AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i341_weak2_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	HI1603	207	conserved hypothetical protein
#2	HI1604	24	phosphate permease, putative
#3	HI1605	65	conserved hypothetical protein

Motif number 1

     TTTTTTACCTTTCAAATTTTCTCGCTTTTAAAGC	1	6	1	TATTTTTTCG	     0.97063	-202
TTCTCGCTTTTAAAGCGAAAAGTGTATTGAGTTACTTAT	1	29	1	TACGTGTTTG	    0.973637	-179
ATAAACCTTTTTTCTTACAAATTTTTTTGAAAAATTTTA	1	113	1	TTTTTTTTTG	    0.988022	-95
TTCGTGCGCATATTACCCGATTTTTGTTGATAGTTAAAA	1	147	0	TACTTTTTTG	    0.997464	-61
      AGTTTATTTCCTATGTTTTGTTGA         	2	2	0	TACTTTTTTG	    0.997467	-23
GCGGTTAAAATTAACCGCACTTTTTATTGAGATCAA   	3	8	0	TTCTTTTTTG	    0.996704	-58
TGCGGTTAATTTTAACCGCACTTTTGTTGTGATGTTTAA	3	28	1	TTCTTTTTTG	    0.996704	-38
          **   *     **** ***

Masking position 13
Map Score:   10.5159

Number of sites scoring better than the average of aligned sites = 83
Number in coding regions = 66
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 2

        TTTTTTACCTTTCAAATTTTCTCGC	1	3	1	TTTTCTTTAA	    0.993815	-205
CTCAATACACTTTTCGCTTTAAAAGCGAGAAAA	1	27	0	TTTTCTTTAA	    0.973356	-181
AAGATAAACCTTTTTTCTTACAAATTTTTTTGA	1	110	1	TTTTCTTAAA	    0.979044	-98
TTTTGAAAAATTTTAACTATCAACAAAAATCGG	1	137	1	TTTTCTATAA	    0.966356	-71
CGCACGAATTTTTAACCCCTTAATTTGGAGTAA	1	178	1	TTTACCCTAA	    0.944721	-30
         TTTTTCCCCTTAAACATCACAACA	3	52	0	TTTTCCTTAA	    0.992203	-14
          ****  **** **

Masking position 3
Map Score:   9.10153

Number of sites scoring better than the average of aligned sites = 137
Number in coding regions = 100
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 3

AATATTTCCTAGTGTGGTAAGATAAGTAAC	1	59	0	AGTGTGGTAA	    0.984921	-149
GTTAAAAATTCGTGCGCATATTACCCGATT	1	164	0	CGTGCGCATA	    0.979989	-44
CTCAATAAAAAGTGCGGTTAATTTTAACCG	3	16	1	AGTGCGGTTA	    0.998468	-50
TCACAACAAAAGTGCGGTTAAAATTAACCG	3	30	0	AGTGCGGTTA	    0.998468	-36
          **********

Masking position 3
Map Score:   6.27593

Number of sites scoring better than the average of aligned sites = 1046
Number in coding regions = 659
Number in noncoding regions = 387
Number of orfs with sites within 600 bp upstream = 265
Fraction of orfs with sites within 600 bp upstream = 0.0425634


Motif number 4

CACACTAGGAAATATTACCCAGTTGCTTAC	1	73	1	AATATTACCC	    0.992759	-135
TACTTAGTCGAAGATAAACCTTTTTTCTTA	1	100	1	AAGATAAACC	    0.948387	-108
TTTTTTGAAAAATTTTAACTATCAACAAAA	1	135	1	AATTTTAACT	    0.931754	-73
AATTCGTGCGCATATTACCCGATTTTTGTT	1	158	0	CATATTACCC	    0.980443	-50
ATGCGCACGAATTTTTAACCCCTTAATTTG	1	175	1	ATTTTTAACC	    0.956254	-33
AAGTGCGGTTAAAATTAACCGCACTTTTTA	3	21	0	AAAATTAACC	    0.980494	-45
          **********

Masking position 5
Map Score:   6.02672

Number of sites scoring better than the average of aligned sites = 243
Number in coding regions = 160
Number in noncoding regions = 83
Number of orfs with sites within 600 bp upstream = 67
Fraction of orfs with sites within 600 bp upstream = 0.0107613


Motif number 5

     TTTTTTACCTTTCAAATTTTCTCGCT	1	6	1	TACTTTCAAA	       0.981	-202
AATACACTTTTCGCTTTAAAAGCGAGAAAAT	1	26	0	TCCTTTAAAA	     0.97518	-182
TTGAGTTACTTATCTTACCACACTAGGAAAT	1	55	1	TACTTACCAC	    0.893006	-153
ATAAACCTTTTTTCTTACAAATTTTTTTGAA	1	113	1	TTCTTACAAA	    0.894767	-95
TGAAAAATTTTAACTATCAACAAAAATCGGG	1	140	1	TACTATCAAC	    0.964447	-68
      TTGATCTCAATAAAAAGTGCGGTTA	3	5	1	TCCAATAAAA	    0.808195	-61
      TTTTTCCCCTTAAACATCACAACAA	3	51	0	TCCCTTAAAC	    0.945531	-15
          ** ********

Masking position 10
Map Score:   2.24807

Number of sites scoring better than the average of aligned sites = 363
Number in coding regions = 311
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 6

          **********

No masking
Map Score:   3.07965e-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:   3.07965e-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 8

          **********

No masking
Map Score:   3.07965e-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