AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i283_hypothetical8_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	HI1678	300	kpsF protein (kpsF)

Motif number 1

GGTAAGAGCGCACCGTGCCGTTGGTAA    	1	7	0	CACCGTGCGT	    0.963524	-294
CGGCACGGTGCGCTCTTACCGCACCCTTTCA	1	18	1	CGCTCTTCCG	    0.974599	-283
CGCACCCTTTCACCCTTACCGTTTACACGGC	1	37	1	CACCCTTCCG	    0.981403	-264
CGGCTCACGCCGCCCGGACGTTATCCGGCAC	1	94	1	CGCCCGGCGT	    0.995083	-207
CGTTATCCGGCACTCTGCCCTGTGTAGCTCG	1	112	1	CACTCTGCCT	    0.993962	-189
TGCCCTGTGTAGCTCGGACTTTCCTCTCGTT	1	127	1	AGCTCGGCTT	    0.904247	-174
TTACTTGTCCCACTAGGTCGTATAAATACGG	1	157	1	CACTAGGCGT	    0.986816	-144
TTGTCTAACCAACTCGGCGCGTAGTATAGGG	1	212	1	AACTCGGGCG	    0.911264	-89
TAGGGGCAATCACTAGTGCGGTCAATAAAAT	1	238	1	CACTAGTCGG	    0.969286	-63
          ******* ***

Masking position 3
Map Score:   10.8163

Number of sites scoring better than the average of aligned sites = 142
Number in coding regions = 124
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

AGAGCGCACCGTGCCGTTGGTAA       	1	4	0	GTGCCGTTGG	    0.973085	-297
GGGTGAAAGGGTGCGGTAAGAGCGCACCGT	1	22	0	GTGCGGTAAG	    0.987066	-279
GTGCAACAGAGAGCAGACCGCCGTGTAAAC	1	57	0	GAGCAGACCG	    0.917014	-244
CGGGCGGCGTGAGCCGACGACCAGTGCAAC	1	80	0	GAGCCGACGA	     0.97866	-221
GCCGGATAACGTCCGGGCGGCGTGAGCCGA	1	93	0	GTCCGGGCGG	    0.977922	-208
ACAGGGCAGAGTGCCGGATAACGTCCGGGC	1	105	0	GTGCCGGATA	    0.904982	-196
ACAAGTAAACGAGAGGAAAGTCCGAGCTAC	1	135	0	GAGAGGAAAG	    0.841658	-166
GCAATCACTAGTGCGGTCAATAAAATCCCC	1	243	1	GTGCGGTCAA	    0.983757	-58
          **********

Masking position 6
Map Score:   5.25142

Number of sites scoring better than the average of aligned sites = 1051
Number in coding regions = 826
Number in noncoding regions = 225
Number of orfs with sites within 600 bp upstream = 186
Fraction of orfs with sites within 600 bp upstream = 0.0298747


Motif number 3

          **********

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 4

          **********

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 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