One-to-n alignments

Command: compare-matrices  -v 1 -format transfac -file $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -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/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab

One-to-n matrix alignment; reference matrix: dyads_m1_shift0 ; 2 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
dyads_m1_shift0 (dyads_m1)
; dyads_m1; m=0 (reference); ncol1=17; shift=0; ncol=17; ccGCCCCCCAGCCCCss ; Alignment reference a 2 6 3 5 0 2 0 0 0 18 1 0 0 2 1 4 5 c 13 11 0 19 22 23 24 25 24 3 3 24 21 22 25 8 8 g 6 5 23 0 2 1 2 1 2 3 22 1 2 1 0 10 9 t 5 4 0 2 2 0 0 0 0 2 0 1 3 1 0 4 4

dyads_m4_shift0 (dyads_m4) 0.843 0.843 9.410 0.827 0.937 2.270 0.933 3 1 3 1 1 3 1 1.857 1
; dyads_m1 versus dyads_m4; m=1/1; ncol2=17; w=17; offset=0; strand=D; shift=0; score= 1.8571; cyGCCCCCCCRCCCCsv ; cor=0.843; Ncor=0.843; logoDP=9.410; NIcor=0.827; NsEucl=0.937; SSD=2.270; NSW=0.933; rcor=3; rNcor=1; rlogoDP=3; rNIcor=1; rNsEucl=1; rSSD=3; rNSW=1; rank_mean=1.857; match_rank=1 a 1 1 2 0 1 1 2 1 0 1 14 0 0 2 1 3 5 c 11 8 2 18 16 15 16 18 19 17 0 18 19 17 18 6 7 g 4 3 13 1 2 2 0 0 0 1 5 0 0 0 0 6 5 t 3 7 2 0 0 1 1 0 0 0 0 1 0 0 0 4 2

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_m1_shift0 (dyads_m1)																		; dyads_m1; m=0 (reference); ncol1=17; shift=0; ncol=17; ccGCCCCCCAGCCCCss ; Alignment reference a 2 6 3 5 0 2 0 0 0 18 1 0 0 2 1 4 5 c 13 11 0 19 22 23 24 25 24 3 3 24 21 22 25 8 8 g 6 5 23 0 2 1 2 1 2 3 22 1 2 1 0 10 9 t 5 4 0 2 2 0 0 0 0 2 0 1 3 1 0 4 4
dyads_m4_shift0 (dyads_m4)		0.843	0.843	9.410	0.827	0.937	2.270	0.933	3	1	3	1	1	3	1	1.857	1	; dyads_m1 versus dyads_m4; m=1/1; ncol2=17; w=17; offset=0; strand=D; shift=0; score= 1.8571; cyGCCCCCCCRCCCCsv ; cor=0.843; Ncor=0.843; logoDP=9.410; NIcor=0.827; NsEucl=0.937; SSD=2.270; NSW=0.933; rcor=3; rNcor=1; rlogoDP=3; rNIcor=1; rNsEucl=1; rSSD=3; rNSW=1; rank_mean=1.857; match_rank=1 a 1 1 2 0 1 1 2 1 0 1 14 0 0 2 1 3 5 c 11 8 2 18 16 15 16 18 19 17 0 18 19 17 18 6 7 g 4 3 13 1 2 2 0 0 0 1 5 0 0 0 0 6 5 t 3 7 2 0 0 1 1 0 0 0 0 1 0 0 0 4 2

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 2 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
dyads_m2_shift0 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; wwTATTTTTATTTTWww ; Alignment reference a 26 26 2 86 4 1 2 7 1 92 1 2 0 1 67 32 30 c 11 11 4 3 0 0 2 0 3 1 2 0 0 1 2 7 9 g 7 12 1 6 0 2 0 4 0 1 1 0 2 2 3 16 17 t 54 49 91 3 94 95 94 87 94 4 94 96 96 94 26 43 42

