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/peak-motifs_motifs_discovered.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_vs_db/peak-motifs_motifs_vs_db_jaspar_core_vertebrates.tab

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 4 1 1 1 9 8 8 4.571 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= 4.5714; ---tyCTTATCTsy------- ; cor=0.803; Ncor=0.589; logoDP=5.942; NIcor=0.568; NsEucl=0.911; SSD=1.907; NSW=0.913; rcor=4; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=9; rSSD=8; rNSW=8; rank_mean=4.571; 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 2 7 6 7 11 3 7 6.143 3
; 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= 6.1429; ----tYTTATCT--------- ; cor=0.858; Ncor=0.458; logoDP=2.390; NIcor=0.043; NsEucl=0.898; SSD=1.327; NSW=0.917; rcor=2; rNcor=7; rlogoDP=6; rNIcor=7; rNsEucl=11; rSSD=3; rNSW=7; rank_mean=6.143; match_rank=3 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 5 2 11 14 5 7 5 7.000 5
; 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= 7; ---yycTTATCWsy------- ; cor=0.798; Ncor=0.585; logoDP=0.537; NIcor=-0.176; NsEucl=0.915; SSD=1.754; NSW=0.920; rcor=5; rNcor=2; rlogoDP=11; rNIcor=14; rNsEucl=5; rSSD=7; rNSW=5; rank_mean=7.000; match_rank=5 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 12 4 3 2 8 13 11 7.571 10
; oligos_7nt_test_vs_ctrl_m3 versus MA0036.2 (GATA2); m=4/6; ncol2=14; w=12; offset=-2; strand=D; shift=0; score= 7.5714; wrrttCTTATCWsh------- ; cor=0.764; Ncor=0.539; logoDP=5.531; NIcor=0.527; NsEucl=0.912; SSD=2.216; NSW=0.908; rcor=12; rNcor=4; rlogoDP=3; rNIcor=2; rNsEucl=8; rSSD=13; rNSW=11; rank_mean=7.571; match_rank=10 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 13 11 14 8 6 10 9 10.143 12
; 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=10.1429; -----cTTATCwsyccscmsc ; cor=0.760; Ncor=0.434; logoDP=0.233; NIcor=0.012; NsEucl=0.915; SSD=2.095; NSW=0.913; rcor=13; rNcor=11; rlogoDP=14; rNIcor=8; rNsEucl=6; rSSD=10; rNSW=9; rank_mean=10.143; match_rank=12 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 14 14 7 5 13 5 14 10.286 14
; 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=10.2857; -------TATrthww------ ; cor=0.751; Ncor=0.400; logoDP=1.587; NIcor=0.205; NsEucl=0.886; SSD=1.676; NSW=0.895; rcor=14; rNcor=14; rlogoDP=7; rNIcor=5; rNsEucl=13; rSSD=5; rNSW=14; rank_mean=10.286; match_rank=14 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	4	1	1	1	9	8	8	4.571	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= 4.5714; ---tyCTTATCTsy------- ; cor=0.803; Ncor=0.589; logoDP=5.942; NIcor=0.568; NsEucl=0.911; SSD=1.907; NSW=0.913; rcor=4; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=9; rSSD=8; rNSW=8; rank_mean=4.571; 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	2	7	6	7	11	3	7	6.143	3	; 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= 6.1429; ----tYTTATCT--------- ; cor=0.858; Ncor=0.458; logoDP=2.390; NIcor=0.043; NsEucl=0.898; SSD=1.327; NSW=0.917; rcor=2; rNcor=7; rlogoDP=6; rNIcor=7; rNsEucl=11; rSSD=3; rNSW=7; rank_mean=6.143; match_rank=3 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	5	2	11	14	5	7	5	7.000	5	; 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= 7; ---yycTTATCWsy------- ; cor=0.798; Ncor=0.585; logoDP=0.537; NIcor=-0.176; NsEucl=0.915; SSD=1.754; NSW=0.920; rcor=5; rNcor=2; rlogoDP=11; rNIcor=14; rNsEucl=5; rSSD=7; rNSW=5; rank_mean=7.000; match_rank=5 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	12	4	3	2	8	13	11	7.571	10	; oligos_7nt_test_vs_ctrl_m3 versus MA0036.2 (GATA2); m=4/6; ncol2=14; w=12; offset=-2; strand=D; shift=0; score= 7.5714; wrrttCTTATCWsh------- ; cor=0.764; Ncor=0.539; logoDP=5.531; NIcor=0.527; NsEucl=0.912; SSD=2.216; NSW=0.908; rcor=12; rNcor=4; rlogoDP=3; rNIcor=2; rNsEucl=8; rSSD=13; rNSW=11; rank_mean=7.571; match_rank=10 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	13	11	14	8	6	10	9	10.143	12	; 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=10.1429; -----cTTATCwsyccscmsc ; cor=0.760; Ncor=0.434; logoDP=0.233; NIcor=0.012; NsEucl=0.915; SSD=2.095; NSW=0.913; rcor=13; rNcor=11; rlogoDP=14; rNIcor=8; rNsEucl=6; rSSD=10; rNSW=9; rank_mean=10.143; match_rank=12 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	14	14	7	5	13	5	14	10.286	14	; 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=10.2857; -------TATrthww------ ; cor=0.751; Ncor=0.400; logoDP=1.587; NIcor=0.205; NsEucl=0.886; SSD=1.676; NSW=0.895; rcor=14; rNcor=14; rlogoDP=7; rNIcor=5; rNsEucl=13; rSSD=5; rNSW=14; rank_mean=10.286; match_rank=14 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

