AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i154_aful_mthe_300.orf -o154_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	RAG50190	144	Archaeoglobus_fulgidus
#2	RAG50188	135	Archaeoglobus_fulgidus
#3	RAG48480	189	Archaeoglobus_fulgidus
#4	RTH01924	221	M.thermo

Motif number 1

TTTTAAATGCATTTAAAAAAGAATAAGAAATTAAA	1	11	1	ATTAAAAATA	    0.983662	-134
AAGAATAAGAAATTAAAAATATTAACTTTTCTGCA	1	29	1	AATAAAAAAA	    0.918429	-116
AAAGATTTCCATTAAAAAAAATGCAGAAAAGTTAA	1	50	0	ATTAAAAACA	     0.93363	-95
ATTTTCAATTAATAAAAAAGATTTCCATTAAAAAA	1	66	0	AATAAAAATC	    0.941268	-79
TAAACCCATAATCCAAAAAAGCAACAACTGTGATA	2	24	0	ATCAAAAAAC	    0.962539	-112
CAAATCTACAATTAAAAAACTTTACTTCCTAAAAA	2	92	0	ATTAAAAAAC	    0.972216	-44
      CCTCATCGAAAAAATTGTACAAATCTACA	2	117	0	ATCAAAAATA	    0.977881	-19
TATCCTCAACATTTAAAAATTTTACTATCTCTTTA	3	22	1	ATTAAAAAAC	    0.972216	-168
AGTATTACTGAACAAAAAATTAATATTATAAACTC	4	68	1	AACAAAAATA	    0.928257	-154
ATAATAAGTGATCTATAAAATGATATAAATAGTTT	4	115	1	ATCATAAATA	    0.813128	-107
TTTTTCAATTATAAAAAAAGTGAAAACTATTTATA	4	138	0	ATAAAAAAAA	    0.844075	-84
TTTTTTTATAATTGAAAAACTTATAACATTTAAAA	4	154	1	ATTAAAAATA	    0.983662	-68
AACTTATAACATTTAAAAATAGTTATAATATTGAA	4	171	1	ATTAAAAATA	    0.983662	-51
TGTTTTTAAAGTTCAAAAAACCTTCAATATTATAA	4	193	0	GTTAAAAATC	    0.888744	-29
          *** *****    **

Masking position 8
Map Score:   22.4907

Number of sites scoring better than the average of aligned sites = 102
Number in coding regions = 58
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 2

CTTTTTTAAATGCATTTAAAA         	1	2	0	TGCATTTAAA	    0.954327	-143
AAAAAGAATAAGAAATTAAAAATATTAACT	1	26	1	AGAAATTAAA	    0.898774	-119
TAAAAAAGATTTCCATTAAAAAAAATGCAG	1	59	0	TTCCATTAAA	    0.859012	-86
CCTTAGCATTTTCAATTAATAAAAAAGATT	1	78	0	TTCAATTAAT	     0.87712	-67
TGTACAAATCTACAATTAAAAAACTTTACT	2	101	0	TACAATTAAA	    0.971333	-35
TTTTATCCTCAACATTTAAAAATTTTACTA	3	19	1	AACATTTAAA	    0.921999	-171
TTCCCAAAGCTGAAATTAAAGAGGTAAGGA	3	120	0	TGAAATTAAA	    0.927988	-70
TTACTGAACAAAAAATTAATATTATAAACT	4	72	1	AAAAATTAAT	    0.671521	-150
TTATAAGTTTTTCAATTATAAAAAAAGTGA	4	150	0	TTCAATTATA	    0.782223	-72
AAAAACTTATAACATTTAAAAATAGTTATA	4	168	1	AACATTTAAA	    0.921999	-54
          **********

Masking position 6
Map Score:   7.84083

Number of sites scoring better than the average of aligned sites = 139
Number in coding regions = 91
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 3

AAAAGTTAATATTTTTAATTTCTTATTCTTT	1	28	0	ATTTTAATTT	    0.774389	-117
CAGACCCTCCATTTTTATCCTTAGCATTTTC	1	95	0	ATTTTATCCT	    0.923695	-50
    TTACCTAATTTTATCCTCAACATTTAA	3	7	1	ATTTTATCCT	    0.923721	-183
AACATTTAAAAATTTTACTATCTCTTTAGAA	3	29	1	ATTTTACTAT	    0.882117	-161
AGAAAACAGAGTTTATAATATTAATTTTTTG	4	80	0	GTTATAATAT	    0.759054	-142
AGTGAAAACTATTTATATCATTTTATAGATC	4	124	0	ATTATATCAT	    0.945527	-98
AATAGTTTTCACTTTTTTTATAATTGAAAAA	4	142	1	ATTTTTTTAT	    0.723662	-80
TAATTGAAAAACTTATAACATTTAAAAATAG	4	162	1	ATTATAACAT	    0.945524	-60
ATTTAAAAATAGTTATAATATTGAAGGTTTT	4	181	1	ATTATAATAT	    0.930868	-41
          * *********

Masking position 6
Map Score:   3.70808

Number of sites scoring better than the average of aligned sites = 93
Number in coding regions = 51
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 4

AAAAATGGAGGGTCTGTGATGATGAGCCTTACCCGA	1	110	1	GTGTGATAGG	    0.974295	-35
ATCTGGCAAAGATAGAGAATCCAGAGGAGTTCAACC	3	75	0	GTAGAATCGG	    0.987517	-115
AAATTAAAGAGGTAAGGAATGCGGCGCATCTGGCAA	3	102	0	GTGGAATCGG	    0.997584	-88
TTTAATTTCAGCTTTGGGAATCAGCGATGTAGTATC	3	130	1	GTGGGAACGG	    0.992672	-60
TTAATTTTTTGTTCAGTAATACTGAGTGTTATATAT	4	55	0	GTGTAATCGG	    0.994572	-167
          * *  ***** * * *

Masking position 9
Map Score:   1.10727

Number of sites scoring better than the average of aligned sites = 67
Number in coding regions = 61
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 5

          **********

No masking
Map Score:   7.34291e-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:   7.34291e-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:   7.34291e-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