One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.tf -format2 tf -file2 /home/rsat/rsa-tools/public_html/data/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey.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 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift1 ; 7 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_mkv5_m1_shift1 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -wwTATYTkKAww ; Alignment reference a | 0 1274 1387 0 4484 0 0 0 0 0 4484 1227 1330 c | 0 685 584 0 0 0 1204 0 0 0 0 707 1019 g | 0 685 1071 0 0 0 0 0 1682 1241 0 715 758 t | 0 1840 1442 4484 0 4484 3280 4484 2802 3243 0 1835 1377

CG12361_Cell_FBgn0250756_shift6 (CG12361_Cell_FBgn0250756) 0.784 0.422 3.808 0.419 0.889 1.216 0.913 3 4 2 2 2 2 2 2.429 1
; oligos_7nt_mkv5_m1 versus CG12361_Cell_FBgn0250756; m=1/6; ncol2=8; w=7; offset=5; strand=D; shift=6; score= 2.4286; ------tTTwATk ; cor=0.784; Ncor=0.422; logoDP=3.808; NIcor=0.419; NsEucl=0.889; SSD=1.216; NSW=0.913; rcor=3; rNcor=4; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.429; match_rank=1 a | 0 0 0 0 0 0 2 2 2 6 16 0 0 c | 0 0 0 0 0 0 2 0 0 0 0 0 2 g | 0 0 0 0 0 0 3 0 0 2 0 0 6 t | 0 0 0 0 0 0 9 14 14 8 0 16 8

br-Z1_FlyReg_FBgn0000210_rc_shift0 (br-Z1_FlyReg_FBgn0000210_rc) 0.832 0.448 2.082 0.158 0.896 1.063 0.924 1 2 6 6 1 1 1 2.571 2
; oligos_7nt_mkv5_m1 versus br-Z1_FlyReg_FBgn0000210_rc; m=2/6; ncol2=8; w=7; offset=-1; strand=R; shift=0; score= 2.5714; TtcTAwTT----- ; cor=0.832; Ncor=0.448; logoDP=2.082; NIcor=0.158; NsEucl=0.896; SSD=1.063; NSW=0.924; rcor=1; rNcor=2; rlogoDP=6; rNIcor=6; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.571; match_rank=2 a | 0 1 3 1 14 8 0 3 0 0 0 0 0 c | 0 2 9 2 0 0 3 2 0 0 0 0 0 g | 1 3 4 0 3 0 2 0 0 0 0 0 0 t | 16 11 1 14 0 9 12 12 0 0 0 0 0

hb_FlyReg_FBgn0001180_shift4 (hb_FlyReg_FBgn0001180) 0.759 0.506 5.738 0.469 0.878 1.919 0.880 4 1 1 1 6 6 6 3.571 3
; oligos_7nt_mkv5_m1 versus hb_FlyReg_FBgn0001180; m=3/6; ncol2=8; w=8; offset=3; strand=D; shift=4; score= 3.5714; ----tTTTTTrt- ; cor=0.759; Ncor=0.506; logoDP=5.738; NIcor=0.469; NsEucl=0.878; SSD=1.919; NSW=0.880; rcor=4; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=6; rSSD=6; rNSW=6; rank_mean=3.571; match_rank=3 a | 0 0 0 0 17 0 1 0 0 1 59 20 0 c | 0 0 0 0 13 0 5 1 0 4 7 17 0 g | 0 0 0 0 7 3 1 0 0 0 29 14 0 t | 0 0 0 0 66 100 96 102 103 98 8 52 0

AbdB_SOLEXA_FBgn0000015_shift6 (AbdB_SOLEXA_FBgn0000015) 0.756 0.407 3.160 0.413 0.889 1.217 0.913 5 5 4 3 3 3 3 3.714 4
; oligos_7nt_mkv5_m1 versus AbdB_SOLEXA_FBgn0000015; m=4/6; ncol2=8; w=7; offset=5; strand=D; shift=6; score= 3.7143; ------tTTwATk ; cor=0.756; Ncor=0.407; logoDP=3.160; NIcor=0.413; NsEucl=0.889; SSD=1.217; NSW=0.913; rcor=5; rNcor=5; rlogoDP=4; rNIcor=3; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.714; match_rank=4 a | 0 0 0 0 0 0 619 344 61 1124 2704 55 449 c | 0 0 0 0 0 0 519 201 0 33 0 630 62 g | 0 0 0 0 0 0 545 252 0 38 0 71 1301 t | 0 0 0 0 0 0 1021 1907 2643 1509 0 1948 892