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m1_shift2 ; 4 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_m1_shift2 (oligos_7nt_test_vs_ctrl_m1)
; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=16; shift=2; ncol=18; --wwcTTTATCTGATAww ; Alignment reference a 0 0 133 133 102 42 41 28 405 14 20 37 33 381 26 326 150 146 c 0 0 69 94 230 28 29 16 14 15 379 6 25 29 16 40 75 105 g 0 0 89 72 44 31 29 14 18 16 19 2 357 16 18 35 69 78 t 0 0 161 153 76 351 353 394 15 407 34 407 37 26 392 51 158 123

MA0037.2_rc_shift4 (GATA3_rc) 0.877 0.438 2.500 0.052 0.904 1.178 0.926 1 10 5 6 10 1 2 5.000 2
; oligos_7nt_test_vs_ctrl_m1 versus MA0037.2_rc (GATA3_rc); m=1/3; ncol2=8; w=8; offset=2; strand=R; shift=4; score= 5; ----tYTTATCT------ ; cor=0.877; Ncor=0.438; logoDP=2.500; NIcor=0.052; NsEucl=0.904; SSD=1.178; NSW=0.926; rcor=1; rNcor=10; rlogoDP=5; rNIcor=6; rNsEucl=10; rSSD=1; rNSW=2; rank_mean=5.000; match_rank=2 a 0 0 0 0 0 0 0 0 4628 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 g 0 0 0 0 712 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

MA0035.2_rc_shift3 (Gata1_rc) 0.797 0.548 0.468 -0.135 0.916 1.718 0.922 6 3 12 13 4 6 3 6.714 4
; oligos_7nt_test_vs_ctrl_m1 versus MA0035.2_rc (Gata1_rc); m=2/3; ncol2=11; w=11; offset=1; strand=R; shift=3; score= 6.7143; ---yycTTATCWsy---- ; cor=0.797; Ncor=0.548; logoDP=0.468; NIcor=-0.135; NsEucl=0.916; SSD=1.718; NSW=0.922; rcor=6; rNcor=3; rlogoDP=12; rNIcor=13; rNsEucl=4; rSSD=6; rNSW=3; rank_mean=6.714; match_rank=4 a 0 0 0 585 311 224 63 107 3835 0 0 1177 424 775 0 0 0 0 c 0 0 0 1099 1360 2296 383 6 109 0 4000 10 1235 1242 0 0 0 0 g 0 0 0 829 897 681 4 0 29 0 0 31 1633 560 0 0 0 0 t 0 0 0 1487 1432 799 3550 3887 27 4000 0 2782 708 1423 0 0 0 0

