AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i087_PTS_sugar_Utilization_bbur_reg_100.orf -o087_borburg_100.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

Purged sequences:
RBB00130	81	3615

Input sequences:
#1	RBB00199	138	3615
#2	RBB00198	20	3615
#3	RBB00129	81	3615

Motif number 1

AAATATAGCATAATAAAGATAGTAATTAAAC	1	23	0	TAATAAGATA	     0.93827	-116
TCCCTTTACATAAGAAATATAGCATAATAAA	1	37	0	TAAGAATATA	    0.924575	-102
TTCTTATGTAAAGGGAATATATAATTTATTT	1	52	1	AAGGAATATA	    0.819073	-87
TTTTACATTATAATACATAAAAATAAATTAT	1	72	0	TAATCATAAA	     0.97476	-67
TTATGTATTATAATGTAAAAAGTTAATCAAA	1	83	1	TAATTAAAAA	    0.928262	-56
TGTAAAAAGTTAATCAAAAAAAACAATATTC	1	96	1	TAATAAAAAA	    0.949861	-43
          AAGTACAGAAACCCCTCATTA	1	128	0	AAGTCAGAAA	    0.859793	-11
ATACACTATATAATATATAAAG         	3	2	0	TAATTATAAA	    0.978983	-80
ATATATTATATAGTGTATATACATTTATTAA	3	15	1	TAGTTATATA	    0.945007	-67
TAAATAGTAAAATTTAATAAATGTATATACA	3	28	0	AATTAATAAA	    0.917844	-54
TTATAAAATCAATTAAATAAATAGTAAAATT	3	45	0	AATTAATAAA	    0.917883	-37
TAATCTCCTTTGATTTATAAAATCAATTAAA	3	59	0	TGATTATAAA	    0.888849	-23
          **** ******

Masking position 7
Map Score:   14.5249

Number of sites scoring better than the average of aligned sites = 1868
Number in coding regions = 1087
Number in noncoding regions = 781
Number of orfs with sites within 600 bp upstream = 155
Fraction of orfs with sites within 600 bp upstream = 0.0248956


Motif number 2

TTGTTAGAATAAGTTTAATTACTATCTTTAT	1	11	1	AAGTTAATTA	    0.919176	-128
ATAATACATAAAAATAAATTATATATTCCCT	1	63	0	AAATAAATTA	    0.957059	-76
TATAATGTAAAAAGTTAATCAAAAAAAACAA	1	91	1	AAATTAATCA	    0.981411	-48
TACATTTATTAAATTTTACTATTTATTTAAT	3	34	1	AAATTTACTA	    0.938983	-48
TTTGATTTATAAAATCAATTAAATAAATAGT	3	51	0	AAATCAATTA	    0.983874	-31
          *** *******

Masking position 5
Map Score:   3.0348

Number of sites scoring better than the average of aligned sites = 312
Number in coding regions = 176
Number in noncoding regions = 136
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 3

GTAATTAAACTTATTCTAACAA        	1	3	0	TTATTCTAAC	    0.875346	-136
ACTATCTTTATTATGCTATATTTCTTATGT	1	31	1	TTATGCTATA	     0.83371	-108
TATGCTATATTTCTTATGTAAAGGGAATAT	1	42	1	TTCTTATGTA	    0.875951	-97
ACATAAAAATAAATTATATATTCCCTTTAC	1	59	0	AAATTATATA	    0.838955	-80
TTAACTTTTTACATTATAATACATAAAAAT	1	79	0	ACATTATAAT	    0.820466	-60
CAGAAACCCCTCATTATGAATATTGTTTTT	1	114	0	TCATTATGAA	    0.938819	-25
  AACTTAAATCCTTCTAAAAT        	2	3	0	TCCTTCTAAA	    0.936158	-18
    CTTTATATATTATATAGTGTATATAC	3	7	1	ATATTATATA	    0.954774	-75
TATTTAATTGATTTTATAAATCAAAGGAGA	3	57	1	ATTTTATAAA	    0.842671	-25
          **********

Masking position 4
Map Score:   3.09318

Number of sites scoring better than the average of aligned sites = 1484
Number in coding regions = 837
Number in noncoding regions = 647
Number of orfs with sites within 600 bp upstream = 142
Fraction of orfs with sites within 600 bp upstream = 0.0228076


Motif number 4

          **********

No masking
Map Score:   -3.31523e-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:   -3.31523e-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:   -3.31523e-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