One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2.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/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/oligos_6nt_mkv4_m2/peak-motifs_oligos_6nt_mkv4_m2_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift4 ; 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
oligos_6nt_mkv4_m2_shift4 (oligos_6nt_mkv4_m2)
; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=4; ncol=15; ----wwAAATTAtw- ; Alignment reference a 0 0 0 0 306 235 792 792 792 0 0 792 152 307 0 c 0 0 0 0 62 44 0 0 0 0 0 0 135 145 0 g 0 0 0 0 126 42 0 0 0 0 0 0 85 79 0 t 0 0 0 0 298 471 0 0 0 792 792 0 420 261 0

MA0075.1_shift7 (Prrx2) 0.998 0.499 8.498 0.498 0.979 0.021 0.998 1 4 1 1 1 1 1 1.429 1
; oligos_6nt_mkv4_m2 versus MA0075.1 (Prrx2); m=1/7; ncol2=5; w=5; offset=3; strand=D; shift=7; score= 1.4286; -------AATTA--- ; cor=0.998; Ncor=0.499; logoDP=8.498; NIcor=0.498; NsEucl=0.979; SSD=0.021; NSW=0.998; rcor=1; rNcor=4; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.429; match_rank=1 a 0 0 0 0 0 0 0 52 59 0 0 58 0 0 0 c 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 4 0 1 0 1 0 0 0 t 0 0 0 0 0 0 0 1 0 58 59 0 0 0 0

MA0132.1_rc_shift7 (Pdx1_rc) 0.897 0.538 0.052 -0.147 0.897 0.762 0.937 2 1 7 7 2 2 2 3.286 2
; oligos_6nt_mkv4_m2 versus MA0132.1_rc (Pdx1_rc); m=2/7; ncol2=6; w=6; offset=3; strand=R; shift=7; score= 3.2857; -------mATTAg-- ; cor=0.897; Ncor=0.538; logoDP=0.052; NIcor=-0.147; NsEucl=0.897; SSD=0.762; NSW=0.937; rcor=2; rNcor=1; rlogoDP=7; rNIcor=7; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=3.286; match_rank=2 a 0 0 0 0 0 0 0 19 30 0 0 31 6 0 0 c 0 0 0 0 0 0 0 10 1 0 0 0 5 0 0 g 0 0 0 0 0 0 0 1 0 0 0 0 19 0 0 t 0 0 0 0 0 0 0 1 0 31 31 0 1 0 0

MA0158.1_rc_shift7 (HOXA5_rc) 0.833 0.530 2.201 0.105 0.889 1.205 0.914 3 3 6 6 3 3 3 3.857 3
; oligos_6nt_mkv4_m2 versus MA0158.1_rc (HOXA5_rc); m=3/7; ncol2=8; w=7; offset=3; strand=R; shift=7; score= 3.8571; -------mATTwvhG ; cor=0.833; Ncor=0.530; logoDP=2.201; NIcor=0.105; NsEucl=0.889; SSD=1.205; NSW=0.914; rcor=3; rNcor=3; rlogoDP=6; rNIcor=6; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.857; match_rank=3 a 0 0 0 0 0 0 0 9 16 0 2 9 4 4 0 c 0 0 0 0 0 0 0 6 0 2 0 1 5 5 0 g 0 0 0 0 0 0 0 1 0 0 0 0 7 0 13 t 0 0 0 0 0 0 0 0 0 14 14 6 0 7 2

MA0135.1_shift6 (Lhx3) 0.798 0.426 8.113 0.399 0.880 1.851 0.884 4 7 2 4 5 5 4 4.429 4
; oligos_6nt_mkv4_m2 versus MA0135.1 (Lhx3); m=4/7; ncol2=13; w=8; offset=2; strand=D; shift=6; score= 4.4286; ------wAATTAATT ; cor=0.798; Ncor=0.426; logoDP=8.113; NIcor=0.399; NsEucl=0.880; SSD=1.851; NSW=0.884; rcor=4; rNcor=7; rlogoDP=2; rNIcor=4; rNsEucl=5; rSSD=5; rNSW=4; rank_mean=4.429; match_rank=4 a 0 0 0 0 0 0 9 16 19 0 0 19 20 2 0 c 0 0 0 0 0 0 0 2 0 0 0 0 0 2 1 g 0 0 0 0 0 0 3 2 0 0 0 0 0 0 0 t 0 0 0 0 0 0 8 0 1 20 20 1 0 16 19

