One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.150329_2014-10-07.150329_sPZtpE/results/discovered_motifs/dyads_test_vs_ctrl_m2/peak-motifs_dyads_test_vs_ctrl_m2.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/2014/10/07/peak-motifs.2014-10-07.150329_2014-10-07.150329_sPZtpE/results/discovered_motifs/dyads_test_vs_ctrl_m2/peak-motifs_dyads_test_vs_ctrl_m2_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m2_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_test_vs_ctrl_m2_shift0 (dyads_test_vs_ctrl_m2)
; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; ssgCCCCGCCCCGCCss ; Alignment reference a 239 229 121 81 76 79 109 103 58 57 71 96 98 88 97 187 179 c 726 623 262 1223 1188 1203 1191 103 1270 1239 1224 1096 221 1129 1129 679 609 g 407 484 1065 188 222 230 180 1258 182 216 218 256 1138 270 245 451 559 t 210 246 134 90 96 70 102 118 72 70 69 134 125 95 111 265 235

MA0599.1_shift2 (KLF5) 0.894 0.526 3.877 0.518 0.932 0.936 0.953 1 3 1 3 2 1 1 1.714 1
; dyads_test_vs_ctrl_m2 versus MA0599.1 (KLF5); m=1/6; ncol2=10; w=10; offset=2; strand=D; shift=2; score= 1.7143; --gCCMCrCCCh----- ; cor=0.894; Ncor=0.526; logoDP=3.877; NIcor=0.518; NsEucl=0.932; SSD=0.936; NSW=0.953; rcor=1; rNcor=3; rlogoDP=1; rNIcor=3; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=1.714; match_rank=1 a 0 0 1429 0 0 3477 0 5051 0 0 0 3915 0 0 0 0 0 c 0 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 0 0 0 0 0 g 0 0 7572 0 0 0 0 5182 0 0 0 0 0 0 0 0 0 t 0 0 2587 1711 1603 565 0 3378 0 0 476 4101 0 0 0 0 0

MA0079.3_shift2 (SP1) 0.857 0.554 3.841 0.551 0.927 1.277 0.942 2 2 2 2 3 2 3 2.286 2
; dyads_test_vs_ctrl_m2 versus MA0079.3 (SP1); m=2/6; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 2.2857; --gCCCCkCCCCy---- ; cor=0.857; Ncor=0.554; logoDP=3.841; NIcor=0.551; NsEucl=0.927; SSD=1.277; NSW=0.942; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=3; rSSD=2; rNSW=3; rank_mean=2.286; match_rank=2 a 0 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 0 c 0 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 0 g 0 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 0 t 0 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0 0

MA0516.1_shift2 (SP2) 0.822 0.725 3.755 0.720 0.939 1.699 0.943 5 1 3 1 1 6 2 2.714 3
; dyads_test_vs_ctrl_m2 versus MA0516.1 (SP2); m=3/6; ncol2=15; w=15; offset=2; strand=D; shift=2; score= 2.7143; --gyCCCGCCyCyyccs ; cor=0.822; Ncor=0.725; logoDP=3.755; NIcor=0.720; NsEucl=0.939; SSD=1.699; NSW=0.943; rcor=5; rNcor=1; rlogoDP=3; rNIcor=1; rNsEucl=1; rSSD=6; rNSW=2; rank_mean=2.714; match_rank=3 a 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 c 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 g 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 t 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316

MA0079.2_shift3 (SP1) 0.835 0.491 2.940 0.484 0.919 1.297 0.935 4 5 4 4 4 3 4 4.000 4
; dyads_test_vs_ctrl_m2 versus MA0079.2 (SP1); m=4/6; ncol2=10; w=10; offset=3; strand=D; shift=3; score= 4; ---CCCCkCCCCC---- ; cor=0.835; Ncor=0.491; logoDP=2.940; NIcor=0.484; NsEucl=0.919; SSD=1.297; NSW=0.935; rcor=4; rNcor=5; rlogoDP=4; rNIcor=4; rNsEucl=4; rSSD=3; rNSW=4; rank_mean=4.000; match_rank=4 a 0 0 0 0 0 0 4 2 0 1 0 6 3 0 0 0 0 c 0 0 0 32 30 35 27 5 28 31 24 25 26 0 0 0 0 g 0 0 0 1 1 0 0 15 1 0 3 0 3 0 0 0 0 t 0 0 0 2 4 0 4 13 6 3 8 4 3 0 0 0 0

