AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i211_transcription_translation_bbur_reg_300.orf -o211_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	RBB00509	60	3615
#2	RBB00508	79	3615
#3	RBB00505	32	3615
#4	RBB00504	148	3615

Motif number 1

TTTAATTTACATTAGAAATAATGTCAATTTAT	1	11	0	ATTAAAAAAT	    0.912649	-50
CTTCCTCTTAATCTTCAATAAAGTTTAATTTA	1	34	0	ATCTCAAAAA	     0.95571	-27
CTTATTATTAATTAATAAAAAACACTGACC  	2	9	0	ATTATAAAAA	      0.8933	-71
TAAGAAAGGATTTTATAAAAATCTACTTATTA	2	34	0	TTTTTAAAAT	    0.538841	-46
TACGAATTAAATTTTTAAGAAAGGATTTTATA	2	49	0	ATTTTAAAAA	     0.80948	-31
CTCTAATAAAATCAAAAAGAAAT         	3	2	0	ATCAAAAAAA	    0.968054	-31
   AGCCTAAACCTCTAATAAAATCAAAAAGA	3	14	0	ACCTTAAAAA	    0.910126	-19
TGTTACTAATAATAGTAAAAAAGAGGAAAA  	4	9	0	AATATAAAAA	    0.940076	-140
TTTTACTATTATTAGTAACATAATGGTGTAAT	4	21	1	ATTATAAATA	    0.902517	-128
ATTTAACATTATCATTAATAATTTTATATGAT	4	55	1	ATCATAAAAT	    0.678641	-94
TCCAAAAAATAATACAAAAAAATTAATACTAT	4	85	0	AATAAAAAAA	    0.901077	-64
TAAGCATAACTTTTCCAAAAAATAATACAAAA	4	98	0	TTTTCAAAAA	    0.859032	-51
          **** *** ***

Masking position 7
Map Score:   16.1267

Number of sites scoring better than the average of aligned sites = 2076
Number in coding regions = 1339
Number in noncoding regions = 737
Number of orfs with sites within 600 bp upstream = 127
Fraction of orfs with sites within 600 bp upstream = 0.0203983


Motif number 2

       ATAAATTGACATTATTTCTAATGT	1	4	1	AATTACATTA	    0.974282	-57
AATAAAGTTTAATTTACATTAGAAATAATGT	1	19	0	AATTACATTA	    0.974486	-42
GTTTTTTATTAATTAATAATAAGTAGATTTT	2	18	1	AATTATAATA	    0.971072	-62
TTAAGAAAGGATTTTATAAAAATCTACTTAT	2	36	0	ATTTATAAAA	    0.902623	-44
CTACGAATTAAATTTTTAAGAAAGGATTTTA	2	51	0	AATTTTAAGA	    0.877299	-29
TTTCTTTTTGATTTTATTAGAGGTTTAGGCT	3	12	1	ATTTATTAGA	    0.853165	-21
GGTGTAATATATTTAACATTATCATTAATAA	4	45	1	ATTTACATTA	    0.968702	-104
ATCATTAATAATTTTATATGATAGTATTAAT	4	65	1	ATTTATATGA	    0.973585	-84
AATACAAAAAAATTAATACTATCATATAAAA	4	76	0	AATTATACTA	    0.954018	-73
          **** ******

Masking position 4
Map Score:   11.0994

Number of sites scoring better than the average of aligned sites = 598
Number in coding regions = 334
Number in noncoding regions = 264
Number of orfs with sites within 600 bp upstream = 72
Fraction of orfs with sites within 600 bp upstream = 0.0115644


Motif number 3

ATTGAAGATTAAGAGGAAGGTTTT      	1	47	1	AAGAGGAAGG	    0.992296	-14
ATTTAATTCGTAGAGGAAAAT         	2	69	1	TAGAGGAAAA	    0.987731	-11
AATAGTAAAAAAGAGGAAAA          	4	1	0	AAGAGGAAAA	    0.996239	-148
TGTTACTAATAATAGTAAAAAAGAGGAAAA	4	11	0	AATAGTAAAA	    0.957495	-138
TAGGTATTTAAAGAGTAAAGGGGATT    	4	133	1	AAGAGTAAAG	    0.992182	-16
          **********

Masking position 4
Map Score:   8.42401

Number of sites scoring better than the average of aligned sites = 101
Number in coding regions = 68
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

          **********

No masking
Map Score:   7.69818e-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:   7.69818e-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:   7.69818e-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