AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i092_bsub_mtub_300.orf -o092_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	licT	95	transcriptional antiterminator (BglG family)
#2	yxiP	206	yxiP
#3	bglP	300	phosphotransferase system (PTS) beta-glucoside-specific enzyme IIABC component

Motif number 1

          CCAGCTTCCGTCTTTCCCTG	1	1	1	CCAGCTTCCG	    0.973563	-95
    GCTCTGTCTCCTCTCTGCTGAATCCC	2	191	0	TCTCCTCTCT	    0.937085	-16
TTAGGTTTTGCCTGCTTTCGCAGTAACAAT	3	128	0	CCTGCTTTCG	    0.978093	-173
ATTGCGAGAGTCTCCTCCTGCACCTGCACC	3	160	0	TCTCCTCCTG	    0.907686	-141
AAATGCTGCATCACCTCCTAAAAGAGAATA	3	210	0	TCACCTCCTA	    0.862128	-91
CCGCCTTTCACCAGCTTTTTTTGTATCAAA	3	237	0	CCAGCTTTTT	    0.935283	-64
TGAAAGGTGGCCGCCTTTCACCAGCTTTTT	3	247	0	CCGCCTTTCA	    0.961271	-54
TGAAAGGCGGCCACCTTTCATCCAGCAGTC	3	257	1	CCACCTTTCA	    0.982174	-44
   GTGTATACCTCCTTTTTATGGGGGGAC	3	284	0	CCTCCTTTTT	    0.965569	-17
          **********

Masking position 6
Map Score:   8.72025

Number of sites scoring better than the average of aligned sites = 1107
Number in coding regions = 740
Number in noncoding regions = 367
Number of orfs with sites within 600 bp upstream = 382
Fraction of orfs with sites within 600 bp upstream = 0.0613556


Motif number 2

TGTACTAGGTCAATATCATCAGGGAAAGACG	1	19	0	CAAATCATCA	    0.547149	-77
TGATATTGACCTAGTACAAAAAGAATGTACA	1	32	1	CTATACAAAA	    0.735018	-64
ATTTGAAGCGAAAAAACATAAATATTTTGTA	2	87	0	AAAAACATAA	    0.916596	-120
AACCCCAGCAATAAATCAAAAGTATGATTTG	2	113	0	ATAATCAAAA	     0.87619	-94
CCCTTCTGGAAAATACCATAAAATATAGTTA	2	163	0	AAAACCATAA	    0.933988	-44
ACTATCGTTTCTAGAACAAAAGTAATCATAA	3	16	0	CTAAACAAAA	      0.9562	-285
AAACGATAGTCAACACCAAAAATGAAAGCGT	3	37	1	CAAACCAAAA	    0.979453	-264
GTATACCTACAAACAAATAAAACGACCCGTC	3	94	1	AAAAAATAAA	    0.628679	-207
CGAAAGCAGGCAAAACCTAAATGGTGCAGGT	3	138	1	CAAACCTAAA	    0.949968	-163
AAGAGAATAAAAAAACCTAAATGACACAGAT	3	188	0	AAAACCTAAA	    0.933988	-113
GCAGCATTTGATACAAAAAAAGCTGGTGAAA	3	231	1	ATAAAAAAAA	    0.714789	-70
          *** *******

Masking position 3
Map Score:   7.15731

Number of sites scoring better than the average of aligned sites = 1858
Number in coding regions = 1534
Number in noncoding regions = 324
Number of orfs with sites within 600 bp upstream = 309
Fraction of orfs with sites within 600 bp upstream = 0.0496306


Motif number 3

GATTGTACATTCTTTTTGTACTAGGTCAAT	1	36	0	TCTTTTTGTA	    0.854522	-60
TTTTACAAAATATTTATGTTTTTTCGCTTC	2	84	1	TATTTATGTT	     0.96382	-123
CTTCAAATCATACTTTTGATTTATTGCTGG	2	110	1	TACTTTTGAT	    0.854521	-97
        AATCTTTATGATTACTTTTGTT	3	3	1	TCTTTATGAT	    0.846703	-298
TCTTTATGATTACTTTTGTTCTAGAAACGA	3	13	1	TACTTTTGTT	    0.941324	-288
TCAACGCTTTCATTTTTGGTGTTGACTATC	3	41	0	CATTTTTGGT	    0.892832	-260
GCACCTGCACCATTTAGGTTTTGCCTGCTT	3	141	0	CATTTAGGTT	    0.914837	-160
CAATCTGTGTCATTTAGGTTTTTTTATTCT	3	186	1	CATTTAGGTT	    0.914837	-115
TTTCACCAGCTTTTTTTGTATCAAATGCTG	3	232	0	TTTTTTTGTA	    0.682892	-69
          **********

Masking position 5
Map Score:   4.11275

Number of sites scoring better than the average of aligned sites = 1342
Number in coding regions = 1013
Number in noncoding regions = 329
Number of orfs with sites within 600 bp upstream = 332
Fraction of orfs with sites within 600 bp upstream = 0.0533248


Motif number 4

TAAATGGTACCAGATGCACCTAACCCCAGC	2	135	0	CAGATGCACC	    0.915802	-72
TGTCTCCTCTCTGCTGAATCCCTTCTGGAA	2	183	0	CTGCTGAATC	    0.986182	-24
GCGTTGACATCTCACGAATCTAGTGCTAAA	3	64	1	CTCACGAATC	    0.907508	-237
AGTAACAATCCTGACGGGTCGTTTTATTTG	3	107	0	CTGACGGGTC	    0.917122	-194
CGAGAGTCTCCTCCTGCACCTGCACCATTT	3	156	0	CTCCTGCACC	    0.978568	-145
TTTGTATCAAATGCTGCATCACCTCCTAAA	3	218	0	ATGCTGCATC	     0.95425	-83
TATGGGGGGACTGCTGGATGAAAGGTGGCC	3	265	0	CTGCTGGATG	    0.954994	-36
          **********

Masking position 6
Map Score:   2.71304

Number of sites scoring better than the average of aligned sites = 1619
Number in coding regions = 1492
Number in noncoding regions = 127
Number of orfs with sites within 600 bp upstream = 97
Fraction of orfs with sites within 600 bp upstream = 0.0155798


Motif number 5

          **********

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 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