AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i225_Glutamyl_tRNA_synthase_bbur_reg_300.orf -o225_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	RBB00398	183	3615

Motif number 1

TGTTTATATCTAAGCTTTAAATTTTTATTTTA	1	29	1	TAAGCTTAAT	    0.989308	-155
TTTTATGTATTAAACTAGTACTATTAATAATA	1	56	1	TAAACTGTAT	    0.988687	-128
ATCATGGAAATAAACTATTATTAATAGTACTA	1	71	0	TAAACTTTAT	    0.996748	-113
TTATTGTCAATAAACTTTATTTCCATAATACT	1	107	0	TAAACTTATT	    0.983552	-77
AAACTACATTTAAACTATTTATTGTCAATAAA	1	125	0	TAAACTTTTT	    0.992667	-59
TTATTAAGCTTAAGCTATTAACAAAACTACAT	1	148	0	TAAGCTTTAC	     0.98495	-36
      TCTATGAACTCTTATTATTAAGCTTA	1	168	0	TGAACTTTAT	    0.989819	-16
          ****** *** *

Masking position 3
Map Score:   14.167

Number of sites scoring better than the average of aligned sites = 112
Number in coding regions = 66
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

GGAAATAAACTATTATTAATAGTACTAGTTT	1	67	0	TTTATTAATA	    0.562859	-117
ATACTACATATCATGGAAATAAACTATTATT	1	81	0	TATGGAAATA	    0.971521	-103
ATATGTAGTATTATGGAAATAAAGTTTATTG	1	101	1	TATGGAAATA	    0.971521	-83
TTAAACTATTTATTGTCAATAAACTTTATTT	1	117	0	TTTGTCAATA	    0.539592	-67
TTAAATGTAGTTTTGTTAATAGCTTAAGCTT	1	144	1	TTTGTTAATA	    0.919498	-40
 TCTATGAACTCTTATTATTAAGCTTAAGCT	1	164	0	TTTATTATTA	    0.849412	-20
          * *********

Masking position 4
Map Score:   7.48246

Number of sites scoring better than the average of aligned sites = 259
Number in coding regions = 183
Number in noncoding regions = 76
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

TATTAATAATAGTTTATTTCCATGATATGT	1	77	1	AGTTTATTTC	    0.974864	-107
TTTCCATAATACTACATATCATGGAAATAA	1	90	0	ACTACATATC	     0.98448	-94
TTGTCAATAAACTTTATTTCCATAATACTA	1	106	0	ACTTTATTTC	    0.990471	-78
TATTAACAAAACTACATTTAAACTATTTAT	1	135	0	ACTACATTTA	     0.97589	-49
          **********

Masking position 6
Map Score:   3.5026

Number of sites scoring better than the average of aligned sites = 20
Number in coding regions = 13
Number in noncoding regions = 7
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:   4.00336e-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:   4.00336e-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:   4.00336e-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