One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/JASPAR/jaspar_core_vertebrates_2013-11.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/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 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
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=17; shift=0; ncol=20; cyGCCCCCCCRCCCCsv--- ; Alignment reference a 1 1 2 0 1 1 2 1 0 1 14 0 0 2 1 3 5 0 0 0 c 11 8 2 18 16 15 16 18 19 17 0 18 19 17 18 6 7 0 0 0 g 4 3 13 1 2 2 0 0 0 1 5 0 0 0 0 6 5 0 0 0 t 3 7 2 0 0 1 1 0 0 0 0 1 0 0 0 4 2 0 0 0

MA0079.3_shift5 (SP1) 0.865 0.560 8.778 0.561 0.922 1.475 0.933 2 1 1 1 1 2 2 1.429 1
; dyads_m4 versus MA0079.3 (SP1); m=1/6; ncol2=11; w=11; offset=5; strand=D; shift=5; score= 1.4286; -----gCCCCkCCCCy---- ; cor=0.865; Ncor=0.560; logoDP=8.778; NIcor=0.561; NsEucl=0.922; SSD=1.475; NSW=0.933; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=1.429; match_rank=1 a 0 0 0 0 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 0 c 0 0 0 0 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 0 g 0 0 0 0 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 0 t 0 0 0 0 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0 0

MA0079.2_shift6 (SP1) 0.879 0.517 6.743 0.524 0.921 1.234 0.938 1 2 4 2 2 1 1 1.857 2
; dyads_m4 versus MA0079.2 (SP1); m=2/6; ncol2=10; w=10; offset=6; strand=D; shift=6; score= 1.8571; ------CCCCkCCCCC---- ; cor=0.879; Ncor=0.517; logoDP=6.743; NIcor=0.524; NsEucl=0.921; SSD=1.234; NSW=0.938; rcor=1; rNcor=2; rlogoDP=4; rNIcor=2; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=1.857; match_rank=2 a 0 0 0 0 0 0 0 0 0 4 2 0 1 0 6 3 0 0 0 0 c 0 0 0 0 0 0 32 30 35 27 5 28 31 24 25 26 0 0 0 0 g 0 0 0 0 0 0 1 1 0 0 15 1 0 3 0 3 0 0 0 0 t 0 0 0 0 0 0 2 4 0 4 13 6 3 8 4 3 0 0 0 0

MA0599.1_shift5 (KLF5) 0.860 0.506 8.354 0.490 0.913 1.511 0.924 3 4 2 3 5 3 3 3.286 3
; dyads_m4 versus MA0599.1 (KLF5); m=3/6; ncol2=10; w=10; offset=5; strand=D; shift=5; score= 3.2857; -----gCCMCrCCCh----- ; cor=0.860; Ncor=0.506; logoDP=8.354; NIcor=0.490; NsEucl=0.913; SSD=1.511; NSW=0.924; rcor=3; rNcor=4; rlogoDP=2; rNIcor=3; rNsEucl=5; rSSD=3; rNSW=3; rank_mean=3.286; match_rank=3 a 0 0 0 0 0 1429 0 0 3477 0 5051 0 0 0 3915 0 0 0 0 0 c 0 0 0 0 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 0 0 0 0 0 g 0 0 0 0 0 7572 0 0 0 0 5182 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 2587 1711 1603 565 0 3378 0 0 476 4101 0 0 0 0 0

MA0162.2_shift5 (EGR1) 0.816 0.515 6.724 0.489 0.917 1.986 0.917 4 3 5 4 3 4 4 3.857 4
; dyads_m4 versus MA0162.2 (EGR1); m=4/6; ncol2=14; w=12; offset=5; strand=D; shift=5; score= 3.8571; -----sccCCgCCCMCkCc- ; cor=0.816; Ncor=0.515; logoDP=6.724; NIcor=0.489; NsEucl=0.917; SSD=1.986; NSW=0.917; rcor=4; rNcor=3; rlogoDP=5; rNIcor=4; rNsEucl=3; rSSD=4; rNSW=4; rank_mean=3.857; match_rank=4 a 0 0 0 0 0 1098 1506 1160 1335 233 2911 0 0 0 3652 0 2368 0 3026 0 c 0 0 0 0 0 5728 6847 6049 10431 11574 0 12256 11852 10154 8361 11952 0 9849 5595 0 g 0 0 0 0 0 3083 1359 2250 0 0 6840 0 0 611 0 0 6599 1420 1913 0 t 0 0 0 0 0 2347 2544 2797 490 449 2505 0 404 1491 243 304 3289 987 1722 0

