One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5.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.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift1 ; 9 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_mkv5_m5_shift1 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=11; shift=1; ncol=16; -ckCCCCTCCcs---- ; Alignment reference a 0 122 95 1 1 0 0 4 3 0 98 91 0 0 0 0 c 0 288 176 725 680 704 718 1 734 731 306 278 0 0 0 0 g 0 175 277 12 55 36 20 102 2 10 158 233 0 0 0 0 t 0 156 193 3 5 1 3 634 2 0 179 139 0 0 0 0

MA0079.3_shift2 (SP1) 0.883 0.735 8.087 0.718 0.926 1.097 0.945 2 2 1 2 2 2 2 1.857 1
; oligos_7nt_mkv5_m5 versus MA0079.3 (SP1); m=1/8; ncol2=11; w=10; offset=1; strand=D; shift=2; score= 1.8571; --gCCCCkCCCCy--- ; cor=0.883; Ncor=0.735; logoDP=8.087; NIcor=0.718; NsEucl=0.926; SSD=1.097; NSW=0.945; rcor=2; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.857; match_rank=1 a 0 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 c 0 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 g 0 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 t 0 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0

MA0079.2_shift3 (SP1) 0.905 0.679 6.201 0.665 0.928 0.850 0.953 1 4 4 3 1 1 1 2.143 2
; oligos_7nt_mkv5_m5 versus MA0079.2 (SP1); m=2/8; ncol2=10; w=9; offset=2; strand=D; shift=3; score= 2.1429; ---CCCCkCCCCC--- ; cor=0.905; Ncor=0.679; logoDP=6.201; NIcor=0.665; NsEucl=0.928; SSD=0.850; NSW=0.953; rcor=1; rNcor=4; rlogoDP=4; rNIcor=3; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.143; match_rank=2 a 0 0 0 0 0 0 4 2 0 1 0 6 3 0 0 0 c 0 0 0 32 30 35 27 5 28 31 24 25 26 0 0 0 g 0 0 0 1 1 0 0 15 1 0 3 0 3 0 0 0 t 0 0 0 2 4 0 4 13 6 3 8 4 3 0 0 0

MA0599.1_shift2 (KLF5) 0.857 0.779 7.904 0.765 0.918 1.337 0.933 3 1 2 1 3 4 3 2.429 3
; oligos_7nt_mkv5_m5 versus MA0599.1 (KLF5); m=3/8; ncol2=10; w=10; offset=1; strand=D; shift=2; score= 2.4286; --gCCMCrCCCh---- ; cor=0.857; Ncor=0.779; logoDP=7.904; NIcor=0.765; NsEucl=0.918; SSD=1.337; NSW=0.933; rcor=3; rNcor=1; rlogoDP=2; rNIcor=1; rNsEucl=3; rSSD=4; rNSW=3; rank_mean=2.429; match_rank=3 a 0 0 1429 0 0 3477 0 5051 0 0 0 3915 0 0 0 0 c 0 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 0 0 0 0 g 0 0 7572 0 0 0 0 5182 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

MA0162.2_shift2 (EGR1) 0.801 0.534 5.883 0.509 0.907 1.733 0.913 6 6 5 4 4 6 4 5.000 4
; oligos_7nt_mkv5_m5 versus MA0162.2 (EGR1); m=4/8; ncol2=14; w=10; offset=1; strand=D; shift=2; score= 5; --sccCCgCCCMCkCc ; cor=0.801; Ncor=0.534; logoDP=5.883; NIcor=0.509; NsEucl=0.907; SSD=1.733; NSW=0.913; rcor=6; rNcor=6; rlogoDP=5; rNIcor=4; rNsEucl=4; rSSD=6; rNSW=4; rank_mean=5.000; match_rank=4 a 0 0 1098 1506 1160 1335 233 2911 0 0 0 3652 0 2368 0 3026 c 0 0 5728 6847 6049 10431 11574 0 12256 11852 10154 8361 11952 0 9849 5595 g 0 0 3083 1359 2250 0 0 6840 0 0 611 0 0 6599 1420 1913 t 0 0 2347 2544 2797 490 449 2505 0 404 1491 243 304 3289 987 1722

