AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i091_Sugar_Transport_3_hinf_reg_100.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

TTAAGAGGGAAGAGAAAACTCTTCCCTTAC	1	13	1	AGAGAAAACT	    0.979829	-38
CATCACCTAGAGAGGAAAATGTT       	2	4	0	AGAGGAAAAT	    0.932255	-230
TTCGTATTTTTGTGAAAAACTAACTTTTCA	2	40	1	TGTGAAAAAC	    0.977942	-194
AATAATCAACATAGAAAAATTAAATAACAT	2	76	0	ATAGAAAAAT	    0.920622	-158
GGATCACAGTTGTGAAAAAACGTAATAATG	2	120	1	TGTGAAAAAA	    0.917756	-114
ACGTAATAATGGAGAAAGATTTTATAATTG	2	139	1	GGAGAAAGAT	    0.946706	-95
AGATTTTATAATTGAAAGCCTTTTTTAAAG	2	155	1	ATTGAAAGCC	    0.905022	-79
TTTTTTAAAGTGTGAAAACTAACAACTGGA	2	175	1	TGTGAAAACT	    0.973884	-59
TCAATAGTTAAGTGAAGGACTAGTTATTGC	2	205	0	AGTGAAGGAC	    0.932006	-29
          **********

Masking position 6
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

      CTTTAAGAGGGAAGAGAAAACTCT	1	5	1	AAGAGGGAAG	    0.996065	-46
GTAACTCCCTAAGAGGTAAGGGAAGAGTTT	1	28	0	AAGAGGTAAG	    0.993926	-23
TCATCACCTAGAGAGGAAAATGTT      	2	5	0	GAGAGGAAAA	    0.948857	-229
GCCTTTTTTAAAGTGTGAAAACTAACAACT	2	172	1	AAGTGTGAAA	    0.938095	-62
TTGATACCTCAATAGTTAAGTGAAGGACTA	2	213	0	AATAGTTAAG	    0.932958	-21
          **********

Masking position 8
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	    0.989835	-50
TCTTCCCTTACCTCTTAGGGAGTTACGAT 	1	32	1	CCTCTTAGGG	    0.993332	-19
  AACATTTTCCTCTCTAGGTGATGAAATT	2	9	1	CCTCTCTAGG	    0.962856	-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

TGTGATCCACGCCACAGTTGCAAATAATCA	2	98	0	GCCACAGTTG	    0.998181	-136
TGTGGCGTGGATCACAGTTGTGAAAAAACG	2	112	1	ATCACAGTTG	    0.986627	-122
ACTAGTTATTGCTCCAGTTGTTAGTTTTCA	2	187	0	GCTCCAGTTG	    0.994122	-47
          **********

Masking position 6
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