AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i225_Glutamyl_tRNA_synthase_hpyl_reg_300.orf -o225_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	RHP00088	297	AE000511
#2	RHP00089	82	AE000511
#3	RHP00253	58	AE000511
#4	RHP00255	91	AE000511
#5	RHP00256	76	AE000511

Motif number 1

AGTATGAAAATTTTTAAAAATTTACAAAAATGAGAA	1	81	1	TTTTTAATCA	    0.988526	-217
TTAAGAATGCTTTTTACATATTATATAAAAATATCC	1	222	0	TTTTTAATAT	     0.95549	-76
CATTGTAGCATTTTTAGATTTAAGAATGCTTTTTAC	1	241	0	TTTTTAATAA	    0.595567	-57
TTGCCCTTTCGTTTTAAAGATAAACATTGTAGCATT	1	265	0	GTTTTAATCA	     0.89198	-33
       TAATTTTTAGCGTTTTTAAGAATGATTAG	2	4	1	TTTTTACTAA	     0.98055	-79
GTTAGTAGCGTTATTATAACTAATCATTCTTAAAAA	2	23	0	TTATTAATCA	    0.905936	-60
      GCTCGTTTTATCTCTAAGCATGTTAAACTA	3	5	1	GTTTTACTCA	    0.975974	-54
         GTTTTTAGCCTTACAAAAAATTTAATG	3	42	0	TTTTTACTAA	    0.915403	-17
CTTAGCTTACTTTTTAACAATATCCATGCCTTAATG	4	58	0	TTTTTACTCA	      0.9914	-34
        CTTTTTTATCGCTTCAATTTAATCAAAA	5	3	1	TTTTTACTAT	    0.969759	-74
ATATTATAGTTATTTAAAGCTTAAATAAGGGTCTAG	5	49	1	TATTTAATAT	    0.762839	-28
          ****** *  *   **

Masking position 6
Map Score:   17.7431

Number of sites scoring better than the average of aligned sites = 351
Number in coding regions = 287
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 2

GGTGTTCTTTCTCATTTTTGTAAATTTTTAAAAA	1	91	0	CTCATTTTAA	    0.896688	-207
ATGATAAAATCTAAGCTTTATCAAGCCATTAGCC	1	125	0	CTAACTTTAA	    0.984761	-173
TTTTTTTTACCTAATTCTCATTAAATAGATTTTT	1	159	0	CTAATCTTAA	    0.949358	-139
ATTCTTAAATCTAAAAATGCTACAATGTTTATCT	1	250	1	CTAAAATTCA	    0.933086	-48
GTTATTATAACTAATCATTCTTAAAAACGCTAAA	2	16	0	CTAACATTAA	    0.953322	-67
AATAACGCTACTAACAACACTCAAGCTAAAATCT	2	44	1	CTAAAACTAA	    0.970277	-39
AACACTCAAGCTAAAATCTATTAAGGAAATCAGT	2	59	1	CTAAATCTAA	     0.96332	-24
CGTTTTATCTCTAAGCATGTTAAACTACCATTAA	3	14	1	CTAACATTAA	     0.98629	-45
AACATGCTAGCTAAAAAATCTAAATTATTGTAAC	4	17	0	CTAAAAATAA	    0.922088	-75
ATATTGTAATCTAATTTTGATTAAATTGAAGCGA	5	19	0	CTAATTTTAA	    0.968786	-58
          **** ***  * **

Masking position 4
Map Score:   12.2051

Number of sites scoring better than the average of aligned sites = 172
Number in coding regions = 146
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 3

TCATTATCATTTATGCTATAATTATGGGACAA	1	36	0	TTATGTAAAT	    0.979713	-262
TTCTTTCTCATTTTTGTAAATTTTTAAAAATT	1	89	0	TTTTTTAATT	    0.614068	-209
AAATAGATTTTTATGATAAAATCTAAGCTTTA	1	139	0	TTATGTAAAT	    0.979365	-159
AAAGGGGATATTTTTATATAATATGTAAAAAG	1	217	1	TTTTTTAAAT	     0.81613	-81
TTAAATCTAAAAATGCTACAATGTTTATCTTT	1	254	1	AAATGTAAAT	    0.769131	-44
TTTAAGAATGATTAGTTATAATAACGCTACTA	2	25	1	ATTAGTAAAT	    0.889153	-58
CTAACAACACTCAAGCTAAAATCTATTAAGGA	2	54	1	TCAAGTAAAT	    0.818021	-29
        GCTTTTGTTACAATAATTTAGATT	4	3	1	TTTTGTAAAT	    0.987928	-89
ATTTAGATTTTTTAGCTAGCATGTTAGCAATT	4	26	1	TTTAGTACAT	    0.860043	-66
AAGGCATGGATATTGTTAAAAAGTAAGCTAAG	4	62	1	TATTGTAAAA	    0.743038	-30
TGTAATCTAATTTTGATTAAATTGAAGCGATA	5	17	0	TTTTGTTAAT	    0.910891	-60
          ***** ** ***

Masking position 7
Map Score:   8.34881

Number of sites scoring better than the average of aligned sites = 624
Number in coding regions = 410
Number in noncoding regions = 214
Number of orfs with sites within 600 bp upstream = 230
Fraction of orfs with sites within 600 bp upstream = 0.0369419


Motif number 4

AAATTTTCATACTCTCATTTACTTTTTCAT	1	64	0	ACTCTCATTT	    0.918295	-234
ATTGATGCCAACCCCTTTTTTTTACCTAAT	1	178	0	ACCCCTTTTT	    0.988241	-120
TCCCCTTTTAACCCCCTATTGATGCCAACC	1	195	0	ACCCCCTATT	    0.982922	-103
ATATAAAAATATCCCCTTTTAACCCCCTAT	1	206	0	ATCCCCTTTT	     0.97318	-92
    CGCTAGACCCTTATTTAAGCTTTAAA	5	61	0	ACCCTTATTT	    0.963006	-16
          **********

Masking position 9
Map Score:   3.10317

Number of sites scoring better than the average of aligned sites = 403
Number in coding regions = 326
Number in noncoding regions = 77
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 5

          **********

No masking
Map Score:   1.44541e-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:   1.44541e-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:   1.44541e-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