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Copy pathdrosophila_eve_segmentation_sites.ft
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drosophila_eve_segmentation_sites.ft
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; matrix-scan -v 1 -matrix_format transfac -m $RSAT/public_html/tmp/wwwrun/2014/03/04/matrix-scan_2014-03-04.132548_WKBWyY.matrix -pseudo 1 -decimals 1 -2str -origin genomic -bgfile $RSAT/public_html/data/genomes/Drosophila_melanogaster/oligo-frequencies/1nt_upstream-noorf_Drosophila_melanogaster-ovlp-1str.freq -bg_pseudo 0.01 -return limits -return sites -return pval -lth score 1 -uth pval 1e-4 -i $RSAT/public_html/tmp/wwwrun/2014/03/04/tmp_sequence_2014-03-04.132548_rRkdeQ.fasta -seq_format fasta -n score
; Slow counting mode
; Input files
; input $RSAT/public_html/tmp/wwwrun/2014/03/04/tmp_sequence_2014-03-04.132548_rRkdeQ.fasta
; bg $RSAT/public_html/data/genomes/Drosophila_melanogaster/oligo-frequencies/1nt_upstream-noorf_Drosophila_melanogaster-ovlp-1str.freq
; Matrix files
; matrix 1 $RSAT/public_html/tmp/wwwrun/2014/03/04/matrix-scan_2014-03-04.132548_WKBWyY.matrix
; Sequence format fasta
; Pseudo counts 1
; Background model
; Method file
; Bernoulli model (order=0)
; Strand sensitive
; Background pseudo-frequency 0.01
; Residue probabilities
; a 0.30372
; c 0.20053
; g 0.19830
; t 0.29744
; Thresholds lower upper
; pval NA 0.0001
; score 1 NA
; Output columns
; 1 seq_id
; 2 ft_type
; 3 ft_name
; 4 strand
; 5 start
; 6 end
; 7 sequence
; 8 weight
#seq_id ft_type ft_name strand start end sequence weight Pval ln_Pval sig
chr2R limit START_END D 5861246 5866745 . 0 0 0 0
chr2R site eve D 5861480 5861494 CGCACAGTCAGCGCG 7.2 9.9e-05 -9.218 4.004
chr2R site eve R 5861489 5861503 CAGCAAATTCGCGCT 7.3 9.0e-05 -9.312 4.044
chr2R site ttk D 5861525 5861531 CAGGACC 8.3 2.9e-05 -10.440 4.534
chr2R site prd R 5861736 5861743 CACCGCAC 7.3 9.6e-05 -9.254 4.019
chr2R site eve R 5862541 5862555 CCAATGATTAGCGGT 7.7 6.2e-05 -9.694 4.210
chr2R site hb D 5862633 5862640 TTTTTGTG 7.4 6.9e-05 -9.582 4.162
chr2R site hb D 5862704 5862711 TTTTTATG 7.9 4.2e-05 -10.085 4.380
chr2R site kni R 5863045 5863052 GATCTAGT 6.2 1.9e-05 -10.864 4.718
chr2R site hb D 5863076 5863083 TTTTTGTG 7.4 6.9e-05 -9.582 4.162
chr2R site hb D 5863179 5863186 TTTTTATG 7.9 4.2e-05 -10.085 4.380
chr2R site Stat92E D 5863203 5863211 TTCGCGGAA 10.6 2.6e-06 -12.876 5.592
chr2R site kni R 5863270 5863277 GATCTACT 6.0 3.9e-05 -10.165 4.415
chr2R site Stat92E R 5863324 5863332 TTCGGGGAA 10.0 5.1e-06 -12.188 5.293
chr2R site hb R 5863636 5863643 TTTTTATG 7.9 4.2e-05 -10.085 4.380
chr2R site hb D 5864152 5864159 TTTTTATG 7.9 4.2e-05 -10.085 4.380
