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/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/2014/10/07/peak-motifs.2014-10-07.150329_2014-10-07.150329_sPZtpE/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_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_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)
; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=13; shift=0; ncol=16; ssCcCCGCCCCss--- ; Alignment reference a 247 252 104 141 70 33 57 88 57 56 59 217 245 0 0 0 c 906 695 1474 1334 1581 1765 36 1687 1552 1596 1596 773 681 0 0 0 g 617 749 319 428 307 186 1893 181 354 289 285 799 835 0 0 0 t 262 336 135 129 74 48 46 76 69 91 92 243 271 0 0 0

MA0079.3_shift1 (SP1) 0.901 0.763 4.496 0.760 0.939 0.899 0.959 1 1 1 1 2 1 1 1.143 1
; oligos_7nt_test_vs_ctrl_m3 versus MA0079.3 (SP1); m=1/7; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 1.1429; -gCCCCkCCCCy---- ; cor=0.901; Ncor=0.763; logoDP=4.496; NIcor=0.760; NsEucl=0.939; SSD=0.899; NSW=0.959; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=1.143; match_rank=1 a 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 0 c 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 0 g 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 0 t 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0 0

MA0516.1_shift1 (SP2) 0.886 0.665 4.462 0.671 0.940 1.034 0.957 2 4 2 2 1 2 2 2.143 2
; oligos_7nt_test_vs_ctrl_m3 versus MA0516.1 (SP2); m=2/7; ncol2=15; w=12; offset=1; strand=D; shift=1; score= 2.1429; -gyCCCGCCyCyyccs ; cor=0.886; Ncor=0.665; logoDP=4.462; NIcor=0.671; NsEucl=0.940; SSD=1.034; NSW=0.957; rcor=2; rNcor=4; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=2.143; match_rank=2 a 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 c 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 g 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 t 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316

MA0079.2_shift2 (SP1) 0.870 0.670 3.144 0.647 0.928 1.034 0.948 3 3 5 4 4 3 3 3.571 3
; oligos_7nt_test_vs_ctrl_m3 versus MA0079.2 (SP1); m=3/7; ncol2=10; w=10; offset=2; strand=D; shift=2; score= 3.5714; --CCCCkCCCCC---- ; cor=0.870; Ncor=0.670; logoDP=3.144; NIcor=0.647; NsEucl=0.928; SSD=1.034; NSW=0.948; rcor=3; rNcor=3; rlogoDP=5; rNIcor=4; rNsEucl=4; rSSD=3; rNSW=3; rank_mean=3.571; match_rank=3 a 0 0 0 0 0 4 2 0 1 0 6 3 0 0 0 0 c 0 0 32 30 35 27 5 28 31 24 25 26 0 0 0 0 g 0 0 1 1 0 0 15 1 0 3 0 3 0 0 0 0 t 0 0 2 4 0 4 13 6 3 8 4 3 0 0 0 0

MA0162.2_shift1 (EGR1) 0.848 0.678 3.726 0.664 0.932 1.320 0.945 5 2 4 3 3 5 4 3.714 4
; oligos_7nt_test_vs_ctrl_m3 versus MA0162.2 (EGR1); m=4/7; ncol2=14; w=12; offset=1; strand=D; shift=1; score= 3.7143; -sccCCgCCCMCkCc- ; cor=0.848; Ncor=0.678; logoDP=3.726; NIcor=0.664; NsEucl=0.932; SSD=1.320; NSW=0.945; rcor=5; rNcor=2; rlogoDP=4; rNIcor=3; rNsEucl=3; rSSD=5; rNSW=4; rank_mean=3.714; match_rank=4 a 0 1098 1506 1160 1335 233 2911 0 0 0 3652 0 2368 0 3026 0 c 0 5728 6847 6049 10431 11574 0 12256 11852 10154 8361 11952 0 9849 5595 0 g 0 3083 1359 2250 0 0 6840 0 0 611 0 0 6599 1420 1913 0 t 0 2347 2544 2797 490 449 2505 0 404 1491 243 304 3289 987 1722 0

MA0599.1_shift1 (KLF5) 0.852 0.655 4.321 0.636 0.920 1.279 0.936 4 5 3 5 5 4 5 4.429 5
; oligos_7nt_test_vs_ctrl_m3 versus MA0599.1 (KLF5); m=5/7; ncol2=10; w=10; offset=1; strand=D; shift=1; score= 4.4286; -gCCMCrCCCh----- ; cor=0.852; Ncor=0.655; logoDP=4.321; NIcor=0.636; NsEucl=0.920; SSD=1.279; NSW=0.936; rcor=4; rNcor=5; rlogoDP=3; rNIcor=5; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=4.429; match_rank=5 a 0 1429 0 0 3477 0 5051 0 0 0 3915 0 0 0 0 0 c 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 0 0 0 0 0 g 0 7572 0 0 0 0 5182 0 0 0 0 0 0 0 0 0 t 0 2587 1711 1603 565 0 3378 0 0 476 4101 0 0 0 0 0

