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_m1/peak-motifs_positions_7nt_m1.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_m1/peak-motifs_positions_7nt_m1_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift2 ; 10 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_m1_shift2 (positions_7nt_m1)
; positions_7nt_m1; m=0 (reference); ncol1=15; shift=2; ncol=21; --byCCAGGTCACCtkg---- ; Alignment reference a 0 0 63 54 14 13 282 3 3 6 6 273 5 32 53 54 67 0 0 0 0 c 0 0 79 94 235 262 2 5 5 5 275 4 254 210 68 66 72 0 0 0 0 g 0 0 74 64 18 6 4 279 281 10 6 10 15 17 57 80 109 0 0 0 0 t 0 0 75 79 24 10 3 4 2 270 4 4 17 32 113 91 43 0 0 0 0

MA0112.1_shift4 (ESR1) 0.869 0.565 6.130 0.554 0.935 1.424 0.945 2 3 6 4 1 3 2 3.000 1
; positions_7nt_m1 versus MA0112.1 (ESR1); m=1/9; ncol2=18; w=13; offset=2; strand=D; shift=4; score= 3; ----ccAGGTCaCcrtGrCCy ; cor=0.869; Ncor=0.565; logoDP=6.130; NIcor=0.554; NsEucl=0.935; SSD=1.424; NSW=0.945; rcor=2; rNcor=3; rlogoDP=6; rNIcor=4; rNsEucl=1; rSSD=3; rNSW=2; rank_mean=3.000; match_rank=1 a 0 0 0 0 1 1 7 2 0 0 0 6 1 2 3 1 1 5 0 0 2 c 0 0 0 0 5 5 1 0 0 0 7 0 7 5 2 1 0 1 8 9 4 g 0 0 0 0 1 1 1 7 9 0 2 2 1 1 4 1 8 3 0 0 0 t 0 0 0 0 2 2 0 0 0 9 0 1 0 1 0 6 0 0 1 0 3

MA0258.2_shift6 (ESR2) 0.887 0.513 6.109 0.504 0.935 1.036 0.953 1 5 7 5 3 1 1 3.286 2
; positions_7nt_m1 versus MA0258.2 (ESR2); m=2/9; ncol2=15; w=11; offset=4; strand=D; shift=6; score= 3.2857; ------rGGTCAsmstGaCCy ; cor=0.887; Ncor=0.513; logoDP=6.109; NIcor=0.504; NsEucl=0.935; SSD=1.036; NSW=0.953; rcor=1; rNcor=5; rlogoDP=7; rNIcor=5; rNsEucl=3; rSSD=1; rNSW=1; rank_mean=3.286; 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

MA0071.1_shift2 (RORA_1) 0.832 0.555 8.394 0.568 0.910 1.634 0.918 4 4 1 3 5 4 4 3.571 3
; positions_7nt_m1 versus MA0071.1 (RORA_1); m=3/9; ncol2=10; w=10; offset=0; strand=D; shift=2; score= 3.5714; --wwcwAGGTCA--------- ; cor=0.832; Ncor=0.555; logoDP=8.394; NIcor=0.568; NsEucl=0.910; SSD=1.634; NSW=0.918; rcor=4; rNcor=4; rlogoDP=1; rNIcor=3; rNsEucl=5; rSSD=4; rNSW=4; rank_mean=3.571; match_rank=3 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

MA0112.2_shift1 (ESR1) 0.819 0.614 3.822 0.578 0.935 1.909 0.936 7 1 9 2 2 8 3 4.571 4
; positions_7nt_m1 versus MA0112.2 (ESR1); m=4/9; ncol2=20; w=15; offset=-1; strand=D; shift=1; score= 4.5714; -vkscmaGGtCAcccTGaCCy ; cor=0.819; Ncor=0.614; logoDP=3.822; NIcor=0.578; NsEucl=0.935; SSD=1.909; NSW=0.936; rcor=7; rNcor=1; rlogoDP=9; rNIcor=2; rNsEucl=2; rSSD=8; rNSW=3; rank_mean=4.571; match_rank=4 a 0 122 107 64 83 134 308 36 19 33 4 398 58 63 64 32 21 305 10 59 26 c 0 120 80 173 229 232 28 8 18 41 394 13 250 276 258 19 22 106 436 353 165 g 0 154 164 149 65 47 89 387 420 91 53 27 107 53 97 8 426 31 12 2 22 t 0 71 117 82 93 57 48 43 18 310 24 37 60 83 56 416 6 33 17 61 262

