AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i282_hypothetical7_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	HI0301	300	hemolysin, putative
#2	HI0303	49	conserved hypothetical protein

Motif number 1

TGTTGTGGATAACTTGTGAATAATGGATTTT	1	71	0	AATTGTGAAT	    0.946609	-230
AAAAGTATCTATGTTGTGGATAACTTGTGAA	1	82	0	ATTTGTGGAT	    0.974568	-219
AAATATTCTTATTTTGTTTATATGACGAAAA	1	109	0	ATTTGTTTAT	    0.750303	-192
AAATAAGAATATTTTGTTGTCTAGAATTTTC	1	126	1	ATTTGTTGTC	    0.793514	-175
CTCTCCGTAAAAATTGTGTATTTTTAACCGC	1	159	1	AATTGTGTAT	    0.970657	-142
GTTTAAACCTAAAGTGCGGTTAAAAATACAC	1	174	0	AAGTGCGGTT	    0.984743	-127
GTTTAAACCCAATGTGCGGTTATTTTTTATT	1	197	1	AAGTGCGGTT	    0.984746	-104
CTCTTTTCGCGTTTTGCGATTTTTTCTAAAA	1	235	1	GTTTGCGATT	      0.8642	-66
       ATTGATTTGTGTTTGATGTCTTAT	1	287	0	GATTGTGTTT	    0.955622	-14
CGGTCATTTTAACTGGTGTTT          	2	1	0	AATGGTGTTT	    0.913503	-49
TATGAATGAAAAAGTGCGGTCATTTTAACTG	2	17	0	AAGTGCGGTC	     0.96121	-33
          ** ********

Masking position 6
Map Score:   11.7174

Number of sites scoring better than the average of aligned sites = 1681
Number in coding regions = 1278
Number in noncoding regions = 403
Number of orfs with sites within 600 bp upstream = 267
Fraction of orfs with sites within 600 bp upstream = 0.0428847


Motif number 2

TGAATAATGGATTTTTGATTGTGAATTGATC	1	55	0	ATTTTTATTG	    0.987059	-246
CAAAATAAGAATATTTTGTTGTCTAGAATTT	1	124	1	ATATTTGTTG	    0.885592	-177
AAAAATACACAATTTTTACGGAGAGGGGAAA	1	153	0	AATTTTACGG	    0.941844	-148
AAAATTGTGTATTTTTAACCGCACTTTAGGT	1	168	1	ATTTTTACCG	    0.987866	-133
ATGTGCGGTTATTTTTTATTGATTTTCCTCT	1	208	1	ATTTTTATTG	    0.987059	-93
AAATATGATAATTTTTCGCCGTCAATAAGAC	1	263	1	ATTTTTGCCG	     0.97877	-38
AAAGTGCGGTCATTTTAACTGGTGTTT    	2	7	0	CATTTTACTG	    0.959934	-43
AATGACCGCACTTTTTCATTCATATAAATAA	2	24	1	CTTTTTATTC	    0.877283	-26
          ****** ****

Masking position 6
Map Score:   8.77

Number of sites scoring better than the average of aligned sites = 728
Number in coding regions = 527
Number in noncoding regions = 201
Number of orfs with sites within 600 bp upstream = 173
Fraction of orfs with sites within 600 bp upstream = 0.0277867


Motif number 3

TGATCTCGTAAAAAGAGGGCAAAGATCCTTAT	1	28	0	AAAAGAGGAA	     0.98898	-273
TATTTTGTTTATATGACGAAAAGTATCTATGT	1	99	0	ATATGAGAAA	    0.968844	-202
TCATATAAACAAAATAAGAATATTTTGTTGTC	1	115	1	AAAATAGATA	    0.900243	-186
GCAAAACGCGAAAAGAGGAAAATCAATAAAAA	1	220	0	AAAAGAGAAA	    0.990847	-81
GATTTTTTCTAAAATATGATAATTTTTCGCCG	1	252	1	AAAATAGAAA	    0.973388	-49
ATGTTTATTTATATGAATGAAAAAGTGCGGTC	2	27	0	ATATGATGAA	    0.799531	-23
          ****** ** **

Masking position 6
Map Score:   3.17617

Number of sites scoring better than the average of aligned sites = 365
Number in coding regions = 283
Number in noncoding regions = 82
Number of orfs with sites within 600 bp upstream = 78
Fraction of orfs with sites within 600 bp upstream = 0.0125281


Motif number 4

 TTTTGAAGTTTGATGTGATAAGGATCTTTG	1	10	1	TTGATGTGTA	    0.972337	-291
TGATTGTGAATTGATCTCGTAAAAAGAGGGC	1	40	0	TTGATCTCTA	    0.972337	-261
ACATAGATACTTTTCGTCATATAAACAAAAT	1	99	1	TTTTCGTCTA	    0.913322	-202
TAAGAATATTTTGTTGTCTAGAATTTTCCCC	1	129	1	TTGTTGTCAG	    0.941528	-172
TGATGTCTTATTGACGGCGAAAAATTATCAT	1	267	0	TTGACGGCAA	    0.960872	-34
TGATTTGTGTTTGATGTCTTATTGACGGCGA	1	278	0	TTGATGTCTA	    0.993519	-23
          ******** **

Masking position 2
Map Score:   2.46231

Number of sites scoring better than the average of aligned sites = 211
Number in coding regions = 186
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 5

          **********

No masking
Map Score:   2.79544e-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:   2.79544e-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:   2.79544e-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