AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i322_mixed7_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	HI0179	130	pyruvate formate-lyase activating enzyme (act)
#2	HI0180	27	formate acetyltransferase (pfl)
#3	HI0181	300	formate transporter

Motif number 1

 AAACATGTTTATTTTTGACCGCACTTTGGCGGGAACA	1	10	1	TTTTTACTTT	    0.979743	-121
GGGAACATAATATGTATGAGCCTGATTTAAATCAGGCT	1	41	1	TTTATACTTT	    0.950624	-90
TTTAGTCTATAAAAAATGAGCCTGATTTAAATCAGGCT	1	59	0	AAAATACTTT	    0.936482	-72
TAGATATAGCTAAATTTTACCAAAGATTTAGTCTATAA	1	85	0	TATTTACATT	    0.955834	-46
GAATTCCCCCAGATAATCATCCACTTTTC         	3	2	0	AAAATACTTT	    0.941861	-299
GTAAAGTACTTAATTTGAAACTTGTTTTATTCGCGTAA	3	46	0	TATTGACTTT	    0.939412	-255
TCTGAATGTATGAAATTGAGCGAATATTAATATGGGAA	3	88	1	TAATTACATT	      0.9309	-213
GAATTTTGTCTTTAATTAAACAAACCTTGCAAAATATC	3	123	1	TTATTACCTT	    0.869918	-178
AAAAGCAAAAATTATTTCAACAAACTTTGATATTTTGC	3	151	0	ATTTTACTTT	    0.975867	-150
TGAAAATTTAATACTTTTAACAAGTTTACGACTACAAA	3	238	0	AATTTACTTA	    0.897958	-63
TAAAAGTATTAAATTTTCATCAACTTTTTCAATGTCAA	3	257	1	AATTTACTTT	    0.941083	-44
          * * *** * *    ***

Masking position 9
Map Score:   9.51505

Number of sites scoring better than the average of aligned sites = 1162
Number in coding regions = 816
Number in noncoding regions = 346
Number of orfs with sites within 600 bp upstream = 246
Fraction of orfs with sites within 600 bp upstream = 0.0395117


Motif number 2

        AAACATGTTTATTTTTGACCGCA	1	3	1	ACATTTTATT	    0.781184	-128
TTTACCAAAGATTTAGTCTATAAAAAATGAG	1	77	0	ATTTGTCTAT	    0.846905	-54
        AGATTTATTTATTAATTAACAAA	2	3	1	ATTTTTTATT	    0.915387	-25
        TTCCTTTGTTAATTAATAAATAA	2	15	0	CCTTGTTAAT	    0.903871	-13
TTAATTTGAAACTTGTTTTATTCGCGTAATA	3	44	0	ACTTTTTTAT	    0.943882	-257
TAATATGGGAATTTTGTCTTTAATTAAACAA	3	115	1	ATTTGTCTTT	    0.790879	-186
ATTTTGCAAGGTTTGTTTAATTAAAGACAAA	3	127	0	GTTTTTTAAT	    0.787402	-174
ATTTCAACAAACTTTGATATTTTGCAAGGTT	3	145	0	ACTTGATATT	    0.884274	-156
GACTACAAATACTTCTATAATTGGTGCTATT	3	216	0	ACTTTATAAT	    0.911703	-85
ATTTTCATCAACTTTTTCAATGTCAATAGTT	3	269	1	ACTTTTCAAT	    0.963554	-32
          **** ******

Masking position 4
Map Score:   4.83443

Number of sites scoring better than the average of aligned sites = 969
Number in coding regions = 756
Number in noncoding regions = 213
Number of orfs with sites within 600 bp upstream = 177
Fraction of orfs with sites within 600 bp upstream = 0.0284292


Motif number 3

TTATTCGCGTAATACCGTGAATTCCCCCAGATA	3	25	0	AATACCAATT	    0.886874	-276
GTATTACGCGAATAAAACAAGTTTCAAATTAAG	3	43	1	AATAAAAGTT	      0.7005	-258
CAGAGTAAGTAAAGTACTTAATTTGAAACTTGT	3	59	0	AAAGTAAATT	    0.959544	-242
ACTTACTCTGAATGTATGAAATTGAGCGAATAT	3	82	1	AATGTAAATT	    0.928229	-219
TTTGTTTAATTAAAGACAAAATTCCCATATTAA	3	114	0	TAAAGAAATT	     0.75259	-187
CAAACCTTGCAAAATATCAAAGTTTGTTGAAAT	3	143	1	AAAATAAAGT	    0.821416	-158
CATTGCAAAGAAAAGCAAAAATTATTTCAACAA	3	166	0	AAAAGCAATT	    0.958995	-135
AGGAGAGTAAAATAGCACCAATTATAGAAGTAT	3	206	1	AATAGCAATT	    0.957553	-95
AAACTTGTTAAAAGTATTAAATTTTCATCAACT	3	249	1	AAAGTAAATT	    0.958668	-52
CAACTTTTTCAATGTCAATAGTTGGAGTTTGAT	3	277	1	AATGTCAGTT	    0.917549	-24
          ******   ****

Masking position 10
Map Score:   5.16339

Number of sites scoring better than the average of aligned sites = 514
Number in coding regions = 414
Number in noncoding regions = 100
Number of orfs with sites within 600 bp upstream = 82
Fraction of orfs with sites within 600 bp upstream = 0.0131706


Motif number 4

          **********

No masking
Map Score:   2.79544e-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 5

          **********

No masking
Map Score:   2.79544e-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:   2.79544e-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