AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i312_mixed26_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	HI0549	169	dimethyladenosine transferase (ksgA)

Motif number 1

TTTAGGCGGAAAAGTTAAGAAAAACGGGCG	1	11	1	AAAGTTAAGA	    0.984449	-159
TCTTTCGTAGAAAGCTAAAAACGGCTATAA	1	43	0	AAAGCTAAAA	    0.996614	-127
GCTTTCTACGAAAGAAAAAATAATATTGTT	1	58	1	AAAGAAAAAA	    0.977123	-112
AATGATTTACAAAGCTAAAACAACCCCTAT	1	118	1	AAAGCTAAAA	    0.996614	-52
          **********

Masking position 7
Map Score:   7.34136

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 23
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 2

CGGGCGGATTATAGCCGTTTTTAGCTTTCTA	1	35	1	ATAGCCGTTT	    0.917603	-135
GTTATGCCAAATTGAGTTTTTCATGAACAAT	1	82	0	ATTGAGTTTT	    0.962948	-88
TGCGGTTATTATAGGGGTTGTTTTAGCTTTG	1	127	0	ATAGGGGTTT	    0.991643	-43
TAATAAGAAAAGTGCGGTTATTATAGGGGTT	1	139	0	AGTGCGGTTT	    0.970543	-31
          ********* *

Masking position 8
Map Score:   1.5265

Number of sites scoring better than the average of aligned sites = 191
Number in coding regions = 127
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 3

CGGCTATAATCCGCCCGTTTTTCTTAACTT	1	22	0	CCGCCCGTTT	    0.997916	-148
GGGCGGATTATAGCCGTTTTTAGCTTTCTA	1	36	1	TAGCCGTTTT	    0.976673	-134
CCTATAATAACCGCACTTTTCTTATTAAAT	1	143	1	CCGCACTTTT	    0.995317	-27
          **********

Masking position 8
Map Score:   1.01798

Number of sites scoring better than the average of aligned sites = 728
Number in coding regions = 449
Number in noncoding regions = 279
Number of orfs with sites within 600 bp upstream = 213
Fraction of orfs with sites within 600 bp upstream = 0.0342114


Motif number 4

          **********

No masking
Map Score:   3.08538e-14

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:   3.08538e-14

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:   3.08538e-14

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