AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i136_Transmembrane_Transport_10_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	HI1051	77	ABC transporter, ATP-binding protein
#2	HI1052	111	transcriptional regulator, araC family, putative

Motif number 1

TATTATAGCACAAAAACAAATCAAT     	1	6	0	CAAAAACAAA	    0.929711	-72
TGTGCTATAATAATATGCACTTCTAAAAGG	1	24	1	TAATATGCAC	    0.948656	-54
TATGCACTTCTAAAAGGCAACCTGCGTTGC	1	37	1	TAAAAGGCAA	    0.986823	-41
ATCTTTTCCTTAAAAAGAAAGGCAACGCAG	1	58	0	TAAAAAGAAA	     0.98251	-20
TATATTGAATTAATAACCAACTGGTGTGGC	2	25	1	TAATAACCAA	    0.988623	-87
AAATTGAGATAAATAAGCAAGTATCATAAT	2	73	0	AAATAAGCAA	    0.980594	-39
          **********

Masking position 5
Map Score:   6.16687

Number of sites scoring better than the average of aligned sites = 406
Number in coding regions = 329
Number in noncoding regions = 77
Number of orfs with sites within 600 bp upstream = 67
Fraction of orfs with sites within 600 bp upstream = 0.0107613


Motif number 2

          ATTGATTTGTTTTTGTGCTA	1	1	1	ATTGATTTGT	    0.970884	-77
TCCTAAATATATTGAATTAATAACCAACTG	2	18	1	ATTGAATTAA	    0.955758	-94
AGCGATAAAAATTGAGATAAATAAGCAAGT	2	81	0	ATTGAGATAA	     0.98331	-31
          AATGAGATGTTAGCGATAAA	2	102	0	AATGAGATGT	    0.973027	-10
          **********

Masking position 5
Map Score:   1.04123

Number of sites scoring better than the average of aligned sites = 93
Number in coding regions = 80
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

TGCATATTATTATAGCACAAAAACAAATCA	1	13	0	TATAGCACAA	    0.964797	-65
GCCTTTCTTTTTAAGGAAAAGAT       	1	65	1	TTAAGGAAAA	    0.951665	-13
ATTCAATATATTTAGGAGAACATT      	2	5	0	TTTAGGAGAA	    0.992349	-107
TGTGGCAAATTATAGGCGGATTAGATTATG	2	49	1	TATAGGCGGA	    0.979609	-63
          **********

Masking position 4
Map Score:   0.243743

Number of sites scoring better than the average of aligned sites = 101
Number in coding regions = 69
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 4

          **********

No masking
Map Score:   3.64809e-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:   3.64809e-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:   3.64809e-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