AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -itorR_mtub_opreg_100.orf -g0.656 -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 =  	0.656
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	bisC	106	bisC

Motif number 1

         CGCTGCAGTCTAAAACCTGGT	1	2	1	GCTGCAGTCT	    0.997498	-105
CGCAACGATGGCACCAGGTTTTAGACTGCA	1	14	0	GCACCAGGTT	    0.994934	-93
CGGCAACCTAGCAGCTAGTTGAGCTCAGAA	1	71	0	GCAGCTAGTT	    0.989394	-36
GCAGTCTAGTGCGGCAACCTAGCAGCTAGT	1	82	0	GCGGCAACCT	    0.995483	-25
        TTGCAGCAGTCTAGTGCGGCAA	1	95	0	GCAGCAGTCT	    0.999008	-12
          **********

Masking position 10
Map Score:   10.4689

Number of sites scoring better than the average of aligned sites = 1119
Number in coding regions = 1027
Number in noncoding regions = 92
Number of orfs with sites within 600 bp upstream = 84
Fraction of orfs with sites within 600 bp upstream = 0.0134918


Motif number 2

CCAGGTTTTAGACTGCAGCG          	1	1	0	GACTGCAGCG	    0.900626	-106
GCGTCGCAACGATGGCACCAGGTTTTAGAC	1	18	0	GATGGCACCA	    0.992963	-89
CTAGCTGCTAGGTTGCCGCACTAGACTGCT	1	83	1	GGTTGCCGCA	    0.918314	-24
TGCCGCACTAGACTGCTGCAA         	1	96	1	GACTGCTGCA	     0.98723	-11
          **********

Masking position 5
Map Score:   6.49666

Number of sites scoring better than the average of aligned sites = 671
Number in coding regions = 618
Number in noncoding regions = 53
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 3

          **********

No masking
Map Score:   1.3033e-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 4

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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