MA0516.1_shift5 (SP2) 0.801 0.481 8.265 0.476 0.913 2.164 0.910 5 5 3 5 4 5 5 4.571 5
; dyads_m4 versus MA0516.1 (SP2); m=5/6; ncol2=15; w=12; offset=5; strand=D; shift=5; score= 4.5714; -----gyCCCGCCyCyyccs ; cor=0.801; Ncor=0.481; logoDP=8.265; NIcor=0.476; NsEucl=0.913; SSD=2.164; NSW=0.910; rcor=5; rNcor=5; rlogoDP=3; rNIcor=5; rNsEucl=4; rSSD=5; rNSW=5; rank_mean=4.571; match_rank=5 a 0 0 0 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 c 0 0 0 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 g 0 0 0 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 t 0 0 0 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316

MA0039.2_rc_shift5 (Klf4_rc) 0.793 0.466 0.894 -0.092 0.895 2.218 0.889 6 6 6 6 6 6 6 6.000 6
; dyads_m4 versus MA0039.2_rc (Klf4_rc); m=6/6; ncol2=10; w=10; offset=5; strand=R; shift=5; score= 6; -----gCCmCrCCCw----- ; cor=0.793; Ncor=0.466; logoDP=0.894; NIcor=-0.092; NsEucl=0.895; SSD=2.218; NSW=0.889; rcor=6; rNcor=6; rlogoDP=6; rNIcor=6; rNsEucl=6; rSSD=6; rNSW=6; rank_mean=6.000; match_rank=6 a 0 0 0 0 0 932 289 125 2042 34 2139 16 13 6 1765 0 0 0 0 0 c 0 0 0 0 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 0 0 0 0 0 g 0 0 0 0 0 2858 130 46 80 15 1922 36 13 9 81 0 0 0 0 0 t 0 0 0 0 0 254 123 264 42 22 277 14 14 88 1468 0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_m4_shift0 (dyads_m4)																	; dyads_m4; m=0 (reference); ncol1=17; shift=0; ncol=20; cyGCCCCCCCRCCCCsv--- ; Alignment reference a 1 1 2 0 1 1 2 1 0 1 14 0 0 2 1 3 5 0 0 0 c 11 8 2 18 16 15 16 18 19 17 0 18 19 17 18 6 7 0 0 0 g 4 3 13 1 2 2 0 0 0 1 5 0 0 0 0 6 5 0 0 0 t 3 7 2 0 0 1 1 0 0 0 0 1 0 0 0 4 2 0 0 0
MA0079.3_shift5 (SP1)	0.865	0.560	8.778	0.561	0.922	1.475	0.933	2	1	1	1	1	2	2	1.429	1	; dyads_m4 versus MA0079.3 (SP1); m=1/6; ncol2=11; w=11; offset=5; strand=D; shift=5; score= 1.4286; -----gCCCCkCCCCy---- ; cor=0.865; Ncor=0.560; logoDP=8.778; NIcor=0.561; NsEucl=0.922; SSD=1.475; NSW=0.933; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=1.429; match_rank=1 a 0 0 0 0 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 0 c 0 0 0 0 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 0 g 0 0 0 0 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 0 t 0 0 0 0 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0 0
MA0079.2_shift6 (SP1)	0.879	0.517	6.743	0.524	0.921	1.234	0.938	1	2	4	2	2	1	1	1.857	2	; dyads_m4 versus MA0079.2 (SP1); m=2/6; ncol2=10; w=10; offset=6; strand=D; shift=6; score= 1.8571; ------CCCCkCCCCC---- ; cor=0.879; Ncor=0.517; logoDP=6.743; NIcor=0.524; NsEucl=0.921; SSD=1.234; NSW=0.938; rcor=1; rNcor=2; rlogoDP=4; rNIcor=2; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=1.857; match_rank=2 a 0 0 0 0 0 0 0 0 0 4 2 0 1 0 6 3 0 0 0 0 c 0 0 0 0 0 0 32 30 35 27 5 28 31 24 25 26 0 0 0 0 g 0 0 0 0 0 0 1 1 0 0 15 1 0 3 0 3 0 0 0 0 t 0 0 0 0 0 0 2 4 0 4 13 6 3 8 4 3 0 0 0 0
