AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -ifis_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	secD	109	secD

Motif number 1

   CCGGCAACCGGCCGACCGGAACCGACG	1	8	1	CCGGCCGACC	    0.998228	-102
CCGACCGGAACCGACGAGCCGCTTGCGCGA	1	22	1	CCGACGAGCC	    0.999129	-88
AGCCGCTTGCGCGACGCGCCCCGGCGCGAC	1	38	1	GCGACGCGCC	    0.996401	-72
GCGACGCGCCCCGGCGCGACACGTAGGCTC	1	48	1	CCGGCGCGAC	    0.997784	-62
TTTTCTACCCCCGACAGAGCCTACGTGTCG	1	64	0	CCGACAGAGC	    0.992448	-46
          **********

Masking position 5
Map Score:   11.2941

Number of sites scoring better than the average of aligned sites = 5079
Number in coding regions = 4687
Number in noncoding regions = 392
Number of orfs with sites within 600 bp upstream = 286
Fraction of orfs with sites within 600 bp upstream = 0.0459364


Motif number 2

          CCGGCAACCGGCCGACCGGA	1	1	1	CCGGCAACCG	    0.980286	-109
CAACCGGCCGACCGGAACCGACGAGCCGCT	1	15	1	ACCGGAACCG	    0.995476	-95
CGGGGCGCGTCGCGCAAGCGGCTCGTCGGT	1	31	0	CGCGCAAGCG	    0.765955	-79
ACGTGTCGCGCCGGGGCGCGTCGCGCAAGC	1	42	0	CCGGGGCGCG	    0.674224	-68
CAGTTTTCTACCCCCGACAGAGCCTACGTG	1	67	0	CCCCCGACAG	    0.984381	-43
          **********

Masking position 10
Map Score:   8.22508

Number of sites scoring better than the average of aligned sites = 6075
Number in coding regions = 5582
Number in noncoding regions = 493
Number of orfs with sites within 600 bp upstream = 416
Fraction of orfs with sites within 600 bp upstream = 0.0668166


Motif number 3

          **********

No masking
Map Score:   1.16119e-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:   1.16119e-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:   1.16119e-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