AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00920_mthe_reg_300.orf -o00920_mthe_300.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

          GATCCATCATCAGGTATTTTT	1	1	1	GATCCATCAC	    0.996119	-134
GTATTTTTAGCAACAAACCGCGGCTCATTCT	1	24	1	CAACAAACCC	    0.984293	-111
ATTCTCCTCACAACCATCAGCTGCTCCATCC	1	50	1	CAACCATCAC	    0.999068	-85
TCAGCTGCTCCATCCATCACCAACTATTTTT	1	66	1	CATCCATCAC	    0.999064	-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

ATCATCAGGTATTTTTAGCAACAAACCGCG	1	16	1	ATTTTTAGCA	    0.994476	-119
GCAGCTGATGGTTGTGAGGAGAATGAGCCG	1	44	0	GTTGTGAGGA	    0.989672	-91
ATCACCAACTATTTTTAGCAATAGCCCCAT	1	81	1	ATTTTTAGCA	    0.994476	-54
TTGGACTTCAGTTTTTAGGGTGACATC   	1	118	1	GTTTTTAGGG	    0.993915	-17
          **********

Masking position 5
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	    0.994785	-104
TCACAACCATCAGCTGCTCCATCCATCACCAAC	1	57	1	CGGCTCCATC	    0.998661	-78
CTATTTTTAGCAATAGCCCCATATTAATATTGG	1	89	1	CAGCCCCATA	    0.994515	-46
ACCCTAAAAACTGAAGTCCAATATTAATATGGG	1	106	0	CGGTCCAATA	    0.991827	-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

TGAGGAGAATGAGCCGCGGTTTGTTGCTAA	1	30	0	GAGCCGCGGT	    0.998728	-105
GTGATGGATGGAGCAGCTGATGGTTGTGAG	1	56	0	GAGCAGCTGA	    0.997252	-79
          **********

Masking position 2
Map Score:   0.182209

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 13
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