MA0151.1_shift8 (ARID3A) 0.795 0.477 6.375 0.451 0.861 1.398 0.883 5 6 4 3 6 4 5 4.714 5
; oligos_6nt_mkv4_m2 versus MA0151.1 (ARID3A); m=5/7; ncol2=6; w=6; offset=4; strand=D; shift=8; score= 4.7143; --------ATyAAA- ; cor=0.795; Ncor=0.477; logoDP=6.375; NIcor=0.451; NsEucl=0.861; SSD=1.398; NSW=0.883; rcor=5; rNcor=6; rlogoDP=4; rNIcor=3; rNsEucl=6; rSSD=4; rNSW=5; rank_mean=4.714; match_rank=5 a 0 0 0 0 0 0 0 0 27 0 1 27 27 20 0 c 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 t 0 0 0 0 0 0 0 0 0 27 17 0 0 6 0

MA0485.1_shift0 (Hoxc9) 0.756 0.486 7.356 0.462 0.881 2.279 0.873 7 5 3 2 4 7 6 4.857 6
; oligos_6nt_mkv4_m2 versus MA0485.1 (Hoxc9); m=6/7; ncol2=13; w=9; offset=-4; strand=D; shift=0; score= 4.8571; rgCmATAAATCwy-- ; cor=0.756; Ncor=0.486; logoDP=7.356; NIcor=0.462; NsEucl=0.881; SSD=2.279; NSW=0.873; rcor=7; rNcor=5; rlogoDP=3; rNIcor=2; rNsEucl=4; rSSD=7; rNSW=6; rank_mean=4.857; match_rank=6 a 235 112 88 224 661 0 745 881 879 18 48 567 141 0 0 c 110 171 605 468 3 9 84 0 6 0 715 72 329 0 0 g 401 536 40 1 205 0 35 0 0 0 5 6 160 0 0 t 139 66 152 192 16 876 21 4 0 867 117 240 255 0 0

