AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i185_4_6_1_10_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	HI1190	89	6-pyruvoyl tetrahydrobiopterin synthase, putative
#2	HI1191	155	conserved hypothetical protein

Motif number 1

CGCAGGTTTTTAATTTAGCAAAAAGGTTTA	2	14	0	TAATTTAGCA	    0.986005	-142
AAAACCTGCGAATTGTAGCACAACGACTTC	2	34	1	AATTGTAGCA	    0.990925	-122
GGGGAAGTTCTATTTTAGCAAGACAAGTGA	2	81	0	TATTTTAGCA	    0.994395	-75
CCTAGTTTTTTATTGTAGGAGGTTTGCGAA	2	130	0	TATTGTAGGA	    0.990349	-26
          **********

Masking position 6
Map Score:   5.79766

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 27
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

AGAAAATGCCCAAGCTGTATTTTACGCAATAA	1	30	1	CAAGTTATTT	    0.986941	-60
ATATTTCTTTAAACCTTTATTGCGTAAAATAC	1	46	0	AAACTTATTG	    0.932103	-44
ATAAAGGTTTAAAGAAATATTTGACTCAAAAA	1	58	1	AAAGATATTT	    0.799917	-32
AATTTAGCAAAAAGGTTTACTT          	2	1	0	AAAGTTACTT	    0.983975	-155
CTTCACATCCAACGAAATATTTCACTTGTCTT	2	60	1	AACGATATTT	    0.954338	-96
TTCTAGTGGGGAAGTTCTATTTTAGCAAGACA	2	86	0	GAAGTTATTT	    0.987274	-70
          **** * *****

Masking position 8
Map Score:   4.84278

Number of sites scoring better than the average of aligned sites = 162
Number in coding regions = 130
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 3

AATACAGCTTGGGCATTTTCTGCATCCACC	1	21	0	GGGCATTTTC	     0.98873	-69
GTATTCTAGTGGGGAAGTTCTATTTTAGCA	2	91	0	GGGGAAGTTC	    0.988344	-65
GCGAACTACGGGGGGTATTCTAGTGGGGAA	2	105	0	GGGGGTATTC	    0.995584	-51
TTTTATTGTAGGAGGTTTGCGAACTACGGG	2	123	0	GGAGGTTTGC	    0.983099	-33
          **********

Masking position 8
Map Score:   2.44724

Number of sites scoring better than the average of aligned sites = 34
Number in coding regions = 22
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

CCCAAGCTGTATTTTACGCAATAAAGGTTT	1	38	1	ATTTTACGCA	    0.982655	-52
TTAAAGAAATATTTGACTCAAAAAGGTAGA	1	66	1	ATTTGACTCA	    0.975332	-24
CCAACGAAATATTTCACTTGTCTTGCTAAA	2	68	1	ATTTCACTTG	    0.920096	-88
GGGAAGTTCTATTTTAGCAAGACAAGTGAA	2	80	0	ATTTTAGCAA	    0.915656	-76
          ATTTTACCTAGTTTTTTATT	2	146	0	ATTTTACCTA	    0.985381	-10
          **********

Masking position 6
Map Score:   1.02345

Number of sites scoring better than the average of aligned sites = 307
Number in coding regions = 250
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 5

TATTTCTTTAAACCTTTATTGCGTAAAATA	1	47	0	AACCTTTATT	    0.970816	-43
    TTTTTCTACCTTTTTGAGTCAAATAT	1	74	0	TACCTTTTTG	    0.992433	-16
     AAGTAAACCTTTTTGCTAAATTAAA	2	6	1	AACCTTTTTG	    0.992402	-150
      ATTTTACCTAGTTTTTTATTGTAG	2	142	0	TACCTAGTTT	    0.941241	-14
          **********

Masking position 5
Map Score:   3.31493

Number of sites scoring better than the average of aligned sites = 85
Number in coding regions = 67
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 6

          **********

No masking
Map Score:   3.64809e-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:   3.64809e-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:   3.64809e-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