AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00500_aful_reg_300.orf -o00500_aful_300.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

CCAGCTGCAATGACCGCTGCTGCCCCCAATCCGACGAT	1	27	1	TACGGTCCCA	    0.998739	-195
CCGAATTTAATCACCGTTATTGCCACAATCGTCGGATT	1	54	0	TACGATCACA	    0.990565	-168
ATTCTCTCGAAAACAGGTGTTTCGCCGAATTTAATCAC	1	78	0	AACGGTCCCA	    0.995636	-144
AGAACTTGTTTATCGGAGGTTTTCCCGACCTCTGGCAA	1	118	0	TTCGGTTCCA	    0.993062	-104
AAACAAGTTCTGTCAGCAGATACTCCCATTTGATTTAA	1	145	1	TTCGGTCCCA	    0.998753	-77
TAATCTTTCGTATCTGGGACTACGACAGGTGAGACA  	2	9	0	TTCGATCACG	    0.974762	-55
          * ** *  * * * ** *

Masking position 11
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

TTTCTCCAGCTGCAATGACCGCTGCTGCCC	1	22	1	TGCAATGACC	    0.981084	-200
TTTCGCCGAATTTAATCACCGTTATTGCCA	1	67	0	TTTAATCACC	    0.987137	-155
CCCATTTGATTTAAATCACCTCCTTATGGG	1	169	1	TTAAATCACC	    0.992792	-53
GAGAGTTATTTAAAATTACCCATAAGGAGG	1	187	0	TAAAATTACC	    0.966092	-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

GCGAAACACCTGTTTTCGAGAGAATCTTTGCCA	1	91	1	TGTTTAGAGA	    0.985243	-131
TTCGAGAGAATCTTTGCCAGAGGTCGGGAAAAC	1	105	1	TCTTTAGAGG	    0.975891	-117
TGACAGAACTTGTTTATCGGAGGTTTTCCCGAC	1	127	0	TGTTTGGAGG	    0.997244	-95
    GAAAAATGTTAAAAGGAGAGTTATTTAAA	1	203	0	TGTTAGGAGA	     0.98943	-19
          *****   *****

Masking position 4
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

AGCGGTCATTGCAGCTGGAGAAATATACTG	1	15	0	GCAGCTGGAG	    0.975486	-207
ATTGGGGGCAGCAGCGGTCATTGCAGCTGG	1	27	0	GCAGCGGTCA	    0.993887	-195
AGAATCTTTGCCAGAGGTCGGGAAAACCTC	1	111	1	CCAGAGGTCG	    0.972272	-111
AATGGGAGTATCTGCTGACAGAACTTGTTT	1	145	0	TCTGCTGACA	    0.924321	-77
      TGTCTCACCTGTCGTAGTCCCAGA	2	5	1	TCACCTGTCG	    0.976784	-59
          **********

Masking position 7
Map Score:   0.245621

Number of sites scoring better than the average of aligned sites = 449
Number in coding regions = 418
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


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


Motif number 7

          **********

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