One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o $RSAT/public_html/tmp/wwwrun/2013/01/11/peak-motifs.2013-01-11.110705_2013-01-11.110705_PdhmNx/results/discovered_motifs/oligos_7nt_mkv4_m3/peak-motifs_oligos_7nt_mkv4_m3_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m3_shift1 ; 9 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NIcor NsEucl SSD NSW rcor rNcor rlogoDP rNIcor rNsEucl rSSD rNSW rank_mean match_rank Aligned matrices
oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)
; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=13; shift=1; ncol=16; -ryTTCCmrGAAry-- ; Alignment reference a 0 381 217 0 4 8 1 597 450 1 1213 1217 492 233 0 0 c 0 271 347 0 0 1168 1214 612 1 0 3 2 185 354 0 0 g 0 337 158 3 1 0 4 10 768 1195 0 0 333 244 0 0 t 0 230 497 1216 1214 43 0 0 0 23 3 0 209 388 0 0

MA0137.2_shift0 (STAT1) 0.972 0.842 9.634 0.851 0.969 0.329 0.987 1 1 1 1 1 1 1 1.000 1
; oligos_7nt_mkv4_m3 versus MA0137.2 (STAT1); m=1/8; ncol2=15; w=13; offset=-1; strand=D; shift=0; score= 1; cayTTCChrGAAryc- ; cor=0.972; Ncor=0.842; logoDP=9.634; NIcor=0.851; NsEucl=0.969; SSD=0.329; NSW=0.987; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1 a 208 859 251 10 8 106 23 528 696 53 1900 2030 954 336 417 0 c 1076 496 574 22 14 1921 1900 762 31 30 124 17 263 760 804 0 g 415 279 144 11 38 14 7 115 1292 1700 29 23 552 270 425 0 t 378 446 1112 2038 2023 44 155 680 66 302 32 15 315 714 431 0

MA0144.1_rc_shift2 (Stat3_rc) 0.922 0.709 4.339 0.204 0.934 0.861 0.957 2 2 6 6 2 3 2 3.286 2
; oligos_7nt_mkv4_m3 versus MA0144.1_rc (Stat3_rc); m=2/8; ncol2=10; w=10; offset=1; strand=R; shift=2; score= 3.2857; --yTTCCtGGAA---- ; cor=0.922; Ncor=0.709; logoDP=4.339; NIcor=0.204; NsEucl=0.934; SSD=0.861; NSW=0.957; rcor=2; rNcor=2; rlogoDP=6; rNIcor=6; rNsEucl=2; rSSD=3; rNSW=2; rank_mean=3.286; match_rank=2 a 0 0 14 1 0 13 0 123 65 14 461 549 0 0 0 0 c 0 0 393 5 7 592 605 148 1 9 129 25 0 0 0 0 g 0 0 15 1 21 2 0 21 541 552 10 19 0 0 0 0 t 0 0 191 606 585 6 8 321 6 38 13 20 0 0 0 0

MA0152.1_shift1 (NFATC2) 0.875 0.471 6.581 0.469 0.904 0.901 0.936 4 4 3 3 3 4 4 3.571 3
; oligos_7nt_mkv4_m3 versus MA0152.1 (NFATC2); m=3/8; ncol2=7; w=7; offset=0; strand=D; shift=1; score= 3.5714; -TTTTCCA-------- ; cor=0.875; Ncor=0.471; logoDP=6.581; NIcor=0.469; NsEucl=0.904; SSD=0.901; NSW=0.936; rcor=4; rNcor=4; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=4; rNSW=4; rank_mean=3.571; match_rank=3 a 0 3 1 1 0 1 0 18 0 0 0 0 0 0 0 0 c 0 1 2 1 0 25 26 3 0 0 0 0 0 0 0 0 g 0 2 2 0 0 0 0 1 0 0 0 0 0 0 0 0 t 0 20 21 24 26 0 0 4 0 0 0 0 0 0 0 0

MA0156.1_shift6 (FEV) 0.846 0.521 6.282 0.484 0.901 1.264 0.921 5 3 4 2 5 6 6 4.429 4
; oligos_7nt_mkv4_m3 versus MA0156.1 (FEV); m=4/8; ncol2=8; w=8; offset=5; strand=D; shift=6; score= 4.4286; ------CAGGAArT-- ; cor=0.846; Ncor=0.521; logoDP=6.282; NIcor=0.484; NsEucl=0.901; SSD=1.264; NSW=0.921; rcor=5; rNcor=3; rlogoDP=4; rNIcor=2; rNsEucl=5; rSSD=6; rNSW=6; rank_mean=4.429; match_rank=4 a 0 0 0 0 0 0 2 9 0 0 13 12 7 0 0 0 c 0 0 0 0 0 0 9 3 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 1 1 13 13 0 0 6 0 0 0 t 0 0 0 0 0 0 1 0 0 0 0 1 0 13 0 0

