AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i327_not_clear2_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	lepA	133	GTP-binding protein

Motif number 1

TGGGTTGCTTTTCTCTTTCACGTAC     	1	6	0	TTCTCTTTCA	    0.997837	-128
AAGAGAAAAGTTCCCTATCATATCTGGGTT	1	30	0	TTCCCTATCA	    0.995474	-104
TAGGGAACTTTTCTCTTTCTTGTTTTACAT	1	43	1	TTCTCTTTCT	    0.996202	-91
          **********

Masking position 6
Map Score:   5.10395

Number of sites scoring better than the average of aligned sites = 82
Number in coding regions = 72
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 2

ATATCTGGGTTGCTTTTCTCTTTCACGTAC	1	11	0	TGCTTTTCTC	    0.994389	-123
TATGATAGGGAACTTTTCTCTTTCTTGTTT	1	38	1	AACTTTTCTC	    0.991345	-96
ACACTAGCTTAGATTATATCAATAGGATTG	1	83	0	AGATTATATC	    0.959713	-51
          **********

Masking position 5
Map Score:   0.608161

Number of sites scoring better than the average of aligned sites = 264
Number in coding regions = 221
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 3

GAAAAGTTCCCTATCATATCTGGGTTGCTT	1	26	0	CTATCATATC	     0.97223	-108
TGAATCTTTACAATCCTATTGATATAATCT	1	73	1	CAATCCTATT	    0.995033	-61
   AATCTATCACTCCTACTATTAAACGCA	1	117	0	CACTCCTACT	    0.992984	-17
          **********

Masking position 8
Map Score:   0.650889

Number of sites scoring better than the average of aligned sites = 46
Number in coding regions = 27
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 4

          **********

No masking
Map Score:   1.51646e-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 5

          **********

No masking
Map Score:   1.51646e-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:   1.51646e-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