AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i036_Acetate_Metabolism_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	HI1203	67	phosphate acetyltransferase (pta)
#2	HI1204	214	acetate kinase (ackA)

Motif number 1

ACAACAAGCTGCCGAATTTTTCGGCAGTTTT	1	15	1	GCGAATTTTT	    0.983838	-53
TTTTCGGCAGTTTTTATTTATAAAATATACA	1	32	1	TTTTATTTAT	    0.742746	-36
TAAACCTTAATATGTATATTTTATAAATAAA	1	44	0	TTGTATATTT	     0.88833	-24
TGATAAGTGCGGTCAATTTTTGAGGTGTTTT	2	12	0	GTCAATTTTT	    0.974446	-203
CGCTATTTTAAGTCTATTTTTAGTAAAAATA	2	45	1	ATCTATTTTT	    0.948179	-170
AGTAAAAATAGTTTAATTTTTCAAAAAATAC	2	66	1	GTTAATTTTT	    0.960398	-149
TACAAACTTTATCGTATTTTTTGAAAAATTA	2	79	0	ACGTATTTTT	    0.966897	-136
TACGATAAAGTTTGTATTTTTTCCTTACCGA	2	94	1	TTGTATTTTT	    0.972606	-121
TTTCCTTACCGATGAATTTATTTTATTCATC	2	113	1	GTGAATTTAT	    0.948346	-102
TGTATTCTATGTCTGATTTTTCAAACCATCT	2	150	1	GCTGATTTTT	    0.942987	-65
CATCTTAGATGATGGATTTCTATTAACCTCA	2	176	1	GTGGATTTCT	    0.927501	-39
      AGGAACCCTATATTTGATTGAGGTT	2	200	0	ACCTATATTT	    0.771301	-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

          TTTAACAACAAGCTGCCGAA	1	1	1	TTTAACAACA	    0.942437	-67
ATTAAACTATTTTTACTAAAAATAGACTTA	2	53	0	TTTTACTAAA	    0.813711	-162
AATAGTTTAATTTTTCAAAAAATACGATAA	2	72	1	TTTTTCAAAA	    0.811078	-143
ATTTATTTTATTCATCAAAAGGTGTATTCT	2	128	1	TTCATCAAAA	    0.957746	-87
CTATGTCTGATTTTTCAAACCATCTTAGAT	2	156	1	TTTTTCAAAC	    0.958123	-59
          **********

Masking position 8
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	    0.954521	-30
ACTAAAAATAGACTTAAAATAGCGTATGATA	2	38	0	GCTTAAAATA	    0.969488	-177
AAACTATTTTTACTAAAAATAGACTTAAAAT	2	49	0	TCTAAAAATA	    0.953863	-166
AGTTTAATTTTTCAAAAAATACGATAAAGTT	2	75	1	TCAAAAAATA	    0.979806	-140
CACCTTTTGATGAATAAAATAAATTCATCGG	2	121	0	TAATAAAATA	    0.974119	-94
TGAAAAATCAGACATAGAATACACCTTTTGA	2	142	0	GCATAGAATA	    0.958495	-73
TCTATTAACCTCAATCAAATATAGGGTTCCT	2	194	1	TAATCAAATA	    0.920584	-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

 TTTAACAACAAGCTGCCGAATTTTTCGGC	1	10	1	AAGCTGCCGA	    0.998126	-58
TTATAAATAAAAACTGCCGAAAAATTCGGC	1	25	0	AAACTGCCGA	    0.997239	-43
          **********

Masking position 5
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

         TTTAACAACAAGCTGCCGAAT	1	2	1	TTAACAACAA	    0.921647	-66
       AGTTAAACCTTAATATGTATATT	1	55	0	TAAACCTTAA	    0.962108	-13
       AAAAACACCTCAAAAATTGACCG	2	4	1	AACACCTCAA	    0.965032	-211
TGGATTTCTATTAACCTCAATCAAATATAG	2	188	1	TTAACCTCAA	    0.984265	-27
          **********

Masking position 4
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