AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i182_riboflafin_biosynthesis_aful_reg_300.orf -o182_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	RAG31059	91	Archaeoglobus_fulgidus
#2	RAG30868	101	Archaeoglobus_fulgidus
#3	RAG45953	33	Archaeoglobus_fulgidus
#4	RAG16256	93	Archaeoglobus_fulgidus
#5	RAG16058	122	Archaeoglobus_fulgidus

Motif number 1

TTTCAAAAGAACGAAACATTTAAAAATCTTTTTTCT	1	13	1	AAACTAAAAA	    0.974275	-79
AATAGCCCTAAGGCAACCTTCAATAGAGAAAAAAGA	1	39	0	AAACTAATAG	     0.81906	-53
AGGTTGCCTTAGGGCTATTTTAAAAAGCAAAAACAA	1	56	1	ACTATAAAAA	    0.937824	-36
    GGTTTTATTTCAAGTACAAAAACGTTTGTAAG	2	7	1	ACAATAAAAA	    0.988259	-95
GTTGAAATAGAGTTCCCTTACAAACGTTTTTGTACT	2	23	0	ACCCTAAACG	    0.923839	-79
AGGGAACTCTATTTCAACTCGAAAAATGCAGGTTTG	2	41	1	ACAATAAAAA	    0.988258	-61
GGATACTTTTATTACACCTGAAATCAAACTCCCACC	2	76	1	ACACTAATCA	    0.941326	-26
TCATATATGAGAAGCACCTCAAAAAATTTAAAGGTT	4	67	0	GCACTAAAAA	    0.965508	-27
AAAAAATTTTAAAACCAATGCAAAAATTTCGAATC 	5	10	0	ACCATAAAAA	    0.976271	-113
TGTCACGGATAATAAAAATTCAAAAAATTTTAAAAC	5	31	0	AAAATAAAAA	    0.959594	-92
          *   *** *  *****

Masking position 9
Map Score:   9.98082

Number of sites scoring better than the average of aligned sites = 225
Number in coding regions = 167
Number in noncoding regions = 58
Number of orfs with sites within 600 bp upstream = 65
Fraction of orfs with sites within 600 bp upstream = 0.0104401


Motif number 2

ACATTTAAAAATCTTTTTTCTCTATTGAAG	1	28	1	ATCTTTTTTC	    0.963541	-64
TTCCCTTACAAACGTTTTTGTACTTGAAAT	2	17	0	AACGTTTTTG	    0.975106	-85
TCCCCCGACCAACTTTTTTC          	3	24	1	AACTTTTTTC	    0.990751	-10
AAAAACCTTTAAATTTTTTGAGGTGCTTCT	4	64	1	AAATTTTTTG	    0.985533	-30
    GATTCGAAATTTTTGCATTGGTTTTA	5	7	1	AAATTTTTGC	    0.961405	-116
ATTGGTTTTAAAATTTTTTGAATTTTTATT	5	27	1	AAATTTTTTG	    0.985533	-96
          **********

Masking position 5
Map Score:   9.39396

Number of sites scoring better than the average of aligned sites = 111
Number in coding regions = 70
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 55
Fraction of orfs with sites within 600 bp upstream = 0.00883392


Motif number 3

GTTTTTGTACTTGAAATAAAACC        	2	3	0	TTGAATAAAA	    0.965426	-99
TTGATTTCAGGTGTAATAAAAGTATCCAAAC	2	72	0	GTGAATAAAA	    0.987754	-30
AAGTTGGTCGGGGGAATATAAACTTAAT   	3	8	0	GGGAATATAA	    0.972895	-26
AGTAGTCCAGAGCCAATAAAAGCCTTCCTCA	4	17	1	AGCAATAAAA	    0.883683	-77
ACGATGGTTCGTGATATAAAAACCTTTAAAT	4	47	1	GTGTATAAAA	    0.973276	-47
ATTTTTGCATTGGTTTTAAAATTTTTTGAAT	5	19	1	TGGTTTAAAA	    0.840608	-104
AATCTGTCACGGATAATAAAAATTCAAAAAA	5	40	0	GGAAATAAAA	    0.963886	-83
          *** *******

Masking position 8
Map Score:   4.97552

Number of sites scoring better than the average of aligned sites = 178
Number in coding regions = 141
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 4

          **********

No masking
Map Score:   -7.64954e-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:   -7.64954e-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:   -7.64954e-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