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/positions_7nt_m4/peak-motifs_positions_7nt_m4.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/positions_7nt_m4/peak-motifs_positions_7nt_m4_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift2 ; 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
positions_7nt_m4_shift2 (positions_7nt_m4)
; positions_7nt_m4; m=0 (reference); ncol1=15; shift=2; ncol=21; --ssCCAGGTCAGGgcr---- ; Alignment reference a 0 0 69 66 33 16 319 3 5 6 1 326 11 34 47 67 85 0 0 0 0 c 0 0 85 109 245 316 2 3 7 8 331 4 15 44 56 111 74 0 0 0 0 g 0 0 102 92 39 7 13 332 327 24 5 7 297 242 192 79 117 0 0 0 0 t 0 0 84 73 23 1 6 2 1 302 3 3 17 20 45 83 64 0 0 0 0

MA0071.1_shift2 (RORA_1) 0.825 0.550 8.532 0.567 0.908 1.696 0.915 1 1 1 1 3 2 3 1.714 1
; positions_7nt_m4 versus MA0071.1 (RORA_1); m=1/7; ncol2=10; w=10; offset=0; strand=D; shift=2; score= 1.7143; --wwcwAGGTCA--------- ; cor=0.825; Ncor=0.550; logoDP=8.532; NIcor=0.567; NsEucl=0.908; SSD=1.696; NSW=0.915; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=3; rSSD=2; rNSW=3; rank_mean=1.714; match_rank=1 a 0 0 15 9 6 11 21 0 0 0 0 25 0 0 0 0 0 0 0 0 0 c 0 0 1 1 12 2 0 0 0 0 25 0 0 0 0 0 0 0 0 0 0 g 0 0 2 0 4 5 4 25 25 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 7 15 3 7 0 0 0 25 0 0 0 0 0 0 0 0 0 0 0

MA0258.2_shift6 (ESR2) 0.816 0.473 6.236 0.465 0.917 1.681 0.924 4 4 5 4 1 1 1 2.857 2
; positions_7nt_m4 versus MA0258.2 (ESR2); m=2/7; ncol2=15; w=11; offset=4; strand=D; shift=6; score= 2.8571; ------rGGTCAsmstGaCCy ; cor=0.816; Ncor=0.473; logoDP=6.236; NIcor=0.465; NsEucl=0.917; SSD=1.681; NSW=0.924; rcor=4; rNcor=4; rlogoDP=5; rNIcor=4; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.857; match_rank=2 a 0 0 0 0 0 0 5410 429 59 74 0 8098 502 2092 1808 1602 1121 3278 434 1111 834 c 0 0 0 0 0 0 96 0 0 147 7621 1 4202 3235 2510 975 398 2056 6469 5854 2708 g 0 0 0 0 0 0 2563 7170 8143 989 533 57 2738 1688 2173 533 6658 1391 363 0 606 t 0 0 0 0 0 0 174 644 41 7033 89 87 801 1228 1752 5133 66 1518 977 1278 4095

MA0141.1_shift0 (Esrrb) 0.824 0.485 7.555 0.491 0.907 1.724 0.914 2 2 3 2 4 3 4 2.857 3
; positions_7nt_m4 versus MA0141.1 (Esrrb); m=3/7; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 2.8571; rgsyCAAGGTCA--------- ; cor=0.824; Ncor=0.485; logoDP=7.555; NIcor=0.491; NsEucl=0.907; SSD=1.724; NSW=0.914; rcor=2; rNcor=2; rlogoDP=3; rNIcor=2; rNsEucl=4; rSSD=3; rNSW=4; rank_mean=2.857; match_rank=3 a 1054 673 420 259 310 3326 3567 32 21 182 9 3458 0 0 0 0 0 0 0 0 0 c 800 829 1211 1250 2664 32 2 5 12 46 3376 20 0 0 0 0 0 0 0 0 0 g 985 1370 1209 448 627 248 60 3586 3602 244 170 129 0 0 0 0 0 0 0 0 0 t 793 767 805 1693 52 50 27 31 17 3175 85 27 0 0 0 0 0 0 0 0 0

