; convert-matrix  -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Ubx.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Ubx_parameters.txt
; Input files
;	input	/Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Ubx.tab
; Output files
;	output	html_ready/Ubx_parameters.txt
; pseudo-weight       	1
;
; MATRIX 1/1 : Ubx
;
;
; Matrix type: counts
; Pos	|	1	2	3	4	5	6
; -----	|--------|-------|-------|-------|-------|-------|
a	|	7	24	55	4	0	48
c	|	29	23	2	0	3	0
g	|	12	6	0	1	0	0
t	|	11	6	2	54	56	11
; -----	|--------|-------|-------|-------|-------|-------|
; c.sum	|	59	59	59	59	59	59	354
; c.max	|	29	24	55	54	56	48	56
; c.min	|	7	6	0	0	0	0	0
; Profile matrix
;pos	a	c	g	t	|	sum	max_frq	inf_sum	strict	IUPAC	-----------1-----------2
1	7	29	12	11	|	59	 0.49	 0.48	C	S	Cg
2	24	23	6	6	|	59	 0.41	 0.30	C	M	C
3	55	2	0	2	|	59	 0.93	 0.70	a	a	aaaaaaat
4	4	0	1	54	|	59	 0.92	 0.64	t	t	ttttttt
5	0	3	0	56	|	59	 0.95	 0.79	t	t	ttttttttt
6	48	0	0	11	|	59	 0.81	 0.48	a	a	aaat
;
; Matrix type: information
;P	|    1    2    3    4    5    6
;-	|-----|----|----|----|----|----|
a	| -0.1  0.0  0.8 -0.1 -0.0  0.6
c	|  0.6  0.4 -0.0 -0.0 -0.0 -0.0
g	|  0.1 -0.0 -0.0 -0.0 -0.0 -0.0
t	| -0.1 -0.1 -0.1  0.8  0.9 -0.1
;-	|-----|----|----|----|----|----|
; i.sum	|  0.5  0.3  0.7  0.6  0.8  0.5  3.4
; i.max	|  0.6  0.4  0.8  0.8  0.9  0.6  0.9
; i.min	| -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1
; Sites	59
>Ubx_chr2L_2445914_244592
ccatta
>Ubx_chr3R_2760544_276056
ccatta
>Ubx_chr2L_2446323_244633
ccatta
>Ubx_chr3R_2824501_282456
ccatta
>Ubx_chr2L_2452228_245226
ccatta
>Ubx_chr2L_11455166_11455
gcatta
>Ubx_chr3R_2760273_276028
gcatta
>Ubx_chr3R_12560061_12560
gcatta
>Ubx_chr3R_2760609_276062
gcatta
>Ubx_chr3R_2759096_275911
caatta
>Ubx_chr2R_19816626_19816
caatta
>Ubx_chr2R_19816652_19816
caatta
>Ubx_chr3R_12559840_12559
caatta
>Ubx_chr2L_2446259_244627
caatta
>Ubx_chr2L_21840736_21840
caatta
>Ubx_chr2R_20311248_20311
caatta
>Ubx_chr3R_2759631_275966
caatta
>Ubx_chr3R_2760146_276019
caatta
>Ubx_chr2L_2446190_244619
caatta
>Ubx_chr2L_2446065_244608
ccattt
>Ubx_chr2L_2446084_244609
ccattt
>Ubx_chr3R_2758676_275869
ccattt
>Ubx_chr2L_2446096_244610
ccattt
>Ubx_chr3R_2758978_275899
ccattt
>Ubx_chr3R_2824601_282466
cgatta
>Ubx_chr3R_2760074_276009
tcatta
>Ubx_chr3R_2759180_275920
tcatta
>Ubx_chr3R_2759244_275925
gaatta
>Ubx_chr2L_2445996_244600
tcatta
>Ubx_chr3R_2759001_275901
ggatta
>Ubx_chr3R_2758951_275896
gcattt
>Ubx_chr3R_2830985_283106
ctatta
>Ubx_chr3R_2759514_275952
ctatta
>Ubx_chr3R_2759290_275931
caattt
>Ubx_chr2L_11454614_11454
acatta
>Ubx_chr3R_2758919_275894
acatta
>Ubx_chr2L_11454863_11454
taatta
>Ubx_chr2L_11455018_11455
taatta
>Ubx_chr3R_2759541_275955
taatta
>Ubx_chr3R_2759395_275942
taatta
>Ubx_chr2L_21840626_21840
taatta
>Ubx_chr3R_2760472_276048
ccatct
>Ubx_chr2L_21840808_21840
cactta
>Ubx_chr3R_2759787_275980
tgatta
>Ubx_chr3R_2759484_275950
gcaata
>Ubx_chr3R_2759274_275928
aaatta
>Ubx_chr3R_2760512_276052
aaatta
>Ubx_chr3R_2759464_275948
aaatta
>Ubx_chr3R_2758853_275887
caaata
>Ubx_chr2L_2445884_244589
acatca
>Ubx_chr2L_11454563_11454
ttatta
>Ubx_chr3R_2759820_275982
gtattt
>Ubx_chr3R_2760341_276036
tgattt
>Ubx_chr2L_21840884_21840
atatta
>Ubx_chr3R_2759526_275953
ggaata
>Ubx_chr2L_2446291_244629
caaatt
>Ubx_chr2R_20311071_20311
gattta
>Ubx_chr2L_2446122_244613
gtttta
>Ubx_chr2L_2446281_244628
cgcgca
;
; Matrix parameters
;	Columns                      	6
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.372|c:0.128|g:0.128|t:0.372
;	program                      	meme
;	matrix.nb                    	1
;	command                      	meme Ubx_factor_binding_sites_sequences.fa -dna -nmotifs 1 -revcomp -w 6 -dir /Users/jturatsi
;	sites                        	59
;	meme.llr                     	210
;	meme.E-value                 	34000
;	pseudo                       	1
;	info.log.base                	2.71828
;	min.prior                    	0.128
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	3.38677
;	information.per.column       	0.564462
;	max.possible.info.per.col    	2.05573
;	consensus.strict             	CCatta
;	consensus.strict.rc          	taatGG
;	consensus.IUPAC              	SMatta
;	consensus.IUPAC.rc           	taatKS
;	consensus.regexp             	[CG][AC]atta
;	consensus.regexp.rc          	taat[GT][CG]
;	residues.content.crude.freq  	a:0.3898|c:0.1610|g:0.0537|t:0.3955
;	G+C.content.crude.freq       	0.214689
;	residues.content.corrected.freq	a:0.3895|c:0.1605|g:0.0549|t:0.3951
;	G+C.content.corrected.freq   	0.215378
;	min(P(S|M))                  	2.59918e-13
;	max(P(S|M))                  	0.124916
;	proba_range                  	0.124916
;	Wmin                         	-18.8
;	Wmax                         	6
;	Wrange                       	24.8
; Job started 2007_12_10.132138
; Job done    2007_12_10.132138