AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i174_Biotin_Biosynthesis_aful_reg_300.orf -o174_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	RAG48329	192	Archaeoglobus_fulgidus
#2	RAG47341	128	Archaeoglobus_fulgidus

Motif number 1

GGCTAAGCTGTAAATCGTTTTCGGTGCCTTAGATAA	1	25	1	TAAATCGTTG	    0.972324	-168
TTTATTTCGATAAATTGTTATCTAAGGCACCGAAAA	1	42	0	TAAATTGTTG	    0.870678	-151
TTTATCGAAATAAATAAAATTCTCGGCAACTGCTAC	1	64	1	TAAATAAATG	    0.980317	-129
TGCTACAAATCAAATACGTATTCTTGTTGCAATTAC	1	94	1	CAAATACGTG	    0.934668	-99
AAGAATACGTAAAATCCAAGTAATTGCAACAAGAAT	1	113	0	AAAATCCATG	    0.972053	-80
AACCTTTTTTCAAATAGAACTGCAAGAATACGTAAA	1	136	0	CAAATAGATG	    0.986463	-57
ATGGCAGTATCAAATCAAGGTGATGGT         	2	2	0	CAAATCAATG	    0.989685	-127
GCCATCAACCTAAATAAACTTTCCTGAAGAACGTAA	2	33	1	TAAATAAATG	    0.980335	-96
TGCACCTCAAAAGATCAAGATTTACGTTCTTCAGGA	2	54	0	AAGATCAATG	    0.908695	-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

    CACTGCTGACATTAGGCTAAGCTGTAAA	1	7	1	TGCATAGGCT	    0.997364	-186
TTTAAATCGGTGGCTTTAGCCTTAAAACTGG 	1	172	1	TGCTTAGCCT	    0.936425	-21
GATTTGATACTGCCATCAACCTAAATAAACTT	2	22	1	TGCATAACCT	    0.991002	-107
TTTTTGTATTTCCCATCAGGCTTGAGAC    	2	111	1	TCCATAGGCT	    0.993842	-18
          ** *** *****

Masking position 6
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

CCGAGAATTTTATTTATTTCGATAAATTGTT	1	59	0	TATTTATTCG	    0.949792	-134
CAAGAATACGTATTTGATTTGTAGCAGTTGC	1	89	0	TATTTGATTG	    0.975915	-104
TTGTTGCAATTACTTGGATTTTACGTATTCT	1	117	1	TACTTGGTTT	    0.903269	-76
TGAAAAAAGGTTTTTAAATCGGTGGCTTTAG	1	160	1	TTTTTAATCG	    0.910225	-33
CAGGAAAGTTTATTTAGGTTGATGGCAGTAT	2	28	0	TATTTAGTTG	      0.9681	-101
ATACAAAAATTTTTTGTTTTTAATATTGCTT	2	89	0	TTTTTGTTTT	    0.955733	-40
AAACAAAAAATTTTTGTATTTCCCATCAGGC	2	101	1	TTTTTGTTTT	    0.955733	-28
          ******* ***

Masking position 5
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