AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i135_bsub_mtub_300.orf -o135_bsub_mtub_300.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	yuxL	107	similar to acylaminoacyl-peptidase
#2	hom	200	homoserine dehydrogenase
#3	yutH	152	yutH

Motif number 1

TATCTCCAGCAAAAAAAAGCGCCCTCCGCTG	1	35	0	AAAAAAAAGG	    0.943486	-73
TTTTTGCTGGAGATAAAGGAGTTTTTATTTA	1	51	1	AGATAAAGGG	    0.953491	-57
AATACATGTAAAAAGGAGGAGATGAAT    	1	91	1	AAAAGGAGGG	    0.962364	-17
GATGTCTTGTCAAAACAGGAGCGGGCTTATA	2	99	1	CAAAACAGGG	    0.975973	-102
TCCTCTTGGAAAAGACAATTGTTAACTCAAC	2	155	0	AAAGACAATG	    0.759519	-46
AGGACAATCAAAAGAAAGGTGGAGTTTTT  	2	182	1	AAAGAAAGGG	    0.988109	-19
AGAAGGCGCAAGAAAAAGTCGTAAACTTCTC	3	53	0	AGAAAAAGTG	    0.942408	-100
TATTTTAATCCGAAGAAGGCGCAAGAAAAAG	3	66	0	CGAAGAAGGG	    0.971019	-87
CCCTAATTCAACAGGCAGGTGATC       	3	139	1	ACAGGCAGGG	    0.960886	-14
          ********* *

Masking position 7
Map Score:   7.61522

Number of sites scoring better than the average of aligned sites = 1661
Number in coding regions = 1256
Number in noncoding regions = 405
Number of orfs with sites within 600 bp upstream = 449
Fraction of orfs with sites within 600 bp upstream = 0.0721169


Motif number 2

ATCTCCTCCTTTTTACATGTATTTCGTTTT	1	84	0	TTTTACATGT	     0.88014	-24
  GGAGAAAATCTGACAAAAATAATTAGAA	2	9	1	TCTGACAAAA	    0.902758	-192
AACGCATTGATATGACAAGATTCTTTATTT	2	38	0	TATGACAAGA	    0.960315	-163
CCGCTCCTGTTTTGACAAGACATCATTAGG	2	93	0	TTTGACAAGA	    0.989413	-108
AACAATTGTCTTTTCCAAGAGGACAATCAA	2	163	1	TTTTCCAAGA	    0.951674	-38
ACCCAATCTTTTTTACTAGTTTATACAAAA	3	18	1	TTTTACTAGT	    0.880193	-135
TTTTACTAGTTTATACAAAATGCTTGAGAA	3	28	1	TTATACAAAA	    0.816838	-125
          **********

Masking position 1
Map Score:   3.99231

Number of sites scoring better than the average of aligned sites = 757
Number in coding regions = 632
Number in noncoding regions = 125
Number of orfs with sites within 600 bp upstream = 144
Fraction of orfs with sites within 600 bp upstream = 0.0231288


Motif number 3

AAAACTCCTTTATCTCCAGCAAAAAAAAGC	1	46	0	TATCTCCAGC	    0.939848	-62
TACATTCGCAAAATTCAGCCTAATGATGTC	2	75	1	AAATTCAGCC	    0.956093	-126
AGACAATTGTTAACTCAACACAGACATATA	2	144	0	TAACTCAACA	    0.963016	-57
        AAAAACTCCACCTTTCTTTTGA	2	189	0	AAACTCCACC	    0.984835	-12
TATGTATTCATAATTCCGGCTGTGTATGAC	3	95	1	TAATTCCGGC	    0.970923	-58
TGATGAGCCCTAATTCAACAGGCAGGTGAT	3	132	1	TAATTCAACA	     0.94305	-21
          **********

Masking position 5
Map Score:   3.13213

Number of sites scoring better than the average of aligned sites = 333
Number in coding regions = 278
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 57
Fraction of orfs with sites within 600 bp upstream = 0.00915516


Motif number 4

          **********

No masking
Map Score:   -2.17836e-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:   -2.17836e-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:   -2.17836e-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