AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i008_Uracil_Utilization_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	upp	104	upp

Motif number 1

TCCGCGCGACCGGTCAACCCCGTCCATATAC	1	18	0	CGTCAACCCC	     0.99714	-87
CCGGTCGCGCGGATGGACGCACCCGTATCAG	1	36	1	GGTGGACGCA	    0.987632	-69
GGACGCACCCGTATCAGCCCCCTTTTAGGGG	1	50	1	GTTCAGCCCC	    0.996415	-55
TAACAATCGTGGCTCGGTCCCCTAAAAGGGG	1	68	0	GGTCGGTCCC	    0.787683	-37
TGTTATATAGGGTTCAACGCC          	1	94	1	GGTCAACGCC	    0.997838	-11
          ** ********

Masking position 4
Map Score:   9.15587

Number of sites scoring better than the average of aligned sites = 1842
Number in coding regions = 1684
Number in noncoding regions = 158
Number of orfs with sites within 600 bp upstream = 142
Fraction of orfs with sites within 600 bp upstream = 0.0228076


Motif number 2

CCCGTCCATATACTCCCGGC          	1	1	0	TACTCCCGGC	    0.976787	-104
CGCGACCGGTCAACCCCGTCCATATACTCC	1	15	0	CAACCCCGTC	    0.992238	-90
CGTCCATCCGCGCGACCGGTCAACCCCGTC	1	25	0	CGCGACCGGT	    0.972956	-80
CGCGGATGGACGCACCCGTATCAGCCCCCT	1	43	1	CGCACCCGTA	    0.994736	-62
GCACCCGTATCAGCCCCCTTTTAGGGGACC	1	54	1	CAGCCCCCTT	    0.991574	-51
AATCGTGGCTCGGTCCCCTAAAAGGGGGCT	1	65	0	CGGTCCCCTA	    0.991718	-40
          **********

Masking position 6
Map Score:   6.10821

Number of sites scoring better than the average of aligned sites = 8880
Number in coding regions = 8192
Number in noncoding regions = 688
Number of orfs with sites within 600 bp upstream = 532
Fraction of orfs with sites within 600 bp upstream = 0.0854481


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