AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -icpxR_mthe_opreg_300.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	MTH1338	81	peptidyl-prolyl cis-trans isomerase B
#2	MTH1813	181	serine protease HtrA

Motif number 1

CAGGTCCCCATATAAATTTTTGGTGATATC	1	11	0	TATAAATTTT	     0.86245	-71
TGGGGACCTGTATTAATGTTGAACCTAAAC	1	31	1	TATTAATGTT	    0.974008	-51
ATTTATTATCAGTTTAGGTTCAACATTAAT	1	42	0	AGTTTAGGTT	     0.79285	-40
TGATAATAAATATTTATGTTGAGGTGGTTA	1	61	1	TATTTATGTT	    0.936942	-21
AAGGTATGATTATTAAAGTAAGAGAGGATA	2	14	0	TATTAAAGTA	    0.877156	-168
AGTCCTTATATATAAAGGTTTTCCCGGGGG	2	70	0	TATAAAGGTT	     0.97852	-112
TTTTTAGTTAAATTAAGTTATTAAAAGTCC	2	95	0	AATTAAGTTA	     0.78171	-87
GGTTACTGAATTTTTAGTTAAATTAAGTTA	2	105	0	TTTTTAGTTA	    0.771493	-77
TCTGGAACTTTTTTCAGGTTACTGAATTTT	2	121	0	TTTTCAGGTT	    0.945266	-61
TTAAGTTTATTTTAAATGTTCTGGAACTTT	2	140	0	TTTAAATGTT	    0.942398	-42
TTTAATTGGTTTTTAAGTTTATTTTAAATG	2	152	0	TTTTAAGTTT	    0.959744	-30
TTAAAAACCAATTAAAAGTTAGAAAA    	2	166	1	ATTAAAAGTT	    0.757135	-16
          **********

Masking position 6
Map Score:   14.4002

Number of sites scoring better than the average of aligned sites = 699
Number in coding regions = 506
Number in noncoding regions = 193
Number of orfs with sites within 600 bp upstream = 193
Fraction of orfs with sites within 600 bp upstream = 0.030999


Motif number 2

   TATTATCCTCTCTTACTTTAATAATCA	2	8	1	CTCTCTTACT	    0.972332	-174
ATCATACCTTCTTTCTTACCCTATTTAAAC	2	34	1	CTTTCTTACC	    0.948775	-148
TATAAGGACTTTTAATAACTTAATTTAACT	2	90	1	TTTAATAACT	    0.871507	-92
TAACTAAAAATTCAGTAACCTGAAAAAAGT	2	115	1	TTCAGTAACC	    0.960202	-67
ATTTTAAATGTTCTGGAACTTTTTTCAGGT	2	132	0	TTCTGGAACT	    0.952047	-50
          TTTTCTAACTTTTAATTGGT	2	172	0	TTTTCTAACT	    0.980471	-10
          **********

Masking position 8
Map Score:   2.4759

Number of sites scoring better than the average of aligned sites = 91
Number in coding regions = 67
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 3

CACCAAAAATTTATATGGGGACCTGTATTA	1	16	1	TTATATGGGG	      0.9857	-66
GGTGGTGGGTTTAAATAGGGTAAGAAAGAA	2	42	0	TTAAATAGGG	    0.987936	-140
GAAAACCTTTATATATAAGGACTTTTAATA	2	77	1	ATATATAAGG	     0.95449	-105
GAATTTTTAGTTAAATTAAGTTATTAAAAG	2	98	0	TTAAATTAAG	    0.883047	-84
          **********

Masking position 5
Map Score:   0.535829

Number of sites scoring better than the average of aligned sites = 72
Number in coding regions = 51
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 4

          **********

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 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