AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i320_mixed5_aful_reg_300.orf -o320_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	RAG50400	138	Archaeoglobus_fulgidus
#2	RAG20719	101	Archaeoglobus_fulgidus

Motif number 1

         ATCATAAAAAATAGGATGTTA	1	2	1	TCATAAAAAA	    0.960832	-137
GTGATTACCATCATCACATATCAGTGTTAC	1	47	1	TCATCACATA	    0.963214	-92
CATATCAGTGTTACCAAAACTTTTAAAACT	1	63	1	TTACCAAAAC	    0.898054	-76
ATCACCTCCTTCATCAAATCATCATTCATC	1	116	0	TCATCAAATC	    0.993038	-23
         GTCATCACCTCCTTCATCAAA	1	128	0	TCATCACCTC	     0.96725	-11
GCATAAAAACTCAAAAAAACTTTATTTGTT	2	28	0	TCAAAAAAAC	    0.956871	-74
GAATTTGTGGGCATAAAAACTCAAAAAAAC	2	38	0	GCATAAAAAC	     0.96512	-64
          **********

Masking position 6
Map Score:   7.17702

Number of sites scoring better than the average of aligned sites = 671
Number in coding regions = 606
Number in noncoding regions = 65
Number of orfs with sites within 600 bp upstream = 59
Fraction of orfs with sites within 600 bp upstream = 0.00947639


Motif number 2

ACTGATATGTGATGATGGTAATCACAAGAT	1	42	0	GATGATGGTA	    0.960989	-97
GGGAAGAGCCGATGAATGATGATTTGATGA	1	106	1	GATGAATGAT	    0.979104	-33
ATGATGATTTGATGAAGGAGGTGATGAC  	1	121	1	GATGAAGGAG	    0.995049	-18
          GCTGAATGTGCGCTTCAAAC	2	1	1	GCTGAATGTG	    0.983201	-101
CACCCTTGCCGAAGCTTGAGC         	2	91	1	GAAGCTTGAG	    0.946776	-11
          **********

Masking position 4
Map Score:   3.35022

Number of sites scoring better than the average of aligned sites = 887
Number in coding regions = 858
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 3

TAGGATGTTAATCCATTTAAATCTTGTGATT	1	22	1	ATCCTTTAAA	    0.969302	-117
AGTGTTACCAAAACTTTTAAAACTGCACGGG	1	69	1	AAACTTTAAA	    0.989716	-70
TGTGCGCTTCAAACAAATAAAGTTTTTTTGA	2	17	1	AAACAATAAA	    0.963743	-85
GTGGGCATAAAAACTCAAAAAAACTTTATTT	2	31	0	AAACCAAAAA	    0.922924	-71
TCAACTCTAAAACCTTTTAAACACCCTTGCC	2	70	1	AACCTTTAAA	    0.990466	-32
          **** ******

Masking position 9
Map Score:   3.07456

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 25
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 4

     GCTGAATGTGCGCTTCAAACAAATA	2	6	1	ATGTGCGCTT	    0.899333	-96
TTGAGCGAATTTGTGGGCATAAAAACTCAA	2	44	0	TTGTGGGCAT	    0.986525	-58
GGTTTTAGAGTTGAGCGAATTTGTGGGCAT	2	54	0	TTGAGCGAAT	    0.975392	-48
          **********

Masking position 2
Map Score:   0.0462086

Number of sites scoring better than the average of aligned sites = 39
Number in coding regions = 36
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

          **********

No masking
Map Score:   -1.75204e-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:   -1.75204e-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:   -1.75204e-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