AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i119_aful_mthe_300.orf -o119_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	RAG47245	31	Archaeoglobus_fulgidus
#2	RAG47166	300	Archaeoglobus_fulgidus
#3	RTH00269	18	M.thermo
#4	RTH00068	49	M.thermo
#5	RTH00701	136	M.thermo
#6	RTH00799	91	M.thermo

Motif number 1

AGTGGAAAATGTCCTTAAAAGCGACTTTGG	2	80	1	GTCCTTAAAA	    0.930152	-221
AAGCGACTTTGGTTTTTGAAAATCTAAAAA	2	98	1	GGTTTTTGAA	    0.775866	-203
TCTAAAAACTGTCCTTTTAAAACTAAAATC	2	120	1	GTCCTTTTAA	    0.897944	-181
CATTATCCAAGGTCTGATAAATTTTTGAAA	2	149	1	GGTCTGATAA	    0.945443	-152
AAAAAGTCGGGGTCTTAAAAATAAAGTAGT	4	24	0	GGTCTTAAAA	    0.952997	-26
          GTTCTGGGAATAACTCCCTC	5	1	1	GTTCTGGGAA	    0.955158	-136
ACATGGGATCGTCCTGAAAGATAAAGAAGG	5	39	0	GTCCTGAAAG	    0.832339	-98
ATACATATCGGTTCTGTGAAGGAATGAGAA	5	68	0	GTTCTGTGAA	    0.983141	-69
          GGTCTTTAACCTCCATTAAC	5	127	0	GGTCTTTAAC	    0.853714	-10
TGAATCTGATGTTCAGTGAAAAAATACATT	6	39	1	GTTCAGTGAA	    0.891361	-53
          **********

Masking position 9
Map Score:   6.74144

Number of sites scoring better than the average of aligned sites = 498
Number in coding regions = 468
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 2

AAAAGAGTGGAAAATGTCCTTAAAAGCGACTT	2	75	1	AAAATGCTTA	    0.984836	-226
GAAAATCTAAAAACTGTCCTTTTAAAACTAAA	2	115	1	AAACTGCTTT	    0.925837	-186
CAGACCTTGGATAATGATTTTAGTTTTAAAAG	2	133	0	ATAATGTTTA	    0.937293	-168
TTTACGCAGAAAAAAGAGCTTTAATTGGCATA	2	195	0	AAAAAGCTTT	    0.935661	-106
TTTTCTGCGTAAAAAGCATTTAGAATGTTTAT	2	214	1	AAAAAGTTTA	    0.636459	-87
ATTAGATAAAAAATTGGGCTGACACGAAAGTT	2	250	1	AAATTGCTGA	    0.884556	-51
TTTTTTATACAAAATGGATTGATTGTGTTCT 	2	280	1	AAAATGTTGA	    0.957753	-21
TCTCTCCCCAATAATGTATTTTTTCACTGAAC	6	49	0	ATAATGTTTT	    0.878781	-43
          ******  ****

Masking position 3
Map Score:   4.67041

Number of sites scoring better than the average of aligned sites = 107
Number in coding regions = 82
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 3

GAATCCGGTGATGTCCAAAAGAGTGGAAAA	2	59	1	ATGTCCAAAA	    0.971574	-242
AGAGTGGAAAATGTCCTTAAAAGCGACTTT	2	78	1	ATGTCCTTAA	    0.941262	-223
CAGTTTTTAGATTTTCAAAAACCAAAGTCG	2	101	0	ATTTTCAAAA	     0.77386	-200
TTTTTATCTAATGTTGATAAACATTCTAAA	2	232	0	ATGTTGATAA	    0.976247	-69
ATATATGTCCATGTCGATATAGGTGTTCTG	5	96	1	ATGTCGATAT	    0.904727	-41
GATATATGGAATGGTGATAAC         	6	81	1	ATGGTGATAA	    0.937906	-11
          **********

Masking position 2
Map Score:   2.01258

Number of sites scoring better than the average of aligned sites = 156
Number in coding regions = 151
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 4

GCATAAAATTGAAAATCAGAATTTCAAAAA	2	170	0	GAAAATCAGA	    0.975381	-131
GAATGTTTATCAACATTAGATAAAAAATTG	2	236	1	CAACATTAGA	    0.955609	-65
GAAGGAATGAGAACATGGGATCGTCCTGAA	5	51	0	GAACATGGGA	     0.98045	-86
TTTTTTCACTGAACATCAGATTCATGGACA	6	33	0	GAACATCAGA	    0.993687	-59
          **********

Masking position 5
Map Score:   1.38536

Number of sites scoring better than the average of aligned sites = 31
Number in coding regions = 29
Number in noncoding regions = 2
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:   9.61665e-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:   9.61665e-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:   9.61665e-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