MA0141.1_shift0 (Esrrb) 0.832 0.489 7.555 0.497 0.909 1.660 0.917 5 6 4 6 6 5 5 5.286 5
; positions_7nt_m1 versus MA0141.1 (Esrrb); m=5/9; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 5.2857; rgsyCAAGGTCA--------- ; cor=0.832; Ncor=0.489; logoDP=7.555; NIcor=0.497; NsEucl=0.909; SSD=1.660; NSW=0.917; rcor=5; rNcor=6; rlogoDP=4; rNIcor=6; rNsEucl=6; rSSD=5; rNSW=5; rank_mean=5.286; match_rank=5 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

MA0592.1_shift3 (ESRRA) 0.801 0.587 8.096 0.582 0.904 2.221 0.899 8 2 2 1 8 9 9 5.571 6
; positions_7nt_m1 versus MA0592.1 (ESRRA); m=6/9; ncol2=11; w=11; offset=1; strand=D; shift=3; score= 5.5714; ---yCAAGGTCAcm------- ; cor=0.801; Ncor=0.587; logoDP=8.096; NIcor=0.582; NsEucl=0.904; SSD=2.221; NSW=0.899; rcor=8; rNcor=2; rlogoDP=2; rNIcor=1; rNsEucl=8; rSSD=9; rNSW=9; rank_mean=5.571; match_rank=6 a 0 0 0 17 18 200 198 0 0 6 0 197 23 70 0 0 0 0 0 0 0 c 0 0 0 118 174 2 0 0 0 0 205 1 108 54 0 0 0 0 0 0 0 g 0 0 0 11 15 6 10 203 207 22 3 10 44 40 0 0 0 0 0 0 0 t 0 0 0 62 1 0 0 5 1 180 0 0 33 44 0 0 0 0 0 0 0

MA0141.2_shift0 (Esrrb) 0.831 0.489 7.647 0.496 0.909 1.674 0.916 6 7 3 7 7 6 6 6.000 7
; positions_7nt_m1 versus MA0141.2 (Esrrb); m=7/9; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 6; rgsyCAAGGTCA--------- ; cor=0.831; Ncor=0.489; logoDP=7.647; NIcor=0.496; NsEucl=0.909; SSD=1.674; NSW=0.916; rcor=6; rNcor=7; rlogoDP=3; rNIcor=7; rNsEucl=7; rSSD=6; rNSW=6; rank_mean=6.000; match_rank=7 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

MA0160.1_shift5 (NR4A2) 0.855 0.456 6.404 0.458 0.897 1.347 0.916 3 8 5 8 9 2 7 6.000 8
; positions_7nt_m1 versus MA0160.1 (NR4A2); m=8/9; ncol2=8; w=8; offset=3; strand=D; shift=5; score= 6; -----aAGGTCAc-------- ; cor=0.855; Ncor=0.456; logoDP=6.404; NIcor=0.458; NsEucl=0.897; SSD=1.347; NSW=0.916; rcor=3; rNcor=8; rlogoDP=5; rNIcor=8; rNsEucl=9; rSSD=2; rNSW=7; rank_mean=6.000; match_rank=8 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

MA0159.1_shift6 (RXR::RAR_DR5) 0.780 0.409 5.308 0.406 0.911 1.901 0.914 9 9 8 9 4 7 8 7.714 9
; positions_7nt_m1 versus MA0159.1 (RXR::RAR_DR5); m=9/9; ncol2=17; w=11; offset=4; strand=D; shift=6; score= 7.7143; ------rGkTCAysgrsAGKT ; cor=0.780; Ncor=0.409; logoDP=5.308; NIcor=0.406; NsEucl=0.911; SSD=1.901; NSW=0.914; rcor=9; rNcor=9; rlogoDP=8; rNIcor=9; rNsEucl=4; rSSD=7; rNSW=8; rank_mean=7.714; match_rank=9 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

