AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i156_HYP_operon_mthe_reg_300.orf -o156_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RTH00077	20	M.thermo
#2	RTH01952	83	M.thermo
#3	RTH01119	67	M.thermo
#4	RTH01092	177	M.thermo
#5	RTH00291	110	M.thermo

Motif number 1

GTAATTAACAATTTTTATATAGATAACTCTA	2	27	1	ATTTTTATTA	    0.972221	-57
TCTGACAAAATTTTATAATTAGAATTAATAG	2	55	0	TTTTATAATA	    0.750161	-29
TATCACGATCATATATATATGGAGGAGGCCA	3	18	0	ATATATATTG	    0.888984	-50
TGATAAATAGATCTTTAAGTGTAATGGTGGT	3	44	1	ATCTTTAATG	    0.962716	-24
    TACCTAATTTATAAGTACATCAATATA	4	7	1	ATTTATAATA	    0.943677	-171
GGCACGGTACATTTCTATCTACCTTGAGTTT	4	62	0	ATTTCTATTA	    0.940358	-116
TTTCCCACAAATCTTTATATGTGACGGATCT	5	32	1	ATCTTTATTG	     0.97643	-79
TATGTGACGGATCTTTATCTAAACATTAGTG	5	49	1	ATCTTTATTA	    0.976887	-62
          ******** **

Masking position 7
Map Score:   6.77788

Number of sites scoring better than the average of aligned sites = 99
Number in coding regions = 41
Number in noncoding regions = 58
Number of orfs with sites within 600 bp upstream = 80
Fraction of orfs with sites within 600 bp upstream = 0.0128493


Motif number 2

         AATCCTTTGGCCTCCTCCATATATATA	3	2	1	ACCTTGCCCC	     0.98261	-66
TAGCATAGGAGAACTCATGCAAACTCAAGGTAGATA	4	42	1	GACTAGCACC	    0.988293	-136
AGATAGAAATGTACCGTGCCCATCTCACAGTGGAGG	4	73	1	GACCTCCCCC	    0.993745	-105
CCAACGCCCTGGACTATTCCCTCCACTGTGAGATGG	4	92	0	GACTTCCCCC	    0.997735	-86
GTAGACCGCTGGCCTGAAGCCAACGCCCTGGACTAT	4	111	0	GCCTAGCCCC	    0.997265	-67
ACTTGCAAAGGAACTCAGCCTCACGGGATACGTGAG	4	149	1	GACTACCTCG	    0.950877	-29
          * *** * ***  * *

Masking position 10
Map Score:   3.05161

Number of sites scoring better than the average of aligned sites = 118
Number in coding regions = 106
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 3

TTTATAATTAGAATTAATAGAGTTATCTAT	2	45	0	GAATTAATAG	     0.94694	-39
CAATGCCATTGAATTAATACC         	5	2	0	GAATTAATAC	    0.723065	-109
AACCCTCTCCAAATTAATAGGATTAAAGTC	5	86	0	AAATTAATAG	     0.97017	-25
          **********

Masking position 6
Map Score:   1.65943

Number of sites scoring better than the average of aligned sites = 5
Number in coding regions = 2
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

CTTTAGTCTGACAAAATTTTATAATTAGAA	2	62	0	ACAAAATTTT	    0.847827	-22
ATCGTGATAAATAGATCTTTAAGTGTAATG	3	40	1	ATAGATCTTT	    0.800366	-28
ATTGTTTCCCACAAATCTTTATATGTGACG	5	28	1	ACAAATCTTT	    0.939139	-83
TTTATATGTGACGGATCTTTATCTAAACAT	5	45	1	ACGGATCTTT	    0.967338	-66
GTCAGAATACACTAATGTTTAGATAAAGAT	5	59	0	ACTAATGTTT	    0.916133	-52
          **********

Masking position 5
Map Score:   0.94435

Number of sites scoring better than the average of aligned sites = 39
Number in coding regions = 21
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 5

TATAATCTTAGCATAGGAGAACTCATGCAA	4	34	1	GCATAGGAGA	    0.952272	-144
TCATGCAAACTCAAGGTAGATAGAAATGTA	4	56	1	TCAAGGTAGA	    0.974392	-122
TGTGAGATGGGCACGGTACATTTCTATCTA	4	72	0	GCACGGTACA	    0.984058	-106
CGTGCCCATCTCACAGTGGAGGGAATAGTC	4	87	1	TCACAGTGGA	    0.968034	-91
GAACTCAGCCTCACGGGATACGTGAGAAC 	4	159	1	TCACGGGATA	    0.976499	-19
          **********

Masking position 3
Map Score:   0.716134

Number of sites scoring better than the average of aligned sites = 261
Number in coding regions = 241
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 6

          **********

No masking
Map Score:   9.48026e-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 7

          **********

No masking
Map Score:   9.48026e-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:   9.48026e-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