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_m1/peak-motifs_positions_6nt_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_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: positions_6nt_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_6nt_m1_shift2 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=14; shift=2; ncol=20; --byCCAGGTCACasw---- ; Alignment reference a 0 0 56 38 22 54 254 0 0 0 0 256 4 172 46 75 0 0 0 0 c 0 0 70 96 185 184 1 2 0 0 256 0 229 28 75 56 0 0 0 0 g 0 0 64 53 21 7 1 254 256 0 0 0 12 20 76 58 0 0 0 0 t 0 0 66 69 28 11 0 0 0 256 0 0 11 36 59 67 0 0 0 0

MA0141.1_shift0 (Esrrb) 0.889 0.555 9.310 0.553 0.925 1.123 0.944 3 4 4 4 4 3 3 3.571 1
; positions_6nt_m1 versus MA0141.1 (Esrrb); m=1/9; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 3.5714; rgsyCAAGGTCA-------- ; cor=0.889; Ncor=0.555; logoDP=9.310; NIcor=0.553; NsEucl=0.925; SSD=1.123; NSW=0.944; rcor=3; rNcor=4; rlogoDP=4; rNIcor=4; rNsEucl=4; rSSD=3; rNSW=3; rank_mean=3.571; match_rank=1 a 1054 673 420 259 310 3326 3567 32 21 182 9 3458 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 g 985 1370 1209 448 627 248 60 3586 3602 244 170 129 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

MA0258.2_shift6 (ESR2) 0.907 0.477 7.708 0.476 0.931 0.963 0.952 1 8 6 8 2 1 1 3.857 2
; positions_6nt_m1 versus MA0258.2 (ESR2); m=2/9; ncol2=15; w=10; offset=4; strand=D; shift=6; score= 3.8571; ------rGGTCAsmstGaCC ; cor=0.907; Ncor=0.477; logoDP=7.708; NIcor=0.476; NsEucl=0.931; SSD=0.963; NSW=0.952; rcor=1; rNcor=8; rlogoDP=6; rNIcor=8; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=3.857; match_rank=2 a 0 0 0 0 0 0 5410 429 59 74 0 8098 502 2092 1808 1602 1121 3278 434 1111 c 0 0 0 0 0 0 96 0 0 147 7621 1 4202 3235 2510 975 398 2056 6469 5854 g 0 0 0 0 0 0 2563 7170 8143 989 533 57 2738 1688 2173 533 6658 1391 363 0 t 0 0 0 0 0 0 174 644 41 7033 89 87 801 1228 1752 5133 66 1518 977 1278

MA0071.1_shift2 (RORA_1) 0.877 0.627 10.635 0.649 0.922 1.221 0.939 6 2 1 2 6 5 5 3.857 3
; positions_6nt_m1 versus MA0071.1 (RORA_1); m=3/9; ncol2=10; w=10; offset=0; strand=D; shift=2; score= 3.8571; --wwcwAGGTCA-------- ; cor=0.877; Ncor=0.627; logoDP=10.635; NIcor=0.649; NsEucl=0.922; SSD=1.221; NSW=0.939; rcor=6; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=6; rSSD=5; rNSW=5; rank_mean=3.857; match_rank=3 a 0 0 15 9 6 11 21 0 0 0 0 25 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 g 0 0 2 0 4 5 4 25 25 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

MA0141.2_shift0 (Esrrb) 0.888 0.555 9.423 0.552 0.925 1.134 0.943 4 5 3 5 5 4 4 4.286 4
; positions_6nt_m1 versus MA0141.2 (Esrrb); m=4/9; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 4.2857; rgsyCAAGGTCA-------- ; cor=0.888; Ncor=0.555; logoDP=9.423; NIcor=0.552; NsEucl=0.925; SSD=1.134; NSW=0.943; rcor=4; rNcor=5; rlogoDP=3; rNIcor=5; rNsEucl=5; rSSD=4; rNSW=4; rank_mean=4.286; match_rank=4 a 1055 673 403 260 312 3347 3590 33 12 180 9 3478 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 g 984 1352 1212 449 630 248 60 3597 3622 243 167 128 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

MA0112.1_shift4 (ESR1) 0.883 0.530 7.478 0.533 0.933 1.311 0.945 5 6 7 6 1 6 2 4.714 5
; positions_6nt_m1 versus MA0112.1 (ESR1); m=5/9; ncol2=18; w=12; offset=2; strand=D; shift=4; score= 4.7143; ----ccAGGTCaCcrtGrCC ; cor=0.883; Ncor=0.530; logoDP=7.478; NIcor=0.533; NsEucl=0.933; SSD=1.311; NSW=0.945; rcor=5; rNcor=6; rlogoDP=7; rNIcor=6; rNsEucl=1; rSSD=6; rNSW=2; rank_mean=4.714; match_rank=5 a 0 0 0 0 1 1 7 2 0 0 0 6 1 2 3 1 1 5 0 0 c 0 0 0 0 5 5 1 0 0 0 7 0 7 5 2 1 0 1 8 9 g 0 0 0 0 1 1 1 7 9 0 2 2 1 1 4 1 8 3 0 0 t 0 0 0 0 2 2 0 0 0 9 0 1 0 1 0 6 0 0 1 0

