AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i265_hypothetical10_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	HI0386	300	conserved hypothetical protein

Motif number 1

CGCATAGAAACGCTAAATATCAAGAATAAA	1	29	1	CGCTAAATAT	    0.953574	-272
TAAATATCAAGAATAAAAATACTGGTGGCT	1	42	1	GAATAAAAAT	    0.862404	-259
AAATACTGGTGGCTTAAGATTACATAGAGG	1	58	1	GGCTTAAGAT	    0.947462	-243
CATAACCGTTCTTTAAAAATAGCCTCTATG	1	80	0	CTTTAAAAAT	    0.944457	-221
CAATGAGAAAGGTTAAAAATGATTTGTCAT	1	128	1	GGTTAAAAAT	    0.990304	-173
TTGCTAGTCAGGCTAAAAGTGCGGTAAAAA	1	169	1	GGCTAAAAGT	    0.977145	-132
GCTAAAAGTGCGGTAAAAATTTTAGATGTT	1	180	1	CGGTAAAAAT	     0.97362	-121
AATTTTAGATGTTTTAAAATGAATAAAATC	1	197	1	GTTTTAAAAT	    0.898545	-104
          **********

Masking position 6
Map Score:   8.13202

Number of sites scoring better than the average of aligned sites = 687
Number in coding regions = 527
Number in noncoding regions = 160
Number of orfs with sites within 600 bp upstream = 135
Fraction of orfs with sites within 600 bp upstream = 0.0216833


Motif number 2

         AATAACCGCAAAGATTGTCGC	1	2	1	ATAACCGCAA	    0.898703	-299
ATTGTCGCATAGAAACGCTAAATATCAAGA	1	24	1	AGAAACGCTA	    0.984104	-277
TTAAGATTACATAGAGGCTATTTTTAAAGA	1	71	1	ATAGAGGCTA	    0.970744	-230
CTATTTTTAAAGAACGGTTATGTTTTGAAT	1	88	1	AGAACGGTTA	    0.988473	-213
TTACTCAATGAGAAAGGTTAAAAATGATTT	1	123	1	AGAAAGGTTA	    0.986118	-178
ATCTTTTGCTAGTCAGGCTAAAAGTGCGGT	1	164	1	AGTCAGGCTA	    0.966389	-137
TCAGGCTAAAAGTGCGGTAAAAATTTTAGA	1	176	1	AGTGCGGTAA	    0.930836	-125
          **********

Masking position 1
Map Score:   7.64179

Number of sites scoring better than the average of aligned sites = 539
Number in coding regions = 364
Number in noncoding regions = 175
Number of orfs with sites within 600 bp upstream = 134
Fraction of orfs with sites within 600 bp upstream = 0.0215226


Motif number 3

GCGACAATCTTTGCGGTTATT         	1	2	0	TTGCGGTTAT	    0.962768	-299
TCTTGATATTTAGCGTTTCTATGCGACAAT	1	24	0	TAGCGTTTCT	    0.956849	-277
TAAGATTACATAGAGGCTATTTTTAAAGAA	1	72	1	TAGAGGCTAT	    0.964515	-229
ATGTTTTGAATAGATTTTACTCAATGAGAA	1	107	1	TAGATTTTAC	    0.915952	-194
GTAAAAATTTTAGATGTTTTAAAATGAATA	1	192	1	TAGATGTTTT	    0.958198	-109
AAAACTCAATAAGATTTTATTCATTTTAAA	1	209	0	AAGATTTTAT	     0.88027	-92
TAAAATCTTATTGAGTTTTTCATAGATAGC	1	220	1	TTGAGTTTTT	    0.944613	-81
          **********

Masking position 8
Map Score:   3.54691

Number of sites scoring better than the average of aligned sites = 297
Number in coding regions = 235
Number in noncoding regions = 62
Number of orfs with sites within 600 bp upstream = 60
Fraction of orfs with sites within 600 bp upstream = 0.00963701


Motif number 4

ATCTTAAGCCACCAGTATTTTTATTCTTGA	1	48	0	ACCAGTATTT	    0.990428	-253
TCAAAACATAACCGTTCTTTAAAAATAGCC	1	86	0	ACCGTTCTTT	    0.979254	-215
GTATTCTAGAACCAGTTTTTGGGATAAGCA	1	251	0	ACCAGTTTTT	    0.990406	-50
          **********

Masking position 1
Map Score:   0.544848

Number of sites scoring better than the average of aligned sites = 24
Number in coding regions = 20
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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