AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i039_Mannose_Metabolism_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	pmmA	101	pmmA

Motif number 1

CCGCGAACGACGCGGGCCGAATCGGTCTCG	1	26	0	CGCGGGCCGA	    0.999874	-76
CCGCGTCGTTCGCGGGCCGATAGGCTGGCG	1	41	1	CGCGGGCCGA	    0.999874	-61
GACTCTTGGCCGCCAGCCTATCGGCCCGCG	1	51	0	CGCCAGCCTA	    0.996525	-51
         GCGCGGGCTCCTGACAACCTA	1	91	0	CGCGGGCTCC	    0.998366	-11
          **********

Masking position 6
Map Score:   12.6063

Number of sites scoring better than the average of aligned sites = 684
Number in coding regions = 623
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 71
Fraction of orfs with sites within 600 bp upstream = 0.0114038


Motif number 2

     TCTTCCCATGCTGTTCGAGACCGATTC	1	6	1	CCAGTGTTCG	    0.997726	-96
ACGACGCGGGCCGAATCGGTCTCGAACAGCAT	1	18	0	CCGACGGTCT	    0.994467	-84
CCGATTCGGCCCGCGTCGTTCGCGGGCCGATA	1	31	1	CCGGCGTTCG	    0.999451	-71
CTCCTGACAACCTAGATTTTCTGCGACTCTTG	1	73	0	CCTGTTTTCT	    0.986387	-29
          *** * ******

Masking position 10
Map Score:   2.7867

Number of sites scoring better than the average of aligned sites = 2473
Number in coding regions = 2344
Number in noncoding regions = 129
Number of orfs with sites within 600 bp upstream = 109
Fraction of orfs with sites within 600 bp upstream = 0.0175072


Motif number 3

          **********

No masking
Map Score:   -1.17788e-14

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:   -1.17788e-14

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:   -1.17788e-14

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