AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i195_aful_mthe_100.orf -o195_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	RAG45884	251	Archaeoglobus_fulgidus
#2	RAG50259	146	Archaeoglobus_fulgidus
#3	RTH01882	35	M.thermo

Motif number 1

GAAACACCAATCGGGAGGATTCCTGAGGAT	1	31	1	TCGGGAGGAT	     0.97703	-221
TTCCTGAGGATTGGGAGGTTGTTAGGCTTG	1	50	1	TTGGGAGGTT	    0.994037	-202
TTGTTAGGCTTGGGGACATTTTCAATGTTG	1	68	1	TGGGGACATT	    0.974648	-184
TTTTTGTAGATGGTGTCGTTCCCGTTTCAA	1	95	0	TGGTGTCGTT	    0.960185	-157
ATAGCATTCTTGGTGACGCTTACGAGTGGC	2	29	1	TGGTGACGCT	    0.980082	-118
AGGCCAAAGAGGGGGAGGTTTTCACCCCTT	2	83	1	GGGGGAGGTT	    0.989182	-64
TTTTCACCCCTTCGGAGGTTGTTGAGCTCA	2	101	1	TTCGGAGGTT	    0.983326	-46
GGATCAACAATTCTGACGATGAGCTCAACA	2	120	0	TTCTGACGAT	    0.909323	-27
          **********

Masking position 10
Map Score:   10.6909

Number of sites scoring better than the average of aligned sites = 496
Number in coding regions = 465
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 2

GGAAACACCAATCGGGAGGATTCCTGAGGA	1	30	1	ATCGGGAGGA	    0.989482	-222
ATTCCTGAGGATTGGGAGGTTGTTAGGCTT	1	49	1	ATTGGGAGGT	    0.985868	-203
AAAGAAGAATATTGGGAAAACGGAACAATT	1	124	1	ATTGGGAAAA	    0.945134	-128
AAGTAAACTAAATGGGAGAACACATATTTC	1	177	1	AATGGGAGAA	    0.986146	-75
TTGGCCTTCTGTGGGGCGAAGTAGCCGATA	2	60	0	GTGGGGCGAA	    0.959176	-87
AAGGCCAAAGAGGGGGAGGTTTTCACCCCT	2	82	1	AGGGGGAGGT	    0.980168	-65
ACAACCTCCGAAGGGGTGAAAACCTCCCCC	2	93	0	AAGGGGTGAA	    0.965051	-54
          **********

Masking position 5
Map Score:   7.10126

Number of sites scoring better than the average of aligned sites = 544
Number in coding regions = 515
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

GCATCCAGATACAAGGAAACACCAATCGGGA	1	16	1	ACAAGGAACA	     0.92297	-236
CCATCTACAAAAAAAGAAGAATATTGGGAAA	1	112	1	AAAAAGAAAA	    0.966026	-140
AATATTGGGAAAACGGAACAATTAATTGGCT	1	131	1	AAACGGAAAA	    0.976299	-121
TTTCTTTCTGAAACGGAAATATGTGTTCTCC	1	191	0	AAACGGAATA	    0.947145	-61
TTTCCGTTTCAGAAAGAAAAATAACTGAGAA	1	203	1	AGAAAGAAAA	    0.971701	-49
AAAATAACTGAGAAAGCATTAAGAGATTACA	1	220	1	AGAAAGCATA	    0.909515	-32
TTCGCCCCACAGAAGGCCAAAGAGGGGGAGG	2	70	1	AGAAGGCCAA	     0.94012	-77
TATTTATATTAAAAGGTATAAATTATACAA 	3	16	1	AAAAGGTAAA	    0.947218	-20
          ******** **

Masking position 3
Map Score:   5.61624

Number of sites scoring better than the average of aligned sites = 372
Number in coding regions = 316
Number in noncoding regions = 56
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 4

TCTACAAAAAAAGAAGAATATTGGGAAAAC	1	115	1	AAGAAGAATA	    0.971894	-137
CAACTGATTTAAGTAAACTAAATGGGAGAA	1	167	1	AAGTAAACTA	     0.95678	-85
CCGTTTCAGAAAGAAAAATAACTGAGAAAG	1	206	1	AAGAAAAATA	    0.976267	-46
AAGCGTCACCAAGAATGCTATCACTCGCCC	2	20	0	AAGAATGCTA	    0.953367	-127
          **********

Masking position 5
Map Score:   0.557642

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 39
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 5

          **********

No masking
Map Score:   -5.51791e-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:   -5.51791e-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:   -5.51791e-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