AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i227_rna_methyltransferase_bsub_reg_100.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	    0.988223	-289
CAATGAAGATCCTTTCTGTAATGGCCTAAAG	1	42	0	CTTTCTGTAA	    0.972213	-259
CCGGCTCATGGATCTCTCTCAGCCAATGAAG	1	65	0	GTCTCTCTCA	    0.969825	-236
AAGCAGACTTCTGCTCTCCCAACTTCAGCCT	1	172	0	CGCTCTCCCA	    0.971293	-129
CCGCGCGGTTCCACTCTGTTTGAAAAGCAGA	1	196	0	CACTCTGTTT	     0.88681	-105
GCGGTTAAAGCGTCTCTGTCATGTTTACATG	1	223	1	CTCTCTGTCA	    0.996845	-78
ATAAAAAAAGCGTCTCTGCATGTAAACATGA	1	241	0	CTCTCTGCAT	    0.981817	-60
TGCTTCCCCCCGTTTCTCTATCTGATTTCCT	1	279	0	CTTTCTCTAT	    0.930581	-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

TCAGCCAATGAAGATCCTTTCTGTAATGGC	1	48	0	AAGATCCTTT	    0.986935	-253
TTGGCTGAGAGAGATCCATGAGCCGGGTTT	1	70	1	GAGATCCATG	    0.960486	-231
GTGCGCCCTTAAGACCTTTGAAGAACGTTT	1	105	1	AAGACCTTTG	     0.96419	-196
AAGACCTTTGAAGAACGTTTTTTGAAATCA	1	115	1	AAGAACGTTT	    0.924083	-186
AAACATGACAGAGACGCTTTAACCGCGCGG	1	219	0	GAGACGCTTT	    0.992799	-82
TTTACATGCAGAGACGCTTTTTTTATTGGG	1	246	1	GAGACGCTTT	    0.992799	-55
          **********

Masking position 4
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

GAACGTTTTTTGAAATCAGTATTCAAAGGC	1	127	1	TGAAATCAGT	     0.95937	-174
GCTGAAGTTGGGAGAGCAGAAGTCTGCTTT	1	174	1	GGAGAGCAGA	    0.995369	-127
CACTCTGTTTGAAAAGCAGACTTCTGCTCT	1	186	0	GAAAAGCAGA	    0.989281	-115
ATTGGGTAGAGGAAATCAGATAGAGAAACG	1	270	1	GGAAATCAGA	    0.995798	-31
          **********

Masking position 5
Map Score:   4.49558

Number of sites scoring better than the average of aligned sites = 168
Number in coding regions = 155
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 5

GGTCTTAAGGGCGCACTTCTAAAACCCGGC	1	91	0	GCGCACTTCT	    0.994339	-210
TGTAACGGCGGCGGCCGCCTTTGAATACTG	1	143	0	GCGGCCGCCT	    0.994815	-158
TGTTTGAAAAGCAGACTTCTGCTCTCCCAA	1	181	0	GCAGACTTCT	    0.991634	-120
          **********

Masking position 10
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