AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i192_topoisomerase_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	HI1527	84	lipid A biosynthesis lauroyl acyltransferase (htrB)
#2	HI1528	73	topoisomerase IV, subunit B (parE)
#3	HI1529	66	topoisomerase IV, subunit A (parC)

Motif number 1

TGGTTATTCAAATAGAGAGATTTTAAA    	1	7	0	AATAGAGAAT	    0.893877	-78
TCTCTATTTGAATAACCAAAATTGTGGCGAT	1	20	1	AATAACCAAA	     0.97905	-65
GTTGTGGTAAAATCGCCACAATTTTGGTTAT	1	31	0	AATCGCCAAA	    0.964128	-54
CACAACTCAAATTTACGATAAACTACGCCCC	1	56	1	ATTTACGAAA	     0.98406	-29
AATTTTTTAAATTTGAGAAAATTCTATCAAA	2	37	0	ATTTGAGAAA	    0.973806	-37
AATTTAAAAAATTAACGAATAACCTCACC  	2	55	1	ATTAACGATA	    0.945526	-19
AATTTTAATAAATTAAGAATATATCAATTAA	3	35	1	AATTAAGATA	    0.958066	-32
AGAATATATCAATTAACAGAAACAAAA    	3	50	1	AATTAACAAA	    0.974598	-17
          ******** **

Masking position 8
Map Score:   8.04431

Number of sites scoring better than the average of aligned sites = 667
Number in coding regions = 550
Number in noncoding regions = 117
Number of orfs with sites within 600 bp upstream = 99
Fraction of orfs with sites within 600 bp upstream = 0.0159011


Motif number 2

TTTAAAATCTCTCTATTTGAATAACCAAAA	1	11	1	CTCTATTTGA	    0.964772	-74
GTAAAATCGCCACAATTTTGGTTATTCAAA	1	26	0	CACAATTTTG	    0.920632	-59
TTTACCACAACTCAAATTTACGATAAACTA	1	51	1	CTCAAATTTA	    0.992894	-34
TAAACTACGCCCCTAACTTAC         	1	74	1	CCCTAACTTA	    0.967291	-11
ATAGAATTTTCTCAAATTTAAAAAATTAAC	2	41	1	CTCAAATTTA	    0.992894	-33
CTCAGCAAATCCGAATTTTAATAAATTAAG	3	22	1	CCGAATTTTA	    0.971513	-45
          **********

Masking position 5
Map Score:   6.71484

Number of sites scoring better than the average of aligned sites = 281
Number in coding regions = 238
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 3

AGGTTATTCGTTAATTTTTTAAATTTGAGA	2	50	0	TTAATTTTTT	    0.978627	-24
TTTGCTGAGATTAATTTAGT          	3	1	0	TTAATTTAGT	    0.985506	-66
TGATATATTCTTAATTTATTAAAATTCGGA	3	31	0	TTAATTTATT	    0.991445	-36
TTTGTTTCTGTTAATTGATATATTCTTAAT	3	46	0	TTAATTGATA	    0.964175	-21
          **********

Masking position 5
Map Score:   4.45311

Number of sites scoring better than the average of aligned sites = 83
Number in coding regions = 61
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 4

ATTCAAATAGAGAGATTTTAAA        	1	3	0	AGAGATTTTA	     0.92192	-82
CCAAAATTGTGGCGATTTTACCACAACTCA	1	35	1	GGCGATTTTA	    0.989168	-50
CAAAAAGTGCGGTGATATTCGACCGCACTT	2	11	0	GGTGATATTC	    0.985922	-63
          GGTGAGGTTATTCGTTAATT	2	64	0	GGTGAGGTTA	    0.992971	-10
ATTCGGATTTGCTGAGATTAATTTAGT   	3	8	0	GCTGAGATTA	     0.97948	-59
          **********

Masking position 5
Map Score:   3.77466

Number of sites scoring better than the average of aligned sites = 182
Number in coding regions = 157
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 5

GAATAACCAAAATTGTGGCGATTTTACCAC	1	29	1	AATTGTGGCG	    0.978548	-56
        GTAAGTTAGGGGCGTAGTTTAT	1	73	0	AAGTTAGGGG	    0.978548	-12
          AAGTGCGGTCGAATATCACC	2	1	1	AAGTGCGGTC	    0.995441	-73
TTCTATCAAAAAGTGCGGTGATATTCGACC	2	17	0	AAGTGCGGTG	     0.99828	-57
          **********

Masking position 4
Map Score:   3.51522

Number of sites scoring better than the average of aligned sites = 821
Number in coding regions = 596
Number in noncoding regions = 225
Number of orfs with sites within 600 bp upstream = 184
Fraction of orfs with sites within 600 bp upstream = 0.0295535


Motif number 6

          **********

No masking
Map Score:   -2.46258e-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:   -2.46258e-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 8

          **********

No masking
Map Score:   -2.46258e-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