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_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_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_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift0 ; 8 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_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=11; shift=0; ncol=12; wkCTTATsArw- ; Alignment reference a | 474 394 0 0 0 1796 0 0 1796 611 473 0 c | 435 355 1796 0 0 0 0 1203 0 347 443 0 g | 342 496 0 0 0 0 0 593 0 458 295 0 t | 545 551 0 1796 1796 0 1796 0 0 380 585 0

So_Cell_FBgn0003460_rc_shift4 (So_Cell_FBgn0003460_rc) 0.939 0.598 4.152 0.234 0.932 0.448 0.968 3 1 1 1 3 3 3 2.143 1
; oligos_6nt_mkv4_m1 versus So_Cell_FBgn0003460_rc; m=1/7; ncol2=7; w=7; offset=4; strand=R; shift=4; score= 2.1429; ----TATCAyt- ; cor=0.939; Ncor=0.598; logoDP=4.152; NIcor=0.234; NsEucl=0.932; SSD=0.448; NSW=0.968; rcor=3; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.143; match_rank=1 a | 0 0 0 0 0 26 0 0 26 3 6 0 c | 0 0 0 0 0 1 0 27 1 10 5 0 g | 0 0 0 0 0 0 0 0 0 1 4 0 t | 0 0 0 0 27 0 27 0 0 13 12 0

So_SOLEXA_FBgn0003460_rc_shift4 (So_SOLEXA_FBgn0003460_rc) 0.959 0.559 0.152 -0.080 0.947 0.278 0.980 1 3 6 6 1 1 1 2.714 2
; oligos_6nt_mkv4_m1 versus So_SOLEXA_FBgn0003460_rc; m=2/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score= 2.7143; ----TATCAyww ; cor=0.959; Ncor=0.559; logoDP=0.152; NIcor=-0.080; NsEucl=0.947; SSD=0.278; NSW=0.980; rcor=1; rNcor=3; rlogoDP=6; rNIcor=6; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.714; match_rank=2 a | 0 0 0 0 0 509 0 0 467 122 165 166 c | 0 0 0 0 0 14 0 519 4 151 117 95 g | 0 0 0 0 0 8 0 0 58 87 92 102 t | 0 0 0 0 531 0 531 12 2 171 157 168

Optix_SOLEXA_FBgn0025360_rc_shift4 (Optix_SOLEXA_FBgn0025360_rc) 0.951 0.555 0.123 -0.085 0.942 0.330 0.976 2 4 7 7 2 2 2 3.714 3
; oligos_6nt_mkv4_m1 versus Optix_SOLEXA_FBgn0025360_rc; m=3/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score= 3.7143; ----TATCAcww ; cor=0.951; Ncor=0.555; logoDP=0.123; NIcor=-0.085; NsEucl=0.942; SSD=0.330; NSW=0.976; rcor=2; rNcor=4; rlogoDP=7; rNIcor=7; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=3.714; match_rank=3 a | 0 0 0 0 0 564 0 0 497 116 151 143 c | 0 0 0 0 17 0 0 564 0 216 119 126 g | 0 0 0 0 43 0 0 0 67 93 111 91 t | 0 0 0 0 504 0 564 0 0 139 183 204

Six4_SOLEXA_FBgn0027364_rc_shift4 (Six4_SOLEXA_FBgn0027364_rc) 0.928 0.541 0.246 -0.054 0.931 0.465 0.967 4 5 4 3 4 4 4 4.000 4
; oligos_6nt_mkv4_m1 versus Six4_SOLEXA_FBgn0027364_rc; m=4/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score= 4; ----TaTCAhww ; cor=0.928; Ncor=0.541; logoDP=0.246; NIcor=-0.054; NsEucl=0.931; SSD=0.465; NSW=0.967; rcor=4; rNcor=5; rlogoDP=4; rNIcor=3; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=4.000; match_rank=4 a | 0 0 0 0 0 383 0 38 599 194 203 181 c | 0 0 0 0 0 126 0 556 0 167 83 116 g | 0 0 0 0 40 128 0 0 38 84 91 93 t | 0 0 0 0 597 0 637 43 0 192 260 247

Optix_Cell_FBgn0025360_rc_shift4 (Optix_Cell_FBgn0025360_rc) 0.920 0.537 0.340 -0.056 0.924 0.560 0.960 5 6 3 4 5 5 5 4.714 5
; oligos_6nt_mkv4_m1 versus Optix_Cell_FBgn0025360_rc; m=5/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score= 4.7143; ----TATCAcww ; cor=0.920; Ncor=0.537; logoDP=0.340; NIcor=-0.056; NsEucl=0.924; SSD=0.560; NSW=0.960; rcor=5; rNcor=6; rlogoDP=3; rNIcor=4; rNsEucl=5; rSSD=5; rNSW=5; rank_mean=4.714; match_rank=5 a | 0 0 0 0 0 27 0 0 22 3 7 9 c | 0 0 0 0 1 0 0 27 0 16 3 2 g | 0 0 0 0 0 0 0 0 5 4 4 4 t | 0 0 0 0 26 0 27 0 0 4 13 12