MA0036.2_shift0 (GATA2) 0.765 0.510 5.523 0.505 0.913 2.162 0.910 11 5 4 3 7 11 10 7.286 7
; oligos_7nt_test_vs_ctrl_m1 versus MA0036.2 (GATA2); m=3/3; ncol2=14; w=12; offset=-2; strand=D; shift=0; score= 7.2857; wrrttCTTATCWsh---- ; cor=0.765; Ncor=0.510; logoDP=5.523; NIcor=0.505; NsEucl=0.913; SSD=2.162; NSW=0.910; rcor=11; rNcor=5; rlogoDP=4; rNIcor=3; rNsEucl=7; rSSD=11; rNSW=10; rank_mean=7.286; match_rank=7 a 1569 1125 1555 1051 32 9 0 51 4380 0 0 1225 104 1256 0 0 0 0 c 567 768 729 525 1057 3015 192 0 0 0 4380 0 1765 1185 0 0 0 0 g 754 1709 1220 427 765 914 0 0 0 0 0 0 1967 224 0 0 0 0 t 1490 778 876 2377 2526 442 4188 4329 0 4380 0 3155 544 1715 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_m1_shift2 (oligos_7nt_test_vs_ctrl_m1)																	; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=16; shift=2; ncol=18; --wwcTTTATCTGATAww ; Alignment reference a 0 0 133 133 102 42 41 28 405 14 20 37 33 381 26 326 150 146 c 0 0 69 94 230 28 29 16 14 15 379 6 25 29 16 40 75 105 g 0 0 89 72 44 31 29 14 18 16 19 2 357 16 18 35 69 78 t 0 0 161 153 76 351 353 394 15 407 34 407 37 26 392 51 158 123
MA0037.2_rc_shift4 (GATA3_rc)	0.877	0.438	2.500	0.052	0.904	1.178	0.926	1	10	5	6	10	1	2	5.000	2	; oligos_7nt_test_vs_ctrl_m1 versus MA0037.2_rc (GATA3_rc); m=1/3; ncol2=8; w=8; offset=2; strand=R; shift=4; score= 5; ----tYTTATCT------ ; cor=0.877; Ncor=0.438; logoDP=2.500; NIcor=0.052; NsEucl=0.904; SSD=1.178; NSW=0.926; rcor=1; rNcor=10; rlogoDP=5; rNIcor=6; rNsEucl=10; rSSD=1; rNSW=2; rank_mean=5.000; match_rank=2 a 0 0 0 0 0 0 0 0 4628 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 g 0 0 0 0 712 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
MA0035.2_rc_shift3 (Gata1_rc)	0.797	0.548	0.468	-0.135	0.916	1.718	0.922	6	3	12	13	4	6	3	6.714	4	; oligos_7nt_test_vs_ctrl_m1 versus MA0035.2_rc (Gata1_rc); m=2/3; ncol2=11; w=11; offset=1; strand=R; shift=3; score= 6.7143; ---yycTTATCWsy---- ; cor=0.797; Ncor=0.548; logoDP=0.468; NIcor=-0.135; NsEucl=0.916; SSD=1.718; NSW=0.922; rcor=6; rNcor=3; rlogoDP=12; rNIcor=13; rNsEucl=4; rSSD=6; rNSW=3; rank_mean=6.714; match_rank=4 a 0 0 0 585 311 224 63 107 3835 0 0 1177 424 775 0 0 0 0 c 0 0 0 1099 1360 2296 383 6 109 0 4000 10 1235 1242 0 0 0 0 g 0 0 0 829 897 681 4 0 29 0 0 31 1633 560 0 0 0 0 t 0 0 0 1487 1432 799 3550 3887 27 4000 0 2782 708 1423 0 0 0 0
MA0036.2_shift0 (GATA2)	0.765	0.510	5.523	0.505	0.913	2.162	0.910	11	5	4	3	7	11	10	7.286	7	; oligos_7nt_test_vs_ctrl_m1 versus MA0036.2 (GATA2); m=3/3; ncol2=14; w=12; offset=-2; strand=D; shift=0; score= 7.2857; wrrttCTTATCWsh---- ; cor=0.765; Ncor=0.510; logoDP=5.523; NIcor=0.505; NsEucl=0.913; SSD=2.162; NSW=0.910; rcor=11; rNcor=5; rlogoDP=4; rNIcor=3; rNsEucl=7; rSSD=11; rNSW=10; rank_mean=7.286; match_rank=7 a 1569 1125 1555 1051 32 9 0 51 4380 0 0 1225 104 1256 0 0 0 0 c 567 768 729 525 1057 3015 192 0 0 0 4380 0 1765 1185 0 0 0 0 g 754 1709 1220 427 765 914 0 0 0 0 0 0 1967 224 0 0 0 0 t 1490 778 876 2377 2526 442 4188 4329 0 4380 0 3155 544 1715 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift0 ; 2 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_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=24; shift=0; ncol=24; wwaaTtTTTATCAGATAAAwAwww ; Alignment reference a 43 51 73 75 17 31 18 9 17 104 6 14 114 13 107 6 113 101 91 73 88 33 48 42 c 20 21 17 12 13 10 8 5 6 5 12 87 2 7 9 6 4 6 12 14 8 10 21 20 g 18 18 16 20 5 13 10 12 8 7 11 5 2 98 4 4 3 6 8 8 13 7 20 24 t 47 38 22 21 93 74 92 102 97 12 99 22 10 10 8 112 8 15 17 33 19 78 39 42

