AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i122_Arsenical_Resistance_Pump_mtub_reg_300.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	Rv2641	101	hypothetical protein Rv2641
#2	Rv2642	135	hypothetical protein Rv2642

Motif number 1

CAAGGTATCTGGCAGGGTGGGCCT       	1	4	0	GGCAGGTGGG	    0.985351	-98
TGGCGCCGAACCCAGTGTGCAACATCTCTTT	1	44	0	CCCAGGTGCA	    0.972815	-58
TAGGCCTGACCCCGGGGTGCGTCTCCAAGCC	2	14	1	CCCGGGTGCG	    0.976393	-122
GGGTGGGCTCCGCGGCTTGGAGACGCACCCC	2	27	0	CGCGGTTGGA	    0.995002	-109
CATTGAGTGGCCCGGGGTGGGCTCCGCGGCT	2	41	0	CCCGGGTGGG	     0.98498	-95
AACGGCGCTACGCGGGTTAGGGGGCATTGAG	2	65	0	CGCGGTTAGG	    0.995113	-71
CAAGCGGCCACGCGGTGAACGGCGCTACGCG	2	82	0	CGCGGGAACG	    0.990063	-54
TTCACCGCGTGGCCGCTTGCGGACCTGATTC	2	94	1	GGCCGTTGCG	    0.986559	-42
          ***** *****

Masking position 5
Map Score:   21.0975

Number of sites scoring better than the average of aligned sites = 3537
Number in coding regions = 3251
Number in noncoding regions = 286
Number of orfs with sites within 600 bp upstream = 250
Fraction of orfs with sites within 600 bp upstream = 0.0401542


Motif number 2

TATATGTCAAGGTATCTGGCAGGGTGGGCCT	1	11	0	GGTATTGGCA	    0.995525	-91
ACATCTCTTTGATATATGTCAAGGTATCTGG	1	23	0	GATATTGTCA	     0.99552	-79
ATATATCAAAGAGATGTTGCACACTGGGTTC	1	37	1	GAGATTTGCA	    0.959053	-65
GCGCCATTTTGATATAAGTCAAACAACTGGG	1	69	1	GATATAGTCA	    0.982086	-33
TCAAACAACTGGGAGGTGTCTACCA      	1	87	1	GGGAGTGTCT	    0.945409	-15
CGCTACGCGGGTTAGGGGGCATTGAGTGGCC	2	60	0	GTTAGGGGCA	    0.952535	-76
GACCTGATTCGATATTTGTCAATATTGATGT	2	115	1	GATATTGTCA	     0.99552	-21
          ***** *****

Masking position 4
Map Score:   10.1036

Number of sites scoring better than the average of aligned sites = 186
Number in coding regions = 154
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

GTTGCACACTGGGTTCGGCGCCATTTTGAT	1	52	1	GGGTTCGGCG	    0.994373	-50
ACGCACCCCGGGGTCAGGCCTACAG     	2	6	0	GGGTCAGGCC	    0.989005	-130
GGCCCGGGGTGGGCTCCGCGGCTTGGAGAC	2	34	0	GGGCTCCGCG	    0.998862	-102
AGCCCACCCCGGGCCACTCAATGCCCCCTA	2	49	1	GGGCCACTCA	    0.983741	-87
GCGGTGAACGGCGCTACGCGGGTTAGGGGG	2	72	0	GCGCTACGCG	    0.996588	-64
GGTCCGCAAGCGGCCACGCGGTGAACGGCG	2	89	0	CGGCCACGCG	    0.997302	-47
          **********

Masking position 3
Map Score:   12.5204

Number of sites scoring better than the average of aligned sites = 2034
Number in coding regions = 1870
Number in noncoding regions = 164
Number of orfs with sites within 600 bp upstream = 140
Fraction of orfs with sites within 600 bp upstream = 0.0224863


Motif number 4

          **********

No masking
Map Score:   2.58227e-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:   2.58227e-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:   2.58227e-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