One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_m3.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.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m3/peak-motifs_oligos_7nt_test_vs_ctrl_m3_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m3_shift2 ; 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_test_vs_ctrl_m3_shift2 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=15; shift=2; ncol=21; --wwcTTTATCTCTAww---- ; Alignment reference a 0 0 190 179 84 48 42 38 551 18 45 33 49 37 486 197 196 0 0 0 0 c 0 0 89 122 378 26 37 33 21 25 495 16 451 36 36 118 118 0 0 0 0 g 0 0 128 80 54 14 39 18 16 8 25 7 45 15 39 101 119 0 0 0 0 t 0 0 206 232 97 525 495 524 25 562 48 557 68 525 52 197 180 0 0 0 0

MA0035.3_shift3 (Gata1) 0.803 0.589 5.942 0.568 0.911 1.907 0.913 2 1 1 1 4 4 3 2.286 1
; oligos_7nt_test_vs_ctrl_m3 versus MA0035.3 (Gata1); m=1/6; ncol2=11; w=11; offset=1; strand=D; shift=3; score= 2.2857; ---tyCTTATCTsy------- ; cor=0.803; Ncor=0.589; logoDP=5.942; NIcor=0.568; NsEucl=0.911; SSD=1.907; NSW=0.913; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=4; rSSD=4; rNSW=3; rank_mean=2.286; match_rank=1 a 0 0 0 2035 506 0 0 0 17955 0 0 2166 2502 1886 0 0 0 0 0 0 0 c 0 0 0 4321 6406 14869 697 0 0 0 17955 0 6166 5072 0 0 0 0 0 0 0 g 0 0 0 2530 2792 437 0 0 0 0 0 0 6687 1598 0 0 0 0 0 0 0 t 0 0 0 9069 8251 2649 17258 17955 0 17955 0 15789 2600 9399 0 0 0 0 0 0 0

MA0037.2_rc_shift4 (GATA3_rc) 0.858 0.458 2.390 0.043 0.898 1.327 0.917 1 4 3 4 5 1 2 2.857 2
; oligos_7nt_test_vs_ctrl_m3 versus MA0037.2_rc (GATA3_rc); m=2/6; ncol2=8; w=8; offset=2; strand=R; shift=4; score= 2.8571; ----tYTTATCT--------- ; cor=0.858; Ncor=0.458; logoDP=2.390; NIcor=0.043; NsEucl=0.898; SSD=1.327; NSW=0.917; rcor=1; rNcor=4; rlogoDP=3; rNIcor=4; rNsEucl=5; rSSD=1; rNSW=2; rank_mean=2.857; match_rank=2 a 0 0 0 0 0 0 0 0 4628 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 1120 3338 0 0 0 0 4628 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 712 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 2796 1290 4628 4628 0 4628 0 4628 0 0 0 0 0 0 0 0 0

MA0035.2_rc_shift3 (Gata1_rc) 0.798 0.585 0.537 -0.176 0.915 1.754 0.920 3 2 5 6 1 3 1 3.000 3
; oligos_7nt_test_vs_ctrl_m3 versus MA0035.2_rc (Gata1_rc); m=3/6; ncol2=11; w=11; offset=1; strand=R; shift=3; score= 3; ---yycTTATCWsy------- ; cor=0.798; Ncor=0.585; logoDP=0.537; NIcor=-0.176; NsEucl=0.915; SSD=1.754; NSW=0.920; rcor=3; rNcor=2; rlogoDP=5; rNIcor=6; rNsEucl=1; rSSD=3; rNSW=1; rank_mean=3.000; match_rank=3 a 0 0 0 585 311 224 63 107 3835 0 0 1177 424 775 0 0 0 0 0 0 0 c 0 0 0 1099 1360 2296 383 6 109 0 4000 10 1235 1242 0 0 0 0 0 0 0 g 0 0 0 829 897 681 4 0 29 0 0 31 1633 560 0 0 0 0 0 0 0 t 0 0 0 1487 1432 799 3550 3887 27 4000 0 2782 708 1423 0 0 0 0 0 0 0

MA0036.2_shift0 (GATA2) 0.764 0.539 5.531 0.527 0.912 2.216 0.908 4 3 2 2 3 6 5 3.571 4
; oligos_7nt_test_vs_ctrl_m3 versus MA0036.2 (GATA2); m=4/6; ncol2=14; w=12; offset=-2; strand=D; shift=0; score= 3.5714; wrrttCTTATCWsh------- ; cor=0.764; Ncor=0.539; logoDP=5.531; NIcor=0.527; NsEucl=0.912; SSD=2.216; NSW=0.908; rcor=4; rNcor=3; rlogoDP=2; rNIcor=2; rNsEucl=3; rSSD=6; rNSW=5; rank_mean=3.571; match_rank=4 a 1569 1125 1555 1051 32 9 0 51 4380 0 0 1225 104 1256 0 0 0 0 0 0 0 c 567 768 729 525 1057 3015 192 0 0 0 4380 0 1765 1185 0 0 0 0 0 0 0 g 754 1709 1220 427 765 914 0 0 0 0 0 0 1967 224 0 0 0 0 0 0 0 t 1490 778 876 2377 2526 442 4188 4329 0 4380 0 3155 544 1715 0 0 0 0 0 0 0

