AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00562_mthe_reg_300.orf -o00562_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	MTH870	103	conserved protein
#2	MTH874	113	porphobilinogen deaminase
#3	MTH1639	163	cell division control protein Cdc48

Motif number 1

 TAATCTTACCTCCTGTTAGAATGAGTGATGTG	1	10	1	CTCCGTTAGT	    0.969889	-94
GCTTACTGAATTCCTATAAAGCTTTTATATAAT	1	76	0	TTCCATAAAT	      0.9746	-28
  TGAATCATCTCCAGTAAACGTTAATCATTTG	2	93	0	CTCCGTAAAT	    0.994887	-21
TATATAAATGTTTCGGTAAAGTTTATATACTAT	3	46	0	TTTCGTAAAT	    0.974601	-118
TATATATGATTACCTGTACATGTATTATAGTAA	3	73	1	TACCGTACAT	    0.949868	-91
AACCGGAATATTCTAGTAAATTTAGGTTACTAT	3	99	0	TTCTGTAAAT	    0.974601	-65
TACTAGAATATTCCGGTTAAATTAAATATCAAC	3	114	1	TTCCGTTAAT	    0.995353	-50
ATTATTATGATTCCGGTTGATATTTAATTTAAC	3	129	0	TTCCGTTGAT	    0.985054	-35
          **** *****  *

Masking position 7
Map Score:   10.4582

Number of sites scoring better than the average of aligned sites = 172
Number in coding regions = 149
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 2

GTGGGACTTCAATGTATATCTATTAATTCAGT	1	40	1	AAGATATCTA	    0.878205	-64
GAATTCCTATAAAGCTTTTATATAATGTCCAC	1	70	0	AAGTTTTATA	    0.919726	-34
CCAGTTTATTAAAAATCACATAATTATGGCTA	2	21	0	AAATCACATA	    0.944384	-93
GGAGTTTTTGAAAAGTTATATAATAGGATACA	2	51	1	AAATTATATA	    0.984898	-63
CACATCGCACAAAATCCATCTAATAGTATATA	3	24	1	AAACCATCTA	    0.917615	-140
ATGTTTCGGTAAAGTTTATATACTATTAGATG	3	40	0	AAGTTATATA	    0.984586	-124
ACTTTACCGAAACATTTATATATGATTACCTG	3	57	1	AAATTATATA	    0.984847	-107
GAATCATAATAATAATCATAAAGAG       	3	149	1	AAATCATAAA	    0.919725	-15
          ** * *******

Masking position 2
Map Score:   6.05937

Number of sites scoring better than the average of aligned sites = 75
Number in coding regions = 24
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 61
Fraction of orfs with sites within 600 bp upstream = 0.00979762


Motif number 3

AATTCAGTGGACATTATATAAAAGCTTTATAGG	1	64	1	AATTATATAA	    0.962027	-40
TCAAAAACTCCAGTTTATTAAAAATCACATAAT	2	29	0	CGTTTATTAA	    0.835883	-85
AGTTTTTGAAAAGTTATATAATAGGATACAATA	2	53	1	AGTTATATAA	    0.981238	-61
        CTCTGTTTAATACCACATCGCACAA	3	3	1	CGTTTAATAA	    0.965689	-161
GTTTCGGTAAAGTTTATATACTATTAGATGGAT	3	37	0	ATTTATATAA	    0.946441	-127
TTTACCGAAACATTTATATATGATTACCTGTAC	3	59	1	CTTTATATAA	    0.935834	-105
TTACCTGTACATGTATTATAGTAACCTAAATTT	3	82	1	AGTATTATAA	    0.869749	-82
ATAGTAACCTAAATTTACTAGAATATTCCGGTT	3	99	1	AATTTACTAA	    0.816014	-65
TATTCCGGTTAAATTAAATATCAACCGGAATCA	3	122	1	AATTAAATAA	    0.953615	-42
          * ********  *

Masking position 9
Map Score:   5.0096

Number of sites scoring better than the average of aligned sites = 83
Number in coding regions = 30
Number in noncoding regions = 53
Number of orfs with sites within 600 bp upstream = 52
Fraction of orfs with sites within 600 bp upstream = 0.00835207


Motif number 4

CCGGTGGTAGCCATAATTATGTGATTTTTA	2	14	1	CCATAATTAT	    0.895922	-100
CTCCAGTAAACGTTAATCATTTGAGAAATT	2	86	0	CGTTAATCAT	     0.95915	-28
ATACATGTACAGGTAATCATATATAAATGT	3	68	0	AGGTAATCAT	     0.94702	-96
TTTAATTTAACCGGAATATTCTAGTAAATT	3	110	0	CCGGAATATT	    0.918178	-54
TAAATATCAACCGGAATCATAATAATAATC	3	136	1	CCGGAATCAT	    0.993229	-28
          **********

Masking position 5
Map Score:   0.243299

Number of sites scoring better than the average of aligned sites = 255
Number in coding regions = 236
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 5

          **********

No masking
Map Score:   -1.25466e-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:   -1.25466e-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:   -1.25466e-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