AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i185_bsub_mtub_300.orf -o185_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	ykvJ	300	similar to hypothetical proteins

Motif number 1

TCTTGACAATAAAAAAGTCAGTCCCCGGTTC	1	47	0	AAAAAAGCAG	    0.986183	-254
TTTTATTGTCAAGAAAAACATCATTATGGTA	1	64	1	AAGAAAACAT	    0.962024	-237
GAAAAAATTGAAGAAAATCCGTGCGATATGC	1	108	1	AAGAAAACCG	    0.990365	-193
CACCCTCTATAAAAAACTAAGGACGAGCTGT	1	156	1	AAAAAACAAG	    0.920698	-145
AGAAAAACATAAAAAAGGCCGTATCCAAGGA	1	188	0	AAAAAAGCCG	    0.991244	-113
GAAGGTGCTCTAGAAAAACATAAAAAAGGCC	1	199	0	TAGAAAACAT	    0.902667	-102
AATTCACGCAAAAAAACACCTTTTTTCGGAA	1	227	0	AAAAAACCCT	    0.984724	-74
TTCTCCGCAATAAAAACGCCGGCGAGAGACA	1	269	0	TAAAAACCCG	    0.983706	-32
          ******* ***

Masking position 6
Map Score:   12.3705

Number of sites scoring better than the average of aligned sites = 1084
Number in coding regions = 827
Number in noncoding regions = 257
Number of orfs with sites within 600 bp upstream = 225
Fraction of orfs with sites within 600 bp upstream = 0.0361388


Motif number 2

ACTATAGAGCGATAATTGATCTAGGAACCGGGGA	1	23	1	GAAAGTCTAG	    0.986998	-278
TGCGATATGCGGGAGAGGTTCTAGCTACACCCTC	1	129	1	GGAGGTCTAG	    0.998531	-172
CTTAGTTTTTTATAGAGGGTGTAGCTAGAACCTC	1	143	0	TAAGGTGTAG	    0.989235	-158
ACCTTTTTTCGGAAGGTGCTCTAGAAAAACATAA	1	207	0	GGAGGTCTAG	    0.998531	-94
TTTTTTTGCGTGAATTAGCTGTAGCGATGTCTCT	1	242	1	TGATGTGTAG	    0.981172	-59
          ** **  * *****

Masking position 10
Map Score:   4.4345

Number of sites scoring better than the average of aligned sites = 22
Number in coding regions = 19
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 3

TGGTAAGATAGCAGAAGTGAAAAAATTGAA	1	90	1	GCAGAAGTGA	    0.968831	-211
CGTGCGATATGCGGGAGAGGTTCTAGCTAC	1	127	1	GCGGGAGAGG	    0.996428	-174
GCGTGAATTAGCTGTAGCGATGTCTCTCGC	1	249	1	GCTGTAGCGA	    0.962854	-52
CAATAAAAACGCCGGCGAGAGACATCGCTA	1	263	0	GCCGGCGAGA	    0.991576	-38
TTATTGCGGAGAAGGAGAGGAATC      	1	287	1	GAAGGAGAGG	    0.984748	-14
          **********

Masking position 4
Map Score:   2.69312

Number of sites scoring better than the average of aligned sites = 514
Number in coding regions = 458
Number in noncoding regions = 56
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 4

GGGACTGACTTTTTTATTGTCAAGAAAAAC	1	53	1	TTTTTATTGT	    0.886307	-248
TCCTTAGTTTTTTATAGAGGGTGTAGCTAG	1	149	0	TTTATAGAGG	    0.893542	-152
GGATACGGCCTTTTTTATGTTTTTCTAGAG	1	193	1	TTTTTTATGT	    0.891874	-108
AAAAAAACACCTTTTTTCGGAAGGTGCTCT	1	219	0	CTTTTTTCGG	      0.9496	-82
AAAAAGGTGTTTTTTTGCGTGAATTAGCTG	1	233	1	TTTTTTGCGT	    0.986638	-68
CGCCGGCGTTTTTATTGCGGAGAAGGAGAG	1	276	1	TTTATTGCGG	    0.984185	-25
          **********

Masking position 5
Map Score:   2.69605

Number of sites scoring better than the average of aligned sites = 1342
Number in coding regions = 1104
Number in noncoding regions = 238
Number of orfs with sites within 600 bp upstream = 231
Fraction of orfs with sites within 600 bp upstream = 0.0371025


Motif number 5

TCCTAGATCAATTATCGCTCTATAGTGACG	1	19	0	ATTATCGCTC	    0.941524	-282
ACCTCTCCCGCATATCGCACGGATTTTCTT	1	118	0	CATATCGCAC	     0.95978	-183
CGTATCCAAGGATACAGCTCGTCCTTAGTT	1	170	0	GATACAGCTC	    0.976721	-131
TAGCTGTAGCGATGTCTCTCGCCGGCGTTT	1	257	1	GATGTCTCTC	    0.981606	-44
          GATTCCTCTCCTTCTCCGCA	1	291	0	GATTCCTCTC	    0.975446	-10
          **********

Masking position 3
Map Score:   0.853103

Number of sites scoring better than the average of aligned sites = 567
Number in coding regions = 515
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 6

          **********

No masking
Map Score:   7.91135e-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 7

          **********

No masking
Map Score:   7.91135e-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 8

          **********

No masking
Map Score:   7.91135e-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