MA0516.1_shift2 (SP2) 0.812 0.507 7.501 0.488 0.906 1.755 0.912 4 7 3 5 5 7 5 5.143 5
; oligos_7nt_mkv5_m5 versus MA0516.1 (SP2); m=5/8; ncol2=15; w=10; offset=1; strand=D; shift=2; score= 5.1429; --gyCCCGCCyCyycc ; cor=0.812; Ncor=0.507; logoDP=7.501; NIcor=0.488; NsEucl=0.906; SSD=1.755; NSW=0.912; rcor=4; rNcor=7; rlogoDP=3; rNIcor=5; rNsEucl=5; rSSD=7; rNSW=5; rank_mean=5.143; match_rank=5 a 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 c 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 g 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 t 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256

MA0057.1_rc_shift0 (MZF1_5-13_rc) 0.811 0.609 0.422 -0.223 0.901 1.594 0.911 5 5 7 8 6 5 6 6.000 6
; oligos_7nt_mkv5_m5 versus MA0057.1_rc (MZF1_5-13_rc); m=6/8; ncol2=10; w=9; offset=-1; strand=R; shift=0; score= 6; yymCCCMTmv------ ; cor=0.811; Ncor=0.609; logoDP=0.422; NIcor=-0.223; NsEucl=0.901; SSD=1.594; NSW=0.911; rcor=5; rNcor=5; rlogoDP=7; rNIcor=8; rNsEucl=6; rSSD=5; rNSW=6; rank_mean=6.000; match_rank=6 a 2 2 4 2 0 1 5 0 7 4 0 0 0 0 0 0 c 4 4 8 14 14 15 11 0 7 7 0 0 0 0 0 0 g 2 0 1 0 2 0 0 1 0 4 0 0 0 0 0 0 t 8 10 3 0 0 0 0 15 2 1 0 0 0 0 0 0

MA0039.2_rc_shift2 (Klf4_rc) 0.766 0.696 0.728 -0.213 0.895 2.203 0.890 8 3 6 7 7 8 8 6.714 7
; oligos_7nt_mkv5_m5 versus MA0039.2_rc (Klf4_rc); m=7/8; ncol2=10; w=10; offset=1; strand=R; shift=2; score= 6.7143; --gCCmCrCCCw---- ; cor=0.766; Ncor=0.696; logoDP=0.728; NIcor=-0.213; NsEucl=0.895; SSD=2.203; NSW=0.890; rcor=8; rNcor=3; rlogoDP=6; rNIcor=7; rNsEucl=7; rSSD=8; rNSW=8; rank_mean=6.714; match_rank=7 a 0 0 932 289 125 2042 34 2139 16 13 6 1765 0 0 0 0 c 0 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 0 0 0 0 g 0 0 2858 130 46 80 15 1922 36 13 9 81 0 0 0 0 t 0 0 254 123 264 42 22 277 14 14 88 1468 0 0 0 0