MA0098.1_rc_shift7 (ETS1_rc) 0.876 0.404 0.152 -0.109 0.904 0.662 0.945 3 8 8 7 4 2 3 5.000 5
; oligos_7nt_mkv4_m3 versus MA0098.1_rc (ETS1_rc); m=5/8; ncol2=6; w=6; offset=6; strand=R; shift=7; score= 5; -------mGGAwr--- ; cor=0.876; Ncor=0.404; logoDP=0.152; NIcor=-0.109; NsEucl=0.904; SSD=0.662; NSW=0.945; rcor=3; rNcor=8; rlogoDP=8; rNIcor=7; rNsEucl=4; rSSD=2; rNSW=3; rank_mean=5.000; match_rank=5 a 0 0 0 0 0 0 0 15 1 0 39 23 16 0 0 0 c 0 0 0 0 0 0 0 17 0 1 0 0 4 0 0 0 g 0 0 0 0 0 0 0 3 39 39 1 0 16 0 0 0 t 0 0 0 0 0 0 0 5 0 0 0 17 4 0 0 0

MA0080.2_shift7 (SPI1) 0.842 0.453 5.422 0.442 0.895 1.081 0.923 7 5 5 4 7 5 5 5.429 6
; oligos_7nt_mkv4_m3 versus MA0080.2 (SPI1); m=6/8; ncol2=7; w=7; offset=6; strand=D; shift=7; score= 5.4286; -------AGGAAGT-- ; cor=0.842; Ncor=0.453; logoDP=5.422; NIcor=0.442; NsEucl=0.895; SSD=1.081; NSW=0.923; rcor=7; rNcor=5; rlogoDP=5; rNIcor=4; rNsEucl=7; rSSD=5; rNSW=5; rank_mean=5.429; match_rank=6 a 0 0 0 0 0 0 0 33 4 4 42 41 5 3 0 0 c 0 0 0 0 0 0 0 3 0 0 0 0 3 5 0 0 g 0 0 0 0 0 0 0 6 37 38 0 1 33 2 0 0 t 0 0 0 0 0 0 0 0 1 0 0 0 1 32 0 0

MA0062.2_shift6 (GABPA) 0.845 0.422 7.243 0.402 0.897 1.360 0.915 6 7 2 5 6 7 7 5.714 7
; oligos_7nt_mkv4_m3 versus MA0062.2 (GABPA); m=7/8; ncol2=11; w=8; offset=5; strand=D; shift=6; score= 5.7143; ------CCGGAAGygv ; cor=0.845; Ncor=0.422; logoDP=7.243; NIcor=0.402; NsEucl=0.897; SSD=1.360; NSW=0.915; rcor=6; rNcor=7; rlogoDP=2; rNIcor=5; rNsEucl=6; rSSD=7; rNSW=7; rank_mean=5.714; match_rank=7 a 0 0 0 0 0 0 32 70 0 0 991 989 94 56 154 264 c 0 0 0 0 0 0 768 914 0 0 1 2 32 261 137 262 g 0 0 0 0 0 0 188 4 990 991 1 0 866 37 603 415 t 0 0 0 0 0 0 1 1 1 0 0 2 0 637 96 49

