AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i152_bsub_mtub_100.orf -o152_bsub_mtub_100.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	yurD	21	similar to 4-hydroxybenzoyl-CoA reductase
#2	yurF	228	yurF
#3	Rv0375c	75	hypothetical protein Rv0375c
#4	Rv0376c	48	hypothetical protein Rv0376c

Motif number 1

GCTTGCGGAGTTCCGCAAGCTTTTCT    	2	7	0	TTCCGCAAGC	    0.996886	-222
GCTTGCGGAACTCCGCAAGCTTTTTAACGA	2	17	1	CTCCGCAAGC	    0.996247	-212
          TGCCGCATCCTCCTCTCGAA	2	219	0	TGCCGCATCC	    0.983213	-10
CCCCAGTGTCGGCCGCCCGCGAAAAGGGCG	3	11	0	GGCCGCCCGC	     0.99326	-65
GCCGACACTGGGGCGCATGCAAGTACCTGG	3	28	1	GGGCGCATGC	    0.979095	-48
AATACGAACGTGCCACCAGC          	3	66	1	TGCCACCAGC	    0.976644	-10
GGCAAGCACTTCACGCACGCTTCCCAAAGT	4	23	0	TCACGCACGC	    0.952361	-26
       CAGCTCGGCAAGCACTTCACGCA	4	36	0	CTCGGCAAGC	    0.977741	-13
          **********

Masking position 6
Map Score:   12.8742

Number of sites scoring better than the average of aligned sites = 1204
Number in coding regions = 1131
Number in noncoding regions = 73
Number of orfs with sites within 600 bp upstream = 66
Fraction of orfs with sites within 600 bp upstream = 0.0106007


Motif number 2

AATCAGATTGGAGAAAACACGAAATCATATCG	2	44	0	GAGAAAAAGA	    0.995138	-185
GAGTCAAACGAAGAAAATCAGATTGGAGAAAA	2	59	0	AAGAAAACGA	    0.979422	-170
TTCATTTTCTGACAAATCATGAGTCATTTTTT	2	117	1	GACAAATAGA	    0.934487	-112
TAGACGATGGAAGAAAAAATGACTCATGATTT	2	130	0	AAGAAAAAGA	    0.992376	-99
AACTTGTATAAAGAATAGACGATGGAAGAAAA	2	145	0	AAGAATAAGA	      0.9698	-84
AAATTGCCGTGAGAAACAACTAGTTCAGCGTG	2	188	0	GAGAAACATA	    0.934487	-41
          ******* * **

Masking position 5
Map Score:   4.63578

Number of sites scoring better than the average of aligned sites = 607
Number in coding regions = 495
Number in noncoding regions = 112
Number of orfs with sites within 600 bp upstream = 139
Fraction of orfs with sites within 600 bp upstream = 0.0223257


Motif number 3

GTTTCTCACGGCAATTTTCGAGAGGAGGAT	2	203	1	GCAATTTTCG	     0.98266	-26
         CGCCCTTTTCGCGGGCGGCCG	3	2	1	GCCCTTTTCG	    0.994966	-74
GCAAGTACCTGGGCCTTTCGAATACGAACG	3	46	1	GGGCCTTTCG	    0.987581	-30
    GCTGGTGGCACGTTCGTATTCGAAAG	3	60	0	GGCACGTTCG	    0.965224	-16
AGCTCGGCAAGCACTTCACGCACGCTTCCC	4	28	0	GCACTTCACG	    0.945934	-21
          **********

Masking position 9
Map Score:   2.23606

Number of sites scoring better than the average of aligned sites = 338
Number in coding regions = 275
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 4

GAGGATTTGTAAAAAGAGTCAAACGAAGAAA	2	75	0	AAAAAGATCA	     0.98748	-154
GATTTGTCAGAAAATGAAACACATAGAAAGA	2	104	0	AAAATGAACA	     0.98748	-125
GATGGAAGAAAAAATGACTCATGATTTGTCA	2	126	0	AAAATGATCA	    0.992825	-103
          ******* ***

Masking position 7
Map Score:   0.997362

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 40
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 5

          **********

No masking
Map Score:   -7.57276e-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:   -7.57276e-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 7

          **********

No masking
Map Score:   -7.57276e-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