AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -icytR_mthe_opreg_100.orf -g0.495 -x5 
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 =  	0.495
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	MTH816	43	sporulation protein IVFB related protein
#2	MTH817	56	conserved protein
#3	MTH1591	30	phosphonopyruvate decarboxylase
#4	MTH1592	21	conserved protein
#5	MTH1593	205	ribosomal protein S3a

Motif number 1

GGTGCTATGAATAAATCATTTTTTATAGC 	1	10	0	ATAAATCATT	    0.894415	-34
GCTCGAGTTTTTTGATCCTGG         	2	2	0	TTTGATCCTG	    0.902223	-55
     AGATCATAAATCTAGGAAGGTGGGT	3	6	1	ATAAATCTAG	    0.895257	-25
AAGGGAGTATTTAAATCTTGACATGGTGGT	5	56	0	TTAAATCTTG	    0.984298	-150
GTATGTAACTCTAAATCATGGTTAACCAGT	5	117	1	CTAAATCATG	    0.975363	-89
TGAATTTATGTTAAATCCAGCTGTTTTTAC	5	162	1	TTAAATCCAG	     0.96741	-44
  TATATCACCTTAATCTTTAACACCGTAA	5	188	0	CTTAATCTTT	    0.887514	-18
          **********

Masking position 5
Map Score:   5.90397

Number of sites scoring better than the average of aligned sites = 120
Number in coding regions = 80
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 2

ATGATTTATTCATAGCACCCCATATAATAG	1	21	1	CATAGCACCC	    0.989563	-23
       GATTAACCCACCTTCCTAGATTT	3	18	0	TAACCCACCT	    0.954047	-13
TTCATGACCACACAGCACCCCAAACCACCA	5	33	1	CACAGCACCC	    0.993227	-173
CACAGCACCCCAAACCACCATGTCAAGATT	5	43	1	CAAACCACCA	    0.988924	-163
TAGAGTTACATACACCGCCAGTATGGAATA	5	100	0	TACACCGCCA	    0.969801	-106
          TATATCACCTTAATCTTTAA	5	196	0	TATATCACCT	    0.934602	-10
          **********

Masking position 2
Map Score:   4.76492

Number of sites scoring better than the average of aligned sites = 340
Number in coding regions = 313
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 3

ATTCTGTACATCATATCCATTCGGTTTTTC	2	35	0	TCATATCCAT	    0.989143	-22
AACTGGCTGTTCATATTCATGACCACACAG	5	18	1	TCATATTCAT	    0.990857	-188
TTCAAAAAATTCATATTTAACTGGTTAACC	5	136	0	TCATATTTAA	    0.956056	-70
          **********

Masking position 5
Map Score:   0.961174

Number of sites scoring better than the average of aligned sites = 57
Number in coding regions = 48
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

          **********

No masking
Map Score:   3.07965e-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:   3.07965e-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:   3.07965e-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