AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i027_bsub_mtub_300.orf -o027_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 =  	0.55
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	citG	300	fumarate hydratase
#2	fum	30	fum
#3	Rv1099c	100	hypothetical protein Rv1099c

Motif number 1

GCACAGGTAAGGCTAGCTGGAAAACAAGAA	1	62	1	GGCTAGCTGG	     0.95575	-239
AATATTCAAAGGATTCCCGCGTATATCTTG	1	180	1	GGATTCCCGC	    0.982556	-121
CCCTCCATAACGGTTGCTTCAATAGATCAT	1	273	0	CGGTTGCTTC	    0.950591	-28
     TGATCGGGTTCCTTGTGTGTCGTGG	2	16	0	GGGTTCCTTG	     0.95059	-15
GTCGACGAACCGGATCCCTCAGCTGTC   	3	8	0	CGGATCCCTC	     0.93441	-93
TCCGGTTCGTCGACGGCCGCGGTGGCCAGC	3	24	1	CGACGGCCGC	    0.936162	-77
GACGGGTCGTGGCTGGCCACCGCGGCCGTC	3	35	0	GGCTGGCCAC	    0.946356	-66
CTTCCCGGCGCGATGGCCTGGTGTGCGACG	3	61	0	CGATGGCCTG	    0.965638	-40
TGCGGTCCGGGGCTTCCCGGCGCGATGGCC	3	73	0	GGCTTCCCGG	    0.991478	-28
AGCCCCGGACCGCAACCTGGCC        	3	89	1	CGCAACCTGG	     0.87221	-12
          **********

Masking position 7
Map Score:   8.79128

Number of sites scoring better than the average of aligned sites = 2855
Number in coding regions = 2623
Number in noncoding regions = 232
Number of orfs with sites within 600 bp upstream = 158
Fraction of orfs with sites within 600 bp upstream = 0.0253774


Motif number 2

     CACACCCACGACACACAAGGAACCC	2	6	1	CCACGACACA	     0.96851	-25
CCGCGGCCGTCGACGAACCGGATCCCTCAG	3	16	0	CGACGAACCG	    0.987705	-85
CGGTGGCCAGCCACGACCCGTCGCACACCA	3	43	1	CCACGACCCG	    0.998434	-58
GTCCGGGGCTTCCCGGCGCGATGGCCTGGT	3	69	0	TCCCGGCGCG	    0.981519	-32
CGCCGGGAAGCCCCGGACCGCAACCTGGCC	3	81	1	CCCCGGACCG	    0.996975	-20
          **********

Masking position 5
Map Score:   5.32578

Number of sites scoring better than the average of aligned sites = 116
Number in coding regions = 112
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

AGCTCATTAGATCATTTGAACAGCATTATG	1	102	1	ATCATTTGAA	    0.961873	-199
TCCTGCCGTACTCCTTTGATGTATAAGAGA	1	135	0	CTCCTTTGAT	     0.95835	-166
ATACGCGGGAATCCTTTGAATATTTGTATT	1	174	0	ATCCTTTGAA	    0.993531	-127
GACACAAAAAATCCTTTTTATTTTTCGATC	1	232	0	ATCCTTTTTA	    0.914236	-69
GCGAATTATGATCTATTGAAGCAACCGTTA	1	266	1	ATCTATTGAA	    0.917258	-35
          **********

Masking position 6
Map Score:   3.07023

Number of sites scoring better than the average of aligned sites = 329
Number in coding regions = 298
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 4

      TAGAGTATTTCATGGAGTAAGTTT	1	5	1	GTATTTCATG	     0.94849	-296
ATGGAGTAAGTTTTTTTATGAAAGCGGAGG	1	22	1	TTTTTTTATG	    0.796859	-279
AGCTGTTCAATTTCTTCTTGTTTTCCAGCT	1	76	0	TTTCTTCTTG	    0.818651	-225
CTTTGAATATTTGTATTTTGGATTTGTCCT	1	161	0	TTGTATTTTG	    0.858511	-140
GGATTCCCGCGTATATCTTGAATTAAAATT	1	190	1	GTATATCTTG	     0.94849	-111
AAAATCCTTTTTATTTTTCGATCTTGGCAG	1	225	0	TTATTTTTCG	    0.841524	-76
AAAATAAAAAGGATTTTTTGTGTCATTGGC	1	238	1	GGATTTTTTG	    0.947249	-63
     TGATCGGGTTCCTTGTGTGTCGTGG	2	16	0	GGGTTCCTTG	    0.862482	-15
          **********

Masking position 10
Map Score:   0.485067

Number of sites scoring better than the average of aligned sites = 1696
Number in coding regions = 1424
Number in noncoding regions = 272
Number of orfs with sites within 600 bp upstream = 266
Fraction of orfs with sites within 600 bp upstream = 0.0427241


Motif number 5

          **********

No masking
Map Score:   -7.57849e-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:   -7.57849e-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 7

          **********

No masking
Map Score:   -7.57849e-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