MA0056.1_rc_shift2 (MZF1_1-4_rc) 0.795 0.433 0.230 -0.153 0.865 1.318 0.890 7 8 8 6 8 3 7 6.714 8
; oligos_7nt_mkv5_m5 versus MA0056.1_rc (MZF1_1-4_rc); m=8/8; ncol2=6; w=6; offset=1; strand=R; shift=2; score= 6.7143; --TCCCCr-------- ; cor=0.795; Ncor=0.433; logoDP=0.230; NIcor=-0.153; NsEucl=0.865; SSD=1.318; NSW=0.890; rcor=7; rNcor=8; rlogoDP=8; rNIcor=6; rNsEucl=8; rSSD=3; rNSW=7; rank_mean=6.714; match_rank=8 a 0 0 0 0 1 0 1 8 0 0 0 0 0 0 0 0 c 0 0 2 20 19 18 19 4 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 t 0 0 18 0 0 2 0 3 0 0 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_mkv5_m5_shift1 (oligos_7nt_mkv5_m5)																	; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=11; shift=1; ncol=16; -ckCCCCTCCcs---- ; Alignment reference a 0 122 95 1 1 0 0 4 3 0 98 91 0 0 0 0 c 0 288 176 725 680 704 718 1 734 731 306 278 0 0 0 0 g 0 175 277 12 55 36 20 102 2 10 158 233 0 0 0 0 t 0 156 193 3 5 1 3 634 2 0 179 139 0 0 0 0
MA0079.3_shift2 (SP1)	0.883	0.735	8.087	0.718	0.926	1.097	0.945	2	2	1	2	2	2	2	1.857	1	; oligos_7nt_mkv5_m5 versus MA0079.3 (SP1); m=1/8; ncol2=11; w=10; offset=1; strand=D; shift=2; score= 1.8571; --gCCCCkCCCCy--- ; cor=0.883; Ncor=0.735; logoDP=8.087; NIcor=0.718; NsEucl=0.926; SSD=1.097; NSW=0.945; rcor=2; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.857; match_rank=1 a 0 0 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0 c 0 0 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0 g 0 0 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0 t 0 0 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0
MA0079.2_shift3 (SP1)	0.905	0.679	6.201	0.665	0.928	0.850	0.953	1	4	4	3	1	1	1	2.143	2	; oligos_7nt_mkv5_m5 versus MA0079.2 (SP1); m=2/8; ncol2=10; w=9; offset=2; strand=D; shift=3; score= 2.1429; ---CCCCkCCCCC--- ; cor=0.905; Ncor=0.679; logoDP=6.201; NIcor=0.665; NsEucl=0.928; SSD=0.850; NSW=0.953; rcor=1; rNcor=4; rlogoDP=4; rNIcor=3; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.143; match_rank=2 a 0 0 0 0 0 0 4 2 0 1 0 6 3 0 0 0 c 0 0 0 32 30 35 27 5 28 31 24 25 26 0 0 0 g 0 0 0 1 1 0 0 15 1 0 3 0 3 0 0 0 t 0 0 0 2 4 0 4 13 6 3 8 4 3 0 0 0
MA0599.1_shift2 (KLF5)	0.857	0.779	7.904	0.765	0.918	1.337	0.933	3	1	2	1	3	4	3	2.429	3	; oligos_7nt_mkv5_m5 versus MA0599.1 (KLF5); m=3/8; ncol2=10; w=10; offset=1; strand=D; shift=2; score= 2.4286; --gCCMCrCCCh---- ; cor=0.857; Ncor=0.779; logoDP=7.904; NIcor=0.765; NsEucl=0.918; SSD=1.337; NSW=0.933; rcor=3; rNcor=1; rlogoDP=2; rNIcor=1; rNsEucl=3; rSSD=4; rNSW=3; rank_mean=2.429; match_rank=3 a 0 0 1429 0 0 3477 0 5051 0 0 0 3915 0 0 0 0 c 0 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595 0 0 0 0 g 0 0 7572 0 0 0 0 5182 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