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_7nt_m1_shift2 (positions_7nt_m1)																	; positions_7nt_m1; m=0 (reference); ncol1=15; shift=2; ncol=21; --byCCAGGTCACCtkg---- ; Alignment reference a 0 0 63 54 14 13 282 3 3 6 6 273 5 32 53 54 67 0 0 0 0 c 0 0 79 94 235 262 2 5 5 5 275 4 254 210 68 66 72 0 0 0 0 g 0 0 74 64 18 6 4 279 281 10 6 10 15 17 57 80 109 0 0 0 0 t 0 0 75 79 24 10 3 4 2 270 4 4 17 32 113 91 43 0 0 0 0
MA0112.1_shift4 (ESR1)	0.869	0.565	6.130	0.554	0.935	1.424	0.945	2	3	6	4	1	3	2	3.000	1	; positions_7nt_m1 versus MA0112.1 (ESR1); m=1/9; ncol2=18; w=13; offset=2; strand=D; shift=4; score= 3; ----ccAGGTCaCcrtGrCCy ; cor=0.869; Ncor=0.565; logoDP=6.130; NIcor=0.554; NsEucl=0.935; SSD=1.424; NSW=0.945; rcor=2; rNcor=3; rlogoDP=6; rNIcor=4; rNsEucl=1; rSSD=3; rNSW=2; rank_mean=3.000; match_rank=1 a 0 0 0 0 1 1 7 2 0 0 0 6 1 2 3 1 1 5 0 0 2 c 0 0 0 0 5 5 1 0 0 0 7 0 7 5 2 1 0 1 8 9 4 g 0 0 0 0 1 1 1 7 9 0 2 2 1 1 4 1 8 3 0 0 0 t 0 0 0 0 2 2 0 0 0 9 0 1 0 1 0 6 0 0 1 0 3
MA0258.2_shift6 (ESR2)	0.887	0.513	6.109	0.504	0.935	1.036	0.953	1	5	7	5	3	1	1	3.286	2	; positions_7nt_m1 versus MA0258.2 (ESR2); m=2/9; ncol2=15; w=11; offset=4; strand=D; shift=6; score= 3.2857; ------rGGTCAsmstGaCCy ; cor=0.887; Ncor=0.513; logoDP=6.109; NIcor=0.504; NsEucl=0.935; SSD=1.036; NSW=0.953; rcor=1; rNcor=5; rlogoDP=7; rNIcor=5; rNsEucl=3; rSSD=1; rNSW=1; rank_mean=3.286; 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
MA0071.1_shift2 (RORA_1)	0.832	0.555	8.394	0.568	0.910	1.634	0.918	4	4	1	3	5	4	4	3.571	3	; positions_7nt_m1 versus MA0071.1 (RORA_1); m=3/9; ncol2=10; w=10; offset=0; strand=D; shift=2; score= 3.5714; --wwcwAGGTCA--------- ; cor=0.832; Ncor=0.555; logoDP=8.394; NIcor=0.568; NsEucl=0.910; SSD=1.634; NSW=0.918; rcor=4; rNcor=4; rlogoDP=1; rNIcor=3; rNsEucl=5; rSSD=4; rNSW=4; rank_mean=3.571; match_rank=3 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
MA0112.2_shift1 (ESR1)	0.819	0.614	3.822	0.578	0.935	1.909	0.936	7	1	9	2	2	8	3	4.571	4	; positions_7nt_m1 versus MA0112.2 (ESR1); m=4/9; ncol2=20; w=15; offset=-1; strand=D; shift=1; score= 4.5714; -vkscmaGGtCAcccTGaCCy ; cor=0.819; Ncor=0.614; logoDP=3.822; NIcor=0.578; NsEucl=0.935; SSD=1.909; NSW=0.936; rcor=7; rNcor=1; rlogoDP=9; rNIcor=2; rNsEucl=2; rSSD=8; rNSW=3; rank_mean=4.571; match_rank=4 a 0 122 107 64 83 134 308 36 19 33 4 398 58 63 64 32 21 305 10 59 26 c 0 120 80 173 229 232 28 8 18 41 394 13 250 276 258 19 22 106 436 353 165 g 0 154 164 149 65 47 89 387 420 91 53 27 107 53 97 8 426 31 12 2 22 t 0 71 117 82 93 57 48 43 18 310 24 37 60 83 56 416 6 33 17 61 262
