AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i339_bsub_mtub_100.orf -o339_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	ykrW	196	similar to ribulose-bisphosphate carboxylase

Motif number 1

CGGGCTCGTCCCTCTGCCTGCTCTTGATAAGA	1	50	0	CTCTCCTGCT	     0.99618	-147
GGTTGCCGGGCTTCATCGGGCTCGTCCCTCTG	1	66	0	CTCACGGGCT	    0.997505	-131
CGATGAAGCCCGGCAACCGACTTATAAAGCAC	1	80	1	CGCACCGACT	    0.994647	-117
CTGCAAGAATTAGCACCGTGCTTTATAAGTCG	1	97	0	TGCACGTGCT	    0.984092	-100
CTAATTCTTGCAGCTAGCGGCTGAGAGATAAG	1	116	1	CGCTGCGGCT	    0.994569	-81
CAAAAAACCTCTTCAAACTGCAATCGCGTCTA	1	173	0	CTCAACTGCA	    0.958336	-24
          * *** ******

Masking position 4
Map Score:   6.79381

Number of sites scoring better than the average of aligned sites = 1188
Number in coding regions = 1120
Number in noncoding regions = 68
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 2

TTATTTTGAATTATCCCATCG         	1	2	0	TTATCCCATC	    0.977635	-195
AAAATCTATATTTTCTTATCAAGAGCAGGC	1	37	1	TTTTCTTATC	    0.958469	-160
TTTCTCGTCCGAATCTTATCTCTCAGCCGC	1	132	0	GAATCTTATC	    0.972375	-65
AAGAGGTTTCGTTTCTCGTCCGAATCTTAT	1	143	0	GTTTCTCGTC	    0.988584	-54
CTTCAAACTGCAATCGCGTCTAAAGAGGTT	1	165	0	CAATCGCGTC	    0.965083	-32
          **********

Masking position 4
Map Score:   1.64215

Number of sites scoring better than the average of aligned sites = 521
Number in coding regions = 469
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 3

ATCGCGTCTAAAGAGGTTTCGTTTCTCGTC	1	153	0	AAGAGGTTTC	    0.994362	-44
TTGCAGTTTGAAGAGGTTTTTTGAT     	1	182	1	AAGAGGTTTT	    0.977344	-15
          **********

Masking position 4
Map Score:   1.032

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 12
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

          **********

No masking
Map Score:   3.50598e-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 5

          **********

No masking
Map Score:   3.50598e-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:   3.50598e-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