AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i087_PTS_sugar_Utilization_bbur_reg_300.orf -o087_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

Purged sequences:
RBB00130	81	3615

Input sequences:
#1	RBB00202	261	3615
#2	RBB00199	138	3615
#3	RBB00198	20	3615
#4	RBB00129	81	3615

Motif number 1

AGAAAACATCTATAATTTATAATGTTAGCA	1	30	1	TATAATTTAT	     0.94001	-232
TTTTATCTCTTTTGATAAATGGACAAATTA	1	60	0	TTTGATAAAT	     0.88564	-202
CGGGGGCTATTTTTATTGACAAATAGTGCT	1	95	1	TTTTATTGAC	    0.830188	-167
TAAGTGAATTTTTTATTAATTTATTTTAAG	1	141	1	TTTTATTAAT	    0.959476	-121
GTTTTTGAGGTTTTATTTTTTAATCCTTTT	1	200	1	TTTTATTTTT	    0.888274	-62
TTTTAATCCTTTTTATTTATGCAATGTTAG	1	217	1	TTTTATTTAT	    0.976845	-45
TTTTTACTAATTTAATTTTTTTGT      	1	248	1	TTTAATTTTT	    0.916215	-14
TTAGAATAAGTTTAATTACTATCTTTATTA	2	14	1	TTTAATTACT	    0.854269	-125
AAAGGGAATATATAATTTATTTTTATGTAT	2	61	1	TATAATTTAT	     0.94001	-78
TATAATTTATTTTTATGTATTATAATGTAA	2	71	1	TTTTATGTAT	    0.879152	-68
TATTGTTTTTTTTGATTAACTTTTTACATT	2	94	0	TTTGATTAAC	     0.87651	-45
ATATACACTATATAATATATAAAG      	4	5	0	TATAATATAT	    0.821101	-77
AATAGTAAAATTTAATAAATGTATATACAC	4	27	0	TTTAATAAAT	    0.904644	-55
TTACTATTTATTTAATTGATTTTATAAATC	4	49	1	TTTAATTGAT	    0.961322	-33
GATAATCTCCTTTGATTTATAAAATCAATT	4	62	0	TTTGATTTAT	    0.976482	-20
          **********

Masking position 5
Map Score:   22.9572

Number of sites scoring better than the average of aligned sites = 1383
Number in coding regions = 849
Number in noncoding regions = 534
Number of orfs with sites within 600 bp upstream = 140
Fraction of orfs with sites within 600 bp upstream = 0.0224863


Motif number 2

TGATAAATGGACAAATTATGCTAACATTATAAATTA	1	42	0	ACAAATTAAA	    0.916012	-220
TCCATTTATCAAAAGAGATAAAAATAGCCGGGGGCT	1	67	1	AAAAATAAAA	    0.960334	-195
AAATTCACTTAAAACTAATTTGAAAACAGCACTATT	1	116	0	AAAAATGAAA	    0.916012	-146
GAATTTTTTATTAATTTATTTTAAGATTGTTGCATG	1	146	1	TTAAATTAAA	     0.96032	-116
TTGCATAAATAAAAAGGATTAAAAAATAAAACCTCA	1	205	0	AAAAATAAAA	    0.960333	-57
AGATAGTAATTAAACTTATTCTAACAA         	2	2	0	TAAAATTAAA	    0.976225	-137
TTTTTACATTATAATACATAAAAATAAATTATATAT	2	68	0	ATAAATAAAA	    0.934531	-71
TATTATAATGTAAAAAGTTAATCAAAAAAAACAATA	2	88	1	TAAATTTCAA	    0.666937	-51
GTTAATCAAAAAAAACAATATTCATAATGAGGGGTT	2	104	1	AAAAATTCAA	    0.940331	-35
       AACTTAAATCCTTCTAAAAT         	3	2	0	TTAACTTAAA	    0.820121	-19
ATAGTAAAATTTAATAAATGTATATACACTATATAA	4	20	0	TTAAATATAA	    0.666182	-62
TAAAATCAATTAAATAAATAGTAAAATTTAATAAAT	4	37	0	TAAAATTAAA	    0.976195	-45
          ****   **  *** *

Masking position 4
Map Score:   11.6505

Number of sites scoring better than the average of aligned sites = 1549
Number in coding regions = 944
Number in noncoding regions = 605
Number of orfs with sites within 600 bp upstream = 124
Fraction of orfs with sites within 600 bp upstream = 0.0199165


Motif number 3

TTTTTATTCAGAAAACATCTATAATTTATA	1	21	1	GAAAACATCT	    0.912838	-241
CAAAAGAGATAAAAATAGCCGGGGGCTATT	1	76	1	AAAAATAGCC	    0.989522	-186
ATTTGTCAATAAAAATAGCCCCCGGCTATT	1	89	0	AAAAATAGCC	    0.989522	-173
AAACTAATTTGAAAACAGCACTATTTGTCA	1	111	0	GAAAACAGCA	    0.982037	-151
ATAAAACCTCAAAAACATCCGACCCTACCC	1	186	0	AAAAACATCC	    0.980465	-76
TTTACATAAGAAATATAGCATAATAAAGAT	2	34	0	AAATATAGCA	    0.911857	-105
          **********

Masking position 5
Map Score:   7.07405

Number of sites scoring better than the average of aligned sites = 187
Number in coding regions = 138
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

AATGGACAAATTATGCTAACATTATAAATT	1	43	0	TTATGCTAAC	    0.985168	-219
TTTTATTAATTTATTTTAAGATTGTTGCAT	1	151	1	TTATTTTAAG	    0.917385	-111
TCCTTTTTATTTATGCAATGTTAGGTTTTT	1	223	1	TTATGCAATG	    0.965369	-39
GTAATTAAACTTATTCTAACAA        	2	3	0	TTATTCTAAC	    0.957554	-136
ACTATCTTTATTATGCTATATTTCTTATGT	2	31	1	TTATGCTATA	    0.929106	-108
GCTATATTTCTTATGTAAAGGGAATATATA	2	45	1	TTATGTAAAG	    0.946208	-94
          **********

Masking position 4
Map Score:   4.48516

Number of sites scoring better than the average of aligned sites = 84
Number in coding regions = 61
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 5

          **********

No masking
Map Score:   6.84553e-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:   6.84553e-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:   6.84553e-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