MA0039.2_rc_shift1 (Klf4_rc) 0.791 0.608 2.178 0.045 0.905 1.805 0.910 6 6 6 6 7 7 7 6.429 6
; oligos_7nt_test_vs_ctrl_m3 versus MA0039.2_rc (Klf4_rc); m=6/7; ncol2=10; w=10; offset=1; strand=R; shift=1; score= 6.4286; -gCCmCrCCCw----- ; cor=0.791; Ncor=0.608; logoDP=2.178; NIcor=0.045; NsEucl=0.905; SSD=1.805; NSW=0.910; rcor=6; rNcor=6; rlogoDP=6; rNIcor=6; rNsEucl=7; rSSD=7; rNSW=7; rank_mean=6.429; match_rank=6 a 0 932 289 125 2042 34 2139 16 13 6 1765 0 0 0 0 0 c 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 0 0 0 0 0 g 0 2858 130 46 80 15 1922 36 13 9 81 0 0 0 0 0 t 0 254 123 264 42 22 277 14 14 88 1468 0 0 0 0 0

MA0079.1_rc_shift1 (SP1_rc) 0.770 0.592 0.961 -0.075 0.910 1.628 0.919 7 7 7 7 6 6 6 6.571 7
; oligos_7nt_test_vs_ctrl_m3 versus MA0079.1_rc (SP1_rc); m=7/7; ncol2=10; w=10; offset=1; strand=R; shift=1; score= 6.5714; -WCMmhsCCym----- ; cor=0.770; Ncor=0.592; logoDP=0.961; NIcor=-0.075; NsEucl=0.910; SSD=1.628; NSW=0.919; rcor=7; rNcor=7; rlogoDP=7; rNIcor=7; rNsEucl=6; rSSD=6; rNSW=6; rank_mean=6.571; match_rank=7 a 0 6 0 2 2 2 1 0 0 1 2 0 0 0 0 0 c 0 0 6 6 5 4 2 8 8 4 4 0 0 0 0 0 g 0 0 1 0 1 0 5 0 0 1 1 0 0 0 0 0 t 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
oligos_7nt_test_vs_ctrl_m3_shift0 (oligos_7nt_test_vs_ctrl_m3)																	; oligos_7nt_test_vs_ctrl_m3; m=0 (reference); ncol1=13; shift=0; ncol=16; ssCcCCGCCCCss--- ; Alignment reference a 247 252 104 141 70 33 57 88 57 56 59 217 245 0 0 0 c 906 695 1474 1334 1581 1765 36 1687 1552 1596 1596 773 681 0 0 0 g 617 749 319 428 307 186 1893 181 354 289 285 799 835 0 0 0 t 262 336 135 129 74 48 46 76 69 91 92 243 271 0 0 0
MA0079.3_shift1 (SP1)	0.901	0.763	4.496	0.760	0.939	0.899	0.959	1	1	1	1	2	1	1	1.143	1	; oligos_7nt_test_vs_ctrl_m3 versus MA0079.3 (SP1); m=1/7; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 1.1429; -gCCCCkCCCCy---- ; cor=0.901; Ncor=0.763; logoDP=4.496; NIcor=0.760; NsEucl=0.939; SSD=0.899; NSW=0.959; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=1.143; match_rank=1 a 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 0 c 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 0 g 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 0 t 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0 0
MA0516.1_shift1 (SP2)	0.886	0.665	4.462	0.671	0.940	1.034	0.957	2	4	2	2	1	2	2	2.143	2	; oligos_7nt_test_vs_ctrl_m3 versus MA0516.1 (SP2); m=2/7; ncol2=15; w=12; offset=1; strand=D; shift=1; score= 2.1429; -gyCCCGCCyCyyccs ; cor=0.886; Ncor=0.665; logoDP=4.462; NIcor=0.671; NsEucl=0.940; SSD=1.034; NSW=0.957; rcor=2; rNcor=4; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=2; rNSW=2; rank_mean=2.143; match_rank=2 a 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203 c 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745 g 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422 t 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316