MA0599.1_shift5 (KLF5)	0.860	0.506	8.354	0.490	0.913	1.511	0.924	3	4	2	3	5	3	3	3.286	3	; dyads_m4 versus MA0599.1 (KLF5); m=3/6; ncol2=10; w=10; offset=5; strand=D; shift=5; score= 3.2857; -----gCCMCrCCCh----- ; cor=0.860; Ncor=0.506; logoDP=8.354; NIcor=0.490; NsEucl=0.913; SSD=1.511; NSW=0.924; rcor=3; rNcor=4; rlogoDP=2; rNIcor=3; rNsEucl=5; rSSD=3; rNSW=3; rank_mean=3.286; match_rank=3 a 0 0 0 0 0 1429 0 0 3477 0 5051 0 0 0 3915 0 0 0 0 0 c 0 0 0 0 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 0 0 0 0 0 g 0 0 0 0 0 7572 0 0 0 0 5182 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 2587 1711 1603 565 0 3378 0 0 476 4101 0 0 0 0 0
MA0162.2_shift5 (EGR1)	0.816	0.515	6.724	0.489	0.917	1.986	0.917	4	3	5	4	3	4	4	3.857	4	; dyads_m4 versus MA0162.2 (EGR1); m=4/6; ncol2=14; w=12; offset=5; strand=D; shift=5; score= 3.8571; -----sccCCgCCCMCkCc- ; cor=0.816; Ncor=0.515; logoDP=6.724; NIcor=0.489; NsEucl=0.917; SSD=1.986; NSW=0.917; rcor=4; rNcor=3; rlogoDP=5; rNIcor=4; rNsEucl=3; rSSD=4; rNSW=4; rank_mean=3.857; match_rank=4 a 0 0 0 0 0 1098 1506 1160 1335 233 2911 0 0 0 3652 0 2368 0 3026 0 c 0 0 0 0 0 5728 6847 6049 10431 11574 0 12256 11852 10154 8361 11952 0 9849 5595 0 g 0 0 0 0 0 3083 1359 2250 0 0 6840 0 0 611 0 0 6599 1420 1913 0 t 0 0 0 0 0 2347 2544 2797 490 449 2505 0 404 1491 243 304 3289 987 1722 0
MA0516.1_shift5 (SP2)	0.801	0.481	8.265	0.476	0.913	2.164	0.910	5	5	3	5	4	5	5	4.571	5	; dyads_m4 versus MA0516.1 (SP2); m=5/6; ncol2=15; w=12; offset=5; strand=D; shift=5; score= 4.5714; -----gyCCCGCCyCyyccs ; cor=0.801; Ncor=0.481; logoDP=8.265; NIcor=0.476; NsEucl=0.913; SSD=2.164; NSW=0.910; rcor=5; rNcor=5; rlogoDP=3; rNIcor=5; rNsEucl=4; rSSD=5; rNSW=5; rank_mean=4.571; match_rank=5 a 0 0 0 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 c 0 0 0 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 g 0 0 0 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 t 0 0 0 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316
MA0039.2_rc_shift5 (Klf4_rc)	0.793	0.466	0.894	-0.092	0.895	2.218	0.889	6	6	6	6	6	6	6	6.000	6	; dyads_m4 versus MA0039.2_rc (Klf4_rc); m=6/6; ncol2=10; w=10; offset=5; strand=R; shift=5; score= 6; -----gCCmCrCCCw----- ; cor=0.793; Ncor=0.466; logoDP=0.894; NIcor=-0.092; NsEucl=0.895; SSD=2.218; NSW=0.889; rcor=6; rNcor=6; rlogoDP=6; rNIcor=6; rNsEucl=6; rSSD=6; rNSW=6; rank_mean=6.000; match_rank=6 a 0 0 0 0 0 932 289 125 2042 34 2139 16 13 6 1765 0 0 0 0 0 c 0 0 0 0 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 0 0 0 0 0 g 0 0 0 0 0 2858 130 46 80 15 1922 36 13 9 81 0 0 0 0 0 t 0 0 0 0 0 254 123 264 42 22 277 14 14 88 1468 0 0 0 0 0