AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i119_aful_mthe_100.orf -o119_aful_mthe_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	RAG47245	31	Archaeoglobus_fulgidus
#2	RAG47166	300	Archaeoglobus_fulgidus
#3	RTH00269	18	M.thermo
#4	RTH00068	49	M.thermo
#5	RTH00701	136	M.thermo

Motif number 1

AGTGGAAAATGTCCTTAAAAGCGACTTTGG	2	80	1	GTCCTTAAAA	    0.951652	-221
AAGCGACTTTGGTTTTTGAAAATCTAAAAA	2	98	1	GGTTTTTGAA	    0.784397	-203
TCTAAAAACTGTCCTTTTAAAACTAAAATC	2	120	1	GTCCTTTTAA	    0.913439	-181
CATTATCCAAGGTCTGATAAATTTTTGAAA	2	149	1	GGTCTGATAA	    0.954966	-152
AAAAAGTCGGGGTCTTAAAAATAAAGTAGT	4	24	0	GGTCTTAAAA	    0.968485	-26
          GTTCTGGGAATAACTCCCTC	5	1	1	GTTCTGGGAA	     0.94347	-136
ACATGGGATCGTCCTGAAAGATAAAGAAGG	5	39	0	GTCCTGAAAG	    0.870667	-98
ATACATATCGGTTCTGTGAAGGAATGAGAA	5	68	0	GTTCTGTGAA	    0.973759	-69
          GGTCTTTAACCTCCATTAAC	5	127	0	GGTCTTTAAC	    0.890855	-10
          **********

Masking position 5
Map Score:   6.62848

Number of sites scoring better than the average of aligned sites = 348
Number in coding regions = 326
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 2

AGAGCTTTAATTGGCATAAAATTGAAAATCAGAA	2	179	0	TTGAAAAATG	    0.969755	-122
AAATGCTTTTTACGCAGAAAAAAGAGCTTTAATT	2	201	0	TAGAAAAAAG	    0.947815	-100
TTATCAACATTAGATAAAAAATTGGGCTGACACG	2	242	1	TAAAAAAATG	    0.984138	-59
ACGAAAGTTTTTTATACAAAATGGATTGATTGTG	2	273	1	TTAAAAAATG	    0.979445	-28
GTCGGGGTCTTAAAAATAAAGTAGTATGTTAACT	4	15	0	TAAAAAAGTG	    0.986829	-35
         CTTCAGAAAAAGTCGGGGTCTTAAA	4	35	0	TTAAAAAGTG	    0.982918	-15
GGATCGTCCTGAAAGATAAAGAAGGACTACTCTG	5	30	0	GAAAAAAGAG	    0.909332	-107
          ** * * ***** *

Masking position 8
Map Score:   5.70838

Number of sites scoring better than the average of aligned sites = 49
Number in coding regions = 36
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 3

TCCAAAAGAGTGGAAAATGTCCTTAAAAGC	2	72	1	TGGAAAATGT	    0.964877	-229
ACTTTGGTTTTTGAAAATCTAAAAACTGTC	2	103	1	TTGAAAATCT	    0.973732	-198
TATCAGACCTTGGATAATGATTTTAGTTTT	2	138	0	TGGATAATGA	    0.964847	-163
TGGCATAAAATTGAAAATCAGAATTTCAAA	2	172	0	TTGAAAATCA	     0.98152	-129
TTATCTAATGTTGATAAACATTCTAAATGC	2	229	0	TTGATAAACA	    0.918459	-72
          **********

Masking position 6
Map Score:   2.88118

Number of sites scoring better than the average of aligned sites = 116
Number in coding regions = 106
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

CCTTAAAAGCGACTTTGGTTTTTGAAAATC	2	92	1	GACTTTGGTT	    0.948623	-209
TAAAAGGACAGTTTTTAGATTTTCAAAAAC	2	109	0	GTTTTTAGAT	    0.934192	-192
CTTGGATAATGATTTTAGTTTTAAAAGGAC	2	130	0	GATTTTAGTT	    0.934192	-171
AAATTTATCAGACCTTGGATAATGATTTTA	2	143	0	GACCTTGGAT	    0.966599	-158
          GTTCTGGGAATAACTCCCTC	5	1	1	GTTCTGGGAA	    0.877731	-136
CGATATAGGTGTTCTGAGTTAATGGAGGTT	5	110	1	GTTCTGAGTT	    0.948731	-27
          **********

Masking position 5
Map Score:   1.30045

Number of sites scoring better than the average of aligned sites = 167
Number in coding regions = 147
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 5

          **********

No masking
Map Score:   -7.43638e-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:   -7.43638e-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:   -7.43638e-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