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

Motif number 1

GATATCACCAAAAATTTATATGGGGACCTG	1	11	1	AAAATTTATA	    0.882033	-71
GTTTAGGTTCAACATTAATACAGGTCCCCA	1	31	0	AACATTAATA	     0.97811	-51
ATTAATGTTGAACCTAAACTGATAATAAAT	1	42	1	AACCTAAACT	    0.820283	-40
TAACCACCTCAACATAAATATTTATTATCA	1	61	0	AACATAAATA	    0.946478	-21
TATCCTCTCTTACTTTAATAATCATACCTT	2	14	1	TACTTTAATA	    0.894892	-168
CCCCCGGGAAAACCTTTATATATAAGGACT	2	70	1	AACCTTTATA	    0.981925	-112
GGACTTTTAATAACTTAATTTAACTAAAAA	2	95	1	TAACTTAATT	    0.810265	-87
TAACTTAATTTAACTAAAAATTCAGTAACC	2	105	1	TAACTAAAAA	    0.801045	-77
AAAATTCAGTAACCTGAAAAAAGTTCCAGA	2	121	1	AACCTGAAAA	    0.953694	-61
AAAGTTCCAGAACATTTAAAATAAACTTAA	2	140	1	AACATTTAAA	    0.951244	-42
CATTTAAAATAAACTTAAAAACCAATTAAA	2	152	1	AAACTTAAAA	    0.966023	-30
    TTTTCTAACTTTTAATTGGTTTTTAA	2	166	0	AACTTTTAAT	    0.788034	-16
          **********

Masking position 8
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

ATGATTATTAAAGTAAGAGAGGATAATA  	2	9	0	AAGTAAGAGA	    0.981874	-173
GGTTTAAATAGGGTAAGAAAGAAGGTATGA	2	35	0	GGGTAAGAAA	    0.912611	-147
TAGTTAAATTAAGTTATTAAAAGTCCTTAT	2	91	0	AAGTTATTAA	    0.896597	-91
AACTTTTTTCAGGTTACTGAATTTTTAGTT	2	116	0	AGGTTACTGA	    0.968584	-66
AACCTGAAAAAAGTTCCAGAACATTTAAAA	2	131	1	AAGTTCCAGA	     0.96208	-51
AACCAATTAAAAGTTAGAAAA         	2	171	1	AAGTTAGAAA	    0.984681	-11
          **********

Masking position 4
Map Score:   3.27334

Number of sites scoring better than the average of aligned sites = 110
Number in coding regions = 92
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 3

          **********

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 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