AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i185_4_6_1_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	HI1190	89	6-pyruvoyl tetrahydrobiopterin synthase, putative
#2	HI1191	155	conserved hypothetical protein

Motif number 1

CGCAGGTTTTTAATTTAGCAAAAAGGTTTA	2	14	0	TAATTTAGCA	    0.987948	-142
AAAACCTGCGAATTGTAGCACAACGACTTC	2	34	1	AATTGTAGCA	    0.992196	-122
GGGGAAGTTCTATTTTAGCAAGACAAGTGA	2	81	0	TATTTTAGCA	    0.995173	-75
CCTAGTTTTTTATTGTAGGAGGTTTGCGAA	2	130	0	TATTGTAGGA	    0.991691	-26
          **********

Masking position 6
Map Score:   5.79766

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 27
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

TTATTGCGTAAAATACAGCTTGGGCATTTTCT	1	30	0	AAATAACTTG	    0.986748	-60
GTATTTTACGCAATAAAGGTTTAAAGAAATAT	1	46	1	CAATAAGTTT	      0.9312	-44
TTTTTGAGTCAAATATTTCTTTAAACCTTTAT	1	58	0	AAATATCTTT	    0.801627	-32
          AAGTAAACCTTTTTGCTAAATT	2	1	1	AAGTAACTTT	    0.983738	-155
AAGACAAGTGAAATATTTCGTTGGATGTGAAG	2	60	0	AAATATCGTT	     0.95416	-96
TGTCTTGCTAAAATAGAACTTCCCCACTAGAA	2	86	1	AAATAACTTC	    0.987076	-70
          ***** * ****

Masking position 5
Map Score:   4.84278

Number of sites scoring better than the average of aligned sites = 162
Number in coding regions = 130
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 3

GGTGGATGCAGAAAATGCCCAAGCTGTATT	1	21	1	GAAAATGCCC	    0.988813	-69
TGCTAAAATAGAACTTCCCCACTAGAATAC	2	91	1	GAACTTCCCC	    0.988446	-65
TTCCCCACTAGAATACCCCCCGTAGTTCGC	2	105	1	GAATACCCCC	    0.995623	-51
CCCGTAGTTCGCAAACCTCCTACAATAAAA	2	123	1	GCAAACCTCC	    0.983245	-33
          **********

Masking position 3
Map Score:   2.44724

Number of sites scoring better than the average of aligned sites = 34
Number in coding regions = 22
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

CCCAAGCTGTATTTTACGCAATAAAGGTTT	1	38	1	ATTTTACGCA	    0.983404	-52
TTAAAGAAATATTTGACTCAAAAAGGTAGA	1	66	1	ATTTGACTCA	     0.97639	-24
CCAACGAAATATTTCACTTGTCTTGCTAAA	2	68	1	ATTTCACTTG	    0.923335	-88
GGGAAGTTCTATTTTAGCAAGACAAGTGAA	2	80	0	ATTTTAGCAA	    0.919059	-76
          ATTTTACCTAGTTTTTTATT	2	146	0	ATTTTACCTA	    0.986014	-10
          **********

Masking position 6
Map Score:   1.02345

Number of sites scoring better than the average of aligned sites = 307
Number in coding regions = 250
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 5

GTATTTTACGCAATAAAGGTTTAAAGAAAT	1	46	1	CAATAAAGGT	    0.975298	-44
AATATTTGACTCAAAAAGGTAGAAAAA   	1	73	1	TCAAAAAGGT	     0.99225	-17
TTTTAATTTAGCAAAAAGGTTTACTT    	2	7	0	GCAAAAAGGT	    0.994755	-149
          **********

Masking position 5
Map Score:   1.32897

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 38
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


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


Motif number 7

          **********

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 8

          **********

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