AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -ifnr_bbur_opreg_300.orf -g0.282 -x5 
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 =  	0.282
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	BB0729	76	glutamate transporter (gltP)
#2	BB0732	263	penicillin-binding protein (pbp-3)

Motif number 1

AGTGCATTCTTTTTTAAACTTAAGGGGGTA	1	36	0	TTTTTAAACT	     0.92287	-41
GCTTCAAATTGTTTTAAACAGTTTTACACA	2	12	1	GTTTTAAACA	    0.984861	-252
GTTTTAAACAGTTTTACACAAATAAAAAAG	2	22	1	GTTTTACACA	    0.993137	-242
TAGCTTAATTGTTTTAAACTTTTTTATTTG	2	40	0	GTTTTAAACT	    0.986038	-224
TATTGTTATAATTTTACACTATGTAAACAG	2	172	0	ATTTTACACT	    0.986274	-92
TATAACAATAATTTTACACTATAACAATCA	2	192	1	ATTTTACACT	    0.986274	-72
          **********

Masking position 5
Map Score:   14.5327

Number of sites scoring better than the average of aligned sites = 30
Number in coding regions = 11
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 2

      AACAAGATTAATTAATTTTTGAATATA	1	5	1	AGTTATTATT	    0.988595	-72
CTCTTATATAAGCTTAGTGCATTCTTTTTTAAA	1	48	0	AGTTATGATT	    0.978079	-29
AATTGTTTTAAACTTTTTTATTTGTGTAAAACT	2	31	0	AATTTTTTTT	    0.930963	-233
GCGTGTTTATAGCTTAATTGTTTTAAACTTTTT	2	46	0	AGTTATTTTT	    0.979543	-218
TTTTAAGGGTAGATTTATTGATTTTTGGCTAAG	2	78	0	AGTTTTTATT	    0.991186	-186
GGATGATGGTATGTTTTTGATTTTAAGGGTAGA	2	98	0	ATTTTTGTTT	    0.789057	-166
GCATTTTGTAAGTTTTGTTAATTGAAAGATGCT	2	140	0	AGTTTTTATT	    0.991151	-124
ATCAACCCATAACATTATTAATTCTTATGCACT	2	218	1	AAATTTTATT	    0.890419	-46
ATGCACTTATAGTATACTTTAGTAAAAAGT   	2	244	1	AGATATTAGT	    0.870764	-20
          ** *** ** ***

Masking position 8
Map Score:   11.2314

Number of sites scoring better than the average of aligned sites = 519
Number in coding regions = 336
Number in noncoding regions = 183
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 3

TTTTTAAACTTAAGGGGGTATATTCAAAAAT	1	25	0	TAAGGGGTAT	    0.964719	-52
AAGAATGCACTAAGCTTATATAAGAGGTAAT	1	55	1	TAAGCTTTAT	    0.977286	-22
TTAATTGTTTTAAACTTTTTTATTTGTGTAA	2	35	0	TAAACTTTTT	    0.810814	-229
GATTTTTGGCTAAGCGTGTTTATAGCTTAAT	2	61	0	TAAGCGTTTT	    0.985556	-203
TTTTTGATTTTAAGGGTAGATTTATTGATTT	2	87	0	TAAGGGTGAT	    0.990768	-177
CAGCATTTTGTAAGTTTTGTTAATTGAAAGA	2	144	0	TAAGTTTGTT	    0.909449	-120
TTAATAATGTTATGGGTTGATTGTTATAGTG	2	208	0	TATGGGTGAT	    0.957043	-56
          ******* ***

Masking position 2
Map Score:   4.9125

Number of sites scoring better than the average of aligned sites = 216
Number in coding regions = 139
Number in noncoding regions = 77
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 4

ATTAATTTTTGAATATACCCCCTTAAGTTT	1	21	1	GAATATACCC	    0.987637	-56
AAAAATCAATAAATCTACCCTTAAAATCAA	2	85	1	AAATCTACCC	    0.993737	-179
TTAAAATCAAAAACATACCATCATCCACCT	2	105	1	AAACATACCA	    0.938103	-159
TACACTATAACAATCAACCCATAACATTAT	2	206	1	CAATCAACCC	    0.981419	-58
          **********

Masking position 7
Map Score:   1.25377

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 25
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 5

         AACAAGATTAATTAATTTTTG	1	2	1	ACAAGATTAA	    0.834467	-75
GGGGGTATATTCAAAAATTAATTAATCTTG	1	13	0	TCAAAAATTA	    0.887864	-64
AAACAGTTTTACACAAATAAAAAAGTTTAA	2	27	1	ACACAAATAA	    0.887991	-237
AAAAAAGTTTAAAACAATTAAGCTATAAAC	2	45	1	AAAACAATTA	    0.891939	-219
ACACGCTTAGCCAAAAATCAATAAATCTAC	2	73	1	CCAAAAATCA	    0.906794	-191
CTTTCAATTAACAAAACTTACAAAATGCTG	2	145	1	ACAAAACTTA	    0.921477	-119
GTGTAAAATTATAACAATAATTTTACACTA	2	183	1	ATAACAATAA	    0.941233	-81
ATTTTACACTATAACAATCAACCCATAACA	2	202	1	ATAACAATCA	    0.945326	-62
CTATAAGTGCATAAGAATTAATAATGTTAT	2	226	0	ATAAGAATTA	    0.934716	-38
          **********

Masking position 6
Map Score:   5.61355

Number of sites scoring better than the average of aligned sites = 915
Number in coding regions = 619
Number in noncoding regions = 296
Number of orfs with sites within 600 bp upstream = 81
Fraction of orfs with sites within 600 bp upstream = 0.01301


Motif number 6

          **********

No masking
Map Score:   -8.99385e-14

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:   -8.99385e-14

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 8

          **********

No masking
Map Score:   -8.99385e-14

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