MA0141.2_shift0 (Esrrb) 0.824 0.484 7.643 0.490 0.907 1.738 0.913 3 3 2 3 5 4 5 3.571 4
; positions_7nt_m4 versus MA0141.2 (Esrrb); m=4/7; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 3.5714; rgsyCAAGGTCA--------- ; cor=0.824; Ncor=0.484; logoDP=7.643; NIcor=0.490; NsEucl=0.907; SSD=1.738; NSW=0.913; rcor=3; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=3.571; match_rank=4 a 1055 673 403 260 312 3347 3590 33 12 180 9 3478 0 0 0 0 0 0 0 0 0 c 801 832 1212 1230 2653 32 2 2 11 43 3394 21 0 0 0 0 0 0 0 0 0 g 984 1352 1212 449 630 248 60 3597 3622 243 167 128 0 0 0 0 0 0 0 0 0 t 773 767 807 1702 51 27 6 29 16 3192 85 26 0 0 0 0 0 0 0 0 0

MA0159.1_shift6 (RXR::RAR_DR5) 0.794 0.416 5.433 0.412 0.913 1.817 0.917 5 6 6 5 2 5 2 4.429 5
; positions_7nt_m4 versus MA0159.1 (RXR::RAR_DR5); m=5/7; ncol2=17; w=11; offset=4; strand=D; shift=6; score= 4.4286; ------rGkTCAysgrsAGKT ; cor=0.794; Ncor=0.416; logoDP=5.433; NIcor=0.412; NsEucl=0.913; SSD=1.817; NSW=0.917; rcor=5; rNcor=6; rlogoDP=6; rNIcor=5; rNsEucl=2; rSSD=5; rNSW=2; rank_mean=4.429; match_rank=5 a 0 0 0 0 0 0 12 0 1 0 0 22 4 5 5 13 5 17 1 0 2 c 0 0 0 0 0 0 0 0 0 0 18 0 7 8 4 1 6 3 1 1 1 g 0 0 0 0 0 0 11 23 13 1 3 1 5 9 11 7 12 3 20 16 3 t 0 0 0 0 0 0 0 0 9 22 2 0 7 1 3 2 0 0 1 6 17

MA0103.2_rc_shift5 (ZEB1_rc) 0.776 0.466 2.348 0.018 0.881 2.305 0.872 6 5 7 7 6 7 6 6.286 6
; positions_7nt_m4 versus MA0103.2_rc (ZEB1_rc); m=6/7; ncol2=9; w=9; offset=3; strand=R; shift=5; score= 6.2857; -----CAGGTGwGg------- ; cor=0.776; Ncor=0.466; logoDP=2.348; NIcor=0.018; NsEucl=0.881; SSD=2.305; NSW=0.872; rcor=6; rNcor=5; rlogoDP=7; rNIcor=7; rNsEucl=6; rSSD=7; rNSW=6; rank_mean=6.286; match_rank=6 a 0 0 0 0 0 0 3555 0 0 0 385 1594 564 414 0 0 0 0 0 0 0 c 0 0 0 0 0 3555 0 0 0 0 0 431 0 830 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 3555 3555 0 3170 333 2991 1455 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 3555 0 1197 0 856 0 0 0 0 0 0 0

