AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i191_dna_gyrase_bbur_reg_300.orf -o191_borburg_300.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	RBB00694	20	3615
#2	RBB00690	187	3615

Motif number 1

          TTTATAAAGCAAGGATTTAG      	1	1	1	TTTAAGCAAT	    0.993403	-20
CTAAAAAAATTTTACATTTCTAGTATGAAAACGAAT	2	48	0	TTTATTCAAT	    0.994102	-140
ATGTAAAATTTTTTTAGTTCTATAATACTTAAGCGT	2	67	1	TTTATTCAAT	      0.9821	-121
AAGTTAGATATTTCAATTGCAATAATTTTTCAATTG	2	110	1	TTTATGCAAT	    0.997143	-78
TGCAATAATTTTTCAATTGTGATAATTTAGTAGTTA	2	127	1	TTTATGTAAT	      0.9916	-61
TTGTGATAATTTAGTAGTTAAATTATTAGTATGCTT	2	143	1	TTAATTAAAT	    0.870163	-45
 AAAACAACCTTTAATAAGTAAGCATACTAATAATT	2	163	0	TTTTAGTAAT	     0.91425	-25
          ***  * *** *  **

Masking position 12
Map Score:   9.00307

Number of sites scoring better than the average of aligned sites = 249
Number in coding regions = 184
Number in noncoding regions = 65
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 2

ACTAAAAAAATTTTACATTTCTAGTATGAAA	2	54	0	TTTTACATTC	     0.98858	-134
AATGTAAAATTTTTTTAGTTCTATAATACTT	2	66	1	TTTTTTATTC	    0.982159	-122
TTAAGTTAGATATTTCAATTGCAATAATTTT	2	108	1	TATTTCATTG	    0.988416	-80
ATTGCAATAATTTTTCAATTGTGATAATTTA	2	125	1	TTTTTCATTG	    0.995437	-63
          ******* ***

Masking position 7
Map Score:   3.50205

Number of sites scoring better than the average of aligned sites = 75
Number in coding regions = 52
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

CTAAATCCTTGCTTTATAAA          	1	1	0	GCTTTATAAA	    0.946052	-20
ATCTCATTCTCCTTTTTTATCCATAGCGAT	2	20	1	CCTTTTTTAT	    0.893654	-168
TAAGCTATACGCTTAAGTATTATAGAACTA	2	81	0	GCTTAAGTAT	    0.977515	-107
TAAGCGTATAGCTTAAGTTAGATATTTCAA	2	96	1	GCTTAAGTTA	    0.949833	-92
   AAAACAACCTTTAATAAGTAAGCATAC	2	171	0	CCTTTAATAA	    0.957377	-17
          **********

Masking position 4
Map Score:   0.505727

Number of sites scoring better than the average of aligned sites = 410
Number in coding regions = 254
Number in noncoding regions = 156
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 4

          **********

No masking
Map Score:   -2.59896e-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:   -2.59896e-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:   -2.59896e-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