AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i227_rna_methyltransferase_bbur_reg_300.orf -o227_borburg_300.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -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 =  	0.28
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RBB00237	56	3615
#2	RBB00234	23	3615
#3	RBB00232	158	3615
#4	RBB00836	101	3615
#5	RBB00158	51	3615

Motif number 1

      ATCCTTTGTTATTTTTTATGCTTTCA	1	41	0	TTTTTATTTT	     0.95005	-16
TAGTGTTATATTGATACATATTGTTAT     	3	6	0	TTGTACATTT	    0.844306	-153
GATGTATATTTTTCTTAAGCTTTCAGTAATAG	3	35	0	TTTTTAAGTT	    0.964977	-124
TTTAATAAAATTGATTCATTTTGAGCATTTGT	3	69	0	TTGTTCATTT	    0.912707	-90
ATGAATCAATTTTATTAAATTTCAAGAAAGAA	3	82	1	TTTTTAAATT	    0.979921	-77
AAGAAAAAAATTTGTAAAATATTTTTTTTAAA	3	109	1	TTTTAAAAAT	    0.921399	-50
GTAAAATATTTTTTTTAAAGATAAAATGCTTT	3	122	1	TTTTTAAAAT	     0.95724	-37
TTTTCCTCCTTTGATAAAGCATTTTATCTTTA	3	137	0	TTGTAAAGAT	     0.82958	-22
TAATGTATTATTGCTTATTATTTACCT     	4	6	0	TTGTTATTTT	     0.93318	-96
TATTAATTTTTTTGTTGTAATTTAATGTATTA	4	28	0	TTTTTGTATT	    0.809756	-74
TATTAGGGTATTTTTAAAATATGGGTGAGTAT	4	74	0	TTTTAAAAAT	    0.921389	-28
ATAAATTAGATTTTTTATTTTTTCAATTTTGA	5	23	1	TTTTTATTTT	     0.95005	-29
       ACATTTCTCAAAATTGAAAAAATAA	5	37	0	TTTTCAAATT	    0.919373	-15
          *** ***** **

Masking position 5
Map Score:   15.899

Number of sites scoring better than the average of aligned sites = 2902
Number in coding regions = 1892
Number in noncoding regions = 1010
Number of orfs with sites within 600 bp upstream = 155
Fraction of orfs with sites within 600 bp upstream = 0.0248956


Motif number 2

AATTGAAAGCATAAAAAATAACAAAGGAT 	1	38	1	ATAAAAAATA	    0.979355	-19
GAAAGCTTAAGAAAAATATACATCTTACAA	3	43	1	GAAAAATATA	    0.841866	-116
TTTCAAGAAAGAAAAAAATTTGTAAAATAT	3	101	1	GAAAAAAATT	    0.946561	-58
TTTTATCTTTAAAAAAAATATTTTACAAAT	3	118	0	AAAAAAAATA	    0.979354	-41
        AGGTAAATAATAAGCAATAATA	4	3	1	GTAAATAATA	    0.938626	-99
ATAATAAGCAATAATACATTAAATTACAAC	4	17	1	ATAATACATT	    0.724712	-85
TTACAACAAAAAAATTAATAGCTTGGCAAA	4	40	1	AAAATTAATA	    0.906765	-62
ATAGCTTGGCAAAAATAATACTCACCCATA	4	57	1	AAAAATAATA	    0.955513	-45
 ACGTACTTAATAATAAATTAGATTTTTTA	5	10	1	ATAATAAATT	    0.918482	-42
AATTGAAAAAATAAAAAATCTAATTTATTA	5	21	0	ATAAAAAATC	    0.935882	-31
          **********

Masking position 4
Map Score:   12.4735

Number of sites scoring better than the average of aligned sites = 2119
Number in coding regions = 1371
Number in noncoding regions = 748
Number of orfs with sites within 600 bp upstream = 143
Fraction of orfs with sites within 600 bp upstream = 0.0229682


Motif number 3

GAATTGGCATGAGTTATATACATA      	1	5	0	GAGTTATATA	    0.979612	-52
TAGAAAAAAGGAGGTTTATAAT        	2	12	1	GAGGTTTATA	    0.973131	-12
TTCAGTAATAGTGTTATATTGATACATATT	3	16	0	GTGTTATATT	    0.954421	-143
GCATTTGTAAGATGTATATTTTTCTTAAGC	3	47	0	GATGTATATT	    0.934203	-112
AAATATGGGTGAGTATTATTTTTGCCAAGC	4	60	0	GAGTATTATT	    0.935952	-42
          **********

Masking position 7
Map Score:   3.03161

Number of sites scoring better than the average of aligned sites = 82
Number in coding regions = 44
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

TGTTATTTTTTATGCTTTCAATTATTGAAT	1	31	0	TATGCTTTCA	    0.992581	-26
ATATTTTTCTTAAGCTTTCAGTAATAGTGT	3	32	0	TAAGCTTTCA	    0.981459	-127
TTACAAATTTTTTTCTTTCTTGAAATTTAA	3	96	0	TTTTCTTTCT	    0.931262	-63
TTAGATTTTTTATTTTTTCAATTTTGAGAA	5	28	1	TATTTTTTCA	    0.956083	-24
          **********

Masking position 6
Map Score:   1.69583

Number of sites scoring better than the average of aligned sites = 84
Number in coding regions = 59
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 5

          **********

No masking
Map Score:   -1.17788e-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 6

          **********

No masking
Map Score:   -1.17788e-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:   -1.17788e-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