AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i138_bsub_mtub_100.orf -o138_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	ycdH	187	similar to adhesion protein
#2	ycdI	55	similar to ABC transporter (ATP-binding protein)

Motif number 1

AAGTAGCCCGGCATTTTTAGCCGGGTTTTT	1	17	1	GCATTTTTAG	    0.972093	-171
TTTTAGCCGGGTTTTTTTAGTACATATATT	1	31	1	GTTTTTTTAG	    0.879484	-157
AGAATAAATTTCATTTTCATTTATTTTTCC	1	74	0	TCATTTTCAT	    0.974855	-114
TGACTTCGGTTTATTATGATATAGGATTAC	1	116	1	TTATTATGAT	    0.791688	-72
AAAATCGTTATCATTTTGATTTAAAGTTAC	1	146	1	TCATTTTGAT	      0.9826	-42
GTATATCCCCTCTTTTTCAGTAACTTTAAA	1	165	0	TCTTTTTCAG	    0.983998	-23
GCACACTATTTCTTTGTGAGAAAGGAAGAT	2	32	1	TCTTTGTGAG	    0.970372	-24
          **********

Masking position 9
Map Score:   7.15963

Number of sites scoring better than the average of aligned sites = 1558
Number in coding regions = 1331
Number in noncoding regions = 227
Number of orfs with sites within 600 bp upstream = 240
Fraction of orfs with sites within 600 bp upstream = 0.038548


Motif number 2

TTCATTTTCATTTATTTTTCCCGCCTGCAG	1	65	0	TTTATTTTTC	    0.967731	-123
CAAGAATAAATTTCATTTTCATTTATTTTT	1	76	0	TTTCATTTTC	     0.98411	-112
GAAAATGAAATTTATTCTTGCAAAACGTAA	1	86	1	TTTATTCTTG	    0.963647	-102
ACCGAAGTCATTACGTTTTGCAAGAATAAA	1	96	0	TTACGTTTTG	    0.908324	-92
ACAAAATCGTTATCATTTTGATTTAAAGTT	1	144	1	TATCATTTTG	    0.944096	-44
GTGCACACTATTTCTTTGTGAGAAAGGAAG	2	30	1	TTTCTTTGTG	     0.96159	-26
          GTTAATCTTCCTTTCTCACA	2	46	0	GTTAATCTTC	    0.861235	-10
          **********

Masking position 6
Map Score:   5.08577

Number of sites scoring better than the average of aligned sites = 1764
Number in coding regions = 1434
Number in noncoding regions = 330
Number of orfs with sites within 600 bp upstream = 335
Fraction of orfs with sites within 600 bp upstream = 0.0538066


Motif number 3

AATGATAACGATTTTGTAATCCTATATCATAA	1	129	0	ATTTGTAACC	    0.976314	-59
          ATCGTATATCCCCTCTTTTTCA	1	176	0	ATGTATATCC	    0.976253	-12
         GATAGTGTGCGCCGGAGGGGTGC	2	2	1	ATGTGTGCCC	    0.998549	-54
TCACAAAGAAATAGTGTGCACCCCTCCGGCGC	2	19	0	ATGTGTGCCC	    0.998549	-37
          ** ****** **

Masking position 7
Map Score:   2.59991

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 37
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

TTGAAGTAGCCCGGCATTTTTAGCCGGGTT	1	14	1	CCGGCATTTT	    0.995755	-174
GCATTTTTAGCCGGGTTTTTTTAGTACATA	1	27	1	CCGGGTTTTT	    0.995571	-161
ATCGTATATCCCCTCTTTTTCAGTAACTTT	1	168	0	CCCTCTTTTT	     0.98801	-20
          **********

Masking position 7
Map Score:   1.5764

Number of sites scoring better than the average of aligned sites = 251
Number in coding regions = 204
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 5

          **********

No masking
Map Score:   -3.30951e-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:   -3.30951e-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 7

          **********

No masking
Map Score:   -3.30951e-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