oligos_7nt_mkv5_m1_shift1 (oligos_7nt_mkv5_m1) 0.850 0.600 10.415 0.563 0.917 2.007 0.916 2 3 1 3 2 2 3 2.286 2
; dyads_m2 versus oligos_7nt_mkv5_m1; m=1/1; ncol2=12; w=12; offset=1; strand=D; shift=1; score= 2.2857; -dtATTTTTAdww---- ; cor=0.850; Ncor=0.600; logoDP=10.415; NIcor=0.563; NsEucl=0.917; SSD=2.007; NSW=0.916; rcor=2; rNcor=3; rlogoDP=1; rNIcor=3; rNsEucl=2; rSSD=2; rNSW=3; rank_mean=2.286; match_rank=2 a 0 325 297 1277 0 0 0 0 0 1277 451 425 527 0 0 0 0 c 0 181 246 0 0 0 0 0 0 0 106 113 141 0 0 0 0 g 0 350 120 0 0 0 0 0 0 0 339 158 173 0 0 0 0 t 0 421 614 0 1277 1277 1277 1277 1277 0 381 581 436 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_m2_shift0 (dyads_m2)																		; dyads_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; wwTATTTTTATTTTWww ; Alignment reference a 26 26 2 86 4 1 2 7 1 92 1 2 0 1 67 32 30 c 11 11 4 3 0 0 2 0 3 1 2 0 0 1 2 7 9 g 7 12 1 6 0 2 0 4 0 1 1 0 2 2 3 16 17 t 54 49 91 3 94 95 94 87 94 4 94 96 96 94 26 43 42
oligos_7nt_mkv5_m1_shift1 (oligos_7nt_mkv5_m1)		0.850	0.600	10.415	0.563	0.917	2.007	0.916	2	3	1	3	2	2	3	2.286	2	; dyads_m2 versus oligos_7nt_mkv5_m1; m=1/1; ncol2=12; w=12; offset=1; strand=D; shift=1; score= 2.2857; -dtATTTTTAdww---- ; cor=0.850; Ncor=0.600; logoDP=10.415; NIcor=0.563; NsEucl=0.917; SSD=2.007; NSW=0.916; rcor=2; rNcor=3; rlogoDP=1; rNIcor=3; rNsEucl=2; rSSD=2; rNSW=3; rank_mean=2.286; match_rank=2 a 0 325 297 1277 0 0 0 0 0 1277 451 425 527 0 0 0 0 c 0 181 246 0 0 0 0 0 0 0 106 113 141 0 0 0 0 g 0 350 120 0 0 0 0 0 0 0 339 158 173 0 0 0 0 t 0 421 614 0 1277 1277 1277 1277 1277 0 381 581 436 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift3 ; 2 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_m3_shift3 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=11; shift=3; ncol=14; ---cyCTGTCTCwa ; Alignment reference a 0 0 0 101 91 8 8 9 11 4 12 4 253 409 c 0 0 0 459 305 766 142 1 3 780 0 785 124 126 g 0 0 0 87 90 13 13 779 4 3 20 0 88 128 t 0 0 0 142 303 2 626 0 771 2 757 0 324 126

oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5) 0.872 0.560 7.480 0.521 0.912 1.262 0.930 1 4 6 5 3 1 2 3.143 3
; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m5; m=1/1; ncol2=12; w=9; offset=-3; strand=D; shift=0; score= 3.1429; wsaCTCTGTCtc-- ; cor=0.872; Ncor=0.560; logoDP=7.480; NIcor=0.521; NsEucl=0.912; SSD=1.262; NSW=0.930; rcor=1; rNcor=4; rlogoDP=6; rNIcor=5; rNsEucl=3; rSSD=1; rNSW=2; rank_mean=3.143; match_rank=3 a 243 134 299 7 14 7 10 5 6 4 169 82 0 0 c 113 209 106 708 4 719 68 0 6 723 94 437 0 0 g 73 235 175 11 28 3 17 723 2 0 146 74 0 0 t 301 152 150 4 684 1 635 2 716 3 321 137 0 0

