AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00500_aful_reg_100.orf -o00500_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -x5 -e 
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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	AF1142	221	glucose-1-phosphate cytidylyltransferase (rfbF)
#2	AF1232	63	conserved hypothetical protein

Motif number 1

ATCGTCGGATTGGGGGCAGCAGCGGTCATTGCAGCTGG	1	27	0	TGGGACCGTA	    0.998763	-195
AATCCGACGATTGTGGCAATAACGGTGATTAAATTCGG	1	54	1	TGTGATCGTA	    0.990815	-168
GTGATTAAATTCGGCGAAACACCTGTTTTCGAGAGAAT	1	78	1	TGGGACCGTT	    0.995754	-144
TTGCCAGAGGTCGGGAAAACCTCCGATAAACAAGTTCT	1	118	1	TGGAACCGAA	    0.993249	-104
TTAAATCAAATGGGAGTATCTGCTGACAGAACTTGTTT	1	145	0	TGGGACCGAA	    0.998778	-77
  TGTCTCACCTGTCGTAGTCCCAGATACGAAAGATTA	2	9	1	CGTGATCGAA	     0.97543	-55
          * ** * * *  * ** *

Masking position 8
Map Score:   7.53283

Number of sites scoring better than the average of aligned sites = 93
Number in coding regions = 86
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

GGGCAGCAGCGGTCATTGCAGCTGGAGAAA	1	22	0	GGTCATTGCA	    0.983587	-200
TGGCAATAACGGTGATTAAATTCGGCGAAA	1	67	1	GGTGATTAAA	    0.988854	-155
CCCATAAGGAGGTGATTTAAATCAAATGGG	1	169	0	GGTGATTTAA	    0.993796	-53
CCTCCTTATGGGTAATTTTAAATAACTCTC	1	187	1	GGTAATTTTA	    0.970659	-35
          **********

Masking position 5
Map Score:   2.48506

Number of sites scoring better than the average of aligned sites = 56
Number in coding regions = 48
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

TGGCAAAGATTCTCTCGAAAACAGGTGTTTCGC	1	91	0	TCTCTAAACA	    0.985145	-131
GTTTTCCCGACCTCTGGCAAAGATTCTCTCGAA	1	105	0	CCTCTAAAGA	    0.975786	-117
GTCGGGAAAACCTCCGATAAACAAGTTCTGTCA	1	127	1	CCTCCAAACA	     0.99736	-95
TTTAAATAACTCTCCTTTTAACATTTTTC    	1	203	1	TCTCCTAACA	    0.989879	-19
          *****   *****

Masking position 10
Map Score:   1.21929

Number of sites scoring better than the average of aligned sites = 35
Number in coding regions = 29
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

          **********

No masking
Map Score:   1.01908e-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:   1.01908e-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:   1.01908e-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