MA0162.2_shift2 (EGR1)	0.801	0.534	5.883	0.509	0.907	1.733	0.913	6	6	5	4	4	6	4	5.000	4	; oligos_7nt_mkv5_m5 versus MA0162.2 (EGR1); m=4/8; ncol2=14; w=10; offset=1; strand=D; shift=2; score= 5; --sccCCgCCCMCkCc ; cor=0.801; Ncor=0.534; logoDP=5.883; NIcor=0.509; NsEucl=0.907; SSD=1.733; NSW=0.913; rcor=6; rNcor=6; rlogoDP=5; rNIcor=4; rNsEucl=4; rSSD=6; rNSW=4; rank_mean=5.000; match_rank=4 a 0 0 1098 1506 1160 1335 233 2911 0 0 0 3652 0 2368 0 3026 c 0 0 5728 6847 6049 10431 11574 0 12256 11852 10154 8361 11952 0 9849 5595 g 0 0 3083 1359 2250 0 0 6840 0 0 611 0 0 6599 1420 1913 t 0 0 2347 2544 2797 490 449 2505 0 404 1491 243 304 3289 987 1722
MA0516.1_shift2 (SP2)	0.812	0.507	7.501	0.488	0.906	1.755	0.912	4	7	3	5	5	7	5	5.143	5	; oligos_7nt_mkv5_m5 versus MA0516.1 (SP2); m=5/8; ncol2=15; w=10; offset=1; strand=D; shift=2; score= 5.1429; --gyCCCGCCyCyycc ; cor=0.812; Ncor=0.507; logoDP=7.501; NIcor=0.488; NsEucl=0.906; SSD=1.755; NSW=0.912; rcor=4; rNcor=7; rlogoDP=3; rNIcor=5; rNsEucl=5; rSSD=7; rNSW=5; rank_mean=5.143; match_rank=5 a 0 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 c 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 g 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 t 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256
MA0057.1_rc_shift0 (MZF1_5-13_rc)	0.811	0.609	0.422	-0.223	0.901	1.594	0.911	5	5	7	8	6	5	6	6.000	6	; oligos_7nt_mkv5_m5 versus MA0057.1_rc (MZF1_5-13_rc); m=6/8; ncol2=10; w=9; offset=-1; strand=R; shift=0; score= 6; yymCCCMTmv------ ; cor=0.811; Ncor=0.609; logoDP=0.422; NIcor=-0.223; NsEucl=0.901; SSD=1.594; NSW=0.911; rcor=5; rNcor=5; rlogoDP=7; rNIcor=8; rNsEucl=6; rSSD=5; rNSW=6; rank_mean=6.000; match_rank=6 a 2 2 4 2 0 1 5 0 7 4 0 0 0 0 0 0 c 4 4 8 14 14 15 11 0 7 7 0 0 0 0 0 0 g 2 0 1 0 2 0 0 1 0 4 0 0 0 0 0 0 t 8 10 3 0 0 0 0 15 2 1 0 0 0 0 0 0
MA0039.2_rc_shift2 (Klf4_rc)	0.766	0.696	0.728	-0.213	0.895	2.203	0.890	8	3	6	7	7	8	8	6.714	7	; oligos_7nt_mkv5_m5 versus MA0039.2_rc (Klf4_rc); m=7/8; ncol2=10; w=10; offset=1; strand=R; shift=2; score= 6.7143; --gCCmCrCCCw---- ; cor=0.766; Ncor=0.696; logoDP=0.728; NIcor=-0.213; NsEucl=0.895; SSD=2.203; NSW=0.890; rcor=8; rNcor=3; rlogoDP=6; rNIcor=7; rNsEucl=7; rSSD=8; rNSW=8; rank_mean=6.714; match_rank=7 a 0 0 932 289 125 2042 34 2139 16 13 6 1765 0 0 0 0 c 0 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022 0 0 0 0 g 0 0 2858 130 46 80 15 1922 36 13 9 81 0 0 0 0 t 0 0 254 123 264 42 22 277 14 14 88 1468 0 0 0 0
MA0056.1_rc_shift2 (MZF1_1-4_rc)	0.795	0.433	0.230	-0.153	0.865	1.318	0.890	7	8	8	6	8	3	7	6.714	8	; oligos_7nt_mkv5_m5 versus MA0056.1_rc (MZF1_1-4_rc); m=8/8; ncol2=6; w=6; offset=1; strand=R; shift=2; score= 6.7143; --TCCCCr-------- ; cor=0.795; Ncor=0.433; logoDP=0.230; NIcor=-0.153; NsEucl=0.865; SSD=1.318; NSW=0.890; rcor=7; rNcor=8; rlogoDP=8; rNIcor=6; rNsEucl=8; rSSD=3; rNSW=7; rank_mean=6.714; match_rank=8 a 0 0 0 0 1 0 1 8 0 0 0 0 0 0 0 0 c 0 0 2 20 19 18 19 4 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 5 0 0 0 0 0 0 0 0 t 0 0 18 0 0 2 0 3 0 0 0 0 0 0 0 0