AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i296_bsub_mtub_100.orf -o296_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	yqjC	201	similar to hypothetical proteins
#2	accD5	49	accD5

Motif number 1

GTTTCTATAACGATAAAAAAGCAGGCGCC   	1	8	0	CGATAAAAGC	    0.995004	-194
CCCAAAATCACGATCAAAACGCTTTTCATCAG	1	79	1	CGATCAACGC	     0.98978	-123
ATTCAAAACACGCTAAAATATAGACAGATTGT	1	139	0	CGCTAAAATA	    0.988813	-63
TCCCTGCTTTCGCTAATAGATATCGCTTGTCC	1	175	0	CGCTAAAATA	    0.988813	-27
GTGCGGCAGCCGATAACATCGACTCCC     	2	33	1	CGATAAACGA	    0.995004	-17
          ****** * ***

Masking position 6
Map Score:   5.13022

Number of sites scoring better than the average of aligned sites = 103
Number in coding regions = 88
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 2

ATAACGATAAAAAAGCAGGCGCC       	1	4	0	AAAAGCAGGC	    0.991503	-198
TTATCGTTATAGAAACATGACGATTCCTGA	1	24	1	AGAAACATGA	    0.920207	-178
AAAAACTCCCAAAATCACGATCAAAACGCT	1	72	1	AAAATCACGA	    0.979914	-130
TTAAGGAGAGAAAATCATGTCTCAAAAACT	1	109	0	AAAATCATGT	    0.947048	-93
TCCGCCCATTCAAAACACGCTAAAATATAG	1	148	0	CAAAACACGC	    0.971425	-54
ATCTATTAGCGAAAGCAGGGATGAAA    	1	186	1	GAAAGCAGGG	    0.966179	-16
          **********

Masking position 4
Map Score:   2.83712

Number of sites scoring better than the average of aligned sites = 1415
Number in coding regions = 1231
Number in noncoding regions = 184
Number of orfs with sites within 600 bp upstream = 185
Fraction of orfs with sites within 600 bp upstream = 0.0297141


Motif number 3

AAAAACTGATGAAAAGCGTTTTGATCGTGA	1	86	0	GAAAAGCGTT	    0.959067	-116
TGAATGGGCGGACAAGCGATATCTATTAGC	1	166	1	GACAAGCGAT	    0.993841	-36
AGTAGTGTGCGGCAGCCGATAACATCGACT	2	27	1	GGCAGCCGAT	    0.995241	-23
          GGGAGTCGATGTTATCGGCT	2	40	0	GGGAGTCGAT	    0.987174	-10
          **********

Masking position 4
Map Score:   1.65194

Number of sites scoring better than the average of aligned sites = 327
Number in coding regions = 294
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 4

TTCAACTGTACTCTCAGGAATCGTCATGTT	1	37	0	CTCTCAGGAA	    0.982552	-165
TGAGAGTACAGTTGAAAGAATAAAAACTCC	1	51	1	GTTGAAAGAA	    0.944285	-151
AGAAAATCATGTCTCAAAAACTGATGAAAA	1	101	0	GTCTCAAAAA	     0.94545	-101
TAGACAGATTGTTTAAGGAGAGAAAATCAT	1	121	0	GTTTAAGGAG	    0.974371	-81
   CGCCCCAGCCTAAGGAAGTAGTGTGCG	2	8	1	GCCTAAGGAA	    0.988513	-42
          **********

Masking position 6
Map Score:   0.997208

Number of sites scoring better than the average of aligned sites = 633
Number in coding regions = 569
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


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


Motif number 7

          **********

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