MA0160.1_shift5 (NR4A2) 0.765 0.408 6.432 0.409 0.871 2.139 0.866 7 7 4 6 7 6 7 6.286 7
; positions_7nt_m4 versus MA0160.1 (NR4A2); m=7/7; ncol2=8; w=8; offset=3; strand=D; shift=5; score= 6.2857; -----aAGGTCAc-------- ; cor=0.765; Ncor=0.408; logoDP=6.432; NIcor=0.409; NsEucl=0.871; SSD=2.139; NSW=0.866; rcor=7; rNcor=7; rlogoDP=4; rNIcor=6; rNsEucl=7; rSSD=6; rNSW=7; rank_mean=6.286; match_rank=7 a 0 0 0 0 0 8 13 0 3 2 0 14 3 0 0 0 0 0 0 0 0 c 0 0 0 0 0 1 0 0 0 2 13 0 8 0 0 0 0 0 0 0 0 g 0 0 0 0 0 3 1 13 11 0 0 0 2 0 0 0 0 0 0 0 0 t 0 0 0 0 0 1 0 1 0 10 1 0 0 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
positions_7nt_m4_shift2 (positions_7nt_m4)																	; positions_7nt_m4; m=0 (reference); ncol1=15; shift=2; ncol=21; --ssCCAGGTCAGGgcr---- ; Alignment reference a 0 0 69 66 33 16 319 3 5 6 1 326 11 34 47 67 85 0 0 0 0 c 0 0 85 109 245 316 2 3 7 8 331 4 15 44 56 111 74 0 0 0 0 g 0 0 102 92 39 7 13 332 327 24 5 7 297 242 192 79 117 0 0 0 0 t 0 0 84 73 23 1 6 2 1 302 3 3 17 20 45 83 64 0 0 0 0
MA0071.1_shift2 (RORA_1)	0.825	0.550	8.532	0.567	0.908	1.696	0.915	1	1	1	1	3	2	3	1.714	1	; positions_7nt_m4 versus MA0071.1 (RORA_1); m=1/7; ncol2=10; w=10; offset=0; strand=D; shift=2; score= 1.7143; --wwcwAGGTCA--------- ; cor=0.825; Ncor=0.550; logoDP=8.532; NIcor=0.567; NsEucl=0.908; SSD=1.696; NSW=0.915; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=3; rSSD=2; rNSW=3; rank_mean=1.714; match_rank=1 a 0 0 15 9 6 11 21 0 0 0 0 25 0 0 0 0 0 0 0 0 0 c 0 0 1 1 12 2 0 0 0 0 25 0 0 0 0 0 0 0 0 0 0 g 0 0 2 0 4 5 4 25 25 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 7 15 3 7 0 0 0 25 0 0 0 0 0 0 0 0 0 0 0
MA0258.2_shift6 (ESR2)	0.816	0.473	6.236	0.465	0.917	1.681	0.924	4	4	5	4	1	1	1	2.857	2	; positions_7nt_m4 versus MA0258.2 (ESR2); m=2/7; ncol2=15; w=11; offset=4; strand=D; shift=6; score= 2.8571; ------rGGTCAsmstGaCCy ; cor=0.816; Ncor=0.473; logoDP=6.236; NIcor=0.465; NsEucl=0.917; SSD=1.681; NSW=0.924; rcor=4; rNcor=4; rlogoDP=5; rNIcor=4; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=2.857; match_rank=2 a 0 0 0 0 0 0 5410 429 59 74 0 8098 502 2092 1808 1602 1121 3278 434 1111 834 c 0 0 0 0 0 0 96 0 0 147 7621 1 4202 3235 2510 975 398 2056 6469 5854 2708 g 0 0 0 0 0 0 2563 7170 8143 989 533 57 2738 1688 2173 533 6658 1391 363 0 606 t 0 0 0 0 0 0 174 644 41 7033 89 87 801 1228 1752 5133 66 1518 977 1278 4095
MA0141.1_shift0 (Esrrb)	0.824	0.485	7.555	0.491	0.907	1.724	0.914	2	2	3	2	4	3	4	2.857	3	; positions_7nt_m4 versus MA0141.1 (Esrrb); m=3/7; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 2.8571; rgsyCAAGGTCA--------- ; cor=0.824; Ncor=0.485; logoDP=7.555; NIcor=0.491; NsEucl=0.907; SSD=1.724; NSW=0.914; rcor=2; rNcor=2; rlogoDP=3; rNIcor=2; rNsEucl=4; rSSD=3; rNSW=4; rank_mean=2.857; match_rank=3 a 1054 673 420 259 310 3326 3567 32 21 182 9 3458 0 0 0 0 0 0 0 0 0 c 800 829 1211 1250 2664 32 2 5 12 46 3376 20 0 0 0 0 0 0 0 0 0 g 985 1370 1209 448 627 248 60 3586 3602 244 170 129 0 0 0 0 0 0 0 0 0 t 793 767 805 1693 52 50 27 31 17 3175 85 27 0 0 0 0 0 0 0 0 0
