AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i276_bsub_mtub_100.orf -o276_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	yurN	57	similar to sugar permease
#2	yurO	80	similar to multiple sugar-binding protein
#3	yurP	215	similar to opine catabolism

Motif number 1

ATAATGTTATATAACATTATAGTCTAATGC	2	33	0	ATAACATTAT	    0.545742	-48
ATAATGTTATATAACATTATAGTCTAATGT	2	43	1	ATAACATTAT	    0.545742	-38
GGACTTTAATATAACAATATATAATGTTAT	3	161	1	ATAACAATAT	    0.810959	-55
ATAACGTTATATAACATTATATATTGTTAT	3	171	0	ATAACATTAT	    0.545742	-45
ATAATGTTATATAACGTTATATAATAAAAA	3	181	1	ATAACGTTAT	    0.499972	-35
          **********

Masking position 4
Map Score:   14.9567

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 6
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 2

TGCGAAGCTTCACCTTTTCTTTGAT       	1	4	0	CCTTTTCTTT	    0.995601	-54
TGAAGCTTCGCACCTTTTCTTTTTATAAAGGA	1	24	1	CCTTTTCTTT	    0.995601	-34
    GGGTATCTCATCTCCTTTATAAAAAGAA	1	40	0	CCTCTCCTTT	    0.990996	-18
CGCATATAGACCCTTTGTCTGTCATCCGAATA	3	84	1	CCTTGTCTGT	    0.990996	-132
  ATCCTTCACTCCTCGTTTTTATTATATAAC	3	196	0	CCTCGTTTTT	    0.980598	-20
          * * ********

Masking position 5
Map Score:   5.30838

Number of sites scoring better than the average of aligned sites = 227
Number in coding regions = 187
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 3

GTTATATAACATTATAGTCTAATGCATAAT	2	28	0	ATTATAGTCT	    0.962616	-53
AGACTATAATGTTATATAACATTATAGTCT	2	38	1	GTTATATAAC	    0.496948	-43
GTTATATAACATTATAGTCTAATGTCCAGA	2	48	1	ATTATAGTCT	    0.962616	-33
CATTTTTTCGCATATAGACCCTTTGTCTGT	3	76	1	CATATAGACC	    0.833759	-140
CTGTCATCCGAATAAATTATTGAGAAATTT	3	102	1	AATAAATTAT	    0.653393	-114
GATTGTCAATATTATTTTCTGAAATTTCTC	3	123	0	ATTATTTTCT	    0.768473	-93
ATATTGTTATATTAAAGTCCGCGGGTAGGA	3	151	0	ATTAAAGTCC	    0.920563	-65
TTAATATAACAATATATAATGTTATATAAC	3	166	1	AATATATAAT	    0.606412	-50
AATATATAATGTTATATAACGTTATATAAT	3	176	1	GTTATATAAC	    0.496948	-40
CCTCGTTTTTATTATATAACGTTATATAAC	3	186	0	ATTATATAAC	    0.519059	-30
          **********

Masking position 4
Map Score:   7.68018

Number of sites scoring better than the average of aligned sites = 528
Number in coding regions = 376
Number in noncoding regions = 152
Number of orfs with sites within 600 bp upstream = 140
Fraction of orfs with sites within 600 bp upstream = 0.0224863


Motif number 4

AACCATTATGCATTAGACTATAATGTTATA	2	24	1	CATTAGACTA	    0.992388	-57
CTCCTCTGGACATTAGACTATAATGTTATA	2	52	0	CATTAGACTA	    0.992388	-29
CTTTGTCTGTCATCCGAATAAATTATTGAG	3	96	1	CATCCGAATA	     0.95251	-120
          **********

Masking position 7
Map Score:   1.64524

Number of sites scoring better than the average of aligned sites = 9
Number in coding regions = 3
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 5

          TCTGAAAATGAAGAACCATT	2	1	1	TCTGAAAATG	      0.9449	-80
GTTGGCCTCCTCTGGACATTAGACTATAAT	2	58	0	TCTGGACATT	    0.967802	-23
TGACTTAAGCTCTGGCTTCGCTGTTCAATC	3	25	0	TCTGGCTTCG	    0.964187	-191
TAAGTCAAGTTCTGGCTTTTGATTTGGGCA	3	48	1	TCTGGCTTTT	    0.982257	-168
AATATTATTTTCTGAAATTTCTCAATAATT	3	116	0	TCTGAAATTT	    0.957917	-100
          **********

Masking position 3
Map Score:   1.14538

Number of sites scoring better than the average of aligned sites = 325
Number in coding regions = 284
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 6

          **********

No masking
Map Score:   -6.15168e-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:   -6.15168e-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 8

          **********

No masking
Map Score:   -6.15168e-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