AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i205_dna_mismatch_repair_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	HI0701	108	conserved hypothetical protein
#2	HI0706	23	lipoprotein
#3	HI0707	132	DNA mismatch repair protein (mutS)

Motif number 1

CAACAAGAACAAAAGTGCGGTTATTTTAGT	1	23	1	AAAAGTGCGG	    0.999069	-86
TTTTCGATAAAAAAGAGCCCTTAACT    	1	93	1	AAAAGAGCCC	    0.993198	-16
TCTTCCTGTAAAAAGTGCGGTAAAAAATCT	3	11	1	AAAAGTGCGG	    0.999069	-122
AAAGCCAGATAAAAGTGCGGTAAAAATTTG	3	44	0	AAAAGTGCGG	    0.999069	-89
TTCGGCACCTAAAATAGCCGCCACAAAACC	3	81	1	AAAATAGCCG	    0.989951	-52
          **********

Masking position 4
Map Score:   15.0214

Number of sites scoring better than the average of aligned sites = 731
Number in coding regions = 442
Number in noncoding regions = 289
Number of orfs with sites within 600 bp upstream = 219
Fraction of orfs with sites within 600 bp upstream = 0.0351751


Motif number 2

AGTGCGGTTATTTTAGTGGATAAATCACGA	1	36	1	TTTTAGTGGA	    0.957528	-73
AAGGGCTCTTTTTTATCGAAAATAATTGTG	1	85	0	TTTTATCGAA	    0.955992	-24
TTACCGCACTTTTTACAGGAAGA       	3	4	0	TTTTACAGGA	    0.990669	-129
TGTTGAGATTTTTTACCGCACTTTTTACAG	3	16	0	TTTTACCGCA	    0.997147	-117
CTCAACAAATTTTTACCGCACTTTTATCTG	3	39	1	TTTTACCGCA	    0.997147	-94
CTTTATTCAGTTTCAAAGCAGGTAATTAG 	3	114	1	TTTCAAAGCA	     0.93458	-19
          **********

Masking position 5
Map Score:   9.00346

Number of sites scoring better than the average of aligned sites = 576
Number in coding regions = 381
Number in noncoding regions = 195
Number of orfs with sites within 600 bp upstream = 146
Fraction of orfs with sites within 600 bp upstream = 0.02345


Motif number 3

TATCCACTAAAATAACCGCACTTTTGTTCT	1	28	0	AATAACCGCA	     0.98951	-81
ATAAATCACGAAAAGTCGCATAGAATTTCG	1	55	1	AAAAGTCGCA	    0.992656	-54
AAGTGCGGTAAAAAATCTCAACAAATTTTT	3	23	1	AAAAATCTCA	    0.937887	-110
CGAAAGGGGAAAAAGCCAGATAAAAGTGCG	3	55	0	AAAAGCCAGA	    0.956083	-78
CGGCACCTAAAATAGCCGCCACAAAACCTA	3	83	1	AATAGCCGCC	    0.989664	-50
          **********

Masking position 4
Map Score:   4.7021

Number of sites scoring better than the average of aligned sites = 298
Number in coding regions = 218
Number in noncoding regions = 80
Number of orfs with sites within 600 bp upstream = 57
Fraction of orfs with sites within 600 bp upstream = 0.00915516


Motif number 4

AACCGCACTTTTGTTCTTGTTGAAGGATTT	1	15	0	TTGTTCTTGT	    0.950669	-94
TTATTCCTTATTGTTCCGTTA         	2	2	0	TTGTTCCGTT	    0.992837	-22
        AGTTATTCCTTATTGTTCCGTT	2	12	0	TTATTCCTTA	    0.958195	-12
AAACCTATCTTTATTCAGTTTCAAAGCAGG	3	106	1	TTATTCAGTT	    0.970459	-27
          **********

Masking position 5
Map Score:   0.631344

Number of sites scoring better than the average of aligned sites = 97
Number in coding regions = 85
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 5

          **********

No masking
Map Score:   -2.39152e-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:   -2.39152e-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:   -2.39152e-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