Exd_SOLEXA_FBgn0000611_rc_shift4 (Exd_SOLEXA_FBgn0000611_rc) 0.777 0.453 0.344 -0.025 0.880 1.404 0.900 6 7 2 2 7 6 6 5.143 6
; oligos_6nt_mkv4_m1 versus Exd_SOLEXA_FBgn0000611_rc; m=6/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score= 5.1429; ----yrTCAaaw ; cor=0.777; Ncor=0.453; logoDP=0.344; NIcor=-0.025; NsEucl=0.880; SSD=1.404; NSW=0.900; rcor=6; rNcor=7; rlogoDP=2; rNIcor=2; rNsEucl=7; rSSD=6; rNSW=6; rank_mean=5.143; match_rank=6 a | 0 0 0 0 77 323 0 0 883 541 408 266 c | 0 0 0 0 259 0 0 883 0 168 143 207 g | 0 0 0 0 26 505 0 0 0 40 172 152 t | 0 0 0 0 521 55 883 0 0 134 160 258

exd_SOLEXA_2_FBgn0000611_rc_shift3 (exd_SOLEXA_2_FBgn0000611_rc) 0.770 0.560 0.192 -0.070 0.886 1.674 0.895 7 2 5 5 6 7 7 5.571 7
; oligos_6nt_mkv4_m1 versus exd_SOLEXA_2_FBgn0000611_rc; m=7/7; ncol2=8; w=8; offset=3; strand=R; shift=3; score= 5.5714; ---wyrTCAaa- ; cor=0.770; Ncor=0.560; logoDP=0.192; NIcor=-0.070; NsEucl=0.886; SSD=1.674; NSW=0.895; rcor=7; rNcor=2; rlogoDP=5; rNIcor=5; rNsEucl=6; rSSD=7; rNSW=7; rank_mean=5.571; match_rank=7 a | 0 0 0 483 259 1228 0 0 2672 1314 1025 0 c | 0 0 0 145 914 86 0 2672 0 598 458 0 g | 0 0 0 91 14 1169 0 0 0 204 568 0 t | 0 0 0 474 1470 189 2672 0 0 539 587 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)																	; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=11; shift=0; ncol=12; wkCTTATsArw- ; Alignment reference a \| 474 394 0 0 0 1796 0 0 1796 611 473 0 c \| 435 355 1796 0 0 0 0 1203 0 347 443 0 g \| 342 496 0 0 0 0 0 593 0 458 295 0 t \| 545 551 0 1796 1796 0 1796 0 0 380 585 0
So_Cell_FBgn0003460_rc_shift4 (So_Cell_FBgn0003460_rc)	0.939	0.598	4.152	0.234	0.932	0.448	0.968	3	1	1	1	3	3	3	2.143	1	; oligos_6nt_mkv4_m1 versus So_Cell_FBgn0003460_rc; m=1/7; ncol2=7; w=7; offset=4; strand=R; shift=4; score= 2.1429; ----TATCAyt- ; cor=0.939; Ncor=0.598; logoDP=4.152; NIcor=0.234; NsEucl=0.932; SSD=0.448; NSW=0.968; rcor=3; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.143; match_rank=1 a \| 0 0 0 0 0 26 0 0 26 3 6 0 c \| 0 0 0 0 0 1 0 27 1 10 5 0 g \| 0 0 0 0 0 0 0 0 0 1 4 0 t \| 0 0 0 0 27 0 27 0 0 13 12 0
So_SOLEXA_FBgn0003460_rc_shift4 (So_SOLEXA_FBgn0003460_rc)	0.959	0.559	0.152	-0.080	0.947	0.278	0.980	1	3	6	6	1	1	1	2.714	2	; oligos_6nt_mkv4_m1 versus So_SOLEXA_FBgn0003460_rc; m=2/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score= 2.7143; ----TATCAyww ; cor=0.959; Ncor=0.559; logoDP=0.152; NIcor=-0.080; NsEucl=0.947; SSD=0.278; NSW=0.980; rcor=1; rNcor=3; rlogoDP=6; rNIcor=6; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.714; match_rank=2 a \| 0 0 0 0 0 509 0 0 467 122 165 166 c \| 0 0 0 0 0 14 0 519 4 151 117 95 g \| 0 0 0 0 0 8 0 0 58 87 92 102 t \| 0 0 0 0 531 0 531 12 2 171 157 168