MA0036.2_rc_shift10 (GATA2_rc) 0.784 0.457 1.090 -0.022 0.929 2.003 0.928 9 8 10 11 1 9 1 7.000 6
; oligos_6nt_test_vs_ctrl_m3 versus MA0036.2_rc (GATA2_rc); m=1/1; ncol2=14; w=14; offset=10; strand=R; shift=10; score= 7; ----------dsWGATAAGaayyw ; cor=0.784; Ncor=0.457; logoDP=1.090; NIcor=-0.022; NsEucl=0.929; SSD=2.003; NSW=0.928; rcor=9; rNcor=8; rlogoDP=10; rNIcor=11; rNsEucl=1; rSSD=9; rNSW=1; rank_mean=7.000; match_rank=6 a 0 0 0 0 0 0 0 0 0 0 1715 544 3155 0 4380 0 4329 4188 442 2526 2377 876 778 1490 c 0 0 0 0 0 0 0 0 0 0 224 1967 0 0 0 0 0 0 914 765 427 1220 1709 754 g 0 0 0 0 0 0 0 0 0 0 1185 1765 0 4380 0 0 0 192 3015 1057 525 729 768 567 t 0 0 0 0 0 0 0 0 0 0 1256 104 1225 0 0 4380 51 0 9 32 1051 1555 1125 1569