MA0039.2_rc_shift2 (Klf4_rc) 0.848 0.499 1.408 -0.011 0.919 1.320 0.934 3 4 5 5 5 4 5 4.429 5
; dyads_test_vs_ctrl_m2 versus MA0039.2_rc (Klf4_rc); m=5/6; ncol2=10; w=10; offset=2; strand=R; shift=2; score= 4.4286; --gCCmCrCCCw----- ; cor=0.848; Ncor=0.499; logoDP=1.408; NIcor=-0.011; NsEucl=0.919; SSD=1.320; NSW=0.934; rcor=3; rNcor=4; rlogoDP=5; rNIcor=5; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=4.429; match_rank=5 a 0 0 932 289 125 2042 34 2139 16 13 6 1765 0 0 0 0 0 c 0 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 0 0 0 0 0 g 0 0 2858 130 46 80 15 1922 36 13 9 81 0 0 0 0 0 t 0 0 254 123 264 42 22 277 14 14 88 1468 0 0 0 0 0

MA0079.1_rc_shift2 (SP1_rc) 0.760 0.447 0.760 -0.066 0.910 1.635 0.918 6 6 6 6 6 5 6 5.857 6
; dyads_test_vs_ctrl_m2 versus MA0079.1_rc (SP1_rc); m=6/6; ncol2=10; w=10; offset=2; strand=R; shift=2; score= 5.8571; --WCMmhsCCym----- ; cor=0.760; Ncor=0.447; logoDP=0.760; NIcor=-0.066; NsEucl=0.910; SSD=1.635; NSW=0.918; rcor=6; rNcor=6; rlogoDP=6; rNIcor=6; rNsEucl=6; rSSD=5; rNSW=6; rank_mean=5.857; match_rank=6 a 0 0 6 0 2 2 2 1 0 0 1 2 0 0 0 0 0 c 0 0 0 6 6 5 4 2 8 8 4 4 0 0 0 0 0 g 0 0 0 1 0 1 0 5 0 0 1 1 0 0 0 0 0 t 0 0 2 1 0 0 2 0 0 0 2 1 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_test_vs_ctrl_m2_shift0 (dyads_test_vs_ctrl_m2)																	; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; ssgCCCCGCCCCGCCss ; Alignment reference a 239 229 121 81 76 79 109 103 58 57 71 96 98 88 97 187 179 c 726 623 262 1223 1188 1203 1191 103 1270 1239 1224 1096 221 1129 1129 679 609 g 407 484 1065 188 222 230 180 1258 182 216 218 256 1138 270 245 451 559 t 210 246 134 90 96 70 102 118 72 70 69 134 125 95 111 265 235
MA0599.1_shift2 (KLF5)	0.894	0.526	3.877	0.518	0.932	0.936	0.953	1	3	1	3	2	1	1	1.714	1	; dyads_test_vs_ctrl_m2 versus MA0599.1 (KLF5); m=1/6; ncol2=10; w=10; offset=2; strand=D; shift=2; score= 1.7143; --gCCMCrCCCh----- ; cor=0.894; Ncor=0.526; logoDP=3.877; NIcor=0.518; NsEucl=0.932; SSD=0.936; NSW=0.953; rcor=1; rNcor=3; rlogoDP=1; rNIcor=3; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=1.714; match_rank=1 a 0 0 1429 0 0 3477 0 5051 0 0 0 3915 0 0 0 0 0 c 0 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 0 0 0 0 0 g 0 0 7572 0 0 0 0 5182 0 0 0 0 0 0 0 0 0 t 0 0 2587 1711 1603 565 0 3378 0 0 476 4101 0 0 0 0 0
MA0079.3_shift2 (SP1)	0.857	0.554	3.841	0.551	0.927	1.277	0.942	2	2	2	2	3	2	3	2.286	2	; dyads_test_vs_ctrl_m2 versus MA0079.3 (SP1); m=2/6; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 2.2857; --gCCCCkCCCCy---- ; cor=0.857; Ncor=0.554; logoDP=3.841; NIcor=0.551; NsEucl=0.927; SSD=1.277; NSW=0.942; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=3; rSSD=2; rNSW=3; rank_mean=2.286; match_rank=2 a 0 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 0 c 0 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 0 g 0 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 0 t 0 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0 0
