AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i305_bsub_mtub_300.orf -o305_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	tesA	238	tesA
#2	fadD26	286	fadD26

Motif number 1

CCCGACACACCGGCGCCACCAGTGCAGTCACA	1	73	0	CGCGCCACCG	    0.979618	-166
ATTTCATATTCGACGAGCCCGGGCGACCACTC	1	110	1	CACGAGCCCG	    0.967467	-129
GCCCAGCAGGCCGCGTGATCTGAGTGGTCGCC	1	131	0	CGCGTGATCG	    0.970544	-108
ACGGTCTACGACACGCGCCCAGCAGGCCGCGT	1	147	0	AACGCGCCCG	    0.975869	-92
ACGTAGGCTCACCCGTCAGCCGCCGAACGGTC	1	173	0	ACCGTCAGCG	    0.946195	-66
ACGGGTGAGCCTACGTCGTCTGGGCGATCTTG	1	189	1	CACGTCGTCG	    0.965678	-50
CCTACGTTGTCGGCACGCTCGGGCAAGATCGC	1	212	0	CGCACGCTCG	    0.792298	-27
    CTACCAATTCGTCACCGGCATCGCACAC	2	7	1	ATCGTCACCG	    0.865837	-280
GCGTGCCGTGCCGCGTCCGCTGTGGTTGGTGT	2	42	0	CGCGTCCGCG	    0.696596	-245
AACGTCCCTTCCGCGTGCCGTGCCGCGTCCGC	2	54	0	CGCGTGCCGG	    0.912202	-233
CTAGCACCACCACCGTGCCCAGGCAACGACGC	2	94	1	CCCGTGCCCG	    0.969667	-193
GCCCAGGCAACGACGCCGGCCGTCGCTAAGAA	2	110	1	CACGCCGGCG	    0.985774	-177
ATGAATAAGGCCGCGCCCGCCCCGACAAATGA	2	156	1	CGCGCCCGCC	    0.773793	-131
CATGTCTGCGCAGCGCCAGCCGATCTCCCCCT	2	236	0	CGCGCCAGCG	    0.622608	-51
TTACGCAGTTCTGCTTCCGCAGCATGTCTGCG	2	258	0	CGCTTCCGCG	    0.797952	-29
          * ******** *

Masking position 4
Map Score:   34.9519

Number of sites scoring better than the average of aligned sites = 1128
Number in coding regions = 1080
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 2

    GGCCACACCCTCCTGGCATCTTGCAAG	1	7	1	ACCTCCTGGC	    0.841308	-232
AACACCAGGCACACTGGTAACAACAGGGATC	1	37	0	ACCTGGTAAC	    0.734669	-202
GTCTGTGACTGCACTGGTGGCGCCGGTGTGT	1	70	1	GCCTGGTGGC	    0.984996	-169
TATTCGACGAGCCCGGGCGACCACTCAGATC	1	116	1	GCCGGGCGAC	     0.99565	-123
CCGGGCGACCACTCAGATCACGCGGCCTGCT	1	128	1	ACCAGATCAC	    0.733186	-111
TACGACACGCGCCCAGCAGGCCGCGTGATCT	1	142	0	GCCAGCAGGC	    0.967447	-97
GTAGACCGTTCGGCGGCTGACGGGTGAGCCT	1	170	1	CGCGGCTGAC	    0.917664	-69
GGGCAAGATCGCCCAGACGACGTAGGCTCAC	1	193	0	GCCAGACGAC	    0.966761	-46
TTGTCGGCACGCTCGGGCAAGATCGCCCAGA	1	207	0	GCCGGGCAAG	    0.830882	-32
CACCGGCATCGCACACGTCACACCAACCACA	2	23	1	GCCACGTCAC	     0.91444	-264
GTCACACCAACCACAGCGGACGCGGCACGGC	2	39	1	CCCAGCGGAC	    0.908089	-248
AGCGGACGCGGCACGGCACGCGGAAGGGACG	2	53	1	GCCGGCACGC	    0.966044	-234
GGGACGTTAGACTCGGCTAGCACCACCACCG	2	78	1	ACCGGCTAGC	    0.966587	-209
CCACCACCGTGCCCAGGCAACGACGCCGGCC	2	100	1	GCCAGGCAAC	     0.97338	-187
AATTTCTTAGCGACGGCCGGCGTCGTTGCCT	2	114	0	CGCGGCCGGC	    0.962029	-173
ATAAGGCCGCGCCCGCCCCGACAAATGATTA	2	160	1	GCCGCCCCGA	    0.769463	-127
GCTCCGCTATGCCTAGCCCGCAAATGTAAGG	2	191	0	GCTAGCCCGC	    0.894285	-96
TCTAGGGGGAGATCGGCTGGCGCTGCGCAGA	2	233	1	GACGGCTGGC	    0.957136	-54
          ** ********

Masking position 4
Map Score:   23.7803

Number of sites scoring better than the average of aligned sites = 4001
Number in coding regions = 3745
Number in noncoding regions = 256
Number of orfs with sites within 600 bp upstream = 186
Fraction of orfs with sites within 600 bp upstream = 0.0298747


Motif number 3

GATGCCAGGAGGGTGTGGCC          	1	1	0	GGGTGTGGCC	    0.985766	-238
GCAAGATCCCTGTTGTTACCAGTGTGCCTG	1	33	1	TGTTGTTACC	     0.92277	-206
CCAGTGTGCCTGGTGTTTCGTCTGTGACTG	1	51	1	TGGTGTTTCG	    0.989111	-188
CTGGTGGCGCCGGTGTGTCGGGACACAATT	1	83	1	CGGTGTGTCG	    0.991734	-156
CCGCTGTGGTTGGTGTGACGTGTGCGATGC	2	28	0	TGGTGTGACG	    0.995136	-259
          **********

Masking position 6
Map Score:   4.46338

Number of sites scoring better than the average of aligned sites = 136
Number in coding regions = 110
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 4

CACACCCTCCTGGCATCTTGCAAGATCCCT	1	14	1	TGGCATCTTG	    0.987361	-225
TGGTAACAACAGGGATCTTGCAAGATGCCA	1	24	0	AGGGATCTTG	    0.993004	-215
ACGTCGTCTGGGCGATCTTGCCCGAGCGTG	1	201	1	GGCGATCTTG	    0.991349	-38
          **********

Masking position 5
Map Score:   0.0707066

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 13
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 5

          **********

No masking
Map Score:   1.74326e-12

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:   1.74326e-12

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:   1.74326e-12

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