MA0592.1_shift3 (ESRRA) 0.864 0.679 9.939 0.661 0.920 1.542 0.930 7 1 2 1 7 7 8 4.714 6
; positions_6nt_m1 versus MA0592.1 (ESRRA); m=6/9; ncol2=11; w=11; offset=1; strand=D; shift=3; score= 4.7143; ---yCAAGGTCAcm------ ; cor=0.864; Ncor=0.679; logoDP=9.939; NIcor=0.661; NsEucl=0.920; SSD=1.542; NSW=0.930; rcor=7; rNcor=1; rlogoDP=2; rNIcor=1; rNsEucl=7; rSSD=7; rNSW=8; rank_mean=4.714; match_rank=6 a 0 0 0 17 18 200 198 0 0 6 0 197 23 70 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 g 0 0 0 11 15 6 10 203 207 22 3 10 44 40 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

MA0160.1_shift5 (NR4A2) 0.904 0.517 7.972 0.518 0.912 0.998 0.938 2 7 5 7 8 2 6 5.286 7
; positions_6nt_m1 versus MA0160.1 (NR4A2); m=7/9; ncol2=8; w=8; offset=3; strand=D; shift=5; score= 5.2857; -----aAGGTCAc------- ; cor=0.904; Ncor=0.517; logoDP=7.972; NIcor=0.518; NsEucl=0.912; SSD=0.998; NSW=0.938; rcor=2; rNcor=7; rlogoDP=5; rNIcor=7; rNsEucl=8; rSSD=2; rNSW=6; rank_mean=5.286; match_rank=7 a 0 0 0 0 0 8 13 0 3 2 0 14 3 0 0 0 0 0 0 0 c 0 0 0 0 0 1 0 0 0 2 13 0 8 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 t 0 0 0 0 0 1 0 1 0 10 1 0 0 0 0 0 0 0 0 0

MA0112.2_shift1 (ESR1) 0.821 0.574 4.608 0.557 0.929 1.952 0.930 8 3 9 3 3 8 7 5.857 8
; positions_6nt_m1 versus MA0112.2 (ESR1); m=8/9; ncol2=20; w=14; offset=-1; strand=D; shift=1; score= 5.8571; -vkscmaGGtCAcccTGaCC ; cor=0.821; Ncor=0.574; logoDP=4.608; NIcor=0.557; NsEucl=0.929; SSD=1.952; NSW=0.930; rcor=8; rNcor=3; rlogoDP=9; rNIcor=3; rNsEucl=3; rSSD=8; rNSW=7; rank_mean=5.857; match_rank=8 a 0 122 107 64 83 134 308 36 19 33 4 398 58 63 64 32 21 305 10 59 c 0 120 80 173 229 232 28 8 18 41 394 13 250 276 258 19 22 106 436 353 g 0 154 164 149 65 47 89 387 420 91 53 27 107 53 97 8 426 31 12 2 t 0 71 117 82 93 57 48 43 18 310 24 37 60 83 56 416 6 33 17 61

MA0258.1_shift4 (ESR2) 0.781 0.469 6.610 0.464 0.911 2.297 0.904 9 9 8 9 9 9 9 8.857 9
; positions_6nt_m1 versus MA0258.1 (ESR2); m=9/9; ncol2=18; w=12; offset=2; strand=D; shift=4; score= 8.8571; ----cwrGGTCAsgkTGmCC ; cor=0.781; Ncor=0.469; logoDP=6.610; NIcor=0.464; NsEucl=0.911; SSD=2.297; NSW=0.904; rcor=9; rNcor=9; rlogoDP=8; rNIcor=9; rNsEucl=9; rSSD=9; rNSW=9; rank_mean=8.857; match_rank=9 a 0 0 0 0 78 158 186 27 18 13 0 337 49 64 52 21 63 178 34 46 c 0 0 0 0 161 51 15 0 20 19 357 1 123 63 61 33 25 99 268 289 g 0 0 0 0 63 41 154 275 319 33 0 0 113 149 147 24 265 19 2 0 t 0 0 0 0 55 107 2 55 0 292 0 19 72 81 97 279 4 61 53 22

