AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -iflhCD_mtub_opreg_100.orf -g0.656 -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 =  	0.656
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	Rv3288c	34	hypothetical protein Rv3288c
#2	Rv3289c	33	hypothetical protein Rv3289c
#3	lat	50	lat
#4	Rv3291c	30	hypothetical protein Rv3291c

Motif number 1

CGGCCGACCTGGCCGACGGC          	1	1	0	GGCCGACGGC	    0.827257	-34
CGGCCAGGTCGGCCGCGGTCAACAAATAA 	1	16	1	GGCCGCGGTC	    0.502381	-19
          GGCAGCCGCCAAGAGCGGGA	2	1	1	GGCAGCCGCC	     0.51169	-33
          GGCCGGAGACTATCGCAACG	4	21	0	GGCCGGAGAC	    0.826306	-10
          **********

Masking position 5
Map Score:   8.71269

Number of sites scoring better than the average of aligned sites = 3663
Number in coding regions = 3503
Number in noncoding regions = 160
Number of orfs with sites within 600 bp upstream = 132
Fraction of orfs with sites within 600 bp upstream = 0.0212014


Motif number 2

  GCCGTCGGCCAGGTCGGCCGCGGTCAAC	1	9	1	CCAGGTCGGC	    0.960933	-26
GCCGCCAAGAGCGGGATGGAGATTCGCCG 	2	15	1	GCGGGATGGA	    0.997884	-19
CGCTATGATAGCAGGATTTACGGAATATTG	3	29	0	GCAGGATTTA	    0.981154	-22
          GCGGCACTGCCGTTGCGATA	4	1	1	GCGGCACTGC	    0.782411	-30
          **********

Masking position 4
Map Score:   1.7549

Number of sites scoring better than the average of aligned sites = 4469
Number in coding regions = 4125
Number in noncoding regions = 344
Number of orfs with sites within 600 bp upstream = 296
Fraction of orfs with sites within 600 bp upstream = 0.0475426


Motif number 3

     GCCGTCGGCCAGGTCGGCCGCGGTCA	1	6	1	CGGCCGGTCG	    0.582686	-29
    GGCAGCCGCCAAGAGCGGGATGGAGAT	2	7	1	CGCCAGAGCG	    0.543298	-27
        GACGCTATGATAGCAGGATTTAC	3	38	0	CGCTAGATAG	    0.963894	-13
GCGGCACTGCCGTTGCGATAGTCTCCGGCC 	4	11	1	CGTTGGATAG	    0.981995	-20
          ***** *****

Masking position 7
Map Score:   1.25283

Number of sites scoring better than the average of aligned sites = 2752
Number in coding regions = 2598
Number in noncoding regions = 154
Number of orfs with sites within 600 bp upstream = 154
Fraction of orfs with sites within 600 bp upstream = 0.024735


Motif number 4

          **********

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 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