AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i103_Ferrous_Iron_Transporter_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	ideR	132	ideR

Motif number 1

CCGCCGCTGGCGCGGCGGGCATACCGTCTG	1	35	0	CGCGGCGGGC	    0.996664	-98
CCGCCGCGCCAGCGGCGGGCATACCGCTGC	1	47	1	AGCGGCGGGC	    0.996196	-86
GCCGCCCCACCGCAGCGGTATGCCCGCCGC	1	58	0	CGCAGCGGTA	     0.99348	-75
GCTGCGGTGGGGCGGCGGGCAACCATTTTC	1	72	1	GGCGGCGGGC	    0.937021	-61
CAACCATTTTCGCAGCTGGCCAAGTAGACT	1	91	1	CGCAGCTGGC	    0.829296	-42
GCCAAGTAGACTCAGCTGCAATGGAGGGTG	1	109	1	CTCAGCTGCA	    0.839045	-24
          **********

Masking position 5
Map Score:   21.8191

Number of sites scoring better than the average of aligned sites = 2937
Number in coding regions = 2736
Number in noncoding regions = 201
Number of orfs with sites within 600 bp upstream = 173
Fraction of orfs with sites within 600 bp upstream = 0.0277867


Motif number 2

GGTAGCAGACGGTATGCCCGCCGCGCCAGC	1	30	1	GGTATGCCCG	    0.997833	-103
GTATGCCCGCCGCTGGCGCGGCGGGCATAC	1	41	0	CGCTGGCGCG	    0.992057	-92
CCACCGCAGCGGTATGCCCGCCGCTGGCGC	1	52	0	GGTATGCCCG	    0.997833	-81
CATACCGCTGCGGTGGGGCGGCGGGCAACC	1	66	1	CGGTGGGGCG	    0.987407	-67
GCTGCGAAAATGGTTGCCCGCCGCCCCACC	1	77	0	TGGTTGCCCG	    0.996824	-56
          **********

Masking position 6
Map Score:   10.1734

Number of sites scoring better than the average of aligned sites = 2667
Number in coding regions = 2461
Number in noncoding regions = 206
Number of orfs with sites within 600 bp upstream = 191
Fraction of orfs with sites within 600 bp upstream = 0.0306778


Motif number 3

CATACCGTCTGCTACCTGGCTCAGGATGTC	1	16	0	GCTACCTGGC	    0.772679	-117
GCGGTATGCCCGCCGCTGGCGCGGCGGGCA	1	44	0	CGCCGCTGGC	    0.973227	-89
GTTGCCCGCCGCCCCACCGCAGCGGTATGC	1	65	0	GCCCCACCGC	      0.9846	-68
TGCAGCTGAGTCTACTTGGCCAGCTGCGAA	1	99	0	TCTACTTGGC	    0.969584	-34
   TCAGCACCCTCCATTGCAGCTGAGTCT	1	116	0	CCTCCATTGC	    0.989492	-17
          **********

Masking position 9
Map Score:   1.69926

Number of sites scoring better than the average of aligned sites = 5378
Number in coding regions = 4961
Number in noncoding regions = 417
Number of orfs with sites within 600 bp upstream = 364
Fraction of orfs with sites within 600 bp upstream = 0.0584645


Motif number 4

          **********

No masking
Map Score:   5.21701e-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:   5.21701e-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 6

          **********

No masking
Map Score:   5.21701e-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