MA0079.2_shift2 (SP1)	0.870	0.670	3.144	0.647	0.928	1.034	0.948	3	3	5	4	4	3	3	3.571	3	; oligos_7nt_test_vs_ctrl_m3 versus MA0079.2 (SP1); m=3/7; ncol2=10; w=10; offset=2; strand=D; shift=2; score= 3.5714; --CCCCkCCCCC---- ; cor=0.870; Ncor=0.670; logoDP=3.144; NIcor=0.647; NsEucl=0.928; SSD=1.034; NSW=0.948; rcor=3; rNcor=3; rlogoDP=5; rNIcor=4; rNsEucl=4; rSSD=3; rNSW=3; rank_mean=3.571; match_rank=3 a 0 0 0 0 0 4 2 0 1 0 6 3 0 0 0 0 c 0 0 32 30 35 27 5 28 31 24 25 26 0 0 0 0 g 0 0 1 1 0 0 15 1 0 3 0 3 0 0 0 0 t 0 0 2 4 0 4 13 6 3 8 4 3 0 0 0 0
MA0162.2_shift1 (EGR1)	0.848	0.678	3.726	0.664	0.932	1.320	0.945	5	2	4	3	3	5	4	3.714	4	; oligos_7nt_test_vs_ctrl_m3 versus MA0162.2 (EGR1); m=4/7; ncol2=14; w=12; offset=1; strand=D; shift=1; score= 3.7143; -sccCCgCCCMCkCc- ; cor=0.848; Ncor=0.678; logoDP=3.726; NIcor=0.664; NsEucl=0.932; SSD=1.320; NSW=0.945; rcor=5; rNcor=2; rlogoDP=4; rNIcor=3; rNsEucl=3; rSSD=5; rNSW=4; rank_mean=3.714; match_rank=4 a 0 1098 1506 1160 1335 233 2911 0 0 0 3652 0 2368 0 3026 0 c 0 5728 6847 6049 10431 11574 0 12256 11852 10154 8361 11952 0 9849 5595 0 g 0 3083 1359 2250 0 0 6840 0 0 611 0 0 6599 1420 1913 0 t 0 2347 2544 2797 490 449 2505 0 404 1491 243 304 3289 987 1722 0
MA0599.1_shift1 (KLF5)	0.852	0.655	4.321	0.636	0.920	1.279	0.936	4	5	3	5	5	4	5	4.429	5	; oligos_7nt_test_vs_ctrl_m3 versus MA0599.1 (KLF5); m=5/7; ncol2=10; w=10; offset=1; strand=D; shift=1; score= 4.4286; -gCCMCrCCCh----- ; cor=0.852; Ncor=0.655; logoDP=4.321; NIcor=0.636; NsEucl=0.920; SSD=1.279; NSW=0.936; rcor=4; rNcor=5; rlogoDP=3; rNIcor=5; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=4.429; match_rank=5 a 0 1429 0 0 3477 0 5051 0 0 0 3915 0 0 0 0 0 c 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 0 0 0 0 0 g 0 7572 0 0 0 0 5182 0 0 0 0 0 0 0 0 0 t 0 2587 1711 1603 565 0 3378 0 0 476 4101 0 0 0 0 0
MA0039.2_rc_shift1 (Klf4_rc)	0.791	0.608	2.178	0.045	0.905	1.805	0.910	6	6	6	6	7	7	7	6.429	6	; oligos_7nt_test_vs_ctrl_m3 versus MA0039.2_rc (Klf4_rc); m=6/7; ncol2=10; w=10; offset=1; strand=R; shift=1; score= 6.4286; -gCCmCrCCCw----- ; cor=0.791; Ncor=0.608; logoDP=2.178; NIcor=0.045; NsEucl=0.905; SSD=1.805; NSW=0.910; rcor=6; rNcor=6; rlogoDP=6; rNIcor=6; rNsEucl=7; rSSD=7; rNSW=7; rank_mean=6.429; match_rank=6 a 0 932 289 125 2042 34 2139 16 13 6 1765 0 0 0 0 0 c 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 0 0 0 0 0 g 0 2858 130 46 80 15 1922 36 13 9 81 0 0 0 0 0 t 0 254 123 264 42 22 277 14 14 88 1468 0 0 0 0 0
MA0079.1_rc_shift1 (SP1_rc)	0.770	0.592	0.961	-0.075	0.910	1.628	0.919	7	7	7	7	6	6	6	6.571	7	; oligos_7nt_test_vs_ctrl_m3 versus MA0079.1_rc (SP1_rc); m=7/7; ncol2=10; w=10; offset=1; strand=R; shift=1; score= 6.5714; -WCMmhsCCym----- ; cor=0.770; Ncor=0.592; logoDP=0.961; NIcor=-0.075; NsEucl=0.910; SSD=1.628; NSW=0.919; rcor=7; rNcor=7; rlogoDP=7; rNIcor=7; rNsEucl=6; rSSD=6; rNSW=6; rank_mean=6.571; match_rank=7 a 0 6 0 2 2 2 1 0 0 1 2 0 0 0 0 0 c 0 0 6 6 5 4 2 8 8 4 4 0 0 0 0 0 g 0 0 1 0 1 0 5 0 0 1 1 0 0 0 0 0 t 0 2 1 0 0 2 0 0 0 2 1 0 0 0 0 0