AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00040_bbur_reg_100.orf -o00040_bbur_100.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -x5 -e 
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 =  	0.28
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	BB0207	52	UTP--glucose-1-phosphate uridylyltransferase (gtaB)
#2	BB0544	202	phosphoribosyl pyrophosphate synthetase (prs)

Motif number 1

       TGAATATATAAAATTAAATTTTT	1	4	1	ATATATAAAA	     0.95194	-49
AAATAAGATTATAGCAAAAATTTAATTTTA	1	19	0	ATAGCAAAAA	    0.960867	-34
ACATAATCCTAAAAATAAAATTAAATAAA 	2	10	0	AAAAATAAAA	    0.968954	-193
AGCAAAAACAAATACTATAACATAATCCTA	2	29	0	AATACTATAA	    0.880578	-174
AATTCTATTAATAGCAAAAACAAATACTAT	2	41	0	ATAGCAAAAA	    0.960867	-162
ATAAAAATAAAAATCTAAAAATTCTATTAA	2	60	0	AAATCTAAAA	    0.981462	-143
TTTTAGCTTTAATAATAAAAATAAAAATCT	2	74	0	AATAATAAAA	    0.955161	-129
TTTTATTATTAAAGCTAAAATATTTTAATG	2	84	1	AAAGCTAAAA	    0.988134	-119
ACACACAAATATGACTAAAATTTTTTAAAG	2	120	0	ATGACTAAAA	    0.968813	-83
TAATTTACTAATTAATAAAACTTATACACA	2	145	0	ATTAATAAAA	    0.960584	-58
ATTGTTAAGATTTTCTAAAAAAGAACGAGG	2	177	1	TTTTCTAAAA	    0.795961	-26
          **********

Masking position 7
Map Score:   18.7684

Number of sites scoring better than the average of aligned sites = 1280
Number in coding regions = 815
Number in noncoding regions = 465
Number of orfs with sites within 600 bp upstream = 87
Fraction of orfs with sites within 600 bp upstream = 0.0139737


Motif number 2

TGAATATATAAAATTAAATTTTTGCTATAA	1	11	1	AAATTAAATT	    0.891739	-42
TTTCTCTCTTAAAATAAGATTATAGCAAAA	1	30	0	AAAATAAGAT	    0.984821	-23
CATAATCCTAAAAATAAAATTAAATAAA  	2	9	0	AAAATAAAAT	    0.987351	-194
ATTAATAGCAAAAACAAATACTATAACATA	2	35	0	AAAACAAATA	    0.892767	-168
TTTAATAATAAAAATAAAAATCTAAAAATT	2	67	0	AAAATAAAAA	    0.976995	-136
ATTAATTAGTAAATTAAGATTGTTAAGATT	2	159	1	AAATTAAGAT	     0.96858	-44
          **********

Masking position 6
Map Score:   8.81805

Number of sites scoring better than the average of aligned sites = 1050
Number in coding regions = 679
Number in noncoding regions = 371
Number of orfs with sites within 600 bp upstream = 109
Fraction of orfs with sites within 600 bp upstream = 0.0175072


Motif number 3

AAAATTTAATTTTATATATTCA        	1	3	0	TTTATATATT	    0.737987	-50
ATATATAAAATTAAATTTTTGCTATAATCT	1	14	1	TTAAATTTTT	    0.912844	-39
CTCTCTTAAAATAAGATTATAGCAAAAATT	1	27	0	ATAAGATTAT	    0.762638	-26
     TTTATTTAATTTTATTTTTAGGATT	2	6	1	TTAATTTTAT	    0.701267	-197
AATTTTATTTTTAGGATTATGTTATAGTAT	2	18	1	TTAGGATTAT	    0.936862	-185
TTTGCTATTAATAGAATTTTTAGATTTTTA	2	53	1	ATAGAATTTT	    0.882189	-150
AGCAAGGTCATTAAAATATTTTAGCTTTAA	2	92	0	TTAAAATATT	    0.962969	-111
TGACCTTGCTTTAAAAAATTTTAGTCATAT	2	112	1	TTAAAAAATT	    0.878846	-91
GTTTTATTAATTAGTAAATTAAGATTGTTA	2	154	1	TTAGTAAATT	    0.798658	-49
ATTAAGATTGTTAAGATTTTCTAAAAAAGA	2	171	1	TTAAGATTTT	    0.978664	-32
          **********

Masking position 2
Map Score:   9.32309

Number of sites scoring better than the average of aligned sites = 3227
Number in coding regions = 2100
Number in noncoding regions = 1127
Number of orfs with sites within 600 bp upstream = 190
Fraction of orfs with sites within 600 bp upstream = 0.0305172


Motif number 4

          **********

No masking
Map Score:   -2.39152e-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:   -2.39152e-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:   -2.39152e-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