; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/gcm.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/gcm_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/gcm.tab
; Output files
;	output	html_ready/gcm_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : gcm
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6	7
; -----	|--------|-------|-------|-------|-------|-------|-------|
a	|	0	0	1	2	0	8	0
c	|	8	8	7	0	8	0	0
g	|	0	0	0	5	0	0	1
t	|	0	0	0	1	0	0	7
; -----	|--------|-------|-------|-------|-------|-------|-------|
; c.sum	|	8	8	8	8	8	8	8	56
; c.max	|	8	8	7	5	8	8	7	8
; c.min	|	0	0	0	0	0	0	0	0
; Profile matrix
;pos	a	c	g	t	|	sum	max_frq	inf_sum	strict	IUPAC	-----------1-----------2
1	0	8	0	0	|	8	 1.00	 1.01	C	C	CCCCCCCCCCCCCCCCC
2	0	8	0	0	|	8	 1.00	 1.01	C	C	CCCCCCCCCCCCCCCCC
3	1	7	0	0	|	8	 0.88	 0.74	C	C	aCCCCCCCCCC
4	2	0	5	1	|	8	 0.62	 0.35	g	r	ggg
5	0	8	0	0	|	8	 1.00	 1.01	C	C	CCCCCCCCCCCCCCCCC
6	8	0	0	0	|	8	 1.00	 1.01	A	A	AAAAAAAAAAAAAAAAA
7	0	0	1	7	|	8	 0.88	 0.74	T	T	gTTTTTTTTTT
;
; Matrix type: information
;P	|    1    2    3    4    5    6    7
;-	|-----|----|----|----|----|----|----|
a	| -0.1 -0.1 -0.1  0.0 -0.1  1.2 -0.1
c	|  1.2  1.2  0.9 -0.1  1.2 -0.1 -0.1
g	| -0.1 -0.1 -0.1  0.5 -0.1 -0.1 -0.1
t	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1  0.9
;-	|-----|----|----|----|----|----|----|
; i.sum	|  1.0  1.0  0.7  0.4  1.0  1.0  0.7  5.9
; i.max	|  1.2  1.2  0.9  0.5  1.2  1.2  0.9  1.2
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
; Sites	8
>gcm_chr3R_14058051_14058
cccgcat
>gcm_chr3R_14059835_14059
cccgcat
>gcm_chr3R_14060045_14060
cccgcat
>gcm_chr3R_14059624_14059
cccacat
>gcm_chr3R_14060445_14060
cccacat
>gcm_chr3R_14060762_14060
ccctcat
>gcm_chr3R_14060568_14060
ccagcat
>gcm_chr3R_14059348_14059
cccgcag
;
; Matrix parameters
;	Columns                      	7
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.250|c:0.250|g:0.250|t:0.250
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme ../data/oreganno_data/processed_data/regulons_for_one_factor/gcm_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi
;	sites                        	8
;	meme.llr                     	64
;	meme.E-value                 	5e-07
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.25
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.86092
;	information.per.column       	0.837274
;	max.possible.info.per.col    	1.38629
;	consensus.strict             	CCCgCAT
;	consensus.strict.rc          	ATGcGGG
;	consensus.IUPAC              	CCCrCAT
;	consensus.IUPAC.rc           	ATGyGGG
;	consensus.regexp             	CCC[ag]CAT
;	consensus.regexp.rc          	ATG[ct]GGG
;	residues.content.crude.freq  	a:0.1964|c:0.5536|g:0.1071|t:0.1429
;	G+C.content.crude.freq       	0.660714
;	residues.content.corrected.freq	a:0.2024|c:0.5198|g:0.1230|t:0.1548
;	G+C.content.corrected.freq   	0.642857
;	min(P(S|M))                  	1.27609e-11
;	max(P(S|M))                  	0.267272
;	proba_range                  	0.267272
;	Wmin                         	-15.4
;	Wmax                         	8.5
;	Wrange                       	23.9
; Job started 2007_12_10.132102
; Job done    2007_12_10.132102