AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i255_heat_shock_bbur_reg_300.orf -o255_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	RBB00234	23	3615
#2	RBB00232	158	3615
#3	RBB00836	101	3615
#4	RBB00107	107	3615

Motif number 1

ATAGTGTTATATTGATACATATTGTTAT    	2	7	0	ATTATAATAT	    0.900887	-152
ATTTTGAGCATTTGTAAGATGTATATTTTTCT	2	52	0	TTTTAAATGT	    0.970187	-107
ATGAATCAATTTTATTAAATTTCAAGAAAGAA	2	82	1	TTTTTAATTT	    0.974289	-77
AAGAAAAAAATTTGTAAAATATTTTTTTTAAA	2	109	1	TTTTAAATAT	    0.990632	-50
GTAAAATATTTTTTTTAAAGATAAAATGCTTT	2	122	1	TTTTTAAGAT	    0.936833	-37
TATTAGGGTATTTTTAAAATATGGGTGAGTAT	3	74	0	TTTTAAATAT	    0.990604	-28
  AATTGGTCTTTTAAAAATTTAGGTTTAATT	4	9	1	TTTAAAATTT	    0.939105	-99
TTTAGGTTTAATTATAACATATATAAAGTATA	4	28	1	ATTTAAATAT	    0.979545	-80
TTTTAAATATATTTTAATATTTATACTTTATA	4	49	0	ATTTAAATTT	    0.961709	-59
ATTTATTGTATTTTTTAAATATATTTTAATAT	4	61	0	TTTTTAATAT	    0.985377	-47
          *** *** ****

Masking position 7
Map Score:   18.8584

Number of sites scoring better than the average of aligned sites = 722
Number in coding regions = 435
Number in noncoding regions = 287
Number of orfs with sites within 600 bp upstream = 69
Fraction of orfs with sites within 600 bp upstream = 0.0110826


Motif number 2

AATATGTATCAATATAACACTATTACTGAAAG	2	16	1	AAATAACCTA	     0.85039	-143
CTGAAAGCTTAAGAAAAATATACATCTTACAA	2	41	1	AAAAAAAATA	     0.98263	-118
AATTTCAAGAAAGAAAAAAATTTGTAAAATAT	2	99	1	AAAAAAAATT	    0.970503	-60
TTTTATCTTTAAAAAAAATATTTTACAAATTT	2	116	0	AAAAAAAATT	    0.969356	-43
AATAATAAGCAATAATACATTAAATTACAACA	3	16	1	AAAATACTTA	    0.908821	-86
ATTAAATTACAACAAAAAAATTAATAGCTTGG	3	34	1	AAAAAAAATT	     0.97106	-68
ATAGCTTGGCAAAAATAATACTCACCCATATT	3	57	1	AAAATAAACT	    0.881076	-45
CCCATATTTTAAAAATACCCTAATATTAAAG 	3	81	1	AAAATACCTA	    0.964589	-21
ATTTAGGTTTAATTATAACATATATAAAGTAT	4	27	1	AATATAAATA	    0.895622	-81
ATAAAGTATAAATATTAAAATATATTTAAAAA	4	50	1	AAATTAAATA	    0.913437	-58
AATATATTTAAAAAATACAATAAATAAGGTAG	4	68	1	AAAATACATA	    0.984433	-40
          ** ***** ***

Masking position 7
Map Score:   15.3801

Number of sites scoring better than the average of aligned sites = 1203
Number in coding regions = 766
Number in noncoding regions = 437
Number of orfs with sites within 600 bp upstream = 86
Fraction of orfs with sites within 600 bp upstream = 0.013813


Motif number 3

     ATTATAAACCTCCTTTTTTCTAA  	1	9	0	AAACCTCCTT	    0.959392	-15
GTAAGATGTATATTTTTCTTAAGCTTTCAG	2	41	0	TATTTTTCTT	    0.890072	-118
TACAAATTTTTTTCTTTCTTGAAATTTAAT	2	95	0	TTTCTTTCTT	    0.927761	-64
TTGATAAAGCATTTTATCTTTAAAAAAAAT	2	129	0	ATTTTATCTT	    0.778875	-30
         TTTTCCTCCTTTGATAAAGCA	2	148	0	TTTCCTCCTT	    0.969726	-11
AATCTCCTTCAATCTACCTTATTTATTGTA	4	83	0	AATCTACCTT	    0.951314	-25
      TAAAAAATCTCCTTCAATCTACCT	4	94	0	AAATCTCCTT	    0.919609	-14
          **********

Masking position 9
Map Score:   4.02072

Number of sites scoring better than the average of aligned sites = 491
Number in coding regions = 323
Number in noncoding regions = 168
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 4

          **********

No masking
Map Score:   4.92707e-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:   4.92707e-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:   4.92707e-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