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_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3)																		; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=24; shift=0; ncol=24; wwaaTtTTTATCAGATAAAwAwww ; Alignment reference a 43 51 73 75 17 31 18 9 17 104 6 14 114 13 107 6 113 101 91 73 88 33 48 42 c 20 21 17 12 13 10 8 5 6 5 12 87 2 7 9 6 4 6 12 14 8 10 21 20 g 18 18 16 20 5 13 10 12 8 7 11 5 2 98 4 4 3 6 8 8 13 7 20 24 t 47 38 22 21 93 74 92 102 97 12 99 22 10 10 8 112 8 15 17 33 19 78 39 42
MA0036.2_rc_shift10 (GATA2_rc)		0.784	0.457	1.090	-0.022	0.929	2.003	0.928	9	8	10	11	1	9	1	7.000	6	; oligos_6nt_test_vs_ctrl_m3 versus MA0036.2_rc (GATA2_rc); m=1/1; ncol2=14; w=14; offset=10; strand=R; shift=10; score= 7; ----------dsWGATAAGaayyw ; cor=0.784; Ncor=0.457; logoDP=1.090; NIcor=-0.022; NsEucl=0.929; SSD=2.003; NSW=0.928; rcor=9; rNcor=8; rlogoDP=10; rNIcor=11; rNsEucl=1; rSSD=9; rNSW=1; rank_mean=7.000; match_rank=6 a 0 0 0 0 0 0 0 0 0 0 1715 544 3155 0 4380 0 4329 4188 442 2526 2377 876 778 1490 c 0 0 0 0 0 0 0 0 0 0 224 1967 0 0 0 0 0 0 914 765 427 1220 1709 754 g 0 0 0 0 0 0 0 0 0 0 1185 1765 0 4380 0 0 0 192 3015 1057 525 729 768 567 t 0 0 0 0 0 0 0 0 0 0 1256 104 1225 0 0 4380 51 0 9 32 1051 1555 1125 1569

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift0 ; 2 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_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=24; shift=0; ncol=24; watAgAGATAAAaAttaaaawhww ; Alignment reference a 58 80 42 181 36 194 26 197 12 184 187 162 138 151 50 43 140 134 139 139 53 64 80 73 c 43 40 32 1 13 3 6 6 6 6 7 18 19 11 11 26 16 18 21 17 18 55 40 42 g 40 43 32 14 144 4 167 5 6 10 8 9 21 24 16 19 23 20 18 24 22 38 28 35 t 71 49 106 16 19 11 13 4 188 12 10 23 34 26 135 124 33 40 34 32 119 55 64 62

MA0036.2_rc_shift3 (GATA2_rc) 0.785 0.458 1.215 -0.018 0.925 2.209 0.921 8 6 9 10 2 12 4 7.286 8
; oligos_6nt_test_vs_ctrl_m2 versus MA0036.2_rc (GATA2_rc); m=1/1; ncol2=14; w=14; offset=3; strand=R; shift=3; score= 7.2857; ---dsWGATAAGaayyw------- ; cor=0.785; Ncor=0.458; logoDP=1.215; NIcor=-0.018; NsEucl=0.925; SSD=2.209; NSW=0.921; rcor=8; rNcor=6; rlogoDP=9; rNIcor=10; rNsEucl=2; rSSD=12; rNSW=4; rank_mean=7.286; match_rank=8 a 0 0 0 1715 544 3155 0 4380 0 4329 4188 442 2526 2377 876 778 1490 0 0 0 0 0 0 0 c 0 0 0 224 1967 0 0 0 0 0 0 914 765 427 1220 1709 754 0 0 0 0 0 0 0 g 0 0 0 1185 1765 0 4380 0 0 0 192 3015 1057 525 729 768 567 0 0 0 0 0 0 0 t 0 0 0 1256 104 1225 0 0 4380 51 0 9 32 1051 1555 1125 1569 0 0 0 0 0 0 0

