AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i174_Biotin_Biosynthesis_aful_reg_100.orf -o174_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	RAG48329	192	Archaeoglobus_fulgidus
#2	RAG47341	128	Archaeoglobus_fulgidus

Motif number 1

GGCTAAGCTGTAAATCGTTTTCGGTGCCTTAGATAA	1	25	1	TAAATCGTTG	     0.97472	-168
TTTATTTCGATAAATTGTTATCTAAGGCACCGAAAA	1	42	0	TAAATTGTTG	    0.880795	-151
TTTATCGAAATAAATAAAATTCTCGGCAACTGCTAC	1	64	1	TAAATAAATG	    0.982012	-129
TGCTACAAATCAAATACGTATTCTTGTTGCAATTAC	1	94	1	CAAATACGTG	    0.939311	-99
AAGAATACGTAAAATCCAAGTAATTGCAACAAGAAT	1	113	0	AAAATCCATG	    0.974397	-80
AACCTTTTTTCAAATAGAACTGCAAGAATACGTAAA	1	136	0	CAAATAGATG	    0.987643	-57
ATGGCAGTATCAAATCAAGGTGATGGT         	2	2	0	CAAATCAATG	    0.990592	-127
GCCATCAACCTAAATAAACTTTCCTGAAGAACGTAA	2	33	1	TAAATAAATG	    0.982032	-96
TGCACCTCAAAAGATCAAGATTTACGTTCTTCAGGA	2	54	0	AAGATCAATG	    0.916124	-75
          ********  *    *

Masking position 11
Map Score:   6.76453

Number of sites scoring better than the average of aligned sites = 171
Number in coding regions = 147
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 2

TTTACAGCTTAGCCTAATGTCAGCAGTG    	1	7	0	AGCCTATGCA	    0.997459	-186
 CCAGTTTTAAGGCTAAAGCCACCGATTTAAA	1	172	0	AGGCTAAGCA	    0.933821	-21
AAGTTTATTTAGGTTGATGGCAGTATCAAATC	2	22	0	AGGTTATGCA	    0.991457	-107
    GTCTCAAGCCTGATGGGAAATACAAAAA	2	111	0	AGCCTATGGA	    0.994147	-18
          ***** *** **

Masking position 7
Map Score:   3.35262

Number of sites scoring better than the average of aligned sites = 27
Number in coding regions = 25
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

AACAATTTATCGAAATAAATAAAATTCTCGG	1	59	1	CGAATAAATA	    0.954097	-134
GCAACTGCTACAAATCAAATACGTATTCTTG	1	89	1	CAATCAAATA	    0.978032	-104
AGAATACGTAAAATCCAAGTAATTGCAACAA	1	117	0	AAACCAAGTA	    0.911189	-76
CTAAAGCCACCGATTTAAAAACCTTTTTTCA	1	160	0	CGATTAAAAA	    0.917628	-33
ATACTGCCATCAACCTAAATAAACTTTCCTG	2	28	1	CAACTAAATA	    0.970883	-101
AAGCAATATTAAAAACAAAAAATTTTTGTAT	2	89	1	AAAACAAAAA	     0.95955	-40
GCCTGATGGGAAATACAAAAATTTTTTGTTT	2	101	0	AAAACAAAAA	     0.95955	-28
          *** *******

Masking position 7
Map Score:   3.7714

Number of sites scoring better than the average of aligned sites = 186
Number in coding regions = 118
Number in noncoding regions = 68
Number of orfs with sites within 600 bp upstream = 70
Fraction of orfs with sites within 600 bp upstream = 0.0112432


Motif number 4

          **********

No masking
Map Score:   -7.93376e-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:   -7.93376e-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:   -7.93376e-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