AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i132_Transmembrane_Transport_6_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	HI1019	300	thiamin ABC transporter, periplasmic-binding protein (tbpA)

Motif number 1

CTAGTCTATAAAAATGAAGATAACTCATTGTA	1	34	0	AAAATGGATA	    0.919106	-267
TTCTGAAAAAATAAAGGGGCTGACGTAGATTA	1	75	0	ATAAAGGCTG	    0.883778	-226
ATTTTTTCAGAAAATGTAGAAAGTTTATTTCT	1	95	1	AAAATGGAAA	    0.955868	-206
ACGGCTTTTTAAAAAGAAATAAACTTTCTACA	1	109	0	AAAAAGATAA	    0.907442	-192
ATTTCTTTTTAAAAAGCCGTTGGCAATCTTAG	1	121	1	AAAAAGGTTG	    0.955244	-180
GAAACAGTTAATACTGACGTAGGAAACTAGGA	1	217	1	ATACTGGTAG	    0.833983	-84
AATAATGACGAAAAGGAGATAAGGTTATATTC	1	247	0	AAAAGGATAA	    0.939085	-54
ATTTATGATTAAAAGGCAGCAATAATGACGAA	1	267	0	AAAAGGGCAA	    0.981367	-34
TTAATCATAAATAAGGATGTAATA        	1	287	1	ATAAGGGTAA	    0.976224	-14
          ******  ****

Masking position 3
Map Score:   6.75225

Number of sites scoring better than the average of aligned sites = 826
Number in coding regions = 701
Number in noncoding regions = 125
Number of orfs with sites within 600 bp upstream = 113
Fraction of orfs with sites within 600 bp upstream = 0.0181497


Motif number 2

AGCCTAGTCGGGGTGCAATACGCTGAGATC	1	173	1	GGGTGCAATA	    0.989911	-128
AGTTTCCTACGTCAGTATTAACTGTTTCAG	1	215	0	GTCAGTATTA	    0.920961	-86
ATGATTAAAAGGCAGCAATAATGACGAAAA	1	265	0	GGCAGCAATA	    0.994502	-36
TCATAAATAAGGATGTAATA          	1	291	1	GGATGTAATA	    0.977209	-10
          **********

Masking position 7
Map Score:   1.48373

Number of sites scoring better than the average of aligned sites = 65
Number in coding regions = 61
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

AGATAACTCATTGTAAATTAAAGAAATCTA	1	19	0	TTGTAAATTA	    0.848612	-282
TTTTATAGACTAGTGCACTTGCTAATCTAC	1	53	1	TAGTGCACTT	    0.528479	-248
TTTTAAAAAGAAATAAACTTTCTACATTTT	1	105	0	AAATAAACTT	     0.83301	-196
TTGGCAATCTTAGTAAATTTTAATACACTA	1	140	1	TAGTAAATTT	    0.936913	-161
TAGTAAATTTTAATACACTAGAAAGCCTAG	1	150	1	TAATACACTA	    0.692085	-151
AATACTGACGTAGGAAACTAGGAATATAAC	1	226	1	TAGGAAACTA	    0.948717	-75
          **********

Masking position 7
Map Score:   1.20042

Number of sites scoring better than the average of aligned sites = 218
Number in coding regions = 173
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 4

AATAAAGGGGCTGACGTAGATTAGCAAGTG	1	68	0	CTGACGTAGA	     0.99251	-233
ACAGTTAATACTGACGTAGGAAACTAGGAA	1	220	1	CTGACGTAGG	    0.951131	-81
GGCAGCAATAATGACGAAAAGGAGATAAGG	1	255	0	ATGACGAAAA	    0.958582	-46
          **********

Masking position 4
Map Score:   1.20078

Number of sites scoring better than the average of aligned sites = 9
Number in coding regions = 4
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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