MA0516.1_shift2 (SP2)	0.822	0.725	3.755	0.720	0.939	1.699	0.943	5	1	3	1	1	6	2	2.714	3	; dyads_test_vs_ctrl_m2 versus MA0516.1 (SP2); m=3/6; ncol2=15; w=15; offset=2; strand=D; shift=2; score= 2.7143; --gyCCCGCCyCyyccs ; cor=0.822; Ncor=0.725; logoDP=3.755; NIcor=0.720; NsEucl=0.939; SSD=1.699; NSW=0.943; rcor=5; rNcor=1; rlogoDP=3; rNIcor=1; rNsEucl=1; rSSD=6; rNSW=2; rank_mean=2.714; match_rank=3 a 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 c 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 g 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 t 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316
MA0079.2_shift3 (SP1)	0.835	0.491	2.940	0.484	0.919	1.297	0.935	4	5	4	4	4	3	4	4.000	4	; dyads_test_vs_ctrl_m2 versus MA0079.2 (SP1); m=4/6; ncol2=10; w=10; offset=3; strand=D; shift=3; score= 4; ---CCCCkCCCCC---- ; cor=0.835; Ncor=0.491; logoDP=2.940; NIcor=0.484; NsEucl=0.919; SSD=1.297; NSW=0.935; rcor=4; rNcor=5; rlogoDP=4; rNIcor=4; rNsEucl=4; rSSD=3; rNSW=4; rank_mean=4.000; match_rank=4 a 0 0 0 0 0 0 4 2 0 1 0 6 3 0 0 0 0 c 0 0 0 32 30 35 27 5 28 31 24 25 26 0 0 0 0 g 0 0 0 1 1 0 0 15 1 0 3 0 3 0 0 0 0 t 0 0 0 2 4 0 4 13 6 3 8 4 3 0 0 0 0
MA0039.2_rc_shift2 (Klf4_rc)	0.848	0.499	1.408	-0.011	0.919	1.320	0.934	3	4	5	5	5	4	5	4.429	5	; dyads_test_vs_ctrl_m2 versus MA0039.2_rc (Klf4_rc); m=5/6; ncol2=10; w=10; offset=2; strand=R; shift=2; score= 4.4286; --gCCmCrCCCw----- ; cor=0.848; Ncor=0.499; logoDP=1.408; NIcor=-0.011; NsEucl=0.919; SSD=1.320; NSW=0.934; rcor=3; rNcor=4; rlogoDP=5; rNIcor=5; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=4.429; match_rank=5 a 0 0 932 289 125 2042 34 2139 16 13 6 1765 0 0 0 0 0 c 0 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 0 0 0 0 0 g 0 0 2858 130 46 80 15 1922 36 13 9 81 0 0 0 0 0 t 0 0 254 123 264 42 22 277 14 14 88 1468 0 0 0 0 0
MA0079.1_rc_shift2 (SP1_rc)	0.760	0.447	0.760	-0.066	0.910	1.635	0.918	6	6	6	6	6	5	6	5.857	6	; dyads_test_vs_ctrl_m2 versus MA0079.1_rc (SP1_rc); m=6/6; ncol2=10; w=10; offset=2; strand=R; shift=2; score= 5.8571; --WCMmhsCCym----- ; cor=0.760; Ncor=0.447; logoDP=0.760; NIcor=-0.066; NsEucl=0.910; SSD=1.635; NSW=0.918; rcor=6; rNcor=6; rlogoDP=6; rNIcor=6; rNsEucl=6; rSSD=5; rNSW=6; rank_mean=5.857; match_rank=6 a 0 0 6 0 2 2 2 1 0 0 1 2 0 0 0 0 0 c 0 0 0 6 6 5 4 2 8 8 4 4 0 0 0 0 0 g 0 0 0 1 0 1 0 5 0 0 1 1 0 0 0 0 0 t 0 0 2 1 0 0 2 0 0 0 2 1 0 0 0 0 0