; oligo-analysis  -quick -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Trichoderma_atroviride/genome/Trichoderma_atroviride_start_codons.wc -o /software/CC/bio/opt/rsat/rsa-tools//public_html/data/genomes/Trichoderma_atroviride/genome/Trichoderma_atroviride_start_codon_frequencies
; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42. 
; Program version              	1.163
; Quick counting mode          
; Oligomer length              	3
; Input file                   	$RSAT/public_html/data/genomes/Trichoderma_atroviride/genome/Trichoderma_atroviride_start_codons.wc
; Input format                 	wc
; Output file                  	$RSAT/public_html/data/genomes/Trichoderma_atroviride/genome/Trichoderma_atroviride_start_codon_frequencies
; Count overlapping matches
; Counted on a single strand
; Background model             	Bernoulli
; Background estimation method 	
; Sequence type                	DNA
; Nb of sequences              	0
; Sum of sequence lengths      	0
; discarded residues           	NA (quick mode)	 (other letters than ACGT)
; discarded occurrences        	NA (quick mode)	 (contain discarded residues)
; nb possible positions        	NA (quick mode)
; total oligo occurrences      	12114
; alphabet size                	4
; nb possible oligomers        	64
; oligomers tested for significance	0
; Threshold values
;	Parameter      	Lower	Upper
;	ms_P           	none	1
;	occ_P          	none	1
; Sequences:
;
; column headers
;	1	seq            	oligomer sequence
;	2	id             	oligomer identifier
;	3	obs_freq       	observed relative frequency
;	4	occ            	observed occurrences
#seq	id	obs_freq	occ
atg	atg	0.9136536239062	11068
cca	cca	0.0219580650487	266
ctc	ctc	0.0023113752683	28
tcc	tcc	0.0021462770348	26
gag	gag	0.0020637279181	25
atc	atc	0.0020637279181	25
cgc	cgc	0.0019811788014	24
gac	gac	0.0017335314512	21
aag	aag	0.0017335314512	21
gat	gat	0.0016509823345	20
gct	gct	0.0016509823345	20
ccc	ccc	0.0016509823345	20
cct	cct	0.0016509823345	20
cag	cag	0.0015684332178	19
aaa	aaa	0.0015684332178	19
gtc	gtc	0.0015684332178	19
agc	agc	0.0015684332178	19
ctg	ctg	0.0014033349843	17
aac	aac	0.0014033349843	17
ccg	ccg	0.0014033349843	17
ttc	ttc	0.0013207858676	16
tct	tct	0.0013207858676	16
aat	aat	0.0013207858676	16
aca	aca	0.0013207858676	16
gcc	gcc	0.0013207858676	16
att	att	0.0012382367509	15
caa	caa	0.0011556876341	14
ggc	ggc	0.0011556876341	14
tca	tca	0.0011556876341	14
ttg	ttg	0.0011556876341	14
cta	cta	0.0010731385174	13
gaa	gaa	0.0009905894007	12
ctt	ctt	0.0009905894007	12
tac	tac	0.0009905894007	12
acc	acc	0.0009905894007	12
ttt	ttt	0.0009080402840	11
act	act	0.0009080402840	11
gcg	gcg	0.0008254911672	10
cga	cga	0.0008254911672	10
gca	gca	0.0008254911672	10
cac	cac	0.0008254911672	10
agt	agt	0.0008254911672	10
tgt	tgt	0.0007429420505	9
tgc	tgc	0.0007429420505	9
tcg	tcg	0.0007429420505	9
tat	tat	0.0007429420505	9
gta	gta	0.0006603929338	8
gtg	gtg	0.0006603929338	8
gtt	gtt	0.0006603929338	8
acg	acg	0.0005778438171	7
tgg	tgg	0.0005778438171	7
cgg	cgg	0.0005778438171	7
cgt	cgt	0.0004952947003	6
tta	tta	0.0004127455836	5
ata	ata	0.0004127455836	5
gga	gga	0.0004127455836	5
cat	cat	0.0003301964669	4
aga	aga	0.0003301964669	4
agg	agg	0.0002476473502	3
ggg	ggg	0.0002476473502	3
ggt	ggt	0.0002476473502	3
; Host name	nic43
; Job started	2011_11_26.223257
; Job done	2011_11_26.223257
; Seconds	0.16