AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i108_NOS_operon_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	Rv1219c	141	hypothetical protein Rv1219c

Motif number 1

GACGCAAAATCGCCCTGAACCGTGCGTTCCAG	1	22	1	CGCCTGACCG	    0.999027	-120
GACGCAAAATCGCCCTGGAACGCACGGTTCAG	1	36	0	CGCCTGAACG	     0.97932	-106
GTGAAGGCCGCGAACTTTGCCGAGCAGACGCA	1	62	0	CGACTTGCCG	    0.994522	-80
GCAAAGTTCGCGGCCTTCACGGATTCCCAACG	1	74	1	CGCCTTACGG	    0.998381	-68
CAACGGCGCCCTCCCTTGACCGGGGATGAACG	1	101	1	CTCCTTACCG	    0.997782	-41
          ** **** ****

Masking position 6
Map Score:   13.4941

Number of sites scoring better than the average of aligned sites = 507
Number in coding regions = 482
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 2

    TTCGGCGAGCAGACGCAAAATCGCCC	1	7	1	GAGCAGACGC	    0.997231	-135
AATCGCCCTGGAACGCACGGTTCAGGGCGA	1	31	0	GAACGCACGG	    0.978602	-111
GAACTTTGCCGAGCAGACGCAAAATCGCCC	1	53	0	GAGCAGACGC	    0.997231	-89
GGGCGCCGTTGGGAATCCGTGAAGGCCGCG	1	82	0	GGGAATCCGT	    0.938917	-60
CCCCGGTCAAGGGAGGGCGCCGTTGGGAAT	1	96	0	GGGAGGGCGC	    0.988541	-46
GACCGGGGATGAACGTACGTTTAATATCCT	1	118	1	GAACGTACGT	    0.984789	-24
          **********

Masking position 8
Map Score:   8.38103

Number of sites scoring better than the average of aligned sites = 5201
Number in coding regions = 4680
Number in noncoding regions = 521
Number of orfs with sites within 600 bp upstream = 384
Fraction of orfs with sites within 600 bp upstream = 0.0616768


Motif number 3

       TTCGGCGAGCAGACGCAAAATCG	1	4	1	GGCGAGCAGA	     0.99728	-138
CACGGTTCAGGGCGATTTTGCGTCTGCTCG	1	16	0	GGCGATTTTG	    0.993563	-126
TGCGTTCCAGGGCGATTTTGCGTCTGCTCG	1	44	1	GGCGATTTTG	    0.993563	-98
CGCGAACTTTGCCGAGCAGACGCAAAATCG	1	56	0	GCCGAGCAGA	    0.992561	-86
          **********

Masking position 5
Map Score:   4.80137

Number of sites scoring better than the average of aligned sites = 2586
Number in coding regions = 2387
Number in noncoding regions = 199
Number of orfs with sites within 600 bp upstream = 153
Fraction of orfs with sites within 600 bp upstream = 0.0245744


Motif number 4

          **********

No masking
Map Score:   1.51646e-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:   1.51646e-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:   1.51646e-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