AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -ioxyR_tpal_opreg_300.orf -g0.528 -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 =  	0.528
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	TP1038	226	bacterioferrin (TpF1)

Motif number 1

CGTAATTCTCAATCCACCAAGCCTCCCAACAA	1	29	0	AATCCCAAGC	    0.936248	-198
GAGAATTACGTCTCCTGGAAAAAAGATTTCGC	1	51	1	TCTCCGAAAA	    0.978915	-176
GGAAAAAAGATTTCGCTGAAACTTCACGAAAT	1	67	1	TTTCGGAAAC	    0.972367	-160
CTTCACGAAATCTCGGTGAAAATAAATGATTA	1	88	1	TCTCGGAAAA	    0.980064	-139
TTATTTTACCAATCGGTGAAAAAAAGCCGGGA	1	117	1	AATCGGAAAA	    0.982502	-110
CGGTGAAAAAAAGCCGGGAAAAGTCCAAAAAG	1	130	1	AAGCCGAAAA	     0.98112	-97
AGCAAAAACCATGCCAACAAAAAATCGAAAGA	1	181	0	ATGCCCAAAA	    0.957006	-46
   CGTTCTTTCTCCTCCAAACTTTAAAGCAA	1	208	0	TCTCCCAAAC	    0.987988	-19
          *****  *****

Masking position 9
Map Score:   10.2727

Number of sites scoring better than the average of aligned sites = 135
Number in coding regions = 118
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

AAGCCTCCCAACAAACCGGTAAGATCATTG	1	13	0	ACAAACCGGT	    0.991501	-214
TGATTATTTTACCAATCGGTGAAAAAAAGC	1	114	1	ACCAATCGGT	     0.91445	-113
ATCGGTGAAAAAAAGCCGGGAAAAGTCCAA	1	128	1	AAAAGCCGGG	    0.994412	-99
GAAAAGTCCAAAAAGACAGTGGTTATGCTC	1	147	1	AAAAGACAGT	    0.949485	-80
ACTTTAAAGCAAAAACCATGCCAACAAAAA	1	190	0	AAAAACCATG	    0.934714	-37
          **********

Masking position 4
Map Score:   1.93006

Number of sites scoring better than the average of aligned sites = 180
Number in coding regions = 163
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

          **********

No masking
Map Score:   3.36387e-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:   3.36387e-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:   3.36387e-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