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
positions_6nt_m1_shift2 (positions_6nt_m1)																	; positions_6nt_m1; m=0 (reference); ncol1=14; shift=2; ncol=20; --byCCAGGTCACasw---- ; Alignment reference a 0 0 56 38 22 54 254 0 0 0 0 256 4 172 46 75 0 0 0 0 c 0 0 70 96 185 184 1 2 0 0 256 0 229 28 75 56 0 0 0 0 g 0 0 64 53 21 7 1 254 256 0 0 0 12 20 76 58 0 0 0 0 t 0 0 66 69 28 11 0 0 0 256 0 0 11 36 59 67 0 0 0 0
MA0141.1_shift0 (Esrrb)	0.889	0.555	9.310	0.553	0.925	1.123	0.944	3	4	4	4	4	3	3	3.571	1	; positions_6nt_m1 versus MA0141.1 (Esrrb); m=1/9; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 3.5714; rgsyCAAGGTCA-------- ; cor=0.889; Ncor=0.555; logoDP=9.310; NIcor=0.553; NsEucl=0.925; SSD=1.123; NSW=0.944; rcor=3; rNcor=4; rlogoDP=4; rNIcor=4; rNsEucl=4; rSSD=3; rNSW=3; rank_mean=3.571; match_rank=1 a 1054 673 420 259 310 3326 3567 32 21 182 9 3458 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 g 985 1370 1209 448 627 248 60 3586 3602 244 170 129 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
MA0258.2_shift6 (ESR2)	0.907	0.477	7.708	0.476	0.931	0.963	0.952	1	8	6	8	2	1	1	3.857	2	; positions_6nt_m1 versus MA0258.2 (ESR2); m=2/9; ncol2=15; w=10; offset=4; strand=D; shift=6; score= 3.8571; ------rGGTCAsmstGaCC ; cor=0.907; Ncor=0.477; logoDP=7.708; NIcor=0.476; NsEucl=0.931; SSD=0.963; NSW=0.952; rcor=1; rNcor=8; rlogoDP=6; rNIcor=8; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=3.857; match_rank=2 a 0 0 0 0 0 0 5410 429 59 74 0 8098 502 2092 1808 1602 1121 3278 434 1111 c 0 0 0 0 0 0 96 0 0 147 7621 1 4202 3235 2510 975 398 2056 6469 5854 g 0 0 0 0 0 0 2563 7170 8143 989 533 57 2738 1688 2173 533 6658 1391 363 0 t 0 0 0 0 0 0 174 644 41 7033 89 87 801 1228 1752 5133 66 1518 977 1278
MA0071.1_shift2 (RORA_1)	0.877	0.627	10.635	0.649	0.922	1.221	0.939	6	2	1	2	6	5	5	3.857	3	; positions_6nt_m1 versus MA0071.1 (RORA_1); m=3/9; ncol2=10; w=10; offset=0; strand=D; shift=2; score= 3.8571; --wwcwAGGTCA-------- ; cor=0.877; Ncor=0.627; logoDP=10.635; NIcor=0.649; NsEucl=0.922; SSD=1.221; NSW=0.939; rcor=6; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=6; rSSD=5; rNSW=5; rank_mean=3.857; match_rank=3 a 0 0 15 9 6 11 21 0 0 0 0 25 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 g 0 0 2 0 4 5 4 25 25 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
MA0141.2_shift0 (Esrrb)	0.888	0.555	9.423	0.552	0.925	1.134	0.943	4	5	3	5	5	4	4	4.286	4	; positions_6nt_m1 versus MA0141.2 (Esrrb); m=4/9; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 4.2857; rgsyCAAGGTCA-------- ; cor=0.888; Ncor=0.555; logoDP=9.423; NIcor=0.552; NsEucl=0.925; SSD=1.134; NSW=0.943; rcor=4; rNcor=5; rlogoDP=3; rNIcor=5; rNsEucl=5; rSSD=4; rNSW=4; rank_mean=4.286; match_rank=4 a 1055 673 403 260 312 3347 3590 33 12 180 9 3478 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 g 984 1352 1212 449 630 248 60 3597 3622 243 167 128 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
