AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i342_aful_mthe_100.orf -o342_aful_mthe_100.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RTH01601	134	M.thermo
#2	RTH01432	19	M.thermo

Motif number 1

AAAAATACCTGATGATGGATC          	1	1	0	GTGATGGATC	    0.995738	-134
AGAATGAGCCGCGGTTTGTTGCTAAAAATAC	1	24	0	GGGTTTGTTG	    0.980083	-111
GGATGGAGCAGCTGATGGTTGTGAGGAGAAT	1	50	0	GTGATGGTTG	    0.998814	-85
AAAAATAGTTGGTGATGGATGGAGCAGCTGA	1	66	0	GTGATGGATG	     0.99881	-69
          * *********

Masking position 6
Map Score:   6.46468

Number of sites scoring better than the average of aligned sites = 86
Number in coding regions = 81
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 2

CGCGGTTTGTTGCTAAAAATACCTGATGAT	1	16	0	TGCTAAAAAT	    0.993407	-119
CGGCTCATTCTCCTCACAACCATCAGCTGC	1	44	1	TCCTCACAAC	    0.987684	-91
ATGGGGCTATTGCTAAAAATAGTTGGTGAT	1	81	0	TGCTAAAAAT	    0.993407	-54
   GATGTCACCCTAAAAACTGAAGTCCAA	1	118	0	CCCTAAAAAC	    0.992739	-17
          **********

Masking position 6
Map Score:   4.98741

Number of sites scoring better than the average of aligned sites = 80
Number in coding regions = 65
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

TTGTGAGGAGAATGAGCCGCGGTTTGTTGCTA	1	31	0	AATGAGCGCG	    0.989104	-104
TTGGTGATGGATGGAGCAGCTGATGGTTGTGA	1	57	0	ATGGAGCGCG	    0.998363	-78
CAATATTAATATGGGGCTATTGCTAAAAATAG	1	89	0	ATGGGGCATG	    0.989662	-46
CCATATTAATATTGGACTTCAGTTTTTAGGGT	1	107	1	ATTGGACTCG	    0.986881	-28
        CAATGAGACGGGAGGCAAA     	2	3	1	ATGAGACGGG	    0.979699	-17
          ******* ** *

Masking position 1
Map Score:   2.39524

Number of sites scoring better than the average of aligned sites = 458
Number in coding regions = 429
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 4

TAGCAACAAACCGCGGCTCATTCTCCTCAC	1	31	1	CCGCGGCTCA	    0.999134	-104
TCACAACCATCAGCTGCTCCATCCATCACC	1	57	1	CAGCTGCTCC	    0.992391	-78
    TTTGCCTCCCGTCTCATTG       	2	4	0	TCCCGTCTCA	    0.988279	-16
          **********

Masking position 8
Map Score:   0.773343

Number of sites scoring better than the average of aligned sites = 104
Number in coding regions = 93
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 5

          **********

No masking
Map Score:   -1.53887e-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:   -1.53887e-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:   -1.53887e-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