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_6nt_m4/peak-motifs_positions_6nt_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_6nt_m4/peak-motifs_positions_6nt_m4_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift7 ; 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
positions_6nt_m4_shift7 (positions_6nt_m4)
; positions_6nt_m4; m=0 (reference); ncol1=17; shift=7; ncol=24; -------styaaCCTGACCTGgsy ; Alignment reference a 0 0 0 0 0 0 0 32 35 24 74 74 8 4 0 1 158 1 0 2 7 24 35 38 c 0 0 0 0 0 0 0 42 39 45 26 27 122 136 0 0 1 159 160 0 5 26 46 41 g 0 0 0 0 0 0 0 52 39 24 37 35 18 12 0 159 0 0 0 0 142 86 44 34 t 0 0 0 0 0 0 0 34 47 67 23 24 12 8 160 0 1 0 0 158 6 24 35 47

MA0071.1_rc_shift14 (RORA_1_rc) 0.857 0.504 1.382 -0.043 0.916 1.418 0.929 1 2 4 6 3 1 1 2.571 1
; positions_6nt_m4 versus MA0071.1_rc (RORA_1_rc); m=1/6; ncol2=10; w=10; offset=7; strand=R; shift=14; score= 2.5714; --------------TGACCTwgww ; cor=0.857; Ncor=0.504; logoDP=1.382; NIcor=-0.043; NsEucl=0.916; SSD=1.418; NSW=0.929; rcor=1; rNcor=2; rlogoDP=4; rNIcor=6; rNsEucl=3; rSSD=1; rNSW=1; rank_mean=2.571; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0 7 3 15 7 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 4 5 4 0 2 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0 0 2 12 1 1 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0 0 21 11 6 9 15

MA0258.2_rc_shift5 (ESR2_rc) 0.803 0.550 2.699 0.311 0.923 1.998 0.923 4 1 3 3 1 5 2 2.714 2
; positions_6nt_m4 versus MA0258.2_rc (ESR2_rc); m=2/6; ncol2=15; w=13; offset=-2; strand=R; shift=5; score= 2.7143; -----rGGtCasksTGACCy---- ; cor=0.803; Ncor=0.550; logoDP=2.699; NIcor=0.311; NsEucl=0.923; SSD=1.998; NSW=0.923; rcor=4; rNcor=1; rlogoDP=3; rNIcor=3; rNsEucl=1; rSSD=5; rNSW=2; rank_mean=2.714; match_rank=2 a 0 0 0 0 0 4095 1278 977 1518 66 5133 1752 1228 801 87 89 7033 41 644 174 0 0 0 0 c 0 0 0 0 0 606 0 363 1391 6658 533 2173 1688 2738 57 533 989 8143 7170 2563 0 0 0 0 g 0 0 0 0 0 2708 5854 6469 2056 398 975 2510 3235 4202 1 7621 147 0 0 96 0 0 0 0 t 0 0 0 0 0 834 1111 434 3278 1121 1602 1808 2092 502 8098 0 74 59 429 5410 0 0 0 0

MA0141.1_rc_shift14 (Esrrb_rc) 0.822 0.432 0.956 0.009 0.905 1.792 0.910 2 3 5 4 4 2 4 3.429 3
; positions_6nt_m4 versus MA0141.1_rc (Esrrb_rc); m=3/6; ncol2=12; w=10; offset=7; strand=R; shift=14; score= 3.4286; --------------TGACCTTGrs ; cor=0.822; Ncor=0.432; logoDP=0.956; NIcor=0.009; NsEucl=0.905; SSD=1.792; NSW=0.910; rcor=2; rNcor=3; rlogoDP=5; rNIcor=4; rNsEucl=4; rSSD=2; rNSW=4; rank_mean=3.429; match_rank=3 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 85 3175 17 31 27 50 52 1693 805 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 129 170 244 3602 3586 60 248 627 448 1209 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 3376 46 12 5 2 32 2664 1250 1211 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3458 9 182 21 32 3567 3326 310 259 420

MA0112.2_shift0 (ESR1) 0.772 0.418 4.953 0.390 0.917 2.301 0.912 6 5 2 2 2 6 3 3.714 4
; positions_6nt_m4 versus MA0112.2 (ESR1); m=4/6; ncol2=20; w=13; offset=-7; strand=D; shift=0; score= 3.7143; vkscmaGGtCAcccTGaCCy---- ; cor=0.772; Ncor=0.418; logoDP=4.953; NIcor=0.390; NsEucl=0.917; SSD=2.301; NSW=0.912; rcor=6; rNcor=5; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=6; rNSW=3; rank_mean=3.714; match_rank=4 a 122 107 64 83 134 308 36 19 33 4 398 58 63 64 32 21 305 10 59 26 0 0 0 0 c 120 80 173 229 232 28 8 18 41 394 13 250 276 258 19 22 106 436 353 165 0 0 0 0 g 154 164 149 65 47 89 387 420 91 53 27 107 53 97 8 426 31 12 2 22 0 0 0 0 t 71 117 82 93 57 48 43 18 310 24 37 60 83 56 416 6 33 17 61 262 0 0 0 0

