AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i047_aful_mthe_100.orf -o047_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	RAG27764	52	Archaeoglobus_fulgidus
#2	RTH00627	31	M.thermo
#3	RTH00736	144	M.thermo
#4	RTH00235	158	M.thermo

Motif number 1

TTTCAACATCTTTAATACTAAAATGTTCATTTT	3	35	1	TTAAACTAAA	    0.864035	-110
ATAACAATCTTTAAATACAAGAAAACGGCAACA	3	72	1	TTAAACAGAA	    0.965379	-73
AGTATAATAATTGAATACTGGCACTTAAAAGTT	3	118	0	TTAAACTGCA	    0.990246	-27
    TTCACTGTTAAAGCCGGCAACATCCCTTC	4	7	1	GTAAGCCGCA	    0.991126	-152
TCATGGAACATTAAAGGCCGGCATCTCTCCCAC	4	38	1	TTAAGCCGCA	    0.997193	-121
GCATCAATTTTTAAGTGCCAGCACGATATAGTT	4	106	1	TTAGGCCGCA	    0.991122	-53
          TTGAACACCCGAATGAAAGTTAA	4	146	0	TTAAACCGAA	    0.993139	-13
          ** ** *** ***

Masking position 4
Map Score:   9.3088

Number of sites scoring better than the average of aligned sites = 157
Number in coding regions = 142
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 2

GTCGGAAATATGTTGCCGTTTTCTTGTATT	3	85	0	TGTTGCCGTT	    0.989368	-60
CATGAAGGGATGTTGCCGGCTTTAACAGTG	4	13	0	TGTTGCCGGC	    0.998254	-146
GAGGTGGGAGAGATGCCGGCCTTTAATGTT	4	44	0	AGATGCCGGC	    0.995599	-115
ACTTAAAAATTGATGCCCGTCCCCCCGTGC	4	92	0	TGATGCCCGT	    0.992801	-67
          **********

Masking position 4
Map Score:   5.74601

Number of sites scoring better than the average of aligned sites = 24
Number in coding regions = 24
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 3

GTTTTATTAATTGTCCCCTCAAAACTGCAA	1	15	0	TTGTCCCCTC	    0.979648	-38
 CAACAAACCCTCACCCACCAGACTTTCTC	2	10	1	CTCACCCACC	    0.994883	-22
AGGCCGGCATCTCTCCCACCTCAAGTTTAT	4	52	1	CTCTCCCACC	    0.997968	-107
AAATTGATGCCCGTCCCCCCGTGCAGAAAA	4	86	0	CCGTCCCCCC	    0.997761	-73
          **********

Masking position 5
Map Score:   4.16483

Number of sites scoring better than the average of aligned sites = 165
Number in coding regions = 150
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

 GAGCAGTTAAACCATTTAATTTTTTTTCAAC	3	10	1	AACCATTAAT	    0.985986	-135
TAATAAAAATGAACATTTTAGTATTAAAGATG	3	41	0	GAACATTTAT	    0.959332	-104
TTTCCGACACAAACTTTTAAGTGCCAGTATTC	3	107	1	AAACTTTAAT	    0.903121	-38
          GACCAGTATAATAATTGAATAC	3	133	0	GACCATATAT	    0.966086	-12
TCCCTTCATGGAACATTAAAGGCCGGCATCTC	4	33	1	GAACATAAAG	    0.927609	-126
CGTGCAGAAAAATCAATAAACTTGAGGTGGGA	4	65	0	AATCATAAAT	    0.931508	-94
GATATAGTTAAACCAGTTAACTTTCATTCGGG	4	130	1	AACCATTAAT	    0.986033	-29
          ***** **** *

Masking position 10
Map Score:   4.81881

Number of sites scoring better than the average of aligned sites = 34
Number in coding regions = 20
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 5

      GAGCAGTTAAACCATTTAATTTTT	3	5	1	AGTTAAACCA	    0.993001	-140
CCCCCCGTGCAGAAAAATCAATAAACTTGA	4	72	0	AGAAAAATCA	    0.944373	-87
AGCACGATATAGTTAAACCAGTTAACTTTC	4	125	1	AGTTAAACCA	    0.993001	-34
          **********

Masking position 5
Map Score:   1.42603

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 11
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 6

GGGACAATTAATAAAACTTTTGGAGACGAT	1	28	1	ATAAAACTTT	    0.910956	-25
         CAACAAACCCTCACCCACCAG	2	2	1	AACAAACCCT	    0.926992	-30
ACCCTCACCCACCAGACTTTCTCGG     	2	17	1	ACCAGACTTT	    0.953204	-15
TTTTTATTATAACAATCTTTAAATACAAGA	3	64	1	AACAATCTTT	    0.977331	-81
ATATTTCCGACACAAACTTTTAAGTGCCAG	3	104	1	CACAAACTTT	       0.972	-41
GGGGACGGGCATCAATTTTTAAGTGCCAGC	4	98	1	ATCAATTTTT	    0.842571	-61
          **********

Masking position 4
Map Score:   0.981812

Number of sites scoring better than the average of aligned sites = 285
Number in coding regions = 243
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 7

          **********

No masking
Map Score:   6.63809e-14

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:   6.63809e-14

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 9

          **********

No masking
Map Score:   6.63809e-14

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