AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i012_Glycogen_Biosynthesis_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	glgD	23	ADP-glucose pyrophosphorylase
#2	glgB	300	1,4-alpha-glucan branching enzyme

Motif number 1

TATCATGATTTATAAAAACAAAAAAACCTTGCAGG	2	97	0	TAAAACAAAA	    0.985982	-204
GTCTGTTTTTAAAATAAAGAACAAAATCTAAGACA	2	132	0	AAAAAGAAAA	    0.987801	-169
CTTTATTTTAAAAACAGACTACAAAAATCTCCATA	2	148	1	AAAAACAAAA	    0.996505	-153
TCATTTTCTGAAGAAAAACGAAATATATGGAGATT	2	173	0	AAAAACAATA	    0.985982	-128
TATTTATTCGAAGAAATAAAAAAAAGCCCTTTCCT	2	238	0	AAAAAAAAAA	    0.982025	-63
TATTTCTTCGAATAAATACTATAAATGAAAACTAT	2	255	1	AAAAACAAAA	    0.996486	-46
          ** * * ** * ***

Masking position 8
Map Score:   8.97525

Number of sites scoring better than the average of aligned sites = 79
Number in coding regions = 51
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 2

TTACCGCCGTGAAAGGGCGGTGTCTTAACCGC	2	21	0	GAAAGGCGTG	    0.993654	-280
TGCAGGATATGCAAGGCTTCTGGATGACCCGT	2	71	0	GCAAGGTTTG	    0.990464	-230
TGCATATCCTGCAAGGTTTTTTTGTTTTTATA	2	90	1	GCAAGGTTTT	    0.992086	-211
GCCCTTTCCTGAAAGCGCTTATACTTATAGAC	2	216	0	GAAAGCCTAT	     0.92312	-85
GCGCTTTCAGGAAAGGGCTTTTTTTTATTTCT	2	230	1	GAAAGGCTTT	     0.89893	-71
TATGATGTCAGAAAGGATGATTAC        	2	287	1	GAAAGGTGTT	    0.992118	-14
          ****** ** **

Masking position 4
Map Score:   8.08268

Number of sites scoring better than the average of aligned sites = 212
Number in coding regions = 163
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 3

          TTACTGAAGAGGGGGCAGAG	1	1	1	TTACTGAAGA	    0.967973	-23
CATATCATGATTTATAAAAACAAAAAAACC	2	104	0	TTTATAAAAA	    0.698048	-197
AAAAACGAAATATATGGAGATTTTTGTAGT	2	165	0	TATATGGAGA	    0.958486	-136
TTAACTTCATTTTCTGAAGAAAAACGAAAT	2	184	0	TTTCTGAAGA	    0.967255	-117
GTATAAGCGCTTTCAGGAAAGGGCTTTTTT	2	224	1	TTTCAGGAAA	    0.709773	-77
TTATAGTATTTATTCGAAGAAATAAAAAAA	2	249	0	TATTCGAAGA	    0.817458	-52
ATAAATACTATAAATGAAAACTATGATGTC	2	266	1	TAAATGAAAA	    0.880022	-35
          **********

Masking position 8
Map Score:   2.55048

Number of sites scoring better than the average of aligned sites = 1862
Number in coding regions = 1618
Number in noncoding regions = 244
Number of orfs with sites within 600 bp upstream = 277
Fraction of orfs with sites within 600 bp upstream = 0.0444908


Motif number 4

         TGACTCTGCCCCCTCTTCAGT	1	13	0	GACTCTGCCC	    0.993627	-11
AAGCGGTTAAGACACCGCCCTTTCACGGCG	2	19	1	GACACCGCCC	    0.998667	-282
TCGAACCCGTGTTACCGCCGTGAAAGGGCG	2	34	0	GTTACCGCCG	    0.988336	-267
          **********

Masking position 5
Map Score:   1.10012

Number of sites scoring better than the average of aligned sites = 103
Number in coding regions = 95
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 5

AGAAGCCTTGCATATCCTGCAAGGTTTTTT	2	82	1	CATATCCTGC	    0.992732	-219
AAATCTAAGACATATCATGATTTATAAAAA	2	114	0	CATATCATGA	    0.983224	-187
CAATTAACTTCATTTTCTGAAGAAAAACGA	2	187	0	CATTTTCTGA	    0.983224	-114
AAAAAAAAGCCCTTTCCTGAAAGCGCTTAT	2	226	0	CCTTTCCTGA	    0.992732	-75
          **********

Masking position 5
Map Score:   3.90863

Number of sites scoring better than the average of aligned sites = 142
Number in coding regions = 123
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 6

          **********

No masking
Map Score:   -4.38104e-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:   -4.38104e-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:   -4.38104e-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