCTACGCGGG	    0.995061	-66
GTAGCGCCGTTCACCGCGTGGCCGCTTGCG	1	85	1	TCACCGCGTG	    0.996682	-51
          **********

Masking position 5
Map Score:   16.2939

Number of sites scoring better than the average of aligned sites = 964
Number in coding regions = 888
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 83
Fraction of orfs with sites within 600 bp upstream = 0.0133312


Motif number 2

    CTGTAGGCCTGACCCCGGGGTGCGTC	1	7	1	GCCTGACCCC	    0.998927	-129
GCGGCTTGGAGACGCACCCCGGGGTCAGGC	1	17	0	GACGCACCCC	    0.980612	-119
GGGGTGCGTCTCCAAGCCGCGGAGCCCACC	1	27	1	TCCAAGCCGC	    0.952915	-109
AGGGGGCATTGAGTGGCCCGGGGTGGGCTC	1	48	0	GAGTGGCCCG	    0.992706	-88
ACTCAATGCCCCCTAACCCGCGTAGCGCCG	1	64	1	CCCTAACCCG	     0.98437	-72
GCCGTTCACCGCGTGGCCGCTTGCGGACCT	1	90	1	GCGTGGCCGC	     0.89708	-46
          **********

Masking position 7
Map Score:   7.16945

Number of sites scoring better than the average of aligned sites = 7698
Number in coding regions = 7023
Number in noncoding regions = 675
Number of orfs with sites within 600 bp upstream = 527
Fraction of orfs with sites within 600 bp upstream = 0.084645


Motif number 3

          **********

No masking
Map Score:   -1.11255e-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:   -1.11255e-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:   -1.11255e-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