AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i010_Nucleotide_Metabolism_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	yrvI	92	similar to hypothetical proteins
#2	relA	167	GTP pyrophosphokinase
#3	yrvE	66	similar to single-strand DNA-specific exonuclease
#4	yrvD	75	yrvD
#5	yrvC	157	yrvC

Motif number 1

ACCCTGACATGGAGTGCTTTTTCGTTATGCG	2	18	0	GGAGTGTTTT	    0.966487	-150
ACTCCATGTCAGGGTGCTTTTTTCCTATTGT	2	34	1	AGGGTGTTTT	    0.993409	-134
GAAACCCCTCAGCCTGCTCTAGTATAATAGG	3	27	1	AGCCTGTCTA	    0.922658	-40
CTAGTATAATAGGGTGGTTGAGGGGTGAATT	3	45	1	AGGGTGTTGA	    0.917546	-22
GGGTGGTTGAGGGGTGAATTT          	3	56	1	GGGGTGATTT	    0.930816	-11
TTCCCAATCAAGACTGGTTTTAAACATGGCT	4	21	0	AGACTGTTTT	    0.984395	-55
TGCAGAGGACAGCCTGATATTTT        	5	3	0	AGCCTGTATT	    0.962223	-155
TCTGCAGGGCAGCCTGTTTTTTGAAGTTTCA	5	28	1	AGCCTGTTTT	    0.993014	-130
AAAGTGTTTATGGCTGGTTTTCAGATATGTA	5	124	1	TGGCTGTTTT	    0.974848	-34
          ****** ****

Masking position 5
Map Score:   11.1803

Number of sites scoring better than the average of aligned sites = 747
Number in coding regions = 611
Number in noncoding regions = 136
Number of orfs with sites within 600 bp upstream = 107
Fraction of orfs with sites within 600 bp upstream = 0.017186


Motif number 2

         AGGGGTTAGAAAAGAGATTAGTTG	1	2	1	GGTTAGAAAG	    0.982002	-91
GTAAAGAGCAGAAGTTCAAATAGCCAAATATTA	2	82	0	GATTCAAAAG	    0.982623	-86
ATACAGTTTACATTTTAAAAAAGGTGATTCC  	2	147	1	CATTAAAAAG	    0.908631	-21
GCAGGCTGAGGGGTTTCAAATAATATTCGAAAA	3	11	0	GGTTCAAAAA	    0.939293	-56
AATCAAGACTGGTTTTAAACATGGCTTAACACT	4	14	0	GGTTAAACTG	    0.957926	-62
AAGTTTCATTGAACTTAAAATAGACATTTGCTA	5	51	1	GATTAAAAAG	     0.98843	-107
ACATATATATGGTGTTAAAAGTGTTTATGGCTG	5	107	1	GGTTAAAATG	     0.98668	-51
          **  ****** **

Masking position 9
Map Score:   4.58273

Number of sites scoring better than the average of aligned sites = 502
Number in coding regions = 444
Number in noncoding regions = 58
Number of orfs with sites within 600 bp upstream = 61
Fraction of orfs with sites within 600 bp upstream = 0.00979762


Motif number 3

CCACTGTAACGCTTGCTTCTGTTACTCGCT	1	38	0	GCTTGCTTCT	    0.953494	-55
TTTCCTATTGTTTTGCATTTATTTTATATA	2	54	1	TTTTGCATTT	    0.935765	-114
AACTTCTGCTCTTTACATCTTTCGTTTTTT	2	99	1	CTTTACATCT	    0.955739	-69
CTACAATACAGTTTACATTTTAAAAAAGGT	2	142	1	GTTTACATTT	    0.981692	-26
AATGACATACGCTTACATTTAAACATATAT	5	85	1	GCTTACATTT	    0.983018	-73
          **********

Masking position 4
Map Score:   1.59962

Number of sites scoring better than the average of aligned sites = 118
Number in coding regions = 88
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 4

TTATTTGAAACCCCTCAGCCTGCTCTAGTA	3	21	1	CCCCTCAGCC	     0.99698	-46
   AAATTCACCCCTCAACCACCCTATTAT	3	50	0	CCCCTCAACC	    0.997462	-17
  TCTCTTTTCCCCCAAACTTCTTATTGAG	4	58	0	CCCCCAAACT	    0.977973	-18
          **********

Masking position 7
Map Score:   1.12688

Number of sites scoring better than the average of aligned sites = 16
Number in coding regions = 14
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 5

          **********

No masking
Map Score:   3.7902e-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:   3.7902e-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:   3.7902e-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