AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i193_dna_polymerase_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	HI0856	148	DNA polymerase I (polA)
#2	HI0889	123	serine hydroxymethyltransferase (serine methylase) (glyA)
#3	HI0890	58	conserved hypothetical protein

Motif number 1

  TTGATTTCCTTAAATTAAATATTTGAAT	1	9	1	CTTAAATTAA	    0.908827	-140
ATTTGAATGGCTGATATTATGCCATAGCAA	1	31	1	CTGATATTAT	    0.938456	-118
ATTTATGACGAATATTTTTTGCTATGGCAT	1	49	0	AATATTTTTT	    0.601517	-100
AAATATTCGTCATAAATTTTACATTAAACC	1	62	1	CATAAATTTT	    0.976442	-87
CGCTCATCACCATAAATTACGCTATAATGC	1	99	1	CATAAATTAC	    0.928444	-50
CATCACTTAAATGAAATTAATTCATCATAA	2	20	0	ATGAAATTAA	    0.725591	-104
AAATTTCATTCCTAAATTTTCATCACTTAA	2	40	0	CCTAAATTTT	    0.938233	-84
AAATTTAGGAATGAAATTTTAATTAAATTT	2	51	1	ATGAAATTTT	     0.92809	-73
TGAAATTTTAATTAAATTTTTATCCATAAA	2	62	1	ATTAAATTTT	    0.939912	-62
TAATTTATGGCAGATAGTTTAACTGTTTAT	2	87	0	CAGATAGTTT	    0.752652	-37
AACTATCTGCCATAAATTACATAACAGGAG	2	98	1	CATAAATTAC	    0.928444	-26
AATATCGCCGCTTATTTTTT          	3	49	1	CTTATTTTTT	    0.851272	-10
          **********

Masking position 4
Map Score:   11.7291

Number of sites scoring better than the average of aligned sites = 1376
Number in coding regions = 1087
Number in noncoding regions = 289
Number of orfs with sites within 600 bp upstream = 252
Fraction of orfs with sites within 600 bp upstream = 0.0404754


Motif number 2

AGCCATTCAAATATTTAATTTAAGGAAATC	1	13	0	ATATTTAATT	     0.82119	-136
TTCGTCATAAATTTTACATTAAACCCGCCA	1	67	1	ATTTTACATT	    0.918042	-82
TAATGCCCACATTTTTCAGTTTAAAACGAG	1	123	1	ATTTTTCAGT	    0.899944	-26
TATGATGAATTAATTTCATTTAAGTGATGA	2	21	1	TAATTTCATT	    0.923871	-103
TTCATTCCTAAATTTTCATCACTTAAATGA	2	36	0	AATTTTCATC	    0.976261	-88
TTAGGAATGAAATTTTAATTAAATTTTTAT	2	55	1	AATTTTAATT	    0.821542	-69
ATTTTAATTAAATTTTTATCCATAAACAGT	2	66	1	AATTTTTATC	    0.843317	-58
TATCTGCCATAAATTACATAACAGGAGAAC	2	101	1	AAATTACATA	    0.710203	-23
        TTTATTTTCTTTCGTTGATTAT	3	3	1	TATTTTCTTT	     0.78473	-56
          **********

Masking position 5
Map Score:   5.89088

Number of sites scoring better than the average of aligned sites = 1339
Number in coding regions = 1076
Number in noncoding regions = 263
Number of orfs with sites within 600 bp upstream = 222
Fraction of orfs with sites within 600 bp upstream = 0.0356569


Motif number 3

ATAATATCAGCCATTCAAATATTTAATTTAAG	1	19	0	CCATTAAAAT	    0.971028	-130
TGATATTATGCCATAGCAAAAAATATTCGTCA	1	42	1	CCATACAAAA	    0.973174	-107
ATTAAACCCGCCATTCGCTCATCACCATAAAT	1	84	1	CCATTGCTAT	    0.942338	-65
         TCCATATCATTATGATGAATTAA	2	2	1	CCATACATAT	    0.985441	-122
AAATTTTTATCCATAAACAGTTAAACTATCTG	2	75	1	CCATAACATT	    0.927664	-49
TCGCCGCTAACCATATAATCAACGAAAGAAAA	3	15	0	CCATAAATAA	    0.971103	-44
          ***** *** **

Masking position 4
Map Score:   1.6604

Number of sites scoring better than the average of aligned sites = 188
Number in coding regions = 160
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 4

ATGGCATAATATCAGCCATTCAAATATTTA	1	26	0	ATCAGCCATT	    0.985393	-123
TTTACATTAAACCCGCCATTCGCTCATCAC	1	79	1	ACCCGCCATT	     0.98628	-70
CAGTTAAACTATCTGCCATAAATTACATAA	2	92	1	ATCTGCCATA	     0.97945	-32
TTATATGGTTAGCGGCGATTAATATCGCCG	3	29	1	AGCGGCGATT	    0.993291	-30
  AAAAAATAAGCGGCGATATTAATCGCCG	3	41	0	AGCGGCGATA	    0.992714	-18
          **********

Masking position 8
Map Score:   6.40134

Number of sites scoring better than the average of aligned sites = 65
Number in coding regions = 62
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

          **********

No masking
Map Score:   -7.93376e-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:   -7.93376e-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:   -7.93376e-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