AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i091_Sugar_Transport_3_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI1110	50	D-xylose ABC transporter, ATP-binding protein (xylG)
#2	HI1111	233	D-xylose ABC transporter, periplasmic-binding protein (xylF)

Motif number 1

GTAAGGGAAGAGTTTTCTCTTCCCTCTTAA	1	13	0	AGTTTTCTCT	    0.979557	-38
       AACATTTTCCTCTCTAGGTGATG	2	4	1	ATTTTCCTCT	    0.931386	-230
TGAAAAGTTAGTTTTTCACAAAAATACGAA	2	40	0	GTTTTTCACA	    0.977645	-194
ATGTTATTTAATTTTTCTATGTTGATTATT	2	76	1	ATTTTTCTAT	    0.919616	-158
CATTATTACGTTTTTTCACAACTGTGATCC	2	120	0	TTTTTTCACA	    0.916718	-114
CAATTATAAAATCTTTCTCCATTATTACGT	2	139	0	ATCTTTCTCC	    0.946012	-95
CTTTAAAAAAGGCTTTCAATTATAAAATCT	2	155	0	GGCTTTCAAT	     0.90384	-79
TCCAGTTGTTAGTTTTCACACTTTAAAAAA	2	175	0	AGTTTTCACA	    0.973534	-59
GCAATAACTAGTCCTTCACTTAACTATTGA	2	205	1	GTCCTTCACT	    0.931134	-29
          **********

Masking position 5
Map Score:   10.1582

Number of sites scoring better than the average of aligned sites = 876
Number in coding regions = 731
Number in noncoding regions = 145
Number of orfs with sites within 600 bp upstream = 111
Fraction of orfs with sites within 600 bp upstream = 0.0178285


Motif number 2

AGAGTTTTCTCTTCCCTCTTAAAG      	1	5	0	CTTCCCTCTT	    0.996559	-46
AAACTCTTCCCTTACCTCTTAGGGAGTTAC	1	28	1	CTTACCTCTT	    0.994687	-23
      AACATTTTCCTCTCTAGGTGATGA	2	5	1	TTTTCCTCTC	    0.955011	-229
AGTTGTTAGTTTTCACACTTTAAAAAAGGC	2	172	0	TTTCACACTT	     0.94547	-62
TAGTCCTTCACTTAACTATTGAGGTATCAA	2	213	1	CTTAACTATT	    0.940906	-21
          **********

Masking position 3
Map Score:   4.02546

Number of sites scoring better than the average of aligned sites = 140
Number in coding regions = 93
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 3

TTTTCTCTTCCCTCTTAAAG          	1	1	0	CCTCTTAAAG	    0.990362	-50
TCTTCCCTTACCTCTTAGGGAGTTACGAT 	1	32	1	CCTCTTAGGG	    0.993353	-19
  AACATTTTCCTCTCTAGGTGATGAAATT	2	9	1	CCTCTCTAGG	    0.960629	-225
          **********

Masking position 5
Map Score:   1.92652

Number of sites scoring better than the average of aligned sites = 2
Number in coding regions = 1
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

TGATTATTTGCAACTGTGGCGTGGATCACA	2	98	1	CAACTGTGGC	    0.998083	-136
CGTTTTTTCACAACTGTGATCCACGCCACA	2	112	0	CAACTGTGAT	     0.98591	-122
TGAAAACTAACAACTGGAGCAATAACTAGT	2	187	1	CAACTGGAGC	    0.993804	-47
          **********

Masking position 3
Map Score:   1.8838

Number of sites scoring better than the average of aligned sites = 11
Number in coding regions = 10
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

          **********

No masking
Map Score:   -1.17788e-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 6

          **********

No masking
Map Score:   -1.17788e-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:   -1.17788e-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