AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i207_holliday_junction_mtub_reg_300.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

AATTTACCATCGCACGTTCCATAGGCGTGT	1	18	1	CGCACGTTCC	    0.958956	-91
CGACATCCCGCGCAGGACACGCCTATGGAA	1	34	0	CGCAGGACAC	    0.992813	-75
GCGGGATGTCGGGACGATCCGCTAGCGTAT	1	53	1	GGGACGATCC	     0.58881	-56
TCCGAACAATCGTTCGATACGCTAGCGGAT	1	69	0	CGTTCGATAC	    0.987013	-40
          CGCACGCTCCCTCAGCCATT	1	99	0	CGCACGCTCC	    0.996199	-10
          **********

Masking position 6
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

CCTATGGAACGTGCGATGGTAAATTTCCTA	1	13	0	GTGCGATGGT	    0.988207	-96
GCGCAGGACACGCCTATGGAACGTGCGATG	1	25	0	CGCCTATGGA	    0.987205	-84
TAGGCGTGTCCTGCGCGGGATGTCGGGACG	1	39	1	CTGCGCGGGA	    0.988557	-70
TCGGGACGATCCGCTAGCGTATCGAACGAT	1	61	1	CCGCTAGCGT	    0.813232	-48
GTTCGGAAATGGCTGAGGGAGCGTGCG   	1	92	1	GGCTGAGGGA	    0.981791	-17
          **********

Masking position 9
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	    0.992728	-108
TTCCATAGGCGTGTCCTGCGCGGGATGTCG	1	34	1	GTGTCCTGCG	    0.986269	-75
CCTGCGCGGGATGTCGGGACGATCCGCTAG	1	48	1	ATGTCGGGAC	    0.991701	-61
TCCCTCAGCCATTTCCGAACAATCGTTCGA	1	82	0	ATTTCCGAAC	    0.992263	-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