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_m3_shift3 (oligos_7nt_mkv5_m3)																		; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=11; shift=3; ncol=14; ---cyCTGTCTCwa ; Alignment reference a 0 0 0 101 91 8 8 9 11 4 12 4 253 409 c 0 0 0 459 305 766 142 1 3 780 0 785 124 126 g 0 0 0 87 90 13 13 779 4 3 20 0 88 128 t 0 0 0 142 303 2 626 0 771 2 757 0 324 126
oligos_7nt_mkv5_m5_shift0 (oligos_7nt_mkv5_m5)		0.872	0.560	7.480	0.521	0.912	1.262	0.930	1	4	6	5	3	1	2	3.143	3	; oligos_7nt_mkv5_m3 versus oligos_7nt_mkv5_m5; m=1/1; ncol2=12; w=9; offset=-3; strand=D; shift=0; score= 3.1429; wsaCTCTGTCtc-- ; cor=0.872; Ncor=0.560; logoDP=7.480; NIcor=0.521; NsEucl=0.912; SSD=1.262; NSW=0.930; rcor=1; rNcor=4; rlogoDP=6; rNIcor=5; rNsEucl=3; rSSD=1; rNSW=2; rank_mean=3.143; match_rank=3 a 243 134 299 7 14 7 10 5 6 4 169 82 0 0 c 113 209 106 708 4 719 68 0 6 723 94 437 0 0 g 73 235 175 11 28 3 17 723 2 0 146 74 0 0 t 301 152 150 4 684 1 635 2 716 3 321 137 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift0 ; 2 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_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; yyCTGCCTCmg ; Alignment reference a 136 100 1 20 14 7 1 13 2 315 114 c 256 419 890 62 1 865 869 1 890 252 202 g 133 118 2 27 877 1 21 30 0 162 401 t 368 256 0 784 1 20 2 849 1 164 176

oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3) 0.767 0.767 8.477 0.785 0.902 2.338 0.894 5 2 4 2 5 4 4 3.714 4
; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m3; m=1/1; ncol2=11; w=11; offset=0; strand=D; shift=0; score= 3.7143; cyCTGTCTCwa ; cor=0.767; Ncor=0.767; logoDP=8.477; NIcor=0.785; NsEucl=0.902; SSD=2.338; NSW=0.894; rcor=5; rNcor=2; rlogoDP=4; rNIcor=2; rNsEucl=5; rSSD=4; rNSW=4; rank_mean=3.714; match_rank=4 a 101 91 8 8 9 11 4 12 4 253 409 c 459 305 766 142 1 3 780 0 785 124 126 g 87 90 13 13 779 4 3 20 0 88 128 t 142 303 2 626 0 771 2 757 0 324 126

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_m2_shift0 (oligos_7nt_mkv5_m2)																		; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; yyCTGCCTCmg ; Alignment reference a 136 100 1 20 14 7 1 13 2 315 114 c 256 419 890 62 1 865 869 1 890 252 202 g 133 118 2 27 877 1 21 30 0 162 401 t 368 256 0 784 1 20 2 849 1 164 176
oligos_7nt_mkv5_m3_shift0 (oligos_7nt_mkv5_m3)		0.767	0.767	8.477	0.785	0.902	2.338	0.894	5	2	4	2	5	4	4	3.714	4	; oligos_7nt_mkv5_m2 versus oligos_7nt_mkv5_m3; m=1/1; ncol2=11; w=11; offset=0; strand=D; shift=0; score= 3.7143; cyCTGTCTCwa ; cor=0.767; Ncor=0.767; logoDP=8.477; NIcor=0.785; NsEucl=0.902; SSD=2.338; NSW=0.894; rcor=5; rNcor=2; rlogoDP=4; rNIcor=2; rNsEucl=5; rSSD=4; rNSW=4; rank_mean=3.714; match_rank=4 a 101 91 8 8 9 11 4 12 4 253 409 c 459 305 766 142 1 3 780 0 785 124 126 g 87 90 13 13 779 4 3 20 0 88 128 t 142 303 2 626 0 771 2 757 0 324 126