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_test_vs_ctrl_m2_shift0 (oligos_6nt_test_vs_ctrl_m2)																		; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=24; shift=0; ncol=24; watAgAGATAAAaAttaaaawhww ; Alignment reference a 58 80 42 181 36 194 26 197 12 184 187 162 138 151 50 43 140 134 139 139 53 64 80 73 c 43 40 32 1 13 3 6 6 6 6 7 18 19 11 11 26 16 18 21 17 18 55 40 42 g 40 43 32 14 144 4 167 5 6 10 8 9 21 24 16 19 23 20 18 24 22 38 28 35 t 71 49 106 16 19 11 13 4 188 12 10 23 34 26 135 124 33 40 34 32 119 55 64 62
MA0036.2_rc_shift3 (GATA2_rc)		0.785	0.458	1.215	-0.018	0.925	2.209	0.921	8	6	9	10	2	12	4	7.286	8	; oligos_6nt_test_vs_ctrl_m2 versus MA0036.2_rc (GATA2_rc); m=1/1; ncol2=14; w=14; offset=3; strand=R; shift=3; score= 7.2857; ---dsWGATAAGaayyw------- ; cor=0.785; Ncor=0.458; logoDP=1.215; NIcor=-0.018; NsEucl=0.925; SSD=2.209; NSW=0.921; rcor=8; rNcor=6; rlogoDP=9; rNIcor=10; rNsEucl=2; rSSD=12; rNSW=4; rank_mean=7.286; match_rank=8 a 0 0 0 1715 544 3155 0 4380 0 4329 4188 442 2526 2377 876 778 1490 0 0 0 0 0 0 0 c 0 0 0 224 1967 0 0 0 0 0 0 914 765 427 1220 1709 754 0 0 0 0 0 0 0 g 0 0 0 1185 1765 0 4380 0 0 0 192 3015 1057 525 729 768 567 0 0 0 0 0 0 0 t 0 0 0 1256 104 1225 0 0 4380 51 0 9 32 1051 1555 1125 1569 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift0 ; 3 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_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=12; shift=0; ncol=15; wwGATTAATCww--- ; Alignment reference a 62 78 13 184 6 7 185 185 8 29 60 59 0 0 0 c 35 32 0 4 5 2 6 4 4 158 30 44 0 0 0 g 44 30 158 4 4 6 2 5 4 0 32 35 0 0 0 t 59 60 29 8 185 185 7 6 184 13 78 62 0 0 0

MA0151.1_rc_shift3 (ARID3A_rc) 0.834 0.417 5.853 0.398 0.871 1.203 0.900 3 13 2 4 14 2 13 7.286 9
; oligos_7nt_test_vs_ctrl_m4 versus MA0151.1_rc (ARID3A_rc); m=1/2; ncol2=6; w=6; offset=3; strand=R; shift=3; score= 7.2857; ---TTTrAT------ ; cor=0.834; Ncor=0.417; logoDP=5.853; NIcor=0.398; NsEucl=0.871; SSD=1.203; NSW=0.900; rcor=3; rNcor=13; rlogoDP=2; rNIcor=4; rNsEucl=14; rSSD=2; rNSW=13; rank_mean=7.286; match_rank=9 a 0 0 0 6 0 0 17 27 0 0 0 0 0 0 0 c 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 t 0 0 0 20 27 27 1 0 27 0 0 0 0 0 0

MA0467.1_rc_shift4 (Crx_rc) 0.792 0.422 0.344 -0.094 0.889 1.570 0.902 7 12 13 12 12 4 12 10.286 13
; oligos_7nt_test_vs_ctrl_m4 versus MA0467.1_rc (Crx_rc); m=2/2; ncol2=11; w=8; offset=4; strand=R; shift=4; score=10.2857; ----yTAATCCyCTt ; cor=0.792; Ncor=0.422; logoDP=0.344; NIcor=-0.094; NsEucl=0.889; SSD=1.570; NSW=0.902; rcor=7; rNcor=12; rlogoDP=13; rNIcor=12; rNsEucl=12; rSSD=4; rNSW=12; rank_mean=10.286; match_rank=13 a 0 0 0 0 175 102 2068 2097 0 0 8 109 225 183 135 c 0 0 0 0 1326 0 0 0 0 2097 1574 823 1470 417 458 g 0 0 0 0 52 0 29 0 465 0 0 222 55 43 297 t 0 0 0 0 544 1995 0 0 1632 0 515 943 347 1454 1207

