AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i123_Daunorubicin_Resistance_Pump_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	yfiL	143	similar to ABC transporter (ATP-binding protein)

Motif number 1

TTTTGCATATACGCTTCTCTGAAAAGGCCT	1	20	1	ACGCTTCTCT	    0.984966	-124
GGCCTGTAAAAGGCCTTTTCAGAGAAGCGT	1	30	0	AGGCCTTTTC	    0.995422	-114
GGCCTTTTACAGGCCTTTTTTTCATGCCCT	1	45	1	AGGCCTTTTT	    0.997932	-99
TACATGCCGCACGCCTTTCTTTCTTCTACA	1	91	1	ACGCCTTTCT	    0.998683	-53
  GTCGTCTCACTCCTTTTTTTGATCCATT	1	126	0	ACTCCTTTTT	    0.992632	-18
          **********

Masking position 6
Map Score:   11.3831

Number of sites scoring better than the average of aligned sites = 184
Number in coding regions = 165
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 2

ATGAAAAAAAGGCCTGTAAAAGGCCTTTTC	1	40	0	GGCCTGTAAA	    0.995903	-104
TAGAACATAGGGCATGAAAAAAAGGCCTGT	1	53	0	GGCATGAAAA	     0.99394	-91
GGCATGTAGCGGCAGATAGAACATAGGGCA	1	69	0	GGCAGATAGA	    0.989532	-75
AAAGGCGTGCGGCATGTAGCGGCAGATAGA	1	79	0	GGCATGTAGC	    0.997234	-65
          **********

Masking position 8
Map Score:   5.82557

Number of sites scoring better than the average of aligned sites = 100
Number in coding regions = 88
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 3

AGAAGCGTATATGCAAAACGTCATATG   	1	8	0	ATGCAAAACG	    0.987125	-136
CCTTTTTTTCATGCCCTATGTTCTATCTGC	1	58	1	ATGCCCTATG	    0.991276	-86
CTGCCGCTACATGCCGCACGCCTTTCTTTC	1	84	1	ATGCCGCACG	    0.997827	-60
          **********

Masking position 8
Map Score:   0.751151

Number of sites scoring better than the average of aligned sites = 63
Number in coding regions = 57
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

          **********

No masking
Map Score:   -2.17836e-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:   -2.17836e-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:   -2.17836e-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