AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00920_mthe_reg_100.orf -o00920_mthe_100.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -x5 -e 
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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	MTH1819	134	ferredoxin

Motif number 1

AAAAATACCTGATGATGGATC          	1	1	0	GTGATGGATC	    0.995962	-134
AGAATGAGCCGCGGTTTGTTGCTAAAAATAC	1	24	0	GGGTTTGTTG	    0.982357	-111
GGATGGAGCAGCTGATGGTTGTGAGGAGAAT	1	50	0	GTGATGGTTG	    0.998951	-85
AAAAATAGTTGGTGATGGATGGAGCAGCTGA	1	66	0	GTGATGGATG	    0.998948	-69
          * *********

Masking position 6
Map Score:   6.76482

Number of sites scoring better than the average of aligned sites = 107
Number in coding regions = 99
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 2

CGCGGTTTGTTGCTAAAAATACCTGATGAT	1	16	0	TGCTAAAAAT	    0.993916	-119
CGGCTCATTCTCCTCACAACCATCAGCTGC	1	44	1	TCCTCACAAC	     0.98863	-91
ATGGGGCTATTGCTAAAAATAGTTGGTGAT	1	81	0	TGCTAAAAAT	    0.993916	-54
   GATGTCACCCTAAAAACTGAAGTCCAA	1	118	0	CCCTAAAAAC	    0.993299	-17
          **********

Masking position 6
Map Score:   5.31682

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 33
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

TAGCAACAAACCGCGGCTCATTCTCCTCACAAC	1	31	1	CGGCTCATTC	    0.994743	-104
TCACAACCATCAGCTGCTCCATCCATCACCAAC	1	57	1	CGGCTCCATC	     0.99865	-78
CTATTTTTAGCAATAGCCCCATATTAATATTGG	1	89	1	CAGCCCCATA	    0.994474	-46
ACCCTAAAAACTGAAGTCCAATATTAATATGGG	1	106	0	CGGTCCAATA	     0.99176	-29
          * *  ********

Masking position 12
Map Score:   1.60382

Number of sites scoring better than the average of aligned sites = 130
Number in coding regions = 121
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

TTAGCAACAAACCGCGGCTCATTCTCCTCA	1	30	1	ACCGCGGCTC	    0.998728	-105
CTCACAACCATCAGCTGCTCCATCCATCAC	1	56	1	TCAGCTGCTC	    0.997252	-79
          **********

Masking position 9
Map Score:   0.182209

Number of sites scoring better than the average of aligned sites = 5
Number in coding regions = 4
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 5

          **********

No masking
Map Score:   1.09013e-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:   1.09013e-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:   1.09013e-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