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_m4_shift0 (oligos_7nt_test_vs_ctrl_m4)																	; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=12; shift=0; ncol=15; wwGATTAATCww--- ; Alignment reference a 62 78 13 184 6 7 185 185 8 29 60 59 0 0 0 c 35 32 0 4 5 2 6 4 4 158 30 44 0 0 0 g 44 30 158 4 4 6 2 5 4 0 32 35 0 0 0 t 59 60 29 8 185 185 7 6 184 13 78 62 0 0 0
MA0151.1_rc_shift3 (ARID3A_rc)	0.834	0.417	5.853	0.398	0.871	1.203	0.900	3	13	2	4	14	2	13	7.286	9	; oligos_7nt_test_vs_ctrl_m4 versus MA0151.1_rc (ARID3A_rc); m=1/2; ncol2=6; w=6; offset=3; strand=R; shift=3; score= 7.2857; ---TTTrAT------ ; cor=0.834; Ncor=0.417; logoDP=5.853; NIcor=0.398; NsEucl=0.871; SSD=1.203; NSW=0.900; rcor=3; rNcor=13; rlogoDP=2; rNIcor=4; rNsEucl=14; rSSD=2; rNSW=13; rank_mean=7.286; match_rank=9 a 0 0 0 6 0 0 17 27 0 0 0 0 0 0 0 c 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0 t 0 0 0 20 27 27 1 0 27 0 0 0 0 0 0
MA0467.1_rc_shift4 (Crx_rc)	0.792	0.422	0.344	-0.094	0.889	1.570	0.902	7	12	13	12	12	4	12	10.286	13	; oligos_7nt_test_vs_ctrl_m4 versus MA0467.1_rc (Crx_rc); m=2/2; ncol2=11; w=8; offset=4; strand=R; shift=4; score=10.2857; ----yTAATCCyCTt ; cor=0.792; Ncor=0.422; logoDP=0.344; NIcor=-0.094; NsEucl=0.889; SSD=1.570; NSW=0.902; rcor=7; rNcor=12; rlogoDP=13; rNIcor=12; rNsEucl=12; rSSD=4; rNSW=12; rank_mean=10.286; match_rank=13 a 0 0 0 0 175 102 2068 2097 0 0 8 109 225 183 135 c 0 0 0 0 1326 0 0 0 0 2097 1574 823 1470 417 458 g 0 0 0 0 52 0 29 0 465 0 0 222 55 43 297 t 0 0 0 0 544 1995 0 0 1632 0 515 943 347 1454 1207

One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_shift0 ; 2 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_test_vs_ctrl_m1_shift0 (oligos_6nt_test_vs_ctrl_m1)
; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; aaTgAGATAAAaAttaaAaTcTww ; Alignment reference a 44 41 8 20 101 16 108 7 99 112 97 82 83 24 23 80 81 90 80 16 21 16 40 45 c 24 29 1 12 3 12 2 3 6 0 4 13 6 19 16 7 17 7 13 2 67 7 19 25 g 25 22 8 77 6 86 5 4 8 3 8 9 9 11 16 12 6 8 9 11 10 3 25 13 t 28 29 104 12 11 7 6 107 8 6 12 17 23 67 66 22 17 16 19 92 23 95 37 38

MA0036.2_rc_shift2 (GATA2_rc) 0.769 0.448 1.262 -0.016 0.924 2.271 0.919 10 9 8 9 3 14 6 8.429 11
; oligos_6nt_test_vs_ctrl_m1 versus MA0036.2_rc (GATA2_rc); m=1/1; ncol2=14; w=14; offset=2; strand=R; shift=2; score= 8.4286; --dsWGATAAGaayyw-------- ; cor=0.769; Ncor=0.448; logoDP=1.262; NIcor=-0.016; NsEucl=0.924; SSD=2.271; NSW=0.919; rcor=10; rNcor=9; rlogoDP=8; rNIcor=9; rNsEucl=3; rSSD=14; rNSW=6; rank_mean=8.429; match_rank=11 a 0 0 1715 544 3155 0 4380 0 4329 4188 442 2526 2377 876 778 1490 0 0 0 0 0 0 0 0 c 0 0 224 1967 0 0 0 0 0 0 914 765 427 1220 1709 754 0 0 0 0 0 0 0 0 g 0 0 1185 1765 0 4380 0 0 0 192 3015 1057 525 729 768 567 0 0 0 0 0 0 0 0 t 0 0 1256 104 1225 0 0 4380 51 0 9 32 1051 1555 1125 1569 0 0 0 0 0 0 0 0