AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i061_Glutamate_Synthase_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	gltA	146	glutamate synthase (large subunit)

Motif number 1

   GTTTGTCTCACATCCATCTATCTCATTTTG	1	8	1	TCACAATCTA	    0.993739	-139
ATAATTTAGATCAAAAGAATCTCAAAATGAGAT	1	30	0	TCAAAATCTC	    0.993739	-117
ATTCTTTTGATCTAAATTATATATTGTTTATAT	1	43	1	TCTAAATATA	    0.989953	-104
TTGTAGGTTTTCAAAACGATATAAACAATATAT	1	61	0	TCAAAATATA	    0.993516	-86
GGTCATAAAATCTAACAACTCTATAATCATTGT	1	90	0	TCTAACTCTA	    0.990924	-57
          *****   *****

Masking position 5
Map Score:   5.55769

Number of sites scoring better than the average of aligned sites = 109
Number in coding regions = 95
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 2

TTTGATCTAAATTATATATTGTTTATATCG	1	48	1	ATTATATATT	    0.761817	-99
TTATATATTGTTTATATCGTTTTGAAAACC	1	59	1	TTTATATCGT	    0.952751	-88
CTCTATAATCATTGTAGGTTTTCAAAACGA	1	75	0	ATTGTAGGTT	    0.968629	-72
ACCTACAATGATTATAGAGTTGTTAGATTT	1	86	1	ATTATAGAGT	    0.955788	-61
          **********

Masking position 5
Map Score:   1.24046

Number of sites scoring better than the average of aligned sites = 94
Number in coding regions = 62
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 3

          **********

No masking
Map Score:   -1.17788e-14

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 4

          **********

No masking
Map Score:   -1.17788e-14

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 5

          **********

No masking
Map Score:   -1.17788e-14

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