MA0103.2_shift7 (ZEB1) 0.788 0.417 5.458 0.416 0.892 1.892 0.895 5 6 1 1 6 4 6 4.143 5
; positions_6nt_m4 versus MA0103.2 (ZEB1); m=5/6; ncol2=9; w=9; offset=0; strand=D; shift=7; score= 4.1429; -------cCwCACCTG-------- ; cor=0.788; Ncor=0.417; logoDP=5.458; NIcor=0.416; NsEucl=0.892; SSD=1.892; NSW=0.895; rcor=5; rNcor=6; rlogoDP=1; rNIcor=1; rNsEucl=6; rSSD=4; rNSW=6; rank_mean=4.143; match_rank=5 a 0 0 0 0 0 0 0 856 0 1197 0 3555 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 1455 2991 333 3170 0 3555 3555 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 830 0 431 0 0 0 0 0 3555 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 414 564 1594 385 0 0 0 3555 0 0 0 0 0 0 0 0 0

MA0141.2_rc_shift14 (Esrrb_rc) 0.821 0.432 0.945 0.007 0.905 1.804 0.910 3 4 6 5 5 3 5 4.429 6
; positions_6nt_m4 versus MA0141.2_rc (Esrrb_rc); m=6/6; ncol2=12; w=10; offset=7; strand=R; shift=14; score= 4.4286; --------------TGACCTTGrs ; cor=0.821; Ncor=0.432; logoDP=0.945; NIcor=0.007; NsEucl=0.905; SSD=1.804; NSW=0.910; rcor=3; rNcor=4; rlogoDP=6; rNIcor=5; rNsEucl=5; rSSD=3; rNSW=5; rank_mean=4.429; match_rank=6 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 85 3192 16 29 6 27 51 1702 807 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 128 167 243 3622 3597 60 248 630 449 1212 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 3394 43 11 2 2 32 2653 1230 1212 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3478 9 180 12 33 3590 3347 312 260 403