MA0141.2_shift0 (Esrrb)	0.824	0.484	7.643	0.490	0.907	1.738	0.913	3	3	2	3	5	4	5	3.571	4	; positions_7nt_m4 versus MA0141.2 (Esrrb); m=4/7; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 3.5714; rgsyCAAGGTCA--------- ; cor=0.824; Ncor=0.484; logoDP=7.643; NIcor=0.490; NsEucl=0.907; SSD=1.738; NSW=0.913; rcor=3; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=3.571; match_rank=4 a 1055 673 403 260 312 3347 3590 33 12 180 9 3478 0 0 0 0 0 0 0 0 0 c 801 832 1212 1230 2653 32 2 2 11 43 3394 21 0 0 0 0 0 0 0 0 0 g 984 1352 1212 449 630 248 60 3597 3622 243 167 128 0 0 0 0 0 0 0 0 0 t 773 767 807 1702 51 27 6 29 16 3192 85 26 0 0 0 0 0 0 0 0 0
MA0159.1_shift6 (RXR::RAR_DR5)	0.794	0.416	5.433	0.412	0.913	1.817	0.917	5	6	6	5	2	5	2	4.429	5	; positions_7nt_m4 versus MA0159.1 (RXR::RAR_DR5); m=5/7; ncol2=17; w=11; offset=4; strand=D; shift=6; score= 4.4286; ------rGkTCAysgrsAGKT ; cor=0.794; Ncor=0.416; logoDP=5.433; NIcor=0.412; NsEucl=0.913; SSD=1.817; NSW=0.917; rcor=5; rNcor=6; rlogoDP=6; rNIcor=5; rNsEucl=2; rSSD=5; rNSW=2; rank_mean=4.429; match_rank=5 a 0 0 0 0 0 0 12 0 1 0 0 22 4 5 5 13 5 17 1 0 2 c 0 0 0 0 0 0 0 0 0 0 18 0 7 8 4 1 6 3 1 1 1 g 0 0 0 0 0 0 11 23 13 1 3 1 5 9 11 7 12 3 20 16 3 t 0 0 0 0 0 0 0 0 9 22 2 0 7 1 3 2 0 0 1 6 17
MA0103.2_rc_shift5 (ZEB1_rc)	0.776	0.466	2.348	0.018	0.881	2.305	0.872	6	5	7	7	6	7	6	6.286	6	; positions_7nt_m4 versus MA0103.2_rc (ZEB1_rc); m=6/7; ncol2=9; w=9; offset=3; strand=R; shift=5; score= 6.2857; -----CAGGTGwGg------- ; cor=0.776; Ncor=0.466; logoDP=2.348; NIcor=0.018; NsEucl=0.881; SSD=2.305; NSW=0.872; rcor=6; rNcor=5; rlogoDP=7; rNIcor=7; rNsEucl=6; rSSD=7; rNSW=6; rank_mean=6.286; match_rank=6 a 0 0 0 0 0 0 3555 0 0 0 385 1594 564 414 0 0 0 0 0 0 0 c 0 0 0 0 0 3555 0 0 0 0 0 431 0 830 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 3555 3555 0 3170 333 2991 1455 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 3555 0 1197 0 856 0 0 0 0 0 0 0
MA0160.1_shift5 (NR4A2)	0.765	0.408	6.432	0.409	0.871	2.139	0.866	7	7	4	6	7	6	7	6.286	7	; positions_7nt_m4 versus MA0160.1 (NR4A2); m=7/7; ncol2=8; w=8; offset=3; strand=D; shift=5; score= 6.2857; -----aAGGTCAc-------- ; cor=0.765; Ncor=0.408; logoDP=6.432; NIcor=0.409; NsEucl=0.871; SSD=2.139; NSW=0.866; rcor=7; rNcor=7; rlogoDP=4; rNIcor=6; rNsEucl=7; rSSD=6; rNSW=7; rank_mean=6.286; match_rank=7 a 0 0 0 0 0 8 13 0 3 2 0 14 3 0 0 0 0 0 0 0 0 c 0 0 0 0 0 1 0 0 0 2 13 0 8 0 0 0 0 0 0 0 0 g 0 0 0 0 0 3 1 13 11 0 0 0 2 0 0 0 0 0 0 0 0 t 0 0 0 0 0 1 0 1 0 10 1 0 0 0 0 0 0 0 0 0 0