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_300.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

          GCCGTCGGCCAGGTCGGCCG	1	1	1	GCCGTCGGCC	    0.831733	-34
 TTATTTGTTGACCGCGGCCGACCTGGCCG	1	16	0	GACCGCGGCC	    0.502478	-19
TCCCGCTCTTGGCGGCTGCC          	2	1	0	GGCGGCTGCC	    0.512156	-33
CGTTGCGATAGTCTCCGGCC          	4	21	1	GTCTCCGGCC	    0.830736	-10
          **********

Masking position 6
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

TGTTGACCGCGGCCGACCTGGCCGACGGC 	1	10	0	GGCCGACCTG	    0.995457	-25
  CGGCGAATCTCCATCCCGCTCTTGGCGG	2	16	0	CTCCATCCCG	    0.991018	-18
TCAATATTCCGTAAATCCTGCTATCATAGC	3	28	1	GTAAATCCTG	    0.974132	-23
CTATCGCAACGGCAGTGCCGC         	4	2	0	GGCAGTGCCG	    0.995042	-29
          **********

Masking position 8
Map Score:   1.7549

Number of sites scoring better than the average of aligned sites = 4619
Number in coding regions = 4332
Number in noncoding regions = 287
Number of orfs with sites within 600 bp upstream = 258
Fraction of orfs with sites within 600 bp upstream = 0.0414391


Motif number 3

TGACCGCGGCCGACCTGGCCGACGGC     	1	6	0	CGACCGGCCG	    0.586087	-29
ATCTCCATCCCGCTCTTGGCGGCTGCC    	2	7	0	CGCTCTGGCG	    0.545285	-27
GTAAATCCTGCTATCATAGCGTC        	3	38	1	CTATCTAGCG	    0.965166	-13
 GGCCGGAGACTATCGCAACGGCAGTGCCGC	4	11	0	CTATCCAACG	    0.981622	-20
          ***** *****

Masking position 5
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