AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -imelR_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	MTH1142	300	H(2)-dependent N5,N10-methylenetetrahydromethanopterin dehydrogenase 

Motif number 1

TAATCATAATTATTAAGATATTAATATCACGG	1	65	0	TATAAATATT	    0.949066	-236
TATAATATTATATGAAAATAATCATAATTATT	1	83	0	TATAAATAAT	    0.980732	-218
CATATAATATTATATGGATAATGGATGGTAAA	1	101	1	TATTGATAAT	    0.935287	-200
TCAAAAAACTTATAAGGAGAATTTATTCACCT	1	195	0	TATAGAGAAT	    0.987518	-106
AGTTTTTTGATTTGAAAATTATCAAAAAATAT	1	217	1	TTTAAATTAT	    0.850432	-84
CGGTTTCCAATATAAATATATTTTTTGATAAT	1	234	0	TATAAATATT	     0.94888	-67
CTACTTATATTATTAGTAGTACAGATTAATCG	1	264	0	TATAGAGTAC	    0.929087	-37
CTACTAATAATATAAGTAGTATTACAGAAATG	1	277	1	TATAGAGTAT	    0.980129	-24
          *** ** *****

Masking position 8
Map Score:   7.94526

Number of sites scoring better than the average of aligned sites = 140
Number in coding regions = 109
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 2

TCCTAACTGGAAGGCTGCCCTTAA      	1	5	0	AAGGCTGCCC	    0.998818	-296
ATGGATGGTAAAGGCTTCCCAAAGGAGGAT	1	121	1	AAGGCTTCCC	    0.998258	-180
          **********

Masking position 6
Map Score:   1.29507

Number of sites scoring better than the average of aligned sites = 7
Number in coding regions = 6
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

GCCACAGATCCGTGATATTAATATCTTAAT	1	56	1	CGTGATATTA	    0.807155	-245
CATCCATTATCCATATAATATTATATGAAA	1	98	0	CCATATAATA	    0.769187	-203
TCCCAAAGGAGGATAAAATGAAAACATTGC	1	137	1	GGATAAAATG	     0.70361	-164
TGAAAACATTGCTTAAATTGACTTACCCTG	1	155	1	GCTTAAATTG	    0.960436	-146
ATTGACTTACCCTGAAATTGCCACAGGTGA	1	171	1	CCTGAAATTG	    0.966807	-130
AAATCAAAAAACTTATAAGGAGAATTTATT	1	200	0	ACTTATAAGG	    0.722661	-101
CAAAAAATATATTTATATTGGAAACCGATT	1	239	1	ATTTATATTG	    0.824205	-62
CTGTAATACTACTTATATTATTAGTAGTAC	1	274	0	ACTTATATTA	    0.922049	-27
AAGTAGTATTACAGAAATGGA         	1	290	1	ACAGAAATGG	    0.861206	-11
          **********

Masking position 5
Map Score:   1.94288

Number of sites scoring better than the average of aligned sites = 935
Number in coding regions = 823
Number in noncoding regions = 112
Number of orfs with sites within 600 bp upstream = 117
Fraction of orfs with sites within 600 bp upstream = 0.0187922


Motif number 4

AATAATTATGATTATTTTCATATAATATTA	1	83	1	ATTATTTTCA	    0.907532	-218
CAATTTAAGCAATGTTTTCATTTTATCCTC	1	145	0	AATGTTTTCA	    0.973513	-156
TTATAAGGAGAATTTATTCACCTGTGGCAA	1	188	0	AATTTATTCA	    0.950112	-113
TCTCCTTATAAGTTTTTTGATTTGAAAATT	1	207	1	AGTTTTTTGA	     0.96188	-94
AATATAAATATATTTTTTGATAATTTTCAA	1	228	0	TATTTTTTGA	    0.928951	-73
          **********

Masking position 5
Map Score:   1.44507

Number of sites scoring better than the average of aligned sites = 136
Number in coding regions = 84
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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