AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i128_Transmembrane_Transport_2_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	HI0620	300	28 kDa outer membrane protein (hlpA)
#2	HI0621	175	ABC transporter, ATP-binding protein

Motif number 1

GTAGAGCTTCTGACAAATAGAATTTACGAACA	1	16	0	TGACAAAGAA	    0.984923	-285
GTAACTTGGGTGGCAACCATTATTATTGTGCT	1	180	1	TGGCAAATTA	    0.959873	-121
TTTGTCAATTTGACATGTATAAAAGGTAAGAG	2	12	0	TGACATATAA	    0.976864	-164
CATGTCAAATTGACAAAAATTATCTATTTAAT	2	27	1	TGACAAATTA	    0.976841	-149
TCCAAGCAATTAGCAAATATAAGTCATAACTA	2	58	1	TAGCAAATAA	    0.962293	-118
CTAATCTGTCTAAAAAAGATAATCTGACATAT	2	87	1	TAAAAAATAA	    0.911613	-89
ATAGCAATCTAGACATCTAGAATACCAAAACA	2	123	1	AGACATAGAA	    0.810851	-53
AAAACAGATTTAAAAACAATAAATAAAAAGGG	2	149	1	TAAAAAATAA	    0.911633	-27
          ******  ****

Masking position 5
Map Score:   5.67137

Number of sites scoring better than the average of aligned sites = 217
Number in coding regions = 167
Number in noncoding regions = 50
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 2

ATGGCGTTACTCTTACGCTAGTCACTTTAGTTG	1	60	1	TTTAGTAGTC	     0.96056	-241
CTAGTCACTTTAGTTGGTTATTCTGCAATGGCA	1	77	1	TGTTGTATTC	    0.974979	-224
ACATAAGGCATATTGCGATATACGCCCGTAGTT	1	149	0	TTTGGTATAC	    0.946497	-152
CAACCATTATTATTGTGCTATTCGTTATGATTA	1	193	1	TTTGGTATTC	    0.989969	-108
TATCGCCGAGTTTTTGGCTAATCATAACGAATA	1	211	0	TTTTGTAATC	    0.973112	-90
ATGATCCACTTTTTTAGCCAGTGTATCGCCGAG	1	234	0	TTTTGCAGTG	    0.902695	-67
TTTTTAAATCTGTTTTGGTATTCTAGATGTCTA	2	132	0	TTTTGTATTC	     0.99323	-44
  ATAAGCCCTTTTTATTTATTGTTTTTAAATC	2	155	0	TTTTTTATTG	    0.852859	-21
          * *** * *****

Masking position 10
Map Score:   5.60583

Number of sites scoring better than the average of aligned sites = 131
Number in coding regions = 100
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 3

CAGAAGCTCTACCTACGCTAATTAATGGCGTTACT	1	36	1	ACAGCTATAA	    0.994263	-265
CGTAGTTGATAGCGAGGCTACCTAAACCACCGCCC	1	121	0	ACAGCTATAA	    0.994263	-180
AATGGTTGCCACCCAAGTTACATAAGGCATATTGC	1	166	0	ACAGTTATAA	    0.979285	-135
ACTCGGCGATACACTGGCTAAAAAAGTGGATCATC	1	233	1	AATGCTAAAA	    0.882867	-68
AAAAAAGTGGATCATCGTTAATTAAACGCAACTCT	1	252	1	ACTGTTATAA	    0.973194	-49
AAATTGACAAAAATTATCTATTTAATCCAAGCAAT	2	33	1	AATTCTATAA	    0.908291	-143
TATAAGTCATAACTAATCTGTCTAAAAAAGATAAT	2	75	1	ACATCTGTAA	    0.935676	-101
          * * * ****  ***

Masking position 14
Map Score:   4.03317

Number of sites scoring better than the average of aligned sites = 197
Number in coding regions = 165
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

TAAAGTGACTAGCGTAAGAGTAACGCCATT	1	59	0	AGCGTAAGAG	    0.983166	-242
CAGAATAACCAACTAAAGTGACTAGCGTAA	1	72	0	AACTAAAGTG	       0.905	-229
CTTCCTGTTTAAGTTAAGAGTTGCGTTTAA	1	273	0	AAGTTAAGAG	    0.984471	-28
ACATGTATAAAAGGTAAGAGA         	2	2	0	AAGGTAAGAG	    0.990109	-174
          **********

Masking position 6
Map Score:   1.20704

Number of sites scoring better than the average of aligned sites = 10
Number in coding regions = 5
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 5

          **********

No masking
Map Score:   -1.68098e-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:   -1.68098e-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:   -1.68098e-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