MA0112.1_shift4 (ESR1)	0.883	0.530	7.478	0.533	0.933	1.311	0.945	5	6	7	6	1	6	2	4.714	5	; positions_6nt_m1 versus MA0112.1 (ESR1); m=5/9; ncol2=18; w=12; offset=2; strand=D; shift=4; score= 4.7143; ----ccAGGTCaCcrtGrCC ; cor=0.883; Ncor=0.530; logoDP=7.478; NIcor=0.533; NsEucl=0.933; SSD=1.311; NSW=0.945; rcor=5; rNcor=6; rlogoDP=7; rNIcor=6; rNsEucl=1; rSSD=6; rNSW=2; rank_mean=4.714; match_rank=5 a 0 0 0 0 1 1 7 2 0 0 0 6 1 2 3 1 1 5 0 0 c 0 0 0 0 5 5 1 0 0 0 7 0 7 5 2 1 0 1 8 9 g 0 0 0 0 1 1 1 7 9 0 2 2 1 1 4 1 8 3 0 0 t 0 0 0 0 2 2 0 0 0 9 0 1 0 1 0 6 0 0 1 0
MA0592.1_shift3 (ESRRA)	0.864	0.679	9.939	0.661	0.920	1.542	0.930	7	1	2	1	7	7	8	4.714	6	; positions_6nt_m1 versus MA0592.1 (ESRRA); m=6/9; ncol2=11; w=11; offset=1; strand=D; shift=3; score= 4.7143; ---yCAAGGTCAcm------ ; cor=0.864; Ncor=0.679; logoDP=9.939; NIcor=0.661; NsEucl=0.920; SSD=1.542; NSW=0.930; rcor=7; rNcor=1; rlogoDP=2; rNIcor=1; rNsEucl=7; rSSD=7; rNSW=8; rank_mean=4.714; match_rank=6 a 0 0 0 17 18 200 198 0 0 6 0 197 23 70 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 g 0 0 0 11 15 6 10 203 207 22 3 10 44 40 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
MA0160.1_shift5 (NR4A2)	0.904	0.517	7.972	0.518	0.912	0.998	0.938	2	7	5	7	8	2	6	5.286	7	; positions_6nt_m1 versus MA0160.1 (NR4A2); m=7/9; ncol2=8; w=8; offset=3; strand=D; shift=5; score= 5.2857; -----aAGGTCAc------- ; cor=0.904; Ncor=0.517; logoDP=7.972; NIcor=0.518; NsEucl=0.912; SSD=0.998; NSW=0.938; rcor=2; rNcor=7; rlogoDP=5; rNIcor=7; rNsEucl=8; rSSD=2; rNSW=6; rank_mean=5.286; match_rank=7 a 0 0 0 0 0 8 13 0 3 2 0 14 3 0 0 0 0 0 0 0 c 0 0 0 0 0 1 0 0 0 2 13 0 8 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 t 0 0 0 0 0 1 0 1 0 10 1 0 0 0 0 0 0 0 0 0
MA0112.2_shift1 (ESR1)	0.821	0.574	4.608	0.557	0.929	1.952	0.930	8	3	9	3	3	8	7	5.857	8	; positions_6nt_m1 versus MA0112.2 (ESR1); m=8/9; ncol2=20; w=14; offset=-1; strand=D; shift=1; score= 5.8571; -vkscmaGGtCAcccTGaCC ; cor=0.821; Ncor=0.574; logoDP=4.608; NIcor=0.557; NsEucl=0.929; SSD=1.952; NSW=0.930; rcor=8; rNcor=3; rlogoDP=9; rNIcor=3; rNsEucl=3; rSSD=8; rNSW=7; rank_mean=5.857; match_rank=8 a 0 122 107 64 83 134 308 36 19 33 4 398 58 63 64 32 21 305 10 59 c 0 120 80 173 229 232 28 8 18 41 394 13 250 276 258 19 22 106 436 353 g 0 154 164 149 65 47 89 387 420 91 53 27 107 53 97 8 426 31 12 2 t 0 71 117 82 93 57 48 43 18 310 24 37 60 83 56 416 6 33 17 61
MA0258.1_shift4 (ESR2)	0.781	0.469	6.610	0.464	0.911	2.297	0.904	9	9	8	9	9	9	9	8.857	9	; positions_6nt_m1 versus MA0258.1 (ESR2); m=9/9; ncol2=18; w=12; offset=2; strand=D; shift=4; score= 8.8571; ----cwrGGTCAsgkTGmCC ; cor=0.781; Ncor=0.469; logoDP=6.610; NIcor=0.464; NsEucl=0.911; SSD=2.297; NSW=0.904; rcor=9; rNcor=9; rlogoDP=8; rNIcor=9; rNsEucl=9; rSSD=9; rNSW=9; rank_mean=8.857; match_rank=9 a 0 0 0 0 78 158 186 27 18 13 0 337 49 64 52 21 63 178 34 46 c 0 0 0 0 161 51 15 0 20 19 357 1 123 63 61 33 25 99 268 289 g 0 0 0 0 63 41 154 275 319 33 0 0 113 149 147 24 265 19 2 0 t 0 0 0 0 55 107 2 55 0 292 0 19 72 81 97 279 4 61 53 22