AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i231_aful_mthe_300.orf -o231_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	RAG23889	59	Archaeoglobus_fulgidus
#2	RAG47920	34	Archaeoglobus_fulgidus
#3	RTH00791	150	M.thermo
#4	RTH01825	139	M.thermo

Motif number 1

     TGGGAAAGATTTTAAAATGAGTTGT	1	6	1	AAGATTTTAA	    0.987968	-54
          GTTATTTTAACACGTTTGTC	2	1	1	GTTATTTTAA	    0.955975	-34
CTTACAAATTTTTATTTTAATATATGGGGG	3	48	0	TTTATTTTAA	    0.888377	-103
TTGTAAGTAAAATATTTTAAGTAGGAGAAA	3	71	1	AATATTTTAA	    0.981049	-80
ATTGATAACTGTGATTTTAATTTTAACCAC	3	103	1	GTGATTTTAA	    0.971784	-48
CAATGTATTTAAGATTTTAGTGTTCAATAT	4	75	0	AAGATTTTAG	    0.956159	-65
CATCTTGAGTAATATTTTCACCAGCAATGT	4	99	0	AATATTTTCA	    0.967013	-41
AATATTACTCAAGATGTTCATTGTGGGAGA	4	113	1	AAGATGTTCA	    0.925094	-27
          **********

Masking position 4
Map Score:   11.3793

Number of sites scoring better than the average of aligned sites = 144
Number in coding regions = 118
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 2

TCGCTGACCTGTGCAGAAAAAGTATATAAC	1	34	0	GTGCAGAAAA	    0.973024	-26
CTCTCACAAATTGGACAAACGTGTTAAAAT	2	14	0	TTGGACAAAC	    0.968924	-21
ATGCAACATGGTGGAGATACCTTTATAAGG	3	14	1	GTGGAGATAC	     0.98387	-137
ATATTTTAAGTAGGAGAAACAATTGATAAC	3	82	1	TAGGAGAAAC	      0.9644	-69
ATTAAGTGAAGTGGTTAAAATTAAAATCAC	3	113	0	GTGGTTAAAA	    0.941709	-38
AAATACATTGCTGGTGAAAATATTACTCAA	4	95	1	CTGGTGAAAA	    0.969192	-45
          **********

Masking position 7
Map Score:   3.10132

Number of sites scoring better than the average of aligned sites = 588
Number in coding regions = 546
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 3

         CCTCTCACAAATTGGACAAAC	2	24	0	CTCTCACAAA	    0.977623	-11
ATGGGGGTTCCCCTTATAAAGGTATCTCCA	3	25	0	CCCTTATAAA	    0.936559	-126
ATAAGGGGAACCCCCATATATTAAAATAAA	3	38	1	CCCCCATATA	    0.985775	-113
TCAATTGTTTCTCCTACTTAAAATATTTTA	3	78	0	CTCCTACTTA	    0.926199	-73
TATTCAAATGCCTCCATTAAGTGAAGTGGT	3	128	0	CCTCCATTAA	    0.914679	-23
  TTAACCATCTCCCACAATGAACATCTTG	4	122	0	CTCCCACAAT	    0.969603	-18
          **********

Masking position 6
Map Score:   2.61067

Number of sites scoring better than the average of aligned sites = 539
Number in coding regions = 496
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 4

TATAACAACTCATTTTAAAATCTTTCCCA 	1	10	0	CATTTTAAAA	    0.978881	-50
ATTGGACAAACGTGTTAAAATAAC      	2	5	0	CGTGTTAAAA	    0.933672	-30
TACAAATTTTTATTTTAATATATGGGGGTT	3	46	0	TATTTTAATA	    0.783349	-105
GTAGGAGAAACAATTGATAACTGTGATTTT	3	91	1	CAATTGATAA	    0.917063	-60
TTAATGGAGGCATTTGAATAGAA       	3	138	1	CATTTGAATA	    0.953139	-13
GGATCAGCCTCAAGTTATAATAGAAAACCG	4	18	0	CAAGTTATAA	    0.917073	-122
          **********

Masking position 5
Map Score:   1.71446

Number of sites scoring better than the average of aligned sites = 113
Number in coding regions = 70
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 5

GCACAGGTCAGCGAGGTGAT          	1	50	1	GCGAGGTGAT	    0.989311	-10
     ACCATGCAACATGGTGGAGATACCT	3	6	1	GCAACATGGT	     0.97004	-145
CCTCCATTAAGTGAAGTGGTTAAAATTAAA	3	118	0	GTGAAGTGGT	    0.980234	-33
TGTTCATTGTGGGAGATGGTTAA       	4	127	1	GGGAGATGGT	    0.992357	-13
          **********

Masking position 4
Map Score:   0.554122

Number of sites scoring better than the average of aligned sites = 231
Number in coding regions = 216
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 6

          **********

No masking
Map Score:   -7.29427e-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:   -7.29427e-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:   -7.29427e-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