AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i115_Glycine_Transport_bbur_reg_300.orf -o115_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	RBB00590	153	3615
#2	RBB00589	50	3615

Motif number 1

CTTTTGTTAATACAATTTATACCAATTAAACTA	1	16	0	TAAATATACC	    0.947636	-138
AAATTGTATTAACAAAAGATCCTTTAAAGGATC	1	31	1	AAAAAATCCT	    0.986086	-123
GAAATAAAAAAACAAAAGATCCTTTAAAGGATC	1	48	0	AAAAAATCCT	    0.986086	-106
CAGATCGGCAAAAATTTAATAATTTTAGTATAA	1	80	1	AAATTATAAT	    0.902442	-74
AACACATCATTATAAATTATACTAAAATTATTA	1	96	0	TAAATATACT	    0.983222	-58
CATTATGCTTTATAACACATCATTATAAATTAT	1	109	0	TAAAAATCAT	    0.978263	-45
GTCAGAAATTTAAATTTTATCATGGAGGAATGA	2	25	1	TAATTATCAT	    0.962258	-26
          ** ** * *****

Masking position 9
Map Score:   6.77035

Number of sites scoring better than the average of aligned sites = 385
Number in coding regions = 249
Number in noncoding regions = 136
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 2

ATACCAATTAAACTAGAATT          	1	1	0	AACTAGAATT	    0.957093	-153
TAATTGGTATAAATTGTATTAACAAAAGAT	1	21	1	AAATTGTATT	    0.916202	-133
TTATAAATTATACTAAAATTATTAAATTTT	1	90	0	TACTAAAATT	    0.895772	-64
ATTTTAGTATAATTTATAATGATGTGTTAT	1	101	1	AATTTATAAT	    0.789504	-53
CAAAGTCAGAAATTTAAATTTTATCATGGA	2	21	1	AATTTAAATT	    0.499432	-30
          **********

Masking position 4
Map Score:   0.676675

Number of sites scoring better than the average of aligned sites = 806
Number in coding regions = 506
Number in noncoding regions = 300
Number of orfs with sites within 600 bp upstream = 69
Fraction of orfs with sites within 600 bp upstream = 0.0110826


Motif number 3

TTATAAAGCATAATGCAGGCTTATTGAGGA	1	127	1	TAATGCAGGC	    0.983282	-27
TAATGCAGGCTTATTGAGGAGTTTGCT   	1	137	1	TTATTGAGGA	    0.983892	-17
TTAAATTTTATCATGGAGGAATGATAT   	2	34	1	TCATGGAGGA	    0.936796	-17
          **********

Masking position 7
Map Score:   0.340328

Number of sites scoring better than the average of aligned sites = 20
Number in coding regions = 12
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

TATAAATTGTATTAACAAAAGATCCTTTAAA	1	28	1	ATTACAAAAG	    0.990801	-126
TCTGAAATAAAAAAACAAAAGATCCTTTAAA	1	53	0	AAAACAAAAG	    0.960355	-101
TTTATTTCAGATCGGCAAAAATTTAATAATT	1	73	1	ATCGCAAAAA	    0.972457	-81
      AAGGATTTGCCAAAGTCAGAAATTT	2	5	1	ATTGCCAAAG	    0.971754	-46
          *** *******

Masking position 8
Map Score:   0.104971

Number of sites scoring better than the average of aligned sites = 143
Number in coding regions = 100
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 5

          **********

No masking
Map Score:   3.15071e-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:   3.15071e-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 7

          **********

No masking
Map Score:   3.15071e-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