AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -imalT_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	MTH478	49	sulfate transport system permease protein
#2	MTH479	136	conserved protein
#3	MTH922	67	unknown
#4	MTH923	21	unknown
#5	MTH925	32	conserved protein
#6	MTH927	139	ferredoxin

Motif number 1

AAAGATAAAGAAGGACTACTCTGAGGGAGTTATTCCC	2	16	0	AAGACTTAGG	    0.983296	-121
CATTCCTTCACAGAACCGATATGTATATATGTCCATG	2	72	1	CAGACTTTTA	    0.969606	-65
TCCATTAACTCAGAACACCTATATCGACATGGACATA	2	99	0	CAGACTTTGA	     0.99595	-38
GAAAGTAATTCAGCACACCTTTCAGGAGCGTTTCCAG	3	28	0	CAGACTTAGA	    0.998235	-40
        AATAGCACCAGTATAATGGCAATTTCGGG	5	14	0	TAGACTTAGG	    0.983295	-19
TTTTATTTTTCAGGAAATACGTGAGGATATCCATTAT	6	20	1	CAGAACTAGA	    0.957571	-120
CCATGTAAAACAGTACTGTTTTCATGAGGTCCATTAA	6	78	1	CAGACTTAGA	    0.998234	-62
          *** **   * * * **

Masking position 5
Map Score:   8.80588

Number of sites scoring better than the average of aligned sites = 85
Number in coding regions = 79
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

AAAGTCGGGGTCTTAAAAATAAAGTAGTATG	1	21	0	TCTTAAAATA	    0.878641	-29
ATGGGATCGTCCTGAAAGATAAAGAAGGACT	2	36	0	CCTGAAAGTA	    0.995429	-101
TGGAAACGCTCCTGAAAGGTGTGCTGAATTA	3	29	1	CCTGAAAGTG	    0.994492	-39
TTCAAGGTAATCTGAAAGTAATTCAGCACAC	3	47	0	TCTGAAAGAA	    0.975275	-21
TCACGTATTTCCTGAAAAATAAAAAAATTGA	6	13	0	CCTGAAAATA	    0.992831	-127
TAATGGACCTCATGAAAACAGTACTGTTTTA	6	83	0	CATGAAAAAG	    0.904954	-57
          ******** **

Masking position 6
Map Score:   6.01081

Number of sites scoring better than the average of aligned sites = 205
Number in coding regions = 175
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 3

TAAAGAAGGACTACTCTGAGGGAGTTATTCCCAGAA	2	12	0	CTTAGGGAGT	    0.987652	-125
CAGAACACCTATATCGACATGGACATATATACATAT	2	90	0	ATAATGGACT	    0.962348	-47
TATAGGTGTTCTGAGTTAATGGAGGTTAAAGACC  	2	113	1	CTTATGGAGT	    0.995449	-24
AGGACCCCCGCAGTTATAATGGATATCCTCACGTAT	6	36	0	CATATGGATT	    0.951883	-104
ATATATAAATCTTTCTTAATGGACCTCATGAAAACA	6	94	0	CTTATGGACT	    0.996871	-46
ATTAAGAAAGATTTATATATGGACCTGTGGAATATA	6	110	1	ATAATGGACT	    0.982781	-30
          **    * ****** *

Masking position 9
Map Score:   3.65717

Number of sites scoring better than the average of aligned sites = 64
Number in coding regions = 57
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

ATCTTTCAGGACGATCCCATGTTCTCATTC	2	47	1	ACGATCCCAT	    0.855891	-90
TTCACTGCACTGGAAACGCTCCTGAAAGGT	3	19	1	TGGAAACGCT	    0.838686	-49
  TTTAAACCAGGATCTGATACC       	4	9	1	AGGATCTGAT	    0.950399	-13
GCAGTTATAATGGATATCCTCACGTATTTC	6	33	0	TGGATATCCT	    0.677154	-107
ATGGCAGCTGAGGACCCCCGCAGTTATAAT	6	52	0	AGGACCCCCG	     0.98039	-88
TCTTTCTTAATGGACCTCATGAAAACAGTA	6	91	0	TGGACCTCAT	    0.981034	-49
GATTTATATATGGACCTGTGGAATATACGA	6	119	1	TGGACCTGTG	    0.913988	-21
          **********

Masking position 4
Map Score:   1.11055

Number of sites scoring better than the average of aligned sites = 1803
Number in coding regions = 1714
Number in noncoding regions = 89
Number of orfs with sites within 600 bp upstream = 71
Fraction of orfs with sites within 600 bp upstream = 0.0114038


Motif number 5

          **********

No masking
Map Score:   -1.75204e-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:   -1.75204e-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:   -1.75204e-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