AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -ifis_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	MTH176	168	tRNA-guanine transglycosylase
#2	MTH848	103	protein-export membrane protein, SecF 

Motif number 1

    TATGTGATCCAGCCCTGCTTCCAGTGT	1	7	1	ATCCAGCCTG	    0.995823	-162
CTCCCACATAATCCATGCCTCAGAAACACTG	1	32	0	ATCCATCCTC	    0.991411	-137
ATCTGGTGGTAGCCACTGCAGAGTACCTGTT	1	131	1	AGCCACGCAG	    0.982991	-38
TTTTAAAGTCATACAGGCCACTCATAGCCAT	2	63	1	ATACAGCCAC	    0.950679	-41
GGCCACTCATAGCCATACCAGCAGCCATAAC	2	78	1	AGCCATCCAG	    0.997128	-26
CCATACCAGCAGCCATAACTGTAA       	2	90	1	AGCCATACTG	    0.985194	-14
          ****** ****

Masking position 5
Map Score:   7.62891

Number of sites scoring better than the average of aligned sites = 306
Number in coding regions = 279
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 2

ATTTTTAGGGTGCTGATTACATATTAATCA	1	64	1	TGCTGATTAC	    0.996676	-105
TCCACGATGATACTGATTAATATGTAATCA	1	77	0	TACTGATTAA	    0.992083	-92
TGGTAGCCACTGCAGAGTACCTGTTAATCA	1	137	1	TGCAGAGTAC	    0.985837	-32
 GCAGAATGATACTGATTAACAGGTACTCT	1	150	0	TACTGATTAA	    0.992083	-19
          **********

Masking position 6
Map Score:   5.60847

Number of sites scoring better than the average of aligned sites = 11
Number in coding regions = 10
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 3

TCTGAGGCATGGATTATGTGGGAGGATTTTT	1	39	1	GGATTATGGG	    0.983823	-130
TTATGTGGGAGGATTTTTAGGGTGCTGATTA	1	52	1	GGATTTTTGG	    0.946951	-117
ATATTAATCAGTATCATCGTGGATATACACT	1	84	1	GTATCATCTG	    0.983772	-85
ATCTGAGCATGTAGTATCTGGTGGTAGCCAC	1	116	1	GTAGTATCGG	    0.969606	-53
AGAATGATACTGATTAACAGGTACTCTGCAG	1	146	0	TGATTAACGG	    0.923823	-23
CTGTTAATCAGTATCATTCTGC         	1	157	1	GTATCATTTG	    0.953453	-12
ACTTTAAAGGTGATCGTCTTGATTGACCGCA	2	32	1	TGATCGTCTG	    0.925863	-72
          ******** **

Masking position 3
Map Score:   2.86992

Number of sites scoring better than the average of aligned sites = 839
Number in coding regions = 785
Number in noncoding regions = 54
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 4

CCTAAAAATCCTCCCACATAATCCATGCCT	1	43	0	CTCCCACATA	      0.9216	-126
ATACTACATGCTCAGATCAGTGTATATCCA	1	103	0	CTCAGATCAG	    0.941272	-66
TCTGCAGTGGCTACCACCAGATACTACATG	1	123	0	CTACCACCAG	    0.995032	-46
TTTAAAGTTTCTCCCATCTGTCAAATAGA 	2	10	0	CTCCCATCTG	    0.995172	-94
ACTCATAGCCATACCAGCAGCCATAACTGT	2	82	1	ATACCAGCAG	    0.954875	-22
          **********

Masking position 6
Map Score:   1.55678

Number of sites scoring better than the average of aligned sites = 781
Number in coding regions = 734
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 5

          **********

No masking
Map Score:   -3.31523e-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:   -3.31523e-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:   -3.31523e-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