Optix_SOLEXA_FBgn0025360_rc_shift4 (Optix_SOLEXA_FBgn0025360_rc)	0.951	0.555	0.123	-0.085	0.942	0.330	0.976	2	4	7	7	2	2	2	3.714	3	; oligos_6nt_mkv4_m1 versus Optix_SOLEXA_FBgn0025360_rc; m=3/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score= 3.7143; ----TATCAcww ; cor=0.951; Ncor=0.555; logoDP=0.123; NIcor=-0.085; NsEucl=0.942; SSD=0.330; NSW=0.976; rcor=2; rNcor=4; rlogoDP=7; rNIcor=7; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=3.714; match_rank=3 a \| 0 0 0 0 0 564 0 0 497 116 151 143 c \| 0 0 0 0 17 0 0 564 0 216 119 126 g \| 0 0 0 0 43 0 0 0 67 93 111 91 t \| 0 0 0 0 504 0 564 0 0 139 183 204
Six4_SOLEXA_FBgn0027364_rc_shift4 (Six4_SOLEXA_FBgn0027364_rc)	0.928	0.541	0.246	-0.054	0.931	0.465	0.967	4	5	4	3	4	4	4	4.000	4	; oligos_6nt_mkv4_m1 versus Six4_SOLEXA_FBgn0027364_rc; m=4/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score= 4; ----TaTCAhww ; cor=0.928; Ncor=0.541; logoDP=0.246; NIcor=-0.054; NsEucl=0.931; SSD=0.465; NSW=0.967; rcor=4; rNcor=5; rlogoDP=4; rNIcor=3; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=4.000; match_rank=4 a \| 0 0 0 0 0 383 0 38 599 194 203 181 c \| 0 0 0 0 0 126 0 556 0 167 83 116 g \| 0 0 0 0 40 128 0 0 38 84 91 93 t \| 0 0 0 0 597 0 637 43 0 192 260 247
Optix_Cell_FBgn0025360_rc_shift4 (Optix_Cell_FBgn0025360_rc)	0.920	0.537	0.340	-0.056	0.924	0.560	0.960	5	6	3	4	5	5	5	4.714	5	; oligos_6nt_mkv4_m1 versus Optix_Cell_FBgn0025360_rc; m=5/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score= 4.7143; ----TATCAcww ; cor=0.920; Ncor=0.537; logoDP=0.340; NIcor=-0.056; NsEucl=0.924; SSD=0.560; NSW=0.960; rcor=5; rNcor=6; rlogoDP=3; rNIcor=4; rNsEucl=5; rSSD=5; rNSW=5; rank_mean=4.714; match_rank=5 a \| 0 0 0 0 0 27 0 0 22 3 7 9 c \| 0 0 0 0 1 0 0 27 0 16 3 2 g \| 0 0 0 0 0 0 0 0 5 4 4 4 t \| 0 0 0 0 26 0 27 0 0 4 13 12
Exd_SOLEXA_FBgn0000611_rc_shift4 (Exd_SOLEXA_FBgn0000611_rc)	0.777	0.453	0.344	-0.025	0.880	1.404	0.900	6	7	2	2	7	6	6	5.143	6	; oligos_6nt_mkv4_m1 versus Exd_SOLEXA_FBgn0000611_rc; m=6/7; ncol2=8; w=7; offset=4; strand=R; shift=4; score= 5.1429; ----yrTCAaaw ; cor=0.777; Ncor=0.453; logoDP=0.344; NIcor=-0.025; NsEucl=0.880; SSD=1.404; NSW=0.900; rcor=6; rNcor=7; rlogoDP=2; rNIcor=2; rNsEucl=7; rSSD=6; rNSW=6; rank_mean=5.143; match_rank=6 a \| 0 0 0 0 77 323 0 0 883 541 408 266 c \| 0 0 0 0 259 0 0 883 0 168 143 207 g \| 0 0 0 0 26 505 0 0 0 40 172 152 t \| 0 0 0 0 521 55 883 0 0 134 160 258
exd_SOLEXA_2_FBgn0000611_rc_shift3 (exd_SOLEXA_2_FBgn0000611_rc)	0.770	0.560	0.192	-0.070	0.886	1.674	0.895	7	2	5	5	6	7	7	5.571	7	; oligos_6nt_mkv4_m1 versus exd_SOLEXA_2_FBgn0000611_rc; m=7/7; ncol2=8; w=8; offset=3; strand=R; shift=3; score= 5.5714; ---wyrTCAaa- ; cor=0.770; Ncor=0.560; logoDP=0.192; NIcor=-0.070; NsEucl=0.886; SSD=1.674; NSW=0.895; rcor=7; rNcor=2; rlogoDP=5; rNIcor=5; rNsEucl=6; rSSD=7; rNSW=7; rank_mean=5.571; match_rank=7 a \| 0 0 0 483 259 1228 0 0 2672 1314 1025 0 c \| 0 0 0 145 914 86 0 2672 0 598 458 0 g \| 0 0 0 91 14 1169 0 0 0 204 568 0 t \| 0 0 0 474 1470 189 2672 0 0 539 587 0