One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 2 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
dyads_m4_shift0 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=17; shift=0; ncol=17; cyGCCCCCCCRCCCCsv ; Alignment reference a 1 1 2 0 1 1 2 1 0 1 14 0 0 2 1 3 5 c 11 8 2 18 16 15 16 18 19 17 0 18 19 17 18 6 7 g 4 3 13 1 2 2 0 0 0 1 5 0 0 0 0 6 5 t 3 7 2 0 0 1 1 0 0 0 0 1 0 0 0 4 2

oligos_7nt_mkv5_m4_shift5 (oligos_7nt_mkv5_m4) 0.758 0.535 7.780 0.542 0.905 2.600 0.892 6 5 5 4 4 5 5 4.857 5
; dyads_m4 versus oligos_7nt_mkv5_m4; m=1/1; ncol2=12; w=12; offset=5; strand=D; shift=5; score= 4.8571; -----ccyCCACCTCss ; cor=0.758; Ncor=0.535; logoDP=7.780; NIcor=0.542; NsEucl=0.905; SSD=2.600; NSW=0.892; rcor=6; rNcor=5; rlogoDP=5; rNIcor=4; rNsEucl=4; rSSD=5; rNSW=5; rank_mean=4.857; match_rank=5 a 0 0 0 0 0 94 140 65 6 3 595 4 5 35 1 150 89 c 0 0 0 0 0 361 304 239 718 703 3 722 704 2 729 276 248 g 0 0 0 0 0 131 130 122 7 18 130 1 19 60 2 203 234 t 0 0 0 0 0 147 159 307 2 9 5 6 5 636 1 104 162

Matrix name	Aligned logos	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_m4_shift0 (dyads_m4)																		; dyads_m4; m=0 (reference); ncol1=17; shift=0; ncol=17; cyGCCCCCCCRCCCCsv ; Alignment reference a 1 1 2 0 1 1 2 1 0 1 14 0 0 2 1 3 5 c 11 8 2 18 16 15 16 18 19 17 0 18 19 17 18 6 7 g 4 3 13 1 2 2 0 0 0 1 5 0 0 0 0 6 5 t 3 7 2 0 0 1 1 0 0 0 0 1 0 0 0 4 2
oligos_7nt_mkv5_m4_shift5 (oligos_7nt_mkv5_m4)		0.758	0.535	7.780	0.542	0.905	2.600	0.892	6	5	5	4	4	5	5	4.857	5	; dyads_m4 versus oligos_7nt_mkv5_m4; m=1/1; ncol2=12; w=12; offset=5; strand=D; shift=5; score= 4.8571; -----ccyCCACCTCss ; cor=0.758; Ncor=0.535; logoDP=7.780; NIcor=0.542; NsEucl=0.905; SSD=2.600; NSW=0.892; rcor=6; rNcor=5; rlogoDP=5; rNIcor=4; rNsEucl=4; rSSD=5; rNSW=5; rank_mean=4.857; match_rank=5 a 0 0 0 0 0 94 140 65 6 3 595 4 5 35 1 150 89 c 0 0 0 0 0 361 304 239 718 703 3 722 704 2 729 276 248 g 0 0 0 0 0 131 130 122 7 18 130 1 19 60 2 203 234 t 0 0 0 0 0 147 159 307 2 9 5 6 5 636 1 104 162

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 2 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
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=21; shift=0; ncol=21; kmCCyCwGCCTyCCTCCTsCy ; Alignment reference a 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 2 3 3 1 3 0 0 3 3 0 2 3 3 0 3 3 0 1 3 1 g 1 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 2 0 0 t 2 0 0 0 2 0 2 0 0 0 3 1 0 0 3 0 0 3 0 0 2

oligos_7nt_mkv5_m2_shift3 (oligos_7nt_mkv5_m2) 0.771 0.404 9.694 0.376 0.891 2.852 0.870 4 6 2 6 6 6 6 5.143 6
; dyads_m3 versus oligos_7nt_mkv5_m2; m=1/1; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 5.1429; ---yyCTGCCTCmg------- ; cor=0.771; Ncor=0.404; logoDP=9.694; NIcor=0.376; NsEucl=0.891; SSD=2.852; NSW=0.870; rcor=4; rNcor=6; rlogoDP=2; rNIcor=6; rNsEucl=6; rSSD=6; rNSW=6; rank_mean=5.143; match_rank=6 a 0 0 0 136 100 1 20 14 7 1 13 2 315 114 0 0 0 0 0 0 0 c 0 0 0 256 419 890 62 1 865 869 1 890 252 202 0 0 0 0 0 0 0 g 0 0 0 133 118 2 27 877 1 21 30 0 162 401 0 0 0 0 0 0 0 t 0 0 0 368 256 0 784 1 20 2 849 1 164 176 0 0 0 0 0 0 0