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m4_shift7 (positions_6nt_m4)																	; positions_6nt_m4; m=0 (reference); ncol1=17; shift=7; ncol=24; -------styaaCCTGACCTGgsy ; Alignment reference a 0 0 0 0 0 0 0 32 35 24 74 74 8 4 0 1 158 1 0 2 7 24 35 38 c 0 0 0 0 0 0 0 42 39 45 26 27 122 136 0 0 1 159 160 0 5 26 46 41 g 0 0 0 0 0 0 0 52 39 24 37 35 18 12 0 159 0 0 0 0 142 86 44 34 t 0 0 0 0 0 0 0 34 47 67 23 24 12 8 160 0 1 0 0 158 6 24 35 47
MA0071.1_rc_shift14 (RORA_1_rc)	0.857	0.504	1.382	-0.043	0.916	1.418	0.929	1	2	4	6	3	1	1	2.571	1	; positions_6nt_m4 versus MA0071.1_rc (RORA_1_rc); m=1/6; ncol2=10; w=10; offset=7; strand=R; shift=14; score= 2.5714; --------------TGACCTwgww ; cor=0.857; Ncor=0.504; logoDP=1.382; NIcor=-0.043; NsEucl=0.916; SSD=1.418; NSW=0.929; rcor=1; rNcor=2; rlogoDP=4; rNIcor=6; rNsEucl=3; rSSD=1; rNSW=1; rank_mean=2.571; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0 7 3 15 7 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 25 4 5 4 0 2 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0 0 2 12 1 1 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0 0 21 11 6 9 15
MA0258.2_rc_shift5 (ESR2_rc)	0.803	0.550	2.699	0.311	0.923	1.998	0.923	4	1	3	3	1	5	2	2.714	2	; positions_6nt_m4 versus MA0258.2_rc (ESR2_rc); m=2/6; ncol2=15; w=13; offset=-2; strand=R; shift=5; score= 2.7143; -----rGGtCasksTGACCy---- ; cor=0.803; Ncor=0.550; logoDP=2.699; NIcor=0.311; NsEucl=0.923; SSD=1.998; NSW=0.923; rcor=4; rNcor=1; rlogoDP=3; rNIcor=3; rNsEucl=1; rSSD=5; rNSW=2; rank_mean=2.714; match_rank=2 a 0 0 0 0 0 4095 1278 977 1518 66 5133 1752 1228 801 87 89 7033 41 644 174 0 0 0 0 c 0 0 0 0 0 606 0 363 1391 6658 533 2173 1688 2738 57 533 989 8143 7170 2563 0 0 0 0 g 0 0 0 0 0 2708 5854 6469 2056 398 975 2510 3235 4202 1 7621 147 0 0 96 0 0 0 0 t 0 0 0 0 0 834 1111 434 3278 1121 1602 1808 2092 502 8098 0 74 59 429 5410 0 0 0 0
MA0141.1_rc_shift14 (Esrrb_rc)	0.822	0.432	0.956	0.009	0.905	1.792	0.910	2	3	5	4	4	2	4	3.429	3	; positions_6nt_m4 versus MA0141.1_rc (Esrrb_rc); m=3/6; ncol2=12; w=10; offset=7; strand=R; shift=14; score= 3.4286; --------------TGACCTTGrs ; cor=0.822; Ncor=0.432; logoDP=0.956; NIcor=0.009; NsEucl=0.905; SSD=1.792; NSW=0.910; rcor=2; rNcor=3; rlogoDP=5; rNIcor=4; rNsEucl=4; rSSD=2; rNSW=4; rank_mean=3.429; match_rank=3 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 85 3175 17 31 27 50 52 1693 805 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 129 170 244 3602 3586 60 248 627 448 1209 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 3376 46 12 5 2 32 2664 1250 1211 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3458 9 182 21 32 3567 3326 310 259 420
MA0112.2_shift0 (ESR1)	0.772	0.418	4.953	0.390	0.917	2.301	0.912	6	5	2	2	2	6	3	3.714	4	; positions_6nt_m4 versus MA0112.2 (ESR1); m=4/6; ncol2=20; w=13; offset=-7; strand=D; shift=0; score= 3.7143; vkscmaGGtCAcccTGaCCy---- ; cor=0.772; Ncor=0.418; logoDP=4.953; NIcor=0.390; NsEucl=0.917; SSD=2.301; NSW=0.912; rcor=6; rNcor=5; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=6; rNSW=3; rank_mean=3.714; match_rank=4 a 122 107 64 83 134 308 36 19 33 4 398 58 63 64 32 21 305 10 59 26 0 0 0 0 c 120 80 173 229 232 28 8 18 41 394 13 250 276 258 19 22 106 436 353 165 0 0 0 0 g 154 164 149 65 47 89 387 420 91 53 27 107 53 97 8 426 31 12 2 22 0 0 0 0 t 71 117 82 93 57 48 43 18 310 24 37 60 83 56 416 6 33 17 61 262 0 0 0 0
MA0103.2_shift7 (ZEB1)	0.788	0.417	5.458	0.416	0.892	1.892	0.895	5	6	1	1	6	4	6	4.143	5	; positions_6nt_m4 versus MA0103.2 (ZEB1); m=5/6; ncol2=9; w=9; offset=0; strand=D; shift=7; score= 4.1429; -------cCwCACCTG-------- ; cor=0.788; Ncor=0.417; logoDP=5.458; NIcor=0.416; NsEucl=0.892; SSD=1.892; NSW=0.895; rcor=5; rNcor=6; rlogoDP=1; rNIcor=1; rNsEucl=6; rSSD=4; rNSW=6; rank_mean=4.143; match_rank=5 a 0 0 0 0 0 0 0 856 0 1197 0 3555 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 1455 2991 333 3170 0 3555 3555 0 0 0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 830 0 431 0 0 0 0 0 3555 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 414 564 1594 385 0 0 0 3555 0 0 0 0 0 0 0 0 0
MA0141.2_rc_shift14 (Esrrb_rc)	0.821	0.432	0.945	0.007	0.905	1.804	0.910	3	4	6	5	5	3	5	4.429	6	; positions_6nt_m4 versus MA0141.2_rc (Esrrb_rc); m=6/6; ncol2=12; w=10; offset=7; strand=R; shift=14; score= 4.4286; --------------TGACCTTGrs ; cor=0.821; Ncor=0.432; logoDP=0.945; NIcor=0.007; NsEucl=0.905; SSD=1.804; NSW=0.910; rcor=3; rNcor=4; rlogoDP=6; rNIcor=5; rNsEucl=5; rSSD=3; rNSW=5; rank_mean=4.429; match_rank=6 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 85 3192 16 29 6 27 51 1702 807 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 128 167 243 3622 3597 60 248 630 449 1212 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 21 3394 43 11 2 2 32 2653 1230 1212 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3478 9 180 12 33 3590 3347 312 260 403