MA0136.1_rc_shift6 (ELF5_rc) 0.758 0.433 0.210 -0.127 0.888 1.608 0.899 8 6 7 8 8 8 8 7.571 8
; oligos_7nt_mkv4_m3 versus MA0136.1_rc (ELF5_rc); m=8/8; ncol2=9; w=8; offset=5; strand=R; shift=6; score= 7.5714; ------mmGGAwrtw- ; cor=0.758; Ncor=0.433; logoDP=0.210; NIcor=-0.127; NsEucl=0.888; SSD=1.608; NSW=0.899; rcor=8; rNcor=6; rlogoDP=7; rNIcor=8; rNsEucl=8; rSSD=8; rNSW=8; rank_mean=7.571; match_rank=8 a 0 0 0 0 0 0 21 26 0 0 43 29 17 5 20 0 c 0 0 0 0 0 0 11 11 0 0 0 1 5 7 3 0 g 0 0 0 0 0 0 8 3 44 44 1 0 20 3 9 0 t 0 0 0 0 0 0 4 4 0 0 0 14 2 29 12 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv4_m3_shift1 (oligos_7nt_mkv4_m3)																	; oligos_7nt_mkv4_m3; m=0 (reference); ncol1=13; shift=1; ncol=16; -ryTTCCmrGAAry-- ; Alignment reference a 0 381 217 0 4 8 1 597 450 1 1213 1217 492 233 0 0 c 0 271 347 0 0 1168 1214 612 1 0 3 2 185 354 0 0 g 0 337 158 3 1 0 4 10 768 1195 0 0 333 244 0 0 t 0 230 497 1216 1214 43 0 0 0 23 3 0 209 388 0 0
MA0137.2_shift0 (STAT1)	0.972	0.842	9.634	0.851	0.969	0.329	0.987	1	1	1	1	1	1	1	1.000	1	; oligos_7nt_mkv4_m3 versus MA0137.2 (STAT1); m=1/8; ncol2=15; w=13; offset=-1; strand=D; shift=0; score= 1; cayTTCChrGAAryc- ; cor=0.972; Ncor=0.842; logoDP=9.634; NIcor=0.851; NsEucl=0.969; SSD=0.329; NSW=0.987; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1 a 208 859 251 10 8 106 23 528 696 53 1900 2030 954 336 417 0 c 1076 496 574 22 14 1921 1900 762 31 30 124 17 263 760 804 0 g 415 279 144 11 38 14 7 115 1292 1700 29 23 552 270 425 0 t 378 446 1112 2038 2023 44 155 680 66 302 32 15 315 714 431 0
MA0144.1_rc_shift2 (Stat3_rc)	0.922	0.709	4.339	0.204	0.934	0.861	0.957	2	2	6	6	2	3	2	3.286	2	; oligos_7nt_mkv4_m3 versus MA0144.1_rc (Stat3_rc); m=2/8; ncol2=10; w=10; offset=1; strand=R; shift=2; score= 3.2857; --yTTCCtGGAA---- ; cor=0.922; Ncor=0.709; logoDP=4.339; NIcor=0.204; NsEucl=0.934; SSD=0.861; NSW=0.957; rcor=2; rNcor=2; rlogoDP=6; rNIcor=6; rNsEucl=2; rSSD=3; rNSW=2; rank_mean=3.286; match_rank=2 a 0 0 14 1 0 13 0 123 65 14 461 549 0 0 0 0 c 0 0 393 5 7 592 605 148 1 9 129 25 0 0 0 0 g 0 0 15 1 21 2 0 21 541 552 10 19 0 0 0 0 t 0 0 191 606 585 6 8 321 6 38 13 20 0 0 0 0
MA0152.1_shift1 (NFATC2)	0.875	0.471	6.581	0.469	0.904	0.901	0.936	4	4	3	3	3	4	4	3.571	3	; oligos_7nt_mkv4_m3 versus MA0152.1 (NFATC2); m=3/8; ncol2=7; w=7; offset=0; strand=D; shift=1; score= 3.5714; -TTTTCCA-------- ; cor=0.875; Ncor=0.471; logoDP=6.581; NIcor=0.469; NsEucl=0.904; SSD=0.901; NSW=0.936; rcor=4; rNcor=4; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=4; rNSW=4; rank_mean=3.571; match_rank=3 a 0 3 1 1 0 1 0 18 0 0 0 0 0 0 0 0 c 0 1 2 1 0 25 26 3 0 0 0 0 0 0 0 0 g 0 2 2 0 0 0 0 1 0 0 0 0 0 0 0 0 t 0 20 21 24 26 0 0 4 0 0 0 0 0 0 0 0