Abd-B_FlyReg_FBgn0000015_rc_shift6 (Abd-B_FlyReg_FBgn0000015_rc) 0.825 0.444 2.968 0.202 0.888 1.232 0.912 2 3 5 5 4 4 4 3.857 5
; oligos_7nt_mkv5_m1 versus Abd-B_FlyReg_FBgn0000015_rc; m=5/6; ncol2=8; w=7; offset=5; strand=R; shift=6; score= 3.8571; ------TTTTATG ; cor=0.825; Ncor=0.444; logoDP=2.968; NIcor=0.202; NsEucl=0.888; SSD=1.232; NSW=0.912; rcor=2; rNcor=3; rlogoDP=5; rNIcor=5; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=3.857; match_rank=5 a | 0 0 0 0 0 0 1 1 0 0 7 0 0 c | 0 0 0 0 0 0 1 0 0 0 0 1 1 g | 0 0 0 0 0 0 0 0 0 0 0 0 5 t | 0 0 0 0 0 0 5 6 7 7 0 6 1

Cad_Cell_FBgn0000251_shift6 (Cad_Cell_FBgn0000251) 0.751 0.404 3.263 0.386 0.880 1.403 0.900 6 6 3 4 5 5 5 4.857 6
; oligos_7nt_mkv5_m1 versus Cad_Cell_FBgn0000251; m=6/6; ncol2=8; w=7; offset=5; strand=D; shift=6; score= 4.8571; ------wTTwATT ; cor=0.751; Ncor=0.404; logoDP=3.263; NIcor=0.386; NsEucl=0.880; SSD=1.403; NSW=0.900; rcor=6; rNcor=6; rlogoDP=3; rNIcor=4; rNsEucl=5; rSSD=5; rNSW=5; rank_mean=4.857; match_rank=6 a | 0 0 0 0 0 0 12 3 4 12 38 0 4 c | 0 0 0 0 0 0 6 3 0 0 0 0 0 g | 0 0 0 0 0 0 4 3 0 2 0 0 7 t | 0 0 0 0 0 0 16 29 34 24 0 38 27

