AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i228_6_1_1_17_aful_reg_300.orf -o228_aful_300.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	RAG50068	112	Archaeoglobus_fulgidus

Motif number 1

AACCTCAACTTCAAGCAAAATCCA      	1	5	0	TCAAGCAAAA	    0.987625	-108
CTAAAAAATTTTAACCTCAACTTCAAGCAA	1	17	0	TTAACCTCAA	    0.970986	-96
AGCGCATCACCCAACCTAAAAAATTTTAAC	1	32	0	CCAACCTAAA	    0.997204	-81
TTTTATCGGCCCAACCAGAACAACATCA  	1	95	1	CCAACCAGAA	    0.996731	-18
          **********

Masking position 4
Map Score:   5.01796

Number of sites scoring better than the average of aligned sites = 243
Number in coding regions = 213
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 2

TGTCTTGAAGTATTTAGCGCATCACCCAAC	1	47	0	TATTTAGCGC	    0.994262	-66
CAAGACAGGCCTTTTAGCGGTAAATTTTTA	1	70	1	CTTTTAGCGG	    0.997719	-43
TAGCGGTAAATTTTTATCGGCCCAACCAGA	1	84	1	TTTTTATCGG	     0.99516	-29
          **********

Masking position 6
Map Score:   3.65423

Number of sites scoring better than the average of aligned sites = 9
Number in coding regions = 7
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

AAATTTTAACCTCAACTTCAAGCAAAATCC	1	12	0	CTCAACTTCA	    0.982496	-101
ACCCAACCTAAAAAATTTTAACCTCAACTT	1	24	0	AAAAATTTTA	     0.85515	-89
GTGATGCGCTAAATACTTCAAGACAGGCCT	1	52	1	AAATACTTCA	    0.983924	-61
GCCCAACCAGAACAACATCA          	1	103	1	AACAACATCA	    0.989649	-10
          **********

Masking position 5
Map Score:   1.57505

Number of sites scoring better than the average of aligned sites = 713
Number in coding regions = 656
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 4

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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:   1.3033e-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