MA0140.1_rc_shift5 (Tal1::Gata1_rc) 0.760 0.434 0.233 0.012 0.915 2.095 0.913 5 5 6 5 2 5 4 4.571 5
; oligos_7nt_test_vs_ctrl_m3 versus MA0140.1_rc (Tal1::Gata1_rc); m=5/6; ncol2=18; w=12; offset=3; strand=R; shift=5; score= 4.5714; -----cTTATCwsyccscmsc ; cor=0.760; Ncor=0.434; logoDP=0.233; NIcor=0.012; NsEucl=0.915; SSD=2.095; NSW=0.913; rcor=5; rNcor=5; rlogoDP=6; rNIcor=5; rNsEucl=2; rSSD=5; rNSW=4; rank_mean=4.571; match_rank=5 a 0 0 0 0 0 242 134 144 2873 10 0 920 345 603 691 644 599 654 866 706 710 c 0 0 0 0 0 1601 376 23 30 2 2936 37 901 940 862 891 938 903 775 1228 1921 g 0 0 0 0 0 550 51 6 26 7 7 31 1172 407 662 699 745 687 635 746 182 t 0 0 0 0 0 547 2382 2770 16 2928 3 1959 527 996 734 713 664 701 669 265 131

MA0033.1_rc_shift7 (FOXL1_rc) 0.751 0.400 1.587 0.205 0.886 1.676 0.895 6 6 4 3 6 2 6 4.714 6
; oligos_7nt_test_vs_ctrl_m3 versus MA0033.1_rc (FOXL1_rc); m=6/6; ncol2=8; w=8; offset=5; strand=R; shift=7; score= 4.7143; -------TATrthww------ ; cor=0.751; Ncor=0.400; logoDP=1.587; NIcor=0.205; NsEucl=0.886; SSD=1.676; NSW=0.895; rcor=6; rNcor=6; rlogoDP=4; rNIcor=3; rNsEucl=6; rSSD=2; rNSW=6; rank_mean=4.714; match_rank=6 a 0 0 0 0 0 0 0 0 21 0 7 2 8 7 11 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 2 2 4 6 2 4 0 0 0 0 0 0 g 0 0 0 0 0 0 0 1 2 0 10 4 3 4 1 0 0 0 0 0 0 t 0 0 0 0 0 0 0 22 0 21 4 13 6 10 7 0 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
oligos_7nt_test_vs_ctrl_m3_shift2 (oligos_7nt_test_vs_ctrl_m3)																	; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=15; shift=2; ncol=21; --wwcTTTATCTCTAww---- ; Alignment reference a 0 0 190 179 84 48 42 38 551 18 45 33 49 37 486 197 196 0 0 0 0 c 0 0 89 122 378 26 37 33 21 25 495 16 451 36 36 118 118 0 0 0 0 g 0 0 128 80 54 14 39 18 16 8 25 7 45 15 39 101 119 0 0 0 0 t 0 0 206 232 97 525 495 524 25 562 48 557 68 525 52 197 180 0 0 0 0
MA0035.3_shift3 (Gata1)	0.803	0.589	5.942	0.568	0.911	1.907	0.913	2	1	1	1	4	4	3	2.286	1	; oligos_7nt_test_vs_ctrl_m3 versus MA0035.3 (Gata1); m=1/6; ncol2=11; w=11; offset=1; strand=D; shift=3; score= 2.2857; ---tyCTTATCTsy------- ; cor=0.803; Ncor=0.589; logoDP=5.942; NIcor=0.568; NsEucl=0.911; SSD=1.907; NSW=0.913; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=4; rSSD=4; rNSW=3; rank_mean=2.286; match_rank=1 a 0 0 0 2035 506 0 0 0 17955 0 0 2166 2502 1886 0 0 0 0 0 0 0 c 0 0 0 4321 6406 14869 697 0 0 0 17955 0 6166 5072 0 0 0 0 0 0 0 g 0 0 0 2530 2792 437 0 0 0 0 0 0 6687 1598 0 0 0 0 0 0 0 t 0 0 0 9069 8251 2649 17258 17955 0 17955 0 15789 2600 9399 0 0 0 0 0 0 0
MA0037.2_rc_shift4 (GATA3_rc)	0.858	0.458	2.390	0.043	0.898	1.327	0.917	1	4	3	4	5	1	2	2.857	2	; oligos_7nt_test_vs_ctrl_m3 versus MA0037.2_rc (GATA3_rc); m=2/6; ncol2=8; w=8; offset=2; strand=R; shift=4; score= 2.8571; ----tYTTATCT--------- ; cor=0.858; Ncor=0.458; logoDP=2.390; NIcor=0.043; NsEucl=0.898; SSD=1.327; NSW=0.917; rcor=1; rNcor=4; rlogoDP=3; rNIcor=4; rNsEucl=5; rSSD=1; rNSW=2; rank_mean=2.857; match_rank=2 a 0 0 0 0 0 0 0 0 4628 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 1120 3338 0 0 0 0 4628 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 712 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 2796 1290 4628 4628 0 4628 0 4628 0 0 0 0 0 0 0 0 0
