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

Motif number 1

AAAATCCATTATTCACAAGTTATCCACAACA	1	71	1	ATTCACAATT	     0.94259	-230
TTCACAAGTTATCCACAACATAGATACTTTT	1	82	1	ATCCACAAAT	    0.972593	-219
TTTTCGTCATATAAACAAAATAAGAATATTT	1	109	1	ATAAACAAAT	    0.735633	-192
GAAAATTCTAGACAACAAAATATTCTTATTT	1	126	0	GACAACAAAT	    0.780641	-175
GCGGTTAAAAATACACAATTTTTACGGAGAG	1	159	0	ATACACAATT	    0.968388	-142
GTGTATTTTTAACCGCACTTTAGGTTTAAAC	1	174	1	AACCGCACTT	    0.983545	-127
AATAAAAAATAACCGCACATTGGGTTTAAAC	1	197	0	AACCGCACTT	    0.983548	-104
TTTTAGAAAAAATCGCAAAACGCGAAAAGAG	1	235	0	AATCGCAAAC	    0.854928	-66
ATAAGACATCAAACACAAATCAAT       	1	287	1	AAACACAATC	    0.952247	-14
          AAACACCAGTTAAAATGACCG	2	1	1	AAACACCATT	    0.907241	-49
CAGTTAAAATGACCGCACTTTTTCATTCATA	2	17	1	GACCGCACTT	    0.958241	-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	    0.984427	-246
CAAAATAAGAATATTTTGTTGTCTAGAATTT	1	124	1	ATATTTGTTG	    0.865141	-177
AAAAATACACAATTTTTACGGAGAGGGGAAA	1	153	0	AATTTTACGG	    0.930662	-148
AAAATTGTGTATTTTTAACCGCACTTTAGGT	1	168	1	ATTTTTACCG	    0.985396	-133
ATGTGCGGTTATTTTTTATTGATTTTCCTCT	1	208	1	ATTTTTATTG	    0.984427	-93
AAATATGATAATTTTTCGCCGTCAATAAGAC	1	263	1	ATTTTTGCCG	    0.974495	-38
AAAGTGCGGTCATTTTAACTGGTGTTT    	2	7	0	CATTTTACTG	    0.952682	-43
AATGACCGCACTTTTTCATTCATATAAATAA	2	24	1	CTTTTTATTC	     0.85559	-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	    0.989181	-273
TATTTTGTTTATATGACGAAAAGTATCTATGT	1	99	0	ATATGAGAAA	    0.969398	-202
TCATATAAACAAAATAAGAATATTTTGTTGTC	1	115	1	AAAATAGATA	    0.901894	-186
GCAAAACGCGAAAAGAGGAAAATCAATAAAAA	1	220	0	AAAAGAGAAA	    0.991014	-81
GATTTTTTCTAAAATATGATAATTTTTCGCCG	1	252	1	AAAATAGAAA	    0.973863	-49
ATGTTTATTTATATGAATGAAAAAGTGCGGTC	2	27	0	ATATGATGAA	    0.802484	-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	    0.977972	-291
TGATTGTGAATTGATCTCGTAAAAAGAGGGC	1	40	0	TTGATCTCTA	     0.97797	-261
TAAGAATATTTTGTTGTCTAGAATTTTCCCC	1	129	1	TTGTTGTCAG	    0.937258	-172
TGATGTCTTATTGACGGCGAAAAATTATCAT	1	267	0	TTGACGGCAA	    0.956069	-34
TGATTTGTGTTTGATGTCTTATTGACGGCGA	1	278	0	TTGATGTCTA	    0.993643	-23
          ******** **

Masking position 2
Map Score:   1.17369

Number of sites scoring better than the average of aligned sites = 129
Number in coding regions = 118
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


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