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

Motif number 1

CGCATAGAAACGCTAAATATCAAGAATAAA	1	29	1	CGCTAAATAT	    0.956014	-272
TAAATATCAAGAATAAAAATACTGGTGGCT	1	42	1	GAATAAAAAT	    0.868979	-259
AAATACTGGTGGCTTAAGATTACATAGAGG	1	58	1	GGCTTAAGAT	    0.950177	-243
CATAACCGTTCTTTAAAAATAGCCTCTATG	1	80	0	CTTTAAAAAT	    0.947296	-221
CAATGAGAAAGGTTAAAAATGATTTGTCAT	1	128	1	GGTTAAAAAT	     0.99083	-173
TTGCTAGTCAGGCTAAAAGTGCGGTAAAAA	1	169	1	GGCTAAAAGT	    0.978374	-132
GCTAAAAGTGCGGTAAAAATTTTAGATGTT	1	180	1	CGGTAAAAAT	    0.975034	-121
AATTTTAGATGTTTTAAAATGAATAAAATC	1	197	1	GTTTTAAAAT	    0.902268	-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

GCGACAATCTTTGCGGTTATT         	1	2	0	TTGCGGTTAT	    0.889707	-299
TCTTGATATTTAGCGTTTCTATGCGACAAT	1	24	0	TAGCGTTTCT	    0.982545	-277
TCTTTAAAAATAGCCTCTATGTAATCTTAA	1	71	0	TAGCCTCTAT	    0.967917	-230
ATTCAAAACATAACCGTTCTTTAAAAATAG	1	88	0	TAACCGTTCT	    0.987338	-213
AAATCATTTTTAACCTTTCTCATTGAGTAA	1	123	0	TAACCTTTCT	    0.984753	-178
ACCGCACTTTTAGCCTGACTAGCAAAAGAT	1	164	0	TAGCCTGACT	    0.963157	-137
TCTAAAATTTTTACCGCACTTTTAGCCTGA	1	176	0	TTACCGCACT	    0.924454	-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

CTATGCGACAATCTTTGCGGTTATT     	1	6	0	ATCTTTGCGG	    0.886294	-295
TATTTAGCGTTTCTATGCGACAATCTTTGC	1	18	0	TTCTATGCGA	    0.982415	-283
TAAAAATAGCCTCTATGTAATCTTAAGCCA	1	67	0	CTCTATGTAA	     0.95222	-234
AACATAACCGTTCTTTAAAAATAGCCTCTA	1	82	0	TTCTTTAAAA	    0.744323	-219
ATTGAGTAAAATCTATTCAAAACATAACCG	1	102	0	ATCTATTCAA	     0.88642	-199
ATAGATTTTACTCAATGAGAAAGGTTAAAA	1	116	1	CTCAATGAGA	    0.974494	-185
CTATGAAAAACTCAATAAGATTTTATTCAT	1	215	0	CTCAATAAGA	    0.912399	-86
TAAGCAAGCTATCTATGAAAAACTCAATAA	1	227	0	ATCTATGAAA	    0.976636	-74
          **********

Masking position 6
Map Score:   5.24578

Number of sites scoring better than the average of aligned sites = 263
Number in coding regions = 222
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 4

ATCTTAAGCCACCAGTATTTTTATTCTTGA	1	48	0	ACCAGTATTT	    0.941106	-253
TTCAAAACATAACCGTTCTTTAAAAATAGC	1	87	0	AACCGTTCTT	    0.972645	-214
TTATGTTTTGAATAGATTTTACTCAATGAG	1	105	1	AATAGATTTT	    0.840645	-196
GGTAATGACAAATCATTTTTAACCTTTCTC	1	132	0	AATCATTTTT	    0.829483	-169
GTATTCTAGAACCAGTTTTTGGGATAAGCA	1	251	0	ACCAGTTTTT	     0.98125	-50
GGTCGCAATAAACCGTGTATTCTAGAACCA	1	267	0	AACCGTGTAT	    0.917173	-34
          **********

Masking position 1
Map Score:   1.0502

Number of sites scoring better than the average of aligned sites = 516
Number in coding regions = 441
Number in noncoding regions = 75
Number of orfs with sites within 600 bp upstream = 68
Fraction of orfs with sites within 600 bp upstream = 0.0109219


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