MA0141.1_shift0 (Esrrb)	0.832	0.489	7.555	0.497	0.909	1.660	0.917	5	6	4	6	6	5	5	5.286	5	; positions_7nt_m1 versus MA0141.1 (Esrrb); m=5/9; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 5.2857; rgsyCAAGGTCA--------- ; cor=0.832; Ncor=0.489; logoDP=7.555; NIcor=0.497; NsEucl=0.909; SSD=1.660; NSW=0.917; rcor=5; rNcor=6; rlogoDP=4; rNIcor=6; rNsEucl=6; rSSD=5; rNSW=5; rank_mean=5.286; match_rank=5 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
MA0592.1_shift3 (ESRRA)	0.801	0.587	8.096	0.582	0.904	2.221	0.899	8	2	2	1	8	9	9	5.571	6	; positions_7nt_m1 versus MA0592.1 (ESRRA); m=6/9; ncol2=11; w=11; offset=1; strand=D; shift=3; score= 5.5714; ---yCAAGGTCAcm------- ; cor=0.801; Ncor=0.587; logoDP=8.096; NIcor=0.582; NsEucl=0.904; SSD=2.221; NSW=0.899; rcor=8; rNcor=2; rlogoDP=2; rNIcor=1; rNsEucl=8; rSSD=9; rNSW=9; rank_mean=5.571; match_rank=6 a 0 0 0 17 18 200 198 0 0 6 0 197 23 70 0 0 0 0 0 0 0 c 0 0 0 118 174 2 0 0 0 0 205 1 108 54 0 0 0 0 0 0 0 g 0 0 0 11 15 6 10 203 207 22 3 10 44 40 0 0 0 0 0 0 0 t 0 0 0 62 1 0 0 5 1 180 0 0 33 44 0 0 0 0 0 0 0
MA0141.2_shift0 (Esrrb)	0.831	0.489	7.647	0.496	0.909	1.674	0.916	6	7	3	7	7	6	6	6.000	7	; positions_7nt_m1 versus MA0141.2 (Esrrb); m=7/9; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 6; rgsyCAAGGTCA--------- ; cor=0.831; Ncor=0.489; logoDP=7.647; NIcor=0.496; NsEucl=0.909; SSD=1.674; NSW=0.916; rcor=6; rNcor=7; rlogoDP=3; rNIcor=7; rNsEucl=7; rSSD=6; rNSW=6; rank_mean=6.000; match_rank=7 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
MA0160.1_shift5 (NR4A2)	0.855	0.456	6.404	0.458	0.897	1.347	0.916	3	8	5	8	9	2	7	6.000	8	; positions_7nt_m1 versus MA0160.1 (NR4A2); m=8/9; ncol2=8; w=8; offset=3; strand=D; shift=5; score= 6; -----aAGGTCAc-------- ; cor=0.855; Ncor=0.456; logoDP=6.404; NIcor=0.458; NsEucl=0.897; SSD=1.347; NSW=0.916; rcor=3; rNcor=8; rlogoDP=5; rNIcor=8; rNsEucl=9; rSSD=2; rNSW=7; rank_mean=6.000; match_rank=8 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
MA0159.1_shift6 (RXR::RAR_DR5)	0.780	0.409	5.308	0.406	0.911	1.901	0.914	9	9	8	9	4	7	8	7.714	9	; positions_7nt_m1 versus MA0159.1 (RXR::RAR_DR5); m=9/9; ncol2=17; w=11; offset=4; strand=D; shift=6; score= 7.7143; ------rGkTCAysgrsAGKT ; cor=0.780; Ncor=0.409; logoDP=5.308; NIcor=0.406; NsEucl=0.911; SSD=1.901; NSW=0.914; rcor=9; rNcor=9; rlogoDP=8; rNIcor=9; rNsEucl=4; rSSD=7; rNSW=8; rank_mean=7.714; match_rank=9 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