AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i207_holliday_junction_mtub_reg_100.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 =  	0.66
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	ruvC	108	ruvC

Motif number 1

ACACGCCTATGGAACGTGCGATGGTAAATT	1	18	0	GGAACGTGCG	    0.960842	-91
TTCCATAGGCGTGTCCTGCGCGGGATGTCG	1	34	1	GTGTCCTGCG	    0.992429	-75
ATACGCTAGCGGATCGTCCCGACATCCCGC	1	53	0	GGATCGTCCC	    0.592756	-56
ATCCGCTAGCGTATCGAACGATTGTTCGGA	1	69	1	GTATCGAACG	    0.986432	-40
AATGGCTGAGGGAGCGTGCG          	1	99	1	GGAGCGTGCG	    0.996324	-10
          **********

Masking position 5
Map Score:   10.1079

Number of sites scoring better than the average of aligned sites = 1011
Number in coding regions = 923
Number in noncoding regions = 88
Number of orfs with sites within 600 bp upstream = 95
Fraction of orfs with sites within 600 bp upstream = 0.0152586


Motif number 2

TAGGAAATTTACCATCGCACGTTCCATAGG	1	13	1	ACCATCGCAC	    0.989727	-96
CATCGCACGTTCCATAGGCGTGTCCTGCGC	1	25	1	TCCATAGGCG	    0.988623	-84
CGTCCCGACATCCCGCGCAGGACACGCCTA	1	39	0	TCCCGCGCAG	    0.988393	-70
ATCGTTCGATACGCTAGCGGATCGTCCCGA	1	61	0	ACGCTAGCGG	    0.801375	-48
   CGCACGCTCCCTCAGCCATTTCCGAAC	1	92	0	TCCCTCAGCC	    0.984021	-17
          **********

Masking position 2
Map Score:   2.28942

Number of sites scoring better than the average of aligned sites = 7370
Number in coding regions = 6803
Number in noncoding regions = 567
Number of orfs with sites within 600 bp upstream = 457
Fraction of orfs with sites within 600 bp upstream = 0.0734019


Motif number 3

GCGATGGTAAATTTCCTACC          	1	1	0	ATTTCCTACC	    0.992654	-108
TTCCATAGGCGTGTCCTGCGCGGGATGTCG	1	34	1	GTGTCCTGCG	    0.986127	-75
CCTGCGCGGGATGTCGGGACGATCCGCTAG	1	48	1	ATGTCGGGAC	     0.99162	-61
TCCCTCAGCCATTTCCGAACAATCGTTCGA	1	82	0	ATTTCCGAAC	    0.992193	-27
          **********

Masking position 4
Map Score:   2.50911

Number of sites scoring better than the average of aligned sites = 732
Number in coding regions = 663
Number in noncoding regions = 69
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


Motif number 4

          **********

No masking
Map Score:   1.37435e-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:   1.37435e-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:   1.37435e-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