AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i115_Glycine_Transport_mtub_reg_300.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 =  	0.66
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	proX	164	proX

Motif number 1

     CGTTGTACCGCTGAGTGGTTGATCAGCC	1	6	1	TCGCTGGTGG	    0.992891	-159
GCTGAGTGGTTGATCAGCCGAGGAAGAGGGATT	1	20	1	TTCAGCGAGG	    0.989762	-145
TGGTTTGGTTTCATTCTGTGTGGGATAGGACAA	1	72	0	TTTCTGGTGG	    0.984043	-93
GTACTGGGATTTTTCCGGCGTGGTTTGGTTTCA	1	92	0	TTCCGGGTGG	    0.998621	-73
TCCCAGTACATGCCGAGTTGTGGAAGCACGGCG	1	116	1	TCGAGTGTGG	    0.985156	-49
GTTGACACTATCGTCAGCGGCGGCGCCGTGCTT	1	139	0	TTCAGCGCGG	    0.993061	-26
          *  ***** ****

Masking position 1
Map Score:   5.9095

Number of sites scoring better than the average of aligned sites = 1262
Number in coding regions = 1147
Number in noncoding regions = 115
Number of orfs with sites within 600 bp upstream = 111
Fraction of orfs with sites within 600 bp upstream = 0.0178285


Motif number 2

 CGTTGTACCGCTGAGTGGTTGATCAGCCG	1	10	1	GCTGAGTGGT	    0.996517	-155
TGGGATTTTTCCGGCGTGGTTTGGTTTCAT	1	91	0	CCGGCGTGGT	     0.95698	-74
CCCAGTACATGCCGAGTTGTGGAAGCACGG	1	117	1	GCCGAGTTGT	    0.993607	-48
ATCGTCAGCGGCGGCGCCGTGCTTCCACAA	1	133	0	GCGGCGCCGT	    0.606819	-32
          **********

Masking position 10
Map Score:   5.62721

Number of sites scoring better than the average of aligned sites = 1351
Number in coding regions = 1271
Number in noncoding regions = 80
Number of orfs with sites within 600 bp upstream = 75
Fraction of orfs with sites within 600 bp upstream = 0.0120463


Motif number 3

CTGATCAACCACTCAGCGGTACAACG    	1	7	0	ACTCAGCGGT	     0.97172	-158
AATCCCTCTTCCTCGGCTGATCAACCACTC	1	23	0	CCTCGGCTGA	    0.998255	-142
TGAAACCAAACCACGCCGGAAAAATCCCAG	1	92	1	CCACGCCGGA	    0.994666	-73
AAGCACGGCGCCGCCGCTGACGATAGTGTC	1	139	1	CCGCCGCTGA	    0.996134	-26
          **********

Masking position 4
Map Score:   3.69528

Number of sites scoring better than the average of aligned sites = 2896
Number in coding regions = 2714
Number in noncoding regions = 182
Number of orfs with sites within 600 bp upstream = 151
Fraction of orfs with sites within 600 bp upstream = 0.0242531


Motif number 4

          **********

No masking
Map Score:   4.35863e-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:   4.35863e-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:   4.35863e-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