AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -icpxR9_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

CAGGTCCCCATATAAATTTTTGGTGATATC	1	11	0	TATAAATTTT	     0.87142	-71
TGGGGACCTGTATTAATGTTGAACCTAAAC	1	31	1	TATTAATGTT	    0.975906	-51
ATTTATTATCAGTTTAGGTTCAACATTAAT	1	42	0	AGTTTAGGTT	    0.805337	-40
TGATAATAAATATTTATGTTGAGGTGGTTA	1	61	1	TATTTATGTT	    0.941341	-21
AAGGTATGATTATTAAAGTAAGAGAGGATA	2	14	0	TATTAAAGTA	    0.885291	-168
AGTCCTTATATATAAAGGTTTTCCCGGGGG	2	70	0	TATAAAGGTT	    0.980096	-112
TTTTTAGTTAAATTAAGTTATTAAAAGTCC	2	95	0	AATTAAGTTA	    0.794694	-87
GGTTACTGAATTTTTAGTTAAATTAAGTTA	2	105	0	TTTTTAGTTA	    0.784917	-77
TCTGGAACTTTTTTCAGGTTACTGAATTTT	2	121	0	TTTTCAGGTT	    0.949155	-61
TTAAGTTTATTTTAAATGTTCTGGAACTTT	2	140	0	TTTAAATGTT	    0.946479	-42
TTTAATTGGTTTTTAAGTTTATTTTAAATG	2	152	0	TTTTAAGTTT	    0.962645	-30
TTAAAAACCAATTAAAAGTTAGAAAA    	2	166	1	ATTAAAAGTT	    0.771153	-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

TGATTATTAAAGTAAGAGAGGATAATA   	2	8	0	AGTAAGAGAG	    0.974599	-174
GTTTAAATAGGGTAAGAAAGAAGGTATGAT	2	34	0	GGTAAGAAAG	    0.952877	-148
AGTTAAATTAAGTTATTAAAAGTCCTTATA	2	90	0	AGTTATTAAA	     0.88102	-92
ACTTTTTTCAGGTTACTGAATTTTTAGTTA	2	115	0	GGTTACTGAA	    0.963426	-67
ACCTGAAAAAAGTTCCAGAACATTTAAAAT	2	132	1	AGTTCCAGAA	    0.955901	-50
ACCAATTAAAAGTTAGAAAA          	2	172	1	AGTTAGAAAA	    0.982078	-10
          **********

Masking position 3
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

TAATACAGGTCCCCATATAAATTTTTGGTG	1	16	0	CCCCATATAA	    0.985462	-66
TTCTTTCTTACCCTATTTAAACCCACCACC	2	42	1	CCCTATTTAA	    0.987735	-140
TATTAAAAGTCCTTATATATAAAGGTTTTC	2	77	0	CCTTATATAT	    0.953755	-105
CTTTTAATAACTTAATTTAACTAAAAATTC	2	98	1	CTTAATTTAA	    0.881309	-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