AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i039_Mannose_Metabolism_aful_reg_100.orf -o039_aful_100.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/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	RAG46100	59	Archaeoglobus_fulgidus
#2	RAG32589	140	Archaeoglobus_fulgidus

Motif number 1

ATGTCCCCTACCCCACGGGGGCAGAAAAAAGG	2	32	0	CCCCGGGGGC	     0.80262	-109
GGGTAGGGGACATCCTGGTGGCCTTCGGAGCC	2	51	1	CACTGGTGGC	    0.995145	-90
GAATCGAACCCGGGTCTGTGGCTCCGAAGGCC	2	70	0	CGGCTGTGGC	     0.99677	-71
GGGTTCGATTCCCGGCGGGGGCGTCAGAAAGT	2	91	1	CCGCGGGGGC	     0.97299	-50
          ** * *******

Masking position 8
Map Score:   5.20756

Number of sites scoring better than the average of aligned sites = 35
Number in coding regions = 25
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 2

TACCGAGATTCCGAATCACTTTTG         	1	2	0	CCGAATTTTT	    0.986486	-58
AATGAATGTTCAAAAAGTTTTTTACCGAGATTC	1	24	0	CAAAAATTTT	    0.899947	-36
GGCAGCAATTCAGAATGAATGTTCAAAAAGTTT	1	37	0	CAGAATTGTT	    0.994239	-23
CCCACGGGGGCAGAAAAAAGGTTGGTAACAAAT	2	20	0	CAGAAAGGTT	     0.99123	-121
GCGGGGGCGTCAGAAAGTATTTTATTAATTTCA	2	105	1	CAGAAATTTT	      0.9952	-36
          ******   ****

Masking position 5
Map Score:   4.98935

Number of sites scoring better than the average of aligned sites = 78
Number in coding regions = 70
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

CAAAAGTGATTCGGAATCTCGGTAAAAAAC	1	11	1	TCGGAATCTC	    0.979373	-49
GAACATTCATTCTGAATTGCTGCC      	1	46	1	TCTGAATTGC	    0.954697	-14
GGTCTGTGGCTCCGAAGGCCACCAGGATGT	2	60	0	TCCGAAGGCC	    0.992898	-81
CAGACCCGGGTTCGATTCCCGGCGGGGGCG	2	84	1	TTCGATTCCC	    0.963409	-57
TAAAATACTTTCTGACGCCCCCGCCGGGAA	2	99	0	TCTGACGCCC	    0.993013	-42
          **********

Masking position 5
Map Score:   1.96968

Number of sites scoring better than the average of aligned sites = 452
Number in coding regions = 426
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 4

ATGTTCAAAAAGTTTTTTACCGAGATTCCG	1	22	0	AGTTTTTTAC	    0.992602	-38
  CCTTTTTTAATTTGTTACCAACCTTTTT	2	9	1	AATTTGTTAC	    0.976385	-132
GGCGTCAGAAAGTATTTTATTAATTTCACT	2	110	1	AGTATTTTAT	     0.96537	-31
          **********

Masking position 9
Map Score:   0.190917

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 13
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:   -2.32047e-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:   -2.32047e-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:   -2.32047e-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