AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i225_Glutamyl_tRNA_synthase_tpal_reg_100.orf -o225_tpal_100.ace -a/home/amcguire/alignace/lib/ORF_tpal.txt -z/skink1/amcguire/genomes/tpal.fna -g0.53 -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 =  	0.53
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RTP00776	171	AE000520
#2	RTP00777	21	AE000520

Motif number 1

ACCGCGCACAGCCCCCACACCAGCGCGCGC	1	11	1	GCCCCCACAC	    0.993952	-161
CCACACCAGCGCGCGCGTACCCTGCCGAAT	1	25	1	GCGCGCGTAC	    0.957215	-147
AATACTCTCTTCCCCCATACTCGCCCCGAC	1	52	1	TCCCCCATAC	    0.991572	-120
TCCCCCATACTCGCCCCGACAACCTGCTGA	1	62	1	TCGCCCCGAC	    0.996185	-110
GCGCTGCGCAGCGCCTGGTTAAACGTTGCG	1	106	0	GCGCCTGGTT	    0.947902	-66
TTCAGATTTTGCGCCTCTTCTGCACTGAAT	1	140	1	GCGCCTCTTC	    0.988937	-32
         CGCCCCCAGGCTAGCGCAAAA	2	2	1	GCCCCCAGGC	    0.942279	-20
          **********

Masking position 4
Map Score:   11.78

Number of sites scoring better than the average of aligned sites = 539
Number in coding regions = 483
Number in noncoding regions = 56
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 2

         ACCGCGCACAGCCCCCACACC	1	2	1	CCGCGCACAG	    0.947964	-170
TTTCTATTTCAAGCGCAACGTTTAACCAGG	1	93	1	AAGCGCAACG	    0.992937	-79
TAACCAGGCGCTGCGCAGCGCGGTTTTCAG	1	115	1	CTGCGCAGCG	      0.9636	-57
AGTGCAGAAGAGGCGCAAAATCTGAAAACC	1	136	0	AGGCGCAAAA	    0.984469	-36
TCAGTGGATTCAGTGCAGAAGAGGCGCAAA	1	147	0	CAGTGCAGAA	    0.968922	-25
GCCCCCAGGCTAGCGCAAAA          	2	12	1	TAGCGCAAAA	    0.983972	-10
          **********

Masking position 7
Map Score:   8.21945

Number of sites scoring better than the average of aligned sites = 735
Number in coding regions = 695
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 3

CGCACAGCCCCCACACCAGCGCGCGCGTACCC	1	15	1	CCCACAGCGC	    0.996771	-157
GAGTATTCGGCAGGGTACGCGCGCGCTGGTGT	1	27	0	CAGGTCGCGC	    0.789718	-145
TACTCTCTTCCCCCATACTCGCCCCGACAACC	1	54	1	CCCATCTCGC	     0.95712	-118
CCATACTCGCCCCGACAACCTGCTGATTTTCT	1	66	1	CCGACACCTG	     0.92422	-106
TGAAAACCGCGCTGCGCAGCGCCTGGTTAAAC	1	112	0	GCGCGAGCGC	    0.971309	-60
AGGCGCAAAATCTGAAAACCGCGCTGCGCAGC	1	124	0	TCGAAACCGC	    0.950326	-48
     CGCCCCCAGGCTAGCGCAAAA      	2	6	1	CCGGCAGCGC	    0.995792	-16
          ** *** *****

Masking position 10
Map Score:   2.71951

Number of sites scoring better than the average of aligned sites = 1259
Number in coding regions = 1152
Number in noncoding regions = 107
Number of orfs with sites within 600 bp upstream = 83
Fraction of orfs with sites within 600 bp upstream = 0.0133312


Motif number 4

          **********

No masking
Map Score:   4.00336e-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:   4.00336e-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:   4.00336e-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