MA0156.1_shift6 (FEV)	0.846	0.521	6.282	0.484	0.901	1.264	0.921	5	3	4	2	5	6	6	4.429	4	; oligos_7nt_mkv4_m3 versus MA0156.1 (FEV); m=4/8; ncol2=8; w=8; offset=5; strand=D; shift=6; score= 4.4286; ------CAGGAArT-- ; cor=0.846; Ncor=0.521; logoDP=6.282; NIcor=0.484; NsEucl=0.901; SSD=1.264; NSW=0.921; rcor=5; rNcor=3; rlogoDP=4; rNIcor=2; rNsEucl=5; rSSD=6; rNSW=6; rank_mean=4.429; match_rank=4 a 0 0 0 0 0 0 2 9 0 0 13 12 7 0 0 0 c 0 0 0 0 0 0 9 3 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 1 1 13 13 0 0 6 0 0 0 t 0 0 0 0 0 0 1 0 0 0 0 1 0 13 0 0
MA0098.1_rc_shift7 (ETS1_rc)	0.876	0.404	0.152	-0.109	0.904	0.662	0.945	3	8	8	7	4	2	3	5.000	5	; oligos_7nt_mkv4_m3 versus MA0098.1_rc (ETS1_rc); m=5/8; ncol2=6; w=6; offset=6; strand=R; shift=7; score= 5; -------mGGAwr--- ; cor=0.876; Ncor=0.404; logoDP=0.152; NIcor=-0.109; NsEucl=0.904; SSD=0.662; NSW=0.945; rcor=3; rNcor=8; rlogoDP=8; rNIcor=7; rNsEucl=4; rSSD=2; rNSW=3; rank_mean=5.000; match_rank=5 a 0 0 0 0 0 0 0 15 1 0 39 23 16 0 0 0 c 0 0 0 0 0 0 0 17 0 1 0 0 4 0 0 0 g 0 0 0 0 0 0 0 3 39 39 1 0 16 0 0 0 t 0 0 0 0 0 0 0 5 0 0 0 17 4 0 0 0
MA0080.2_shift7 (SPI1)	0.842	0.453	5.422	0.442	0.895	1.081	0.923	7	5	5	4	7	5	5	5.429	6	; oligos_7nt_mkv4_m3 versus MA0080.2 (SPI1); m=6/8; ncol2=7; w=7; offset=6; strand=D; shift=7; score= 5.4286; -------AGGAAGT-- ; cor=0.842; Ncor=0.453; logoDP=5.422; NIcor=0.442; NsEucl=0.895; SSD=1.081; NSW=0.923; rcor=7; rNcor=5; rlogoDP=5; rNIcor=4; rNsEucl=7; rSSD=5; rNSW=5; rank_mean=5.429; match_rank=6 a 0 0 0 0 0 0 0 33 4 4 42 41 5 3 0 0 c 0 0 0 0 0 0 0 3 0 0 0 0 3 5 0 0 g 0 0 0 0 0 0 0 6 37 38 0 1 33 2 0 0 t 0 0 0 0 0 0 0 0 1 0 0 0 1 32 0 0
MA0062.2_shift6 (GABPA)	0.845	0.422	7.243	0.402	0.897	1.360	0.915	6	7	2	5	6	7	7	5.714	7	; oligos_7nt_mkv4_m3 versus MA0062.2 (GABPA); m=7/8; ncol2=11; w=8; offset=5; strand=D; shift=6; score= 5.7143; ------CCGGAAGygv ; cor=0.845; Ncor=0.422; logoDP=7.243; NIcor=0.402; NsEucl=0.897; SSD=1.360; NSW=0.915; rcor=6; rNcor=7; rlogoDP=2; rNIcor=5; rNsEucl=6; rSSD=7; rNSW=7; rank_mean=5.714; match_rank=7 a 0 0 0 0 0 0 32 70 0 0 991 989 94 56 154 264 c 0 0 0 0 0 0 768 914 0 0 1 2 32 261 137 262 g 0 0 0 0 0 0 188 4 990 991 1 0 866 37 603 415 t 0 0 0 0 0 0 1 1 1 0 0 2 0 637 96 49
MA0136.1_rc_shift6 (ELF5_rc)	0.758	0.433	0.210	-0.127	0.888	1.608	0.899	8	6	7	8	8	8	8	7.571	8	; oligos_7nt_mkv4_m3 versus MA0136.1_rc (ELF5_rc); m=8/8; ncol2=9; w=8; offset=5; strand=R; shift=6; score= 7.5714; ------mmGGAwrtw- ; cor=0.758; Ncor=0.433; logoDP=0.210; NIcor=-0.127; NsEucl=0.888; SSD=1.608; NSW=0.899; rcor=8; rNcor=6; rlogoDP=7; rNIcor=8; rNsEucl=8; rSSD=8; rNSW=8; rank_mean=7.571; match_rank=8 a 0 0 0 0 0 0 21 26 0 0 43 29 17 5 20 0 c 0 0 0 0 0 0 11 11 0 0 0 1 5 7 3 0 g 0 0 0 0 0 0 8 3 44 44 1 0 20 3 9 0 t 0 0 0 0 0 0 4 4 0 0 0 14 2 29 12 0