AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i276_hypothetical20_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

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

GCATTAGACTATAATGTTATATAACATTAT	2	33	1	ATAATGTTAT	    0.545742	-48
ACATTAGACTATAATGTTATATAACATTAT	2	43	0	ATAATGTTAT	    0.545742	-38
ATAACATTATATATTGTTATATTAAAGTCC	3	161	0	ATATTGTTAT	    0.810959	-55
ATAACAATATATAATGTTATATAACGTTAT	3	171	1	ATAATGTTAT	    0.545742	-45
ATAATGTTATATAACGTTATATAATAAAAA	3	181	1	ATAACGTTAT	    0.499972	-35
          **********

Masking position 7
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	    0.995366	-54
TGAAGCTTCGCACCTTTTCTTTTTATAAAGGA	1	24	1	CCTTTTCTTT	    0.995366	-34
    GGGTATCTCATCTCCTTTATAAAAAGAA	1	40	0	CCTCTCCTTT	    0.990518	-18
CGCATATAGACCCTTTGTCTGTCATCCGAATA	3	84	1	CCTTGTCTGT	    0.990518	-132
  ATCCTTCACTCCTCGTTTTTATTATATAAC	3	196	0	CCTCGTTTTT	    0.979579	-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	    0.993924	-53
GTTATATAACATTATAGTCTAATGTCCAGA	2	48	1	ATTATAGTCT	    0.993924	-33
GATTGTCAATATTATTTTCTGAAATTTCTC	3	123	0	ATTATTTTCT	    0.942366	-93
ATATTGTTATATTAAAGTCCGCGGGTAGGA	3	151	0	ATTAAAGTCC	    0.974547	-65
          **********

Masking position 4
Map Score:   4.47091

Number of sites scoring better than the average of aligned sites = 33
Number in coding regions = 28
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

TATAACATTATAGTCTAATGCATAATGGTT	2	24	0	TAGTCTAATG	    0.992127	-57
TATAACATTATAGTCTAATGTCCAGAGGAG	2	52	1	TAGTCTAATG	    0.992127	-29
CTCAATAATTTATTCGGATGACAGACAAAG	3	96	0	TATTCGGATG	    0.952522	-120
          **********

Masking position 8
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

          AGGGTTGGCCTCCTCTGGACA	2	70	0	AGGTTGGCCT	    0.975687	-11
ACTTGACTTAAGCTCTGGCTTCGCTGTTCAA	3	27	0	AGTCTGGCTT	    0.996712	-189
GCTTAAGTCAAGTTCTGGCTTTTGATTTGGG	3	45	1	AGTCTGGCTT	    0.996712	-171
          ** ********

Masking position 1
Map Score:   1.13593

Number of sites scoring better than the average of aligned sites = 25
Number in coding regions = 20
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 6

AGAAAAGGTGCGAAGCTTCACCTTTTCTTT	1	14	0	CGAAGCTTCA	    0.899568	-44
CTGTTCAATCCGCAGACTGACGTC      	3	5	0	CGCAGACTGA	    0.989173	-211
GATTGAACAGCGAAGCCAGAGCTTAAGTCA	3	25	1	CGAAGCCAGA	    0.995328	-191
TGCCCAAATCAAAAGCCAGAACTTGACTTA	3	48	0	AAAAGCCAGA	    0.810772	-168
GGCATTTTTTCGCATATAGACCCTTTGTCT	3	74	1	CGCATATAGA	    0.839096	-142
TAATTTATTCGGATGACAGACAAAGGGTCT	3	91	0	GGATGACAGA	    0.909107	-125
ATAATAAAAACGAGGAGTGAAGGAT     	3	201	1	CGAGGAGTGA	    0.933772	-15
          **********

Masking position 10
Map Score:   1.14915

Number of sites scoring better than the average of aligned sites = 1722
Number in coding regions = 1604
Number in noncoding regions = 118
Number of orfs with sites within 600 bp upstream = 89
Fraction of orfs with sites within 600 bp upstream = 0.0142949


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


Motif number 9

          **********

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