MA0035.2_rc_shift3 (Gata1_rc)	0.798	0.585	0.537	-0.176	0.915	1.754	0.920	3	2	5	6	1	3	1	3.000	3	; oligos_7nt_test_vs_ctrl_m3 versus MA0035.2_rc (Gata1_rc); m=3/6; ncol2=11; w=11; offset=1; strand=R; shift=3; score= 3; ---yycTTATCWsy------- ; cor=0.798; Ncor=0.585; logoDP=0.537; NIcor=-0.176; NsEucl=0.915; SSD=1.754; NSW=0.920; rcor=3; rNcor=2; rlogoDP=5; rNIcor=6; rNsEucl=1; rSSD=3; rNSW=1; rank_mean=3.000; match_rank=3 a 0 0 0 585 311 224 63 107 3835 0 0 1177 424 775 0 0 0 0 0 0 0 c 0 0 0 1099 1360 2296 383 6 109 0 4000 10 1235 1242 0 0 0 0 0 0 0 g 0 0 0 829 897 681 4 0 29 0 0 31 1633 560 0 0 0 0 0 0 0 t 0 0 0 1487 1432 799 3550 3887 27 4000 0 2782 708 1423 0 0 0 0 0 0 0
MA0036.2_shift0 (GATA2)	0.764	0.539	5.531	0.527	0.912	2.216	0.908	4	3	2	2	3	6	5	3.571	4	; oligos_7nt_test_vs_ctrl_m3 versus MA0036.2 (GATA2); m=4/6; ncol2=14; w=12; offset=-2; strand=D; shift=0; score= 3.5714; wrrttCTTATCWsh------- ; cor=0.764; Ncor=0.539; logoDP=5.531; NIcor=0.527; NsEucl=0.912; SSD=2.216; NSW=0.908; rcor=4; rNcor=3; rlogoDP=2; rNIcor=2; rNsEucl=3; rSSD=6; rNSW=5; rank_mean=3.571; match_rank=4 a 1569 1125 1555 1051 32 9 0 51 4380 0 0 1225 104 1256 0 0 0 0 0 0 0 c 567 768 729 525 1057 3015 192 0 0 0 4380 0 1765 1185 0 0 0 0 0 0 0 g 754 1709 1220 427 765 914 0 0 0 0 0 0 1967 224 0 0 0 0 0 0 0 t 1490 778 876 2377 2526 442 4188 4329 0 4380 0 3155 544 1715 0 0 0 0 0 0 0
MA0140.1_rc_shift5 (Tal1::Gata1_rc)	0.760	0.434	0.233	0.012	0.915	2.095	0.913	5	5	6	5	2	5	4	4.571	5	; oligos_7nt_test_vs_ctrl_m3 versus MA0140.1_rc (Tal1::Gata1_rc); m=5/6; ncol2=18; w=12; offset=3; strand=R; shift=5; score= 4.5714; -----cTTATCwsyccscmsc ; cor=0.760; Ncor=0.434; logoDP=0.233; NIcor=0.012; NsEucl=0.915; SSD=2.095; NSW=0.913; rcor=5; rNcor=5; rlogoDP=6; rNIcor=5; rNsEucl=2; rSSD=5; rNSW=4; rank_mean=4.571; match_rank=5 a 0 0 0 0 0 242 134 144 2873 10 0 920 345 603 691 644 599 654 866 706 710 c 0 0 0 0 0 1601 376 23 30 2 2936 37 901 940 862 891 938 903 775 1228 1921 g 0 0 0 0 0 550 51 6 26 7 7 31 1172 407 662 699 745 687 635 746 182 t 0 0 0 0 0 547 2382 2770 16 2928 3 1959 527 996 734 713 664 701 669 265 131
MA0033.1_rc_shift7 (FOXL1_rc)	0.751	0.400	1.587	0.205	0.886	1.676	0.895	6	6	4	3	6	2	6	4.714	6	; oligos_7nt_test_vs_ctrl_m3 versus MA0033.1_rc (FOXL1_rc); m=6/6; ncol2=8; w=8; offset=5; strand=R; shift=7; score= 4.7143; -------TATrthww------ ; cor=0.751; Ncor=0.400; logoDP=1.587; NIcor=0.205; NsEucl=0.886; SSD=1.676; NSW=0.895; rcor=6; rNcor=6; rlogoDP=4; rNIcor=3; rNsEucl=6; rSSD=2; rNSW=6; rank_mean=4.714; match_rank=6 a 0 0 0 0 0 0 0 0 21 0 7 2 8 7 11 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 2 2 4 6 2 4 0 0 0 0 0 0 g 0 0 0 0 0 0 0 1 2 0 10 4 3 4 1 0 0 0 0 0 0 t 0 0 0 0 0 0 0 22 0 21 4 13 6 10 7 0 0 0 0 0 0