AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i227_rna_methyltransferase_bbur_reg_100.orf -o227_borburg_100.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	RBB00158	51	3615

Motif number 1

TTTGTTATTTTTTATGCTTTCAATTATTGA	1	33	0	TTTATGCTTT	    0.887568	-24
      ATCCTTTGTTATTTTTTATGCTTT	1	43	0	TTTGTTATTT	    0.941836	-14
ATAAACCTCCTTTTTTCTAA          	2	1	0	TTTTTTCTAA	    0.920076	-23
TAAGATGTATATTTTTCTTAAGCTTTCAGT	3	40	0	ATTTTTCTTA	    0.957882	-119
AAAATGAATCAATTTTATTAAATTTCAAGA	3	79	1	AATTTTATTA	    0.762865	-80
TTTTACAAATTTTTTTCTTTCTTGAAATTT	3	98	0	TTTTTTCTTT	    0.991721	-61
ATTTGTAAAATATTTTTTTTAAAGATAAAA	3	118	1	TATTTTTTTT	     0.83743	-41
TGATAAAGCATTTTATCTTTAAAAAAAATA	3	128	0	TTTTATCTTT	     0.94398	-31
AAAAATCTAATTTATTATTAAGTACGT   	4	8	0	TTTATTATTA	    0.929377	-44
ATAAATTAGATTTTTTATTTTTTCAATTTT	4	23	1	TTTTTTATTT	    0.983861	-29
          **********

Masking position 3
Map Score:   13.115

Number of sites scoring better than the average of aligned sites = 3020
Number in coding regions = 1955
Number in noncoding regions = 1065
Number of orfs with sites within 600 bp upstream = 136
Fraction of orfs with sites within 600 bp upstream = 0.0218439


Motif number 2

CAATAATTGAAAGCATAAAAAATAACAAAGGA	1	34	1	AAATAAAAAA	     0.74514	-23
TAGAAAAAAGGAGGTTTATAAT          	2	12	1	GATTTATAAT	    0.848252	-12
     ATAACAATATGTATCAATATAACACTA	3	6	1	AATGTATCAA	    0.952667	-153
CTATTACTGAAAGCTTAAGAAAAATATACATC	3	35	1	AATTAAGAAA	    0.915475	-124
GAGCATTTGTAAGATGTATATTTTTCTTAAGC	3	47	0	AATGTATATT	    0.682288	-112
ACAAATGCTCAAAATGAATCAATTTTATTAAA	3	69	1	AATGAATCAA	    0.965163	-90
TTCTTTCTTGAAATTTAATAAAATTGATTCAT	3	82	0	AATTAATAAA	    0.976657	-77
GAAAGAAAAAAATTTGTAAAATATTTTTTTTA	3	107	1	AATGTAAAAT	    0.915924	-52
AAAGCATTTTATCTTTAAAAAAAATATTTTAC	3	122	0	ATTTAAAAAA	    0.895626	-37
TAAAGATAAAATGCTTTATCAAAGGAGGAAAA	3	137	1	ATTTTATCAA	    0.859513	-22
        ACGTACTTAATAATAAATTAGATT	4	3	1	GTTTAATAAT	    0.728777	-49
ACATTTCTCAAAATTGAAAAAATAAAAAATCT	4	30	0	AATGAAAAAA	    0.966923	-22
          **  ********

Masking position 8
Map Score:   9.74226

Number of sites scoring better than the average of aligned sites = 3251
Number in coding regions = 2126
Number in noncoding regions = 1125
Number of orfs with sites within 600 bp upstream = 173
Fraction of orfs with sites within 600 bp upstream = 0.0277867


Motif number 3

TTATTTTTTATGCTTTCAATTATTGAATTG	1	29	0	TGCTTTCAAT	    0.957282	-28
ATCTTACAAATGCTCAAAATGAATCAATTT	3	64	1	TGCTCAAAAT	    0.990451	-95
ATTTTTTTCTTTCTTGAAATTTAATAAAAT	3	90	0	TTCTTGAAAT	    0.972305	-69
      ACATTTCTCAAAATTGAAAAAATA	4	38	0	TTCTCAAAAT	    0.984765	-14
          **********

Masking position 4
Map Score:   2.33413

Number of sites scoring better than the average of aligned sites = 106
Number in coding regions = 81
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

          **********

No masking
Map Score:   -4.38104e-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:   -4.38104e-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:   -4.38104e-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