AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i202_aful_mthe_300.orf -o202_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	RAG50345	223	Archaeoglobus_fulgidus
#2	RTH00536	107	M.thermo
#3	RTH00449	194	M.thermo

Motif number 1

AAAAGTTTTAAAAGGCTGAAAAAATAGTTAAA	1	24	0	AAGCTGAAAA	    0.969346	-200
TTAATTTCGTAAAAAGCGAAAAGTTTTAAAAG	1	42	0	AAAGCGAAAA	    0.950774	-182
GAATGGCTTCAGAACCTGAGAATAAATACTTA	1	75	0	AAACTGAGAA	    0.985384	-149
ATATTTTCGCAAAATCTGAAAAATTTGAATGG	1	101	0	AAACTGAAAA	    0.991671	-123
TTGCGAAAATATAATCCAAAAAAGTAATTCAC	1	121	1	AAACCAAAAA	    0.963888	-103
CCTTCACCAGAAAAACCACAAACTATTTATAA	2	54	1	AAACCACAAA	    0.937945	-54
CCTTATTATAACAAGCTGCAATAAAAATAATT	3	16	1	AAACTGCAAT	    0.923558	-179
CTGAGCCCGAGAAAGCTGAGAAGTTCTGTCCA	3	129	1	GAACTGAGAA	    0.947109	-66
          * ** *******

Masking position 3
Map Score:   6.76506

Number of sites scoring better than the average of aligned sites = 322
Number in coding regions = 283
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 2

TTTTAAAAGGCTGAAAAAATAGTTAAAGAC	1	21	0	CTGAAAAAAT	    0.969426	-203
TTCGTAAAAAGCGAAAAGTTTTAAAAGGCT	1	39	0	GCGAAAAGTT	    0.915377	-185
GCTTCAGAACCTGAGAATAAATACTTATTT	1	72	0	CTGAGAATAA	    0.888146	-152
TTCGCAAAATCTGAAAAATTTGAATGGCTT	1	98	0	CTGAAAAATT	    0.951842	-126
TTCAGATTTTGCGAAAATATAATCCAAAAA	1	113	1	GCGAAAATAT	    0.885081	-111
ATGGTTACGAGTGAAGAGATGAAGAGGAGA	3	59	1	GTGAAGAGAT	    0.890584	-136
AGGAGACTCGCTGAGAAAAAGGGTATGAGG	3	83	1	CTGAGAAAAA	    0.919209	-112
CCCGAGAAAGCTGAGAAGTTCTGTCCAAAC	3	134	1	CTGAGAAGTT	    0.968217	-61
          **********

Masking position 4
Map Score:   5.7051

Number of sites scoring better than the average of aligned sites = 573
Number in coding regions = 527
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 3

CACTGTCTTTAACTATTTTTTCAGCCTTTT	1	17	1	AACTATTTTT	    0.982439	-207
GAAATTAAATAAGTATTTATTCTCAGGTTC	1	66	1	AAGTATTTAT	    0.957441	-158
GCTTTTAGTGAATTACTTTTTTGGATTATA	1	130	0	AATTACTTTT	    0.945303	-94
AAAAACCACAAACTATTTATAACATTTATT	2	64	1	AACTATTTAT	     0.97639	-44
ATAACACCATAATTATTTTTATTGCAGCTT	3	28	0	AATTATTTTT	    0.973626	-167
          **********

Masking position 5
Map Score:   4.9415

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 12
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 4

TTATTCTCAGGTTCTGAAGCCATTCAAATTT	1	82	1	GTTCTGAACC	    0.929706	-142
TGCCCCACTAGAGCAGAGACCATGGCAGTGC	2	11	1	GAGCAGAGCC	    0.948427	-97
GCAGAGACCATGGCAGTGCCCCGACTGAGGC	2	23	1	TGGCAGTGCC	    0.854851	-85
GGCAGTGCCCCGACTGAGGCCCTTCACCAGA	2	34	1	CGACTGAGCC	    0.948086	-74
TGAGAAAAAGGGTATGAGGCCTGGAACGGTG	3	94	1	GGTATGAGCC	     0.94942	-101
GGAACGGTGAGATCTGAGCCCGAGAAAGCTG	3	116	1	GATCTGAGCC	    0.781801	-79
AAGGAGTATGGAGCTGACTCCAACTTCTGCG	3	170	1	GAGCTGACCC	    0.984589	-25
          ******** **

Masking position 6
Map Score:   5.79554

Number of sites scoring better than the average of aligned sites = 169
Number in coding regions = 160
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 5

CCAATTGAGCTTTTAGTGAATTACTTTTTT	1	138	0	TTTTAGTGAA	    0.936602	-86
TTTTATTTTGTTTCGTTCAAGTAGTAACGT	1	185	1	TTTCGTTCAA	     0.91174	-39
TTTGTGGTTTTTCTGGTGAAGGGCCTCAGT	2	46	0	TTCTGGTGAA	    0.972942	-62
AACATTTATTTTCTATTCAATATTAAACAT	2	84	1	TTCTATTCAA	    0.960347	-24
CCATAATTATTTTTATTGCAGCTTGTTATA	3	22	0	TTTTATTGCA	     0.86768	-173
AGCTGAGAAGTTCTGTCCAAACTGTGGCAA	3	142	1	TTCTGTCCAA	    0.941634	-53
          **********

Masking position 2
Map Score:   0.788143

Number of sites scoring better than the average of aligned sites = 113
Number in coding regions = 94
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 6

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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 8

          **********

No masking
Map Score:   1.3033e-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