AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i072_Fatty_Acid_Bios___Butirate_Fermentation_hpyl_reg_300.orf -o072_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -x5 -e 
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 =  	0.39
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RHP00119	143	AE000511
#2	RHP00120	20	AE000511
#3	RHP00121	281	AE000511
#4	RHP00124	19	AE000511

Motif number 1

AACGATATAACTAAAAATTAGAAAAACTTTAA	1	30	0	CTAAAATAGA	    0.982565	-114
GACTTTTAATCTAAAAACGATATAACTAAAAA	1	45	0	CTAAAACATA	    0.985341	-99
CGTTTTTAGATTAAAAGTCAGCACTATAGCGC	1	58	1	TTAAAATAGC	    0.926909	-86
TTGTTATATAATAAAAGCGAGACAAGAATGTT	1	101	1	ATAAAACAGA	    0.979128	-43
   AATTCTATTAAAACCCTGAAACTAGGCAA	3	8	1	TTAAAACTGA	    0.880882	-274
GAGTGGGGATCTAAAATCAAGCAGATATGCAC	3	91	0	CTAAAACAGC	    0.992999	-191
TAGATCCCCACTCAAAGCTATATTGTGCAATA	3	110	1	CTCAAACATA	    0.940138	-172
AAAACCTAAAATAAAATCCAACCTGTTAGGGT	3	206	1	ATAAAACAAC	    0.856857	-76
TGTCAATCACCTAAAAGTGATACTATGAATAA	3	237	1	CTAAAATATA	    0.956579	-45
          ****** * ***

Masking position 6
Map Score:   10.7676

Number of sites scoring better than the average of aligned sites = 857
Number in coding regions = 760
Number in noncoding regions = 97
Number of orfs with sites within 600 bp upstream = 75
Fraction of orfs with sites within 600 bp upstream = 0.0120463


Motif number 2

TAATCTAAAAACGATATAACTAAAAATTAGAAA	1	38	0	ACGATAAAAA	    0.916429	-106
GCACTATAGCGCTATAAGACTAATTGTTATATA	1	78	1	GCTATAGAAA	    0.941492	-66
AAGACTAATTGTTATATAATAAAAGCGAGACAA	1	93	1	GTTATAAAAA	    0.971753	-51
TATAATAAAAGCGAGACAAGAATGTTAAAAAAT	1	107	1	GCGAGAAAAT	    0.941366	-37
AGACAAGAATGTTAAAAAATGAAAGGAGCGTGT	1	120	1	GTTAAAAAAA	    0.947699	-24
TTTTTAAAGCGTTAGAGAAACATGAGCCTAAAG	3	59	1	GTTAGAAAAT	     0.88625	-223
TTTGAGTGGGGATCTAAAATCAAGCAGATATGC	3	93	0	GATCTAAAAA	    0.733497	-189
AAGCTATATTGTGCAATAATCATTGAACGATAA	3	124	1	GTGCAAAAAT	    0.840437	-158
TAATCATTGAACGATAAGAATAATATTTTTGTG	3	140	1	ACGATAGAAA	    0.825027	-142
TAATATTTTTGTGAAAAAAATAAACGGATCGCC	3	160	1	GTGAAAAAAA	    0.971802	-122
TCACCTAAAAGTGATACTATGAATAATAAATCA	3	243	1	GTGATATAAA	    0.911725	-39
          ****** **  **

Masking position 6
Map Score:   6.46798

Number of sites scoring better than the average of aligned sites = 764
Number in coding regions = 663
Number in noncoding regions = 101
Number of orfs with sites within 600 bp upstream = 81
Fraction of orfs with sites within 600 bp upstream = 0.01301


Motif number 3

GTTTGAATGCTCCGCATTAAAGTTTTTCTAAT	1	14	1	TCGCATAAAG	    0.980621	-130
AGATTAAAAGTCAGCACTATAGCGCTATAAGA	1	65	1	TAGCATATAG	    0.980998	-79
TATATAACAATTAGTCTTATAGCGCTATAGTG	1	79	0	TAGTCTATAG	    0.889948	-65
    AGAGCAAACGCCATTTAGAT        	2	3	0	ACGCCTTTAG	    0.957258	-18
ATCAAGCAGATATGCACTTTAGGCTCATGTTT	3	76	0	TTGCATTTAG	    0.975399	-206
CAATGATTATTGCACAATATAGCTTTGAGTGG	3	117	0	TCACATATAG	    0.937842	-165
       GTCTTTGCCTTTAAGTTGATTTATT	3	267	0	TTGCCTTAAG	    0.954189	-15
          * **** *****

Masking position 11
Map Score:   4.18251

Number of sites scoring better than the average of aligned sites = 243
Number in coding regions = 222
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 4

TTTCTAAGCAGTCTTTGCCTAGTTTCAGGG	3	24	0	GTCTTTGCCT	    0.997673	-258
          GTCTTTGCCTTTAAGTTGAT	3	272	0	GTCTTTGCCT	    0.997673	-10
          **********

Masking position 5
Map Score:   1.55727

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 9
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

          **********

No masking
Map Score:   2.227e-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:   2.227e-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:   2.227e-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