AlignACE version 2.2  July 7, 1998
alignACE -aORF_aful.txt -zaful.fna -icoldbox_aful_opreg_300.orf -g0.49 -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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	AF2253	78	molybdopterin-guanine dinucleotide biosynthesis protein B (mobB)
#2	AF2254	207	ATP-dependent RNA helicase, DEAD-family (deaD)

Motif number 1

TTAATCTCAAAAGATTTAAACCTCTCCGCATGACGGGA	1	15	0	AATAACTTCG	     0.99764	-64
GATTAAACAAAAGTTAAAAAACTTCCTGGGTTTTCAGA	1	47	1	AATAACTCCG	    0.993572	-32
CTTAATTTTAACTTTACAAAACTTTCACCATGAAAAAG	2	15	0	ACTAACTTCC	    0.987773	-193
ATGCAAATTAAACTTCTAAACATGTCTGAACGCTAGAG	2	81	0	AATAAATTCG	    0.984939	-127
TGAATCCCTCAATCTTCGACTCTCTCCGAGATGCAAAT	2	111	0	AATACCTTCG	    0.997155	-97
ACAGAACAGCAACGTTCCACTCTATCTCCCAACGCTTG	2	174	0	AATACCTTCC	     0.99457	-34
          **  *   ** ** ** *

Masking position 9
Map Score:   6.98346

Number of sites scoring better than the average of aligned sites = 64
Number in coding regions = 54
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 2

AAAGATTTAAACCTCTCCGCATGACGGGAT	1	14	0	ACCTCTCCGC	    0.980919	-65
         AACCTCTGAAAACCCAGGAAG	1	68	0	ACCTCTGAAA	    0.972672	-11
ACTTCTAAACATGTCTGAACGCTAGAGTCT	2	78	0	ATGTCTGAAC	     0.94372	-130
TTTAATTTGCATCTCGGAGAGAGTCGAAGA	2	107	1	ATCTCGGAGA	    0.928628	-101
CTTTGTTTGAATCCCTCAATCTTCGACTCT	2	126	0	ATCCCTCAAT	    0.936588	-82
AGACTTATATACCCTTCAGCCAAGCGTTGG	2	154	1	ACCCTTCAGC	    0.935829	-54
GTTCCACTCTATCTCCCAACGCTTGGCTGA	2	169	0	ATCTCCCAAC	    0.976686	-39
          **********

Masking position 1
Map Score:   2.3729

Number of sites scoring better than the average of aligned sites = 1697
Number in coding regions = 1599
Number in noncoding regions = 98
Number of orfs with sites within 600 bp upstream = 80
Fraction of orfs with sites within 600 bp upstream = 0.0128493


Motif number 3

GTTTAATCTCAAAAGATTTAAACCTCTCCG	1	25	0	AAAAGATTTA	    0.956007	-54
GAGATTAAACAAAAGTTAAAAAACTTCCTG	1	45	1	AAAAGTTAAA	    0.944977	-34
GAAAGTTTTGTAAAGTTAAAATTAAGGAGT	2	27	1	TAAAGTTAAA	    0.871677	-181
AGACATGTTTAGAAGTTTAATTTGCATCTC	2	92	1	AGAAGTTTAA	    0.963714	-116
CGGAGAGAGTCGAAGATTGAGGGATTCAAA	2	121	1	CGAAGATTGA	    0.943881	-87
GGGATTCAAACAAAGACTTATATACCCTTC	2	141	1	CAAAGACTTA	    0.898191	-67
          **********

Masking position 4
Map Score:   1.52707

Number of sites scoring better than the average of aligned sites = 324
Number in coding regions = 221
Number in noncoding regions = 103
Number of orfs with sites within 600 bp upstream = 120
Fraction of orfs with sites within 600 bp upstream = 0.019274


Motif number 4

AGATTTAAACCTCTCCGCATGACGGGATTGT 	1	10	0	CTCCGCATGA	     0.97845	-69
CTTTACAAAACTTTCACCATGAAAAAGAGTT 	2	10	0	CTTCCCATGA	    0.985597	-198
ATTCGCCCGATTTGAGCCGAGACTCTAGCGTT	2	59	1	TTTACCGAGA	    0.967162	-149
CTAAACATGTCTGAACGCTAGAGTCTCGGCTC	2	72	0	CTGAGCTAGA	    0.907401	-136
CAATCTTCGACTCTCTCCGAGATGCAAATTAA	2	108	0	CTCCCCGAGA	    0.995147	-100
GATTGAGGGATTCAAACAAAGACTTATATACC	2	135	1	TTCACAAAGA	    0.878748	-73
CTTATATACCCTTCAGCCAAGCGTTGGGAGAT	2	157	1	CTTACCAAGC	    0.975656	-51
          *** * ******

Masking position 2
Map Score:   2.34239

Number of sites scoring better than the average of aligned sites = 623
Number in coding regions = 577
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 5

          **********

No masking
Map Score:   1.09013e-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 6

          **********

No masking
Map Score:   1.09013e-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 7

          **********

No masking
Map Score:   1.09013e-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