AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00562_mthe_reg_100.orf -o00562_mthe_100.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	MTH874	113	porphobilinogen deaminase
#2	MTH1639	163	cell division control protein Cdc48

Motif number 1

TTTTCAAAAACTCCAGTTTATTAAAAATCA	1	35	0	CTCCAGTTTA	    0.972655	-79
  TGAATCATCTCCAGTAAACGTTAATCAT	1	96	0	CTCCAGTAAA	    0.991049	-18
          CTCTGTTTAATACCACATCG	2	1	1	CTCTGTTTAA	    0.913321	-163
TATATAAATGTTTCGGTAAAGTTTATATAC	2	49	0	TTTCGGTAAA	    0.960832	-115
AACCGGAATATTCTAGTAAATTTAGGTTAC	2	102	0	TTCTAGTAAA	    0.961538	-62
TACTAGAATATTCCGGTTAAATTAAATATC	2	114	1	TTCCGGTTAA	     0.99596	-50
ATTATTATGATTCCGGTTGATATTTAATTT	2	132	0	TTCCGGTTGA	    0.989031	-32
          **********

Masking position 10
Map Score:   11.0881

Number of sites scoring better than the average of aligned sites = 230
Number in coding regions = 181
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 2

AAACCGGTGGTAGCCATAATTATGTGATTT	1	11	1	TAGCCATAAT	    0.848384	-103
GATTTTTAATAAACTGGAGTTTTTGAAAAG	1	36	1	AAACTGGAGT	    0.949686	-78
TGATTAACGTTTACTGGAGATGATTCA   	1	97	1	TTACTGGAGA	    0.922525	-17
TAAATTTAGGTTACTATAATACATGTACAG	2	86	0	TTACTATAAT	    0.920312	-78
TAACCTAAATTTACTAGAATATTCCGGTTA	2	103	1	TTACTAGAAT	    0.972578	-61
ATATTTAATTTAACCGGAATATTCTAGTAA	2	113	0	TAACCGGAAT	    0.992137	-51
AATTAAATATCAACCGGAATCATAATAATA	2	133	1	CAACCGGAAT	    0.980372	-31
          **********

Masking position 8
Map Score:   5.3287

Number of sites scoring better than the average of aligned sites = 320
Number in coding regions = 274
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 3

AGTTTATTAAAAATCACATAATTATGGCTA	1	21	0	AAATCACATA	    0.909016	-93
AAAAGTTATATAATAGGATACAATAAATTT	1	61	1	TAATAGGATA	    0.918747	-53
CAGTAAACGTTAATCATTTGAGAAATTTAT	1	83	0	TAATCATTTG	     0.89008	-31
AAAATCCATCTAATAGTATATAAACTTTAC	2	34	1	TAATAGTATA	    0.961545	-130
CATGTACAGGTAATCATATATAAATGTTTC	2	65	0	TAATCATATA	    0.988857	-99
ATCATAATAATAATCATAAAGAG       	2	151	1	TAATCATAAA	    0.956853	-13
          **********

Masking position 4
Map Score:   3.61418

Number of sites scoring better than the average of aligned sites = 97
Number in coding regions = 54
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 4

          **********

No masking
Map Score:   1.3033e-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 5

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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