AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i263_hypothetical_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	Rv2421c	274	hypothetical protein Rv2421c

Motif number 1

GATACCCGCGGGCAGTGCGGCGCG          	1	1	0	GGCGTCGCGG	    0.982545	-274
CATGGCCTACCGGTGATACCCGCGGGCAGTGCGG	1	15	0	CGGGAACCGG	    0.967144	-260
GTGACTCCCTCGGCGAGCGGCATGGCCTACCGGT	1	35	0	CGGGACGCAG	    0.991955	-240
AGGGAGTCACCGGCGAGGGTCGCGACACCCAGTC	1	59	1	CGGGAGGCGG	    0.997481	-216
TCGTCGCCGACGGGGCGGGACTGGGTGTCGCGAC	1	77	0	CGGGCGGCTG	    0.995978	-198
CCCGCCCCGTCGGCGACGACCTCGACCTCACCCG	1	92	1	CGGGAGACTG	    0.992206	-183
CTAAGCCTTTGCGTGATCATCTTGGTCTCGTTCC	1	125	0	GCGGACACTG	    0.950149	-150
CCATTGATAAGGCAGCACGATTGGTTATTCCTAA	1	155	0	GGCGCCGTTG	    0.990516	-120
CCTTATCAATGGCTGCTCGCTTAGGCTGGCTGGC	1	177	1	GGCGCCGTTG	    0.990504	-98
ATTATCTTGCCGCAGTTCCGTTCGCGGCAACTGC	1	209	0	CGCGTCCTTG	    0.965317	-66
AATCGTGCATGGGCGTCGATTGGGAGTC      	1	257	1	GGGGTGATGG	    0.964801	-18
          *** ** ** ** *

Masking position 5
Map Score:   19.383

Number of sites scoring better than the average of aligned sites = 16387
Number in coding regions = 15428
Number in noncoding regions = 959
Number of orfs with sites within 600 bp upstream = 670
Fraction of orfs with sites within 600 bp upstream = 0.107613


Motif number 2

    CGCGCCGCACTGCCCGCGGGTATCACCGGTA	1	7	1	GCTGCCGGGT	    0.960501	-268
TCGGCGAGCGGCATGGCCTACCGGTGATACCCGCG	1	25	0	GCGGCCCGGT	    0.997569	-250
GCCGCTCGCCGAGGGAGTCACCGGCGAGGGTCGCG	1	48	1	GAGATCCGGC	    0.935822	-227
ACCGGCGAGGGTCGCGACACCCAGTCCCGCCCCGT	1	67	1	GTCGCCCAGT	    0.975543	-208
CGCCCCGTCGGCGACGACCTCGACCTCACCCGGAA	1	94	1	GCCGCCGACC	    0.970854	-181
CTGCCAGCCAGCCTAAGCGAGCAGCCATTGATAAG	1	178	0	GCAACGCAGC	    0.954982	-97
AGTTCCGTTCGCGGCAACTGCCAGCCAGCCTAAGC	1	195	0	GCCACCCAGC	    0.988644	-80
CGGAACTGCGGCAAGATAATCCAGTAAGCTGGCCA	1	223	1	GCGAACCAGT	    0.976134	-52
CGACGCCCATGCACGATTGGCCAGCTTACTGGATT	1	240	0	GCGATCCAGC	    0.920441	-35
          **  ** *  *****

Masking position 1
Map Score:   9.52436

Number of sites scoring better than the average of aligned sites = 16354
Number in coding regions = 15429
Number in noncoding regions = 925
Number of orfs with sites within 600 bp upstream = 654
Fraction of orfs with sites within 600 bp upstream = 0.105043


Motif number 3

CCGGTGATACCCGCGGGCAGTGCGGCGCG  	1	9	0	CCGCGGGCGT	    0.974344	-266
CGGGTATCACCGGTAGGCCATGCCGCTCGCC	1	27	1	CGGTAGGCAT	    0.981631	-248
CGACGGGGCGGGACTGGGTGTCGCGACCCTC	1	73	0	GGACTGGGGT	     0.98169	-202
TAAGGCAGCACGATTGGTTATTCCTAAGCCT	1	151	0	CGATTGGTAT	     0.97173	-124
TCGCTTAGGCTGGCTGGCAGTTGCCGCGAAC	1	193	1	TGGCTGGCGT	    0.988177	-82
CGCCCATGCACGATTGGCCAGCTTACTGGAT	1	241	0	CGATTGGCAG	    0.982205	-34
GCATGGGCGTCGATTGGGAGTC         	1	263	1	CGATTGGGGT	    0.994862	-12
          ******** **

Masking position 6
Map Score:   5.89452

Number of sites scoring better than the average of aligned sites = 4226
Number in coding regions = 3905
Number in noncoding regions = 321
Number of orfs with sites within 600 bp upstream = 283
Fraction of orfs with sites within 600 bp upstream = 0.0454545


Motif number 4

          **********

No masking
Map Score:   -1.17788e-14

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:   -1.17788e-14

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:   -1.17788e-14

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