AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i214_Ribosomal_Operon_1_bbur_reg_300.orf -o214_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	RBB00407	19	3615
#2	RBB00406	49	3615
#3	RBB00398	183	3615

Motif number 1

 TACAATGAATGAGATTTATGCATAAAATT	2	10	1	TGAGATTTAT	    0.637923	-40
GATTTATGCATAAAATTATAAAGGGTATAG	2	23	1	TAAAATTATA	    0.638673	-27
TGTTTATATCTAAGCTTTAAATTTTTATTT	3	29	1	TAAGCTTTAA	    0.960841	-155
GTTTAATACATAAAATAAAAATTTAAAGCT	3	41	0	TAAAATAAAA	    0.831321	-143
TTTTATGTATTAAACTAGTACTATTAATAA	3	56	1	TAAACTAGTA	    0.955084	-128
ATCATGGAAATAAACTATTATTAATAGTAC	3	73	0	TAAACTATTA	     0.96546	-111
TTATTGTCAATAAACTTTATTTCCATAATA	3	109	0	TAAACTTTAT	    0.952721	-75
AAACTACATTTAAACTATTTATTGTCAATA	3	127	0	TAAACTATTT	    0.972875	-57
TTATTAAGCTTAAGCTATTAACAAAACTAC	3	150	0	TAAGCTATTA	     0.97273	-34
      TCTATGAACTCTTATTATTAAGCT	3	170	0	TGAACTCTTA	     0.91002	-14
          **********

Masking position 6
Map Score:   12.7514

Number of sites scoring better than the average of aligned sites = 990
Number in coding regions = 615
Number in noncoding regions = 375
Number of orfs with sites within 600 bp upstream = 72
Fraction of orfs with sites within 600 bp upstream = 0.0115644


Motif number 2

TGCATAAATCTCATTCATTGTA          	2	1	0	TCATTATGTA	    0.861223	-49
TGAATGAGATTTATGCATAAAATTATAAAGGG	2	16	1	TTATGAAAAA	    0.982642	-34
AATTTTTATTTTATGTATTAAACTAGTACTAT	3	48	1	TTATGATAAA	    0.958011	-136
AAATAAACTATTATTAATAGTACTAGTTTAAT	3	64	0	TTATTAAGTA	    0.971868	-120
ATACTACATATCATGGAAATAAACTATTATTA	3	80	0	TCATGAATAA	    0.897467	-104
ATATGTAGTATTATGGAAATAAAGTTTATTGA	3	101	1	TTATGAATAA	    0.627761	-83
GAAATAAAGTTTATTGACAATAAATAGTTTAA	3	116	1	TTATTAAATA	    0.974324	-68
TAAGCTTAAGCTATTAACAAAACTACATTTAA	3	144	0	CTATTAAAAA	    0.921591	-40
TGAACTCTTATTATTAAGCTTAAGCTATTAAC	3	158	0	TTATTACTTA	    0.908033	-26
          ***** * ****

Masking position 7
Map Score:   9.91821

Number of sites scoring better than the average of aligned sites = 769
Number in coding regions = 471
Number in noncoding regions = 298
Number of orfs with sites within 600 bp upstream = 71
Fraction of orfs with sites within 600 bp upstream = 0.0114038


Motif number 3

TTTCCATGATATGTAGTATTATGGAAATAA	3	93	1	ATGTAGTATT	    0.987588	-91
AATAGTTTAAATGTAGTTTTGTTAATAGCT	3	138	1	ATGTAGTTTT	    0.987588	-46
       TCTATGAACTCTTATTATTAAGC	3	171	0	ATGAACTCTT	     0.96867	-13
          **********

Masking position 5
Map Score:   0.526995

Number of sites scoring better than the average of aligned sites = 17
Number in coding regions = 9
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

          **********

No masking
Map Score:   -3.30951e-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:   -3.30951e-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:   -3.30951e-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