AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i020_aful_mthe_300.orf -o020_aful_mthe_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	RAG48032	19	Archaeoglobus_fulgidus
#2	RAG50014	300	Archaeoglobus_fulgidus
#3	RAG46888	145	Archaeoglobus_fulgidus

Motif number 1

CTTAAAGAAAAATTTAAATATCGTCAGTGA	2	13	0	AATTTAAATA	    0.759559	-288
TTAAGTTTTTATCTTAAAGAAAAATTTAAA	2	25	0	ATCTTAAAGA	    0.975138	-276
TTAAGATAAAAACTTAAAACTAATTTGCTT	2	38	1	AACTTAAAAC	    0.967057	-263
TCAAGCTACAAACTTAAAAAGCAAATTAGT	2	56	0	AACTTAAAAA	    0.972657	-245
ACGTACAGAAAAATTCAAGCTACAAACTTA	2	70	0	AAATTCAAGC	    0.826763	-231
CAATGATATTACCTAAAAGAAAGAGAGAAA	2	135	1	ACCTAAAAGA	    0.906343	-166
GTTTCTGACCACCTTAAAAATCTTCTGGAA	2	239	1	ACCTTAAAAA	    0.959532	-62
AACAAACCTAAACTTCAAGCG         	3	2	0	AACTTCAAGC	    0.973537	-144
TACGAAGTGAATTTTAAAGAGAGGCAACAG	3	75	1	ATTTTAAAGA	    0.892858	-71
          **********

Masking position 4
Map Score:   9.50324

Number of sites scoring better than the average of aligned sites = 282
Number in coding regions = 225
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 73
Fraction of orfs with sites within 600 bp upstream = 0.011725


Motif number 2

TTTAAATATCGTCAGTGAGA          	2	1	0	GTCAGTGAGA	    0.965532	-300
ATCATTGTGAGCAAGTGGCAATATTGCAAT	2	112	0	GCAAGTGGCA	    0.940224	-189
TTACCTAAAAGAAAGAGAGAAATCCTGATG	2	143	1	GAAAGAGAGA	    0.951404	-158
TGAGTTTTTGGCAAGTAACATCAGGATTTC	2	161	0	GCAAGTAACA	    0.973915	-140
TTCAGAGTTGGTAAGTGAGTTTTTGGCAAG	2	176	0	GTAAGTGAGT	    0.968589	-125
ATCTAAGATTGCAAGAAATTTCAGAGTTGG	2	195	0	GCAAGAAATT	     0.85418	-106
TTTTAAGGTGGTCAGAAACTGCTGCTGGAC	2	228	0	GTCAGAAACT	    0.893405	-73
AAAATCTTCTGGAAGAAAGATTGATTGAAA	2	255	1	GGAAGAAAGA	     0.94817	-46
          **********

Masking position 4
Map Score:   4.4657

Number of sites scoring better than the average of aligned sites = 463
Number in coding regions = 426
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 3

GTTTTAAGTTTTTATCTTAAAGAAAAATTT	2	28	0	TTTATCTTAA	    0.859795	-273
CGTCGGAAAATTTATATTGCAATATTGCCA	2	97	1	TTTATATTGC	    0.976688	-204
GAAAAAAGATTTTATATAACAAACCTAAAC	3	19	0	TTTATATAAC	    0.654934	-127
CTTCGTATGCTTTGTATTGATTAGTACGCA	3	52	0	TTTGTATTGA	    0.949279	-94
TAGTATAATGTTTATATAGAGGGATTAATA	3	106	1	TTTATATAGA	    0.674318	-40
          **********

Masking position 5
Map Score:   2.24383

Number of sites scoring better than the average of aligned sites = 42
Number in coding regions = 26
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 4

TTTATCTTAAAGAAAAATTTAAATATCGTC	2	18	0	AGAAAAATTT	    0.932808	-283
TTCCGACGTACAGAAAAATTCAAGCTACAA	2	75	0	CAGAAAAATT	    0.864609	-226
TTCTGTACGTCGGAAAATTTATATTGCAAT	2	90	1	CGGAAAATTT	    0.972167	-211
TCTAAGATTGCAAGAAATTTCAGAGTTGGT	2	194	0	CAAGAAATTT	    0.856454	-107
ATCTTTCTTCCAGAAGATTTTTAAGGTGGT	2	246	0	CAGAAGATTT	    0.982611	-55
ATCTTCTGGAAGAAAGATTGATTGAAAAAA	2	258	1	AGAAAGATTG	    0.853969	-43
AAAAAAATGGAAGACGATTTGCCATCACC 	2	282	1	AAGACGATTT	     0.90408	-19
ACGCACGAGAAAAAAGATTTTATATAACAA	3	27	0	AAAAAGATTT	    0.956976	-119
          **********

Masking position 7
Map Score:   6.40208

Number of sites scoring better than the average of aligned sites = 377
Number in coding regions = 291
Number in noncoding regions = 86
Number of orfs with sites within 600 bp upstream = 112
Fraction of orfs with sites within 600 bp upstream = 0.0179891


Motif number 5

          **********

No masking
Map Score:   -8.85746e-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:   -8.85746e-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:   -8.85746e-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