AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i036_Acetate_Metabolism_hinf_reg_300.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	HI1203	67	phosphate acetyltransferase (pta)
#2	HI1204	214	acetate kinase (ackA)

Motif number 1

ACAACAAGCTGCCGAATTTTTCGGCAGTTTT	1	15	1	GCGAATTTTT	    0.981815	-53
TTTTCGGCAGTTTTTATTTATAAAATATACA	1	32	1	TTTTATTTAT	    0.719164	-36
TAAACCTTAATATGTATATTTTATAAATAAA	1	44	0	TTGTATATTT	    0.875864	-24
TGATAAGTGCGGTCAATTTTTGAGGTGTTTT	2	12	0	GTCAATTTTT	    0.971283	-203
CGCTATTTTAAGTCTATTTTTAGTAAAAATA	2	45	1	ATCTATTTTT	    0.941957	-170
AGTAAAAATAGTTTAATTTTTCAAAAAATAC	2	66	1	GTTAATTTTT	    0.955574	-149
TACAAACTTTATCGTATTTTTTGAAAAATTA	2	79	0	ACGTATTTTT	    0.962834	-136
TACGATAAAGTTTGTATTTTTTCCTTACCGA	2	94	1	TTGTATTTTT	    0.969222	-121
TTTCCTTACCGATGAATTTATTTTATTCATC	2	113	1	GTGAATTTAT	    0.942144	-102
TGTATTCTATGTCTGATTTTTCAAACCATCT	2	150	1	GCTGATTTTT	    0.936183	-65
CATCTTAGATGATGGATTTCTATTAACCTCA	2	176	1	GTGGATTTCT	    0.919009	-39
      AGGAACCCTATATTTGATTGAGGTT	2	200	0	ACCTATATTT	    0.749454	-15
          * *********

Masking position 6
Map Score:   16.011

Number of sites scoring better than the average of aligned sites = 1243
Number in coding regions = 969
Number in noncoding regions = 274
Number of orfs with sites within 600 bp upstream = 229
Fraction of orfs with sites within 600 bp upstream = 0.0367812


Motif number 2

TTCGGCAGCTTGTTGTTAAA          	1	1	0	TGTTGTTAAA	    0.947872	-67
TAAGTCTATTTTTAGTAAAAATAGTTTAAT	2	53	1	TTTAGTAAAA	    0.806448	-162
TTATCGTATTTTTTGAAAAATTAAACTATT	2	72	0	TTTTGAAAAA	    0.797352	-143
AGAATACACCTTTTGATGAATAAAATAAAT	2	128	0	TTTTGATGAA	    0.961468	-87
ATCTAAGATGGTTTGAAAAATCAGACATAG	2	156	0	GTTTGAAAAA	    0.959155	-59
          **********

Masking position 3
Map Score:   3.66484

Number of sites scoring better than the average of aligned sites = 336
Number in coding regions = 261
Number in noncoding regions = 75
Number of orfs with sites within 600 bp upstream = 65
Fraction of orfs with sites within 600 bp upstream = 0.0104401


Motif number 3

GCAGTTTTTATTTATAAAATATACATATTAA	1	38	1	TTATAAAATA	    0.953184	-30
ACTAAAAATAGACTTAAAATAGCGTATGATA	2	38	0	GCTTAAAATA	    0.968593	-177
AAACTATTTTTACTAAAAATAGACTTAAAAT	2	49	0	TCTAAAAATA	    0.952514	-166
AGTTTAATTTTTCAAAAAATACGATAAAGTT	2	75	1	TCAAAAAATA	    0.979174	-140
CACCTTTTGATGAATAAAATAAATTCATCGG	2	121	0	TAATAAAATA	    0.973317	-94
TGAAAAATCAGACATAGAATACACCTTTTGA	2	142	0	GCATAGAATA	    0.957226	-73
TCTATTAACCTCAATCAAATATAGGGTTCCT	2	194	1	TAATCAAATA	    0.918256	-21
          * *********

Masking position 8
Map Score:   7.2997

Number of sites scoring better than the average of aligned sites = 339
Number in coding regions = 231
Number in noncoding regions = 108
Number of orfs with sites within 600 bp upstream = 106
Fraction of orfs with sites within 600 bp upstream = 0.0170254


Motif number 4

GCCGAAAAATTCGGCAGCTTGTTGTTAAA 	1	10	0	TCGGCAGCTT	    0.998359	-58
GCCGAATTTTTCGGCAGTTTTTATTTATAA	1	25	1	TCGGCAGTTT	    0.997586	-43
          **********

Masking position 6
Map Score:   1.11019

Number of sites scoring better than the average of aligned sites = 4
Number in coding regions = 3
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 5

ATTCGGCAGCTTGTTGTTAAA         	1	2	0	TTGTTGTTAA	    0.931099	-66
AATATACATATTAAGGTTTAACT       	1	55	1	TTAAGGTTTA	     0.96538	-13
CGGTCAATTTTTGAGGTGTTTTT       	2	4	0	TTGAGGTGTT	    0.969486	-211
CTATATTTGATTGAGGTTAATAGAAATCCA	2	188	0	TTGAGGTTAA	    0.984244	-27
          **********

Masking position 7
Map Score:   0.869191

Number of sites scoring better than the average of aligned sites = 118
Number in coding regions = 102
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 6

          **********

No masking
Map Score:   -7.57276e-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 7

          **********

No masking
Map Score:   -7.57276e-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 8

          **********

No masking
Map Score:   -7.57276e-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