AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i344_weak5_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	HI1578	300	glycosyl transferase, putative

Motif number 1

         CGAAATGGCAAAGTAACACCGTGGTG	1	2	1	GAATGCAAGA	    0.954858	-299
CACCGTGGTGGTTATGAATATGCAATCTGCAACAC	1	27	1	GTATGATAGA	    0.985661	-274
AACCTCTGTAGAAATTCATATAATAATACTACCTT	1	89	0	GAATTATAAA	    0.977884	-212
CAGAGGTTATGATATTCTTAAGCTATATTTAAAGG	1	116	1	GAATTTTAGA	    0.935684	-185
TTAAATCACTGTGATTAAAACGCCATTCATATTCC	1	149	0	GTATTAAAGA	    0.985941	-152
TTTAATCACAGTGATTTAAAAAAACTCAAATTTCT	1	165	1	GTATTAAAAC	    0.915584	-136
ATAACAAAAGGAGATGCATAGATAACCAATTAAAA	1	226	0	GAATGATAAA	    0.977447	-75
TATTTTATACGTTATTTAAATAACAAAAGGAGATG	1	245	0	GTATTAAAAA	    0.977884	-56
          ** *** *** *  *

Masking position 10
Map Score:   6.61843

Number of sites scoring better than the average of aligned sites = 216
Number in coding regions = 186
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 2

GAATATGAATGGCGTTTTAATCACAGTGAT	1	150	1	GGCGTTTTAA	    0.930761	-151
TTTTAATCACAGTGATTTAAAAAAACTCAA	1	164	1	AGTGATTTAA	    0.957645	-137
GTTTTGAAATAGAAATTTGAGTTTTTTTAA	1	180	0	AGAAATTTGA	    0.786415	-121
TCCTAAATTAATTGTTTTGAAATAGAAATT	1	193	0	ATTGTTTTGA	    0.905136	-108
TTAATTTAGGAGAGTTTTAATTGGTTATCT	1	212	1	AGAGTTTTAA	    0.989793	-89
AACGTATAAAATAGTTTAAAGAAGAGTGTA	1	267	1	ATAGTTTAAA	    0.920054	-34
AGTTTAAAGAAGAGTGTAAAATTAGAGCTT	1	279	1	AGAGTGTAAA	    0.928477	-22
          **********

Masking position 10
Map Score:   3.95558

Number of sites scoring better than the average of aligned sites = 429
Number in coding regions = 338
Number in noncoding regions = 91
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 3

GGCAAAGTAACACCGTGGTGGTTATGAATA	1	17	1	CACCGTGGTG	    0.754304	-284
AATAATCGGTAACAGTGTTGCAGATTGCAT	1	46	0	AACAGTGTTG	    0.968454	-255
ATAATAATACTACCTTGTTTATTTTCTCGA	1	75	0	TACCTTGTTT	    0.911466	-226
TATGAATTTCTACAGAGGTTATGATATTCT	1	104	1	TACAGAGGTT	    0.957841	-197
GCGTTTTAATCACAGTGATTTAAAAAAACT	1	161	1	CACAGTGATT	    0.977947	-140
          **********

Masking position 2
Map Score:   1.87185

Number of sites scoring better than the average of aligned sites = 140
Number in coding regions = 125
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 4

ACACCGTGGTGGTTATGAATATGCAATCTG	1	26	1	GGTTATGAAT	    0.990652	-275
GGTAGTATTATTATATGAATTTCTACAGAG	1	91	1	TTATATGAAT	    0.872842	-210
TTTCTACAGAGGTTATGATATTCTTAAGCT	1	110	1	GGTTATGATA	    0.933387	-191
ATATTTAAAGGAATATGAATGGCGTTTTAA	1	140	1	GAATATGAAT	      0.9531	-161
CTAAATTAATTGTTTTGAAATAGAAATTTG	1	191	0	TGTTTTGAAA	     0.82572	-110
AATAACAAAAGGAGATGCATAGATAACCAA	1	232	0	GGAGATGCAT	     0.93412	-69
          **********

Masking position 6
Map Score:   1.57603

Number of sites scoring better than the average of aligned sites = 316
Number in coding regions = 262
Number in noncoding regions = 54
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


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