AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i296_mixed11_aful_reg_300.orf -o296_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	RAG05258	41	Archaeoglobus_fulgidus
#2	RAG05274	111	Archaeoglobus_fulgidus
#3	RAG26611	137	Archaeoglobus_fulgidus

Motif number 1

AACTTTATGATTAAAAAGCTTTGGTTTT      	1	5	0	TAAAAGTTGG	    0.992419	-37
AGCTTTTTAATCATAAAGTTTAGGAGGAGAAGG 	1	19	1	TATAAGTTGG	    0.991409	-23
TTACGCTATATTAAAGCTTTTAGCTAATGACCAT	2	30	1	TAAAGTTTGC	    0.967991	-82
AAAGGTTGCCTTATAACTATTATGGTCATTAGCT	2	51	0	TATAATTTTG	    0.965812	-61
ATTTCAAGTTTAAAAACGCTTTTCAAAAGGTTGC	2	76	0	TAAAAGTTTC	    0.936874	-36
GCCAACTTATTTAAAATTATTTGGAATGAACTTC	3	25	1	TAAAATTTGG	    0.995769	-113
GTCATATAGGTAAAAATTTTTCGGATTAATTCCG	3	97	0	TAAAATTTGG	    0.995511	-41
          * **** * ** **

Masking position 5
Map Score:   11.6609

Number of sites scoring better than the average of aligned sites = 107
Number in coding regions = 75
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 2

TAATTACTTTTAAGGGAGTTGG        	2	3	0	TAAGGGAGTT	    0.986753	-109
AGCTTTAATATAGCGTAATTACTTTTAAGG	2	18	0	TAGCGTAATT	    0.979657	-94
AGAAGGCATTTAGCGGAATTAATCCGAAAA	3	84	1	TAGCGGAATT	      0.9948	-54
      CCCGTAGGGGAGTAGTTGTCATAT	3	124	0	TAGGGGAGTA	    0.991525	-14
          **********

Masking position 7
Map Score:   3.86627

Number of sites scoring better than the average of aligned sites = 31
Number in coding regions = 26
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

AAAGTAATTACGCTATATTAAAGCTTTTAG	2	23	1	CGCTATATTA	    0.964804	-89
TATGGTCATTAGCTAAAAGCTTTAATATAG	2	35	0	AGCTAAAAGC	    0.964158	-77
CTTCTCATCGCCCAAAATTCAAACCTCACA	3	55	1	CCCAAAATTC	    0.948636	-83
GGATTAATTCCGCTAAATGCCTTCTGTGAG	3	79	0	CGCTAAATGC	    0.995008	-59
AAAAATTTTTACCTATATGACAACTACTCC	3	110	1	ACCTATATGA	    0.948703	-28
          **********

Masking position 5
Map Score:   1.98383

Number of sites scoring better than the average of aligned sites = 71
Number in coding regions = 60
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 4

          **********

No masking
Map Score:   -3.17312e-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:   -3.17312e-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:   -3.17312e-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