chr2R site Kr D 5864404 5864411 AACCCATT 7.1 8.8e-05 -9.343 4.058
chr2R site Kr R 5865543 5865550 AACCCGGT 7.2 6.8e-05 -9.602 4.170
chr2R site gt R 5865707 5865716 TTATGACTTT 7.8 2.8e-05 -10.483 4.553
chr2R site hb R 5865712 5865719 TTTTTATG 7.9 4.2e-05 -10.085 4.380
chr2R site Kr D 5865833 5865840 AACCCGTT 8.3 3.3e-05 -10.330 4.486
chr2R site ttk R 5865961 5865967 CAGGACC 8.3 2.9e-05 -10.440 4.534
chr2R site eve D 5866126 5866140 CAAATGGTTATGGCT 8.4 3.1e-05 -10.397 4.515
chr2R site eve R 5866219 5866233 CGCACGTTTAACAGC 8.2 3.8e-05 -10.189 4.425
chr2R site gt R 5866230 5866239 TTATGCCGCA 7.9 1.7e-05 -10.992 4.774
chr2R site eve R 5866257 5866271 CGAATTATTTGCGCT 7.2 9.9e-05 -9.218 4.004
chr2R site gt R 5866361 5866370 TTATGCCGCT 7.4 5.8e-05 -9.750 4.234
chr2R site ttk D 5866551 5866557 CAGGACC 8.3 2.9e-05 -10.440 4.534
chr2R site ttk R 5866565 5866571 CAGGACC 8.3 2.9e-05 -10.440 4.534
chr2R site ttk R 5866607 5866613 CAGGACC 8.3 2.9e-05 -10.440 4.534
chr2R site eve D 5866630 5866644 CGCCTCGTTATCGCC 11.0 1.2e-06 -13.605 5.909
chr2R site prd D 5866683 5866690 CACCGCAC 7.3 9.6e-05 -9.254 4.019
chr2R site eve D 5866686 5866700 CGCACGATTAGCACC 12.8 3.9e-08 -17.049 7.404
;
; Matrices
; matrix name ncol nrow pseudo Wmin Wmax Wrange
; 1 Kr 8 4 1 -23.000 8.700 31.700 a:0.304 c:0.201 g:0.198 t:0.297
; 2 Med 6 4 1 -14.400 6.900 21.300 a:0.304 c:0.201 g:0.198 t:0.297
; 3 Stat92E 9 4 1 -12.500 10.300 22.800 a:0.304 c:0.201 g:0.198 t:0.297
; 4 bcd 6 4 1 -17.600 6.900 24.500 a:0.304 c:0.201 g:0.198 t:0.297
; 5 eve 15 4 1 -33.000 13.400 46.400 a:0.304 c:0.201 g:0.198 t:0.297
; 6 gt 10 4 1 -22.000 9.300 31.300 a:0.304 c:0.201 g:0.198 t:0.297
; 7 hb 8 4 1 -25.600 8.900 34.500 a:0.304 c:0.201 g:0.198 t:0.297
; 8 kni 8 4 1 -13.200 6.500 19.700 a:0.304 c:0.201 g:0.198 t:0.297
; 9 pan 8 4 1 -18.100 7.500 25.600 a:0.304 c:0.201 g:0.198 t:0.297
; 10 prd 8 4 1 -18.500 7.600 26.100 a:0.304 c:0.201 g:0.198 t:0.297
; 11 tin 6 4 1 -15.000 7.500 22.500 a:0.304 c:0.201 g:0.198 t:0.297
; 12 ttk 7 4 1 -15.400 7.700 23.100 a:0.304 c:0.201 g:0.198 t:0.297
; Number of sequences scanned 1
; Genomic coordinate format UCSC
; Organism dm3
; Browser URL http://genome.ucsc.edu/cgi-bin/hgTracks?db=dm3&position=chr2R:5861246-5866745
; Sum of sequence lengths 5500
; N residues 0
; Matches per matrix
; matrix name matches scored
; 1 Kr 3 10986
; 2 Med 0 10990
; 3 Stat92E 2 10984
; 4 bcd 0 10990
; 5 eve 8 10972
; 6 gt 3 10982
; 7 hb 7 10986
; 8 kni 2 10986
; 9 pan 0 10986
; 10 prd 2 10986
; 11 tin 0 10990
; 12 ttk 5 10988
; TOTAL 32 131826
; Host name rsat
; Job started 2014-03-04.132548
; Job done 2014-03-04.132619
; Seconds 30.54
; user 30.54
; system 0.06
; cuser 0
; csystem 0