AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i227_rna_methyltransferase_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 
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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	cysE	300	serine acetyltransferase

Motif number 1

GCTTTATACTCTTCCCTGTCAACAATCATTT	1	12	0	CTCCCTGTCA	    0.990599	-289
CAATGAAGATCCTTTCTGTAATGGCCTAAAG	1	42	0	CTTTCTGTAA	    0.977746	-259
CCGGCTCATGGATCTCTCTCAGCCAATGAAG	1	65	0	GTCTCTCTCA	    0.975821	-236
AAGCAGACTTCTGCTCTCCCAACTTCAGCCT	1	172	0	CGCTCTCCCA	    0.977005	-129
CCGCGCGGTTCCACTCTGTTTGAAAAGCAGA	1	196	0	CACTCTGTTT	    0.907734	-105
GCGGTTAAAGCGTCTCTGTCATGTTTACATG	1	223	1	CTCTCTGTCA	    0.997486	-78
ATAAAAAAAGCGTCTCTGCATGTAAACATGA	1	241	0	CTCTCTGCAT	    0.985466	-60
TGCTTCCCCCCGTTTCTCTATCTGATTTCCT	1	279	0	CTTTCTCTAT	    0.943925	-22
          * *********

Masking position 7
Map Score:   9.59388

Number of sites scoring better than the average of aligned sites = 699
Number in coding regions = 609
Number in noncoding regions = 90
Number of orfs with sites within 600 bp upstream = 90
Fraction of orfs with sites within 600 bp upstream = 0.0144555


Motif number 2

GCCATTACAGAAAGGATCTTCATTGGCTGA	1	48	1	AAAGGATCTT	     0.98728	-253
AAACCCGGCTCATGGATCTCTCTCAGCCAA	1	70	0	CATGGATCTC	    0.961506	-231
AAACGTTCTTCAAAGGTCTTAAGGGCGCAC	1	105	0	CAAAGGTCTT	    0.965109	-196
TGATTTCAAAAAACGTTCTTCAAAGGTCTT	1	115	0	AAACGTTCTT	    0.925969	-186
CCGCGCGGTTAAAGCGTCTCTGTCATGTTT	1	219	1	AAAGCGTCTC	    0.992985	-82
CCCAATAAAAAAAGCGTCTCTGCATGTAAA	1	246	0	AAAGCGTCTC	    0.992985	-55
          **********

Masking position 7
Map Score:   6.14484

Number of sites scoring better than the average of aligned sites = 339
Number in coding regions = 293
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 3

GGCGCACTTCTAAAACCCGGCTCATGGATC	1	82	0	TAAAACCCGG	    0.921018	-219
TTCAAAGGTCTTAAGGGCGCACTTCTAAAA	1	97	0	TTAAGGGCGC	    0.983936	-204
AAATCAGTATTCAAAGGCGGCCGCCGCCGT	1	139	1	TCAAAGGCGG	     0.98792	-162
ACTTCAGCCTGTAACGGCGGCGGCCGCCTT	1	152	0	GTAACGGCGG	    0.996174	-149
CAGAGACGCTTTAACCGCGCGGTTCCACTC	1	211	0	TTAACCGCGC	    0.988482	-90
ATCAGATAGAGAAACGGGGGGAAGCAT   	1	284	1	GAAACGGGGG	    0.976566	-17
          **********

Masking position 4
Map Score:   5.78786

Number of sites scoring better than the average of aligned sites = 776
Number in coding regions = 696
Number in noncoding regions = 80
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 4

AGAACGTTTTTTGAAATCAGTATTCAAAGG	1	126	1	TTGAAATCAG	    0.976398	-175
GGCTGAAGTTGGGAGAGCAGAAGTCTGCTT	1	173	1	GGGAGAGCAG	    0.992686	-128
CCACTCTGTTTGAAAAGCAGACTTCTGCTC	1	187	0	TGAAAAGCAG	     0.98579	-114
TATTGGGTAGAGGAAATCAGATAGAGAAAC	1	269	1	AGGAAATCAG	     0.99007	-32
          **********

Masking position 6
Map Score:   2.48715

Number of sites scoring better than the average of aligned sites = 200
Number in coding regions = 182
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 5

GCCGGGTTTTAGAAGTGCGCCCTTAAGACC	1	91	1	AGAAGTGCGC	    0.994339	-210
CAGTATTCAAAGGCGGCCGCCGCCGTTACA	1	143	1	AGGCGGCCGC	    0.994815	-158
TTGGGAGAGCAGAAGTCTGCTTTTCAAACA	1	181	1	AGAAGTCTGC	    0.991634	-120
          **********

Masking position 1
Map Score:   0.0220249

Number of sites scoring better than the average of aligned sites = 62
Number in coding regions = 57
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


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