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m1_shift1 (oligos_7nt_mkv5_m1)																	; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -wwTATYTkKAww ; Alignment reference a \| 0 1274 1387 0 4484 0 0 0 0 0 4484 1227 1330 c \| 0 685 584 0 0 0 1204 0 0 0 0 707 1019 g \| 0 685 1071 0 0 0 0 0 1682 1241 0 715 758 t \| 0 1840 1442 4484 0 4484 3280 4484 2802 3243 0 1835 1377
CG12361_Cell_FBgn0250756_shift6 (CG12361_Cell_FBgn0250756)	0.784	0.422	3.808	0.419	0.889	1.216	0.913	3	4	2	2	2	2	2	2.429	1	; oligos_7nt_mkv5_m1 versus CG12361_Cell_FBgn0250756; m=1/6; ncol2=8; w=7; offset=5; strand=D; shift=6; score= 2.4286; ------tTTwATk ; cor=0.784; Ncor=0.422; logoDP=3.808; NIcor=0.419; NsEucl=0.889; SSD=1.216; NSW=0.913; rcor=3; rNcor=4; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.429; match_rank=1 a \| 0 0 0 0 0 0 2 2 2 6 16 0 0 c \| 0 0 0 0 0 0 2 0 0 0 0 0 2 g \| 0 0 0 0 0 0 3 0 0 2 0 0 6 t \| 0 0 0 0 0 0 9 14 14 8 0 16 8
br-Z1_FlyReg_FBgn0000210_rc_shift0 (br-Z1_FlyReg_FBgn0000210_rc)	0.832	0.448	2.082	0.158	0.896	1.063	0.924	1	2	6	6	1	1	1	2.571	2	; oligos_7nt_mkv5_m1 versus br-Z1_FlyReg_FBgn0000210_rc; m=2/6; ncol2=8; w=7; offset=-1; strand=R; shift=0; score= 2.5714; TtcTAwTT----- ; cor=0.832; Ncor=0.448; logoDP=2.082; NIcor=0.158; NsEucl=0.896; SSD=1.063; NSW=0.924; rcor=1; rNcor=2; rlogoDP=6; rNIcor=6; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.571; match_rank=2 a \| 0 1 3 1 14 8 0 3 0 0 0 0 0 c \| 0 2 9 2 0 0 3 2 0 0 0 0 0 g \| 1 3 4 0 3 0 2 0 0 0 0 0 0 t \| 16 11 1 14 0 9 12 12 0 0 0 0 0
hb_FlyReg_FBgn0001180_shift4 (hb_FlyReg_FBgn0001180)	0.759	0.506	5.738	0.469	0.878	1.919	0.880	4	1	1	1	6	6	6	3.571	3	; oligos_7nt_mkv5_m1 versus hb_FlyReg_FBgn0001180; m=3/6; ncol2=8; w=8; offset=3; strand=D; shift=4; score= 3.5714; ----tTTTTTrt- ; cor=0.759; Ncor=0.506; logoDP=5.738; NIcor=0.469; NsEucl=0.878; SSD=1.919; NSW=0.880; rcor=4; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=6; rSSD=6; rNSW=6; rank_mean=3.571; match_rank=3 a \| 0 0 0 0 17 0 1 0 0 1 59 20 0 c \| 0 0 0 0 13 0 5 1 0 4 7 17 0 g \| 0 0 0 0 7 3 1 0 0 0 29 14 0 t \| 0 0 0 0 66 100 96 102 103 98 8 52 0
AbdB_SOLEXA_FBgn0000015_shift6 (AbdB_SOLEXA_FBgn0000015)	0.756	0.407	3.160	0.413	0.889	1.217	0.913	5	5	4	3	3	3	3	3.714	4	; oligos_7nt_mkv5_m1 versus AbdB_SOLEXA_FBgn0000015; m=4/6; ncol2=8; w=7; offset=5; strand=D; shift=6; score= 3.7143; ------tTTwATk ; cor=0.756; Ncor=0.407; logoDP=3.160; NIcor=0.413; NsEucl=0.889; SSD=1.217; NSW=0.913; rcor=5; rNcor=5; rlogoDP=4; rNIcor=3; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.714; match_rank=4 a \| 0 0 0 0 0 0 619 344 61 1124 2704 55 449 c \| 0 0 0 0 0 0 519 201 0 33 0 630 62 g \| 0 0 0 0 0 0 545 252 0 38 0 71 1301 t \| 0 0 0 0 0 0 1021 1907 2643 1509 0 1948 892
Abd-B_FlyReg_FBgn0000015_rc_shift6 (Abd-B_FlyReg_FBgn0000015_rc)	0.825	0.444	2.968	0.202	0.888	1.232	0.912	2	3	5	5	4	4	4	3.857	5	; oligos_7nt_mkv5_m1 versus Abd-B_FlyReg_FBgn0000015_rc; m=5/6; ncol2=8; w=7; offset=5; strand=R; shift=6; score= 3.8571; ------TTTTATG ; cor=0.825; Ncor=0.444; logoDP=2.968; NIcor=0.202; NsEucl=0.888; SSD=1.232; NSW=0.912; rcor=2; rNcor=3; rlogoDP=5; rNIcor=5; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=3.857; match_rank=5 a \| 0 0 0 0 0 0 1 1 0 0 7 0 0 c \| 0 0 0 0 0 0 1 0 0 0 0 1 1 g \| 0 0 0 0 0 0 0 0 0 0 0 0 5 t \| 0 0 0 0 0 0 5 6 7 7 0 6 1
Cad_Cell_FBgn0000251_shift6 (Cad_Cell_FBgn0000251)	0.751	0.404	3.263	0.386	0.880	1.403	0.900	6	6	3	4	5	5	5	4.857	6	; oligos_7nt_mkv5_m1 versus Cad_Cell_FBgn0000251; m=6/6; ncol2=8; w=7; offset=5; strand=D; shift=6; score= 4.8571; ------wTTwATT ; cor=0.751; Ncor=0.404; logoDP=3.263; NIcor=0.386; NsEucl=0.880; SSD=1.403; NSW=0.900; rcor=6; rNcor=6; rlogoDP=3; rNIcor=4; rNsEucl=5; rSSD=5; rNSW=5; rank_mean=4.857; match_rank=6 a \| 0 0 0 0 0 0 12 3 4 12 38 0 4 c \| 0 0 0 0 0 0 6 3 0 0 0 0 0 g \| 0 0 0 0 0 0 4 3 0 2 0 0 7 t \| 0 0 0 0 0 0 16 29 34 24 0 38 27