AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i249_min_operon_mthe_reg_300.orf -o249_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	RTH00838	128	M.thermo
#2	RTH01361	158	M.thermo

Motif number 1

    ACTATGCCTCCATAAACAGAGTATTCCA	1	7	1	CCCCATAAAA	    0.986627	-122
ACAGAGTATTCCACCTAAAATATATAGGCTTT	1	26	1	CCCCTAAAAA	    0.954977	-103
GTTAGTCATACCCATTTAATTAATAAATGCTT	1	58	0	CCATTTAATA	     0.97779	-71
   ATAATCACTCCTTTAATACTTGCTGGAAT	1	110	0	CTCTTTAATC	    0.887832	-19
ACATGTAAGTCCGGTATAAAAATATTGTTAGT	2	55	0	CCGTATAAAA	    0.973675	-104
TTTAATTACCCTACTTTAAAGACATGTAAGTC	2	76	0	CTCTTTAAAA	    0.979411	-83
ACACACGTCGCCTTTTTAATTACCCTACTTTA	2	90	0	CCTTTTAATA	     0.96136	-69
ATCAGTCATTCCGATATAAATATTGTTACACA	2	117	0	CCATATAAAA	    0.977789	-42
          ** ******* *

Masking position 8
Map Score:   7.67226

Number of sites scoring better than the average of aligned sites = 206
Number in coding regions = 152
Number in noncoding regions = 54
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 2

TGCCTCCATAAACAGAGTATTCCACCTAAA	1	15	1	AACAGAGTAT	    0.976153	-114
TTTATTAATTAAATGGGTATGACTAACTAA	1	63	1	AAATGGGTAT	    0.940953	-66
AGTATTAAAGGAGTGATTAT          	1	119	1	GAGTGATTAT	     0.96958	-10
GTTAGTTCTGGACAGGATATCCGATCCGGG	2	31	0	GACAGGATAT	    0.973335	-128
ATATCGGAATGACTGATTATTATCTGGAGG	2	132	1	GACTGATTAT	    0.988431	-27
          **********

Masking position 8
Map Score:   2.41554

Number of sites scoring better than the average of aligned sites = 94
Number in coding regions = 87
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

GAATCAAATAGAAACTGTTAATTAGTTAGT	1	84	0	GAAACTGTTA	    0.971842	-45
CCGGTATAAAAATATTGTTAGTTCTGGACA	2	47	0	AATATTGTTA	    0.988539	-112
TTCCGATATAAATATTGTTACACACGTCGC	2	111	0	AATATTGTTA	    0.988539	-48
          **********

Masking position 4
Map Score:   1.01758

Number of sites scoring better than the average of aligned sites = 11
Number in coding regions = 7
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

TACTCTGTTTATGGAGGCATAGT       	1	4	0	ATGGAGGCAT	    0.977559	-125
CTATATATTTTAGGTGGAATACTCTGTTTA	1	23	0	TAGGTGGAAT	    0.980232	-106
CCTTTAATACTTGCTGGAATCAAATAGAAA	1	100	0	TTGCTGGAAT	    0.978621	-29
TGATTATTATCTGGAGGTATTGGA      	2	145	1	CTGGAGGTAT	    0.983512	-14
          **********

Masking position 9
Map Score:   0.877556

Number of sites scoring better than the average of aligned sites = 140
Number in coding regions = 119
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 5

          **********

No masking
Map Score:   -3.38628e-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:   -3.38628e-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:   -3.38628e-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