MA0063.1_rc_shift6 (Nkx2-5_rc) 0.765 0.536 2.977 0.115 0.860 1.910 0.864 6 2 5 5 7 6 7 5.429 7
; oligos_6nt_mkv4_m2 versus MA0063.1_rc (Nkx2-5_rc); m=7/7; ncol2=7; w=7; offset=2; strand=R; shift=6; score= 5.4286; ------camTTAw-- ; cor=0.765; Ncor=0.536; logoDP=2.977; NIcor=0.115; NsEucl=0.860; SSD=1.910; NSW=0.864; rcor=6; rNcor=2; rlogoDP=5; rNIcor=5; rNsEucl=7; rSSD=6; rNSW=7; rank_mean=5.429; match_rank=7 a 0 0 0 0 0 0 3 11 10 0 0 13 9 0 0 c 0 0 0 0 0 0 11 0 7 0 0 0 1 0 0 g 0 0 0 0 0 0 1 2 0 0 0 4 0 0 0 t 0 0 0 0 0 0 2 4 0 17 17 0 7 0 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_6nt_mkv4_m2_shift4 (oligos_6nt_mkv4_m2)																	; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=4; ncol=15; ----wwAAATTAtw- ; Alignment reference a 0 0 0 0 306 235 792 792 792 0 0 792 152 307 0 c 0 0 0 0 62 44 0 0 0 0 0 0 135 145 0 g 0 0 0 0 126 42 0 0 0 0 0 0 85 79 0 t 0 0 0 0 298 471 0 0 0 792 792 0 420 261 0
MA0075.1_shift7 (Prrx2)	0.998	0.499	8.498	0.498	0.979	0.021	0.998	1	4	1	1	1	1	1	1.429	1	; oligos_6nt_mkv4_m2 versus MA0075.1 (Prrx2); m=1/7; ncol2=5; w=5; offset=3; strand=D; shift=7; score= 1.4286; -------AATTA--- ; cor=0.998; Ncor=0.499; logoDP=8.498; NIcor=0.498; NsEucl=0.979; SSD=0.021; NSW=0.998; rcor=1; rNcor=4; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.429; match_rank=1 a 0 0 0 0 0 0 0 52 59 0 0 58 0 0 0 c 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 g 0 0 0 0 0 0 0 4 0 1 0 1 0 0 0 t 0 0 0 0 0 0 0 1 0 58 59 0 0 0 0
MA0132.1_rc_shift7 (Pdx1_rc)	0.897	0.538	0.052	-0.147	0.897	0.762	0.937	2	1	7	7	2	2	2	3.286	2	; oligos_6nt_mkv4_m2 versus MA0132.1_rc (Pdx1_rc); m=2/7; ncol2=6; w=6; offset=3; strand=R; shift=7; score= 3.2857; -------mATTAg-- ; cor=0.897; Ncor=0.538; logoDP=0.052; NIcor=-0.147; NsEucl=0.897; SSD=0.762; NSW=0.937; rcor=2; rNcor=1; rlogoDP=7; rNIcor=7; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=3.286; match_rank=2 a 0 0 0 0 0 0 0 19 30 0 0 31 6 0 0 c 0 0 0 0 0 0 0 10 1 0 0 0 5 0 0 g 0 0 0 0 0 0 0 1 0 0 0 0 19 0 0 t 0 0 0 0 0 0 0 1 0 31 31 0 1 0 0
MA0158.1_rc_shift7 (HOXA5_rc)	0.833	0.530	2.201	0.105	0.889	1.205	0.914	3	3	6	6	3	3	3	3.857	3	; oligos_6nt_mkv4_m2 versus MA0158.1_rc (HOXA5_rc); m=3/7; ncol2=8; w=7; offset=3; strand=R; shift=7; score= 3.8571; -------mATTwvhG ; cor=0.833; Ncor=0.530; logoDP=2.201; NIcor=0.105; NsEucl=0.889; SSD=1.205; NSW=0.914; rcor=3; rNcor=3; rlogoDP=6; rNIcor=6; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.857; match_rank=3 a 0 0 0 0 0 0 0 9 16 0 2 9 4 4 0 c 0 0 0 0 0 0 0 6 0 2 0 1 5 5 0 g 0 0 0 0 0 0 0 1 0 0 0 0 7 0 13 t 0 0 0 0 0 0 0 0 0 14 14 6 0 7 2
MA0135.1_shift6 (Lhx3)	0.798	0.426	8.113	0.399	0.880	1.851	0.884	4	7	2	4	5	5	4	4.429	4	; oligos_6nt_mkv4_m2 versus MA0135.1 (Lhx3); m=4/7; ncol2=13; w=8; offset=2; strand=D; shift=6; score= 4.4286; ------wAATTAATT ; cor=0.798; Ncor=0.426; logoDP=8.113; NIcor=0.399; NsEucl=0.880; SSD=1.851; NSW=0.884; rcor=4; rNcor=7; rlogoDP=2; rNIcor=4; rNsEucl=5; rSSD=5; rNSW=4; rank_mean=4.429; match_rank=4 a 0 0 0 0 0 0 9 16 19 0 0 19 20 2 0 c 0 0 0 0 0 0 0 2 0 0 0 0 0 2 1 g 0 0 0 0 0 0 3 2 0 0 0 0 0 0 0 t 0 0 0 0 0 0 8 0 1 20 20 1 0 16 19
MA0151.1_shift8 (ARID3A)	0.795	0.477	6.375	0.451	0.861	1.398	0.883	5	6	4	3	6	4	5	4.714	5	; oligos_6nt_mkv4_m2 versus MA0151.1 (ARID3A); m=5/7; ncol2=6; w=6; offset=4; strand=D; shift=8; score= 4.7143; --------ATyAAA- ; cor=0.795; Ncor=0.477; logoDP=6.375; NIcor=0.451; NsEucl=0.861; SSD=1.398; NSW=0.883; rcor=5; rNcor=6; rlogoDP=4; rNIcor=3; rNsEucl=6; rSSD=4; rNSW=5; rank_mean=4.714; match_rank=5 a 0 0 0 0 0 0 0 0 27 0 1 27 27 20 0 c 0 0 0 0 0 0 0 0 0 0 9 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 t 0 0 0 0 0 0 0 0 0 27 17 0 0 6 0
MA0485.1_shift0 (Hoxc9)	0.756	0.486	7.356	0.462	0.881	2.279	0.873	7	5	3	2	4	7	6	4.857	6	; oligos_6nt_mkv4_m2 versus MA0485.1 (Hoxc9); m=6/7; ncol2=13; w=9; offset=-4; strand=D; shift=0; score= 4.8571; rgCmATAAATCwy-- ; cor=0.756; Ncor=0.486; logoDP=7.356; NIcor=0.462; NsEucl=0.881; SSD=2.279; NSW=0.873; rcor=7; rNcor=5; rlogoDP=3; rNIcor=2; rNsEucl=4; rSSD=7; rNSW=6; rank_mean=4.857; match_rank=6 a 235 112 88 224 661 0 745 881 879 18 48 567 141 0 0 c 110 171 605 468 3 9 84 0 6 0 715 72 329 0 0 g 401 536 40 1 205 0 35 0 0 0 5 6 160 0 0 t 139 66 152 192 16 876 21 4 0 867 117 240 255 0 0
MA0063.1_rc_shift6 (Nkx2-5_rc)	0.765	0.536	2.977	0.115	0.860	1.910	0.864	6	2	5	5	7	6	7	5.429	7	; oligos_6nt_mkv4_m2 versus MA0063.1_rc (Nkx2-5_rc); m=7/7; ncol2=7; w=7; offset=2; strand=R; shift=6; score= 5.4286; ------camTTAw-- ; cor=0.765; Ncor=0.536; logoDP=2.977; NIcor=0.115; NsEucl=0.860; SSD=1.910; NSW=0.864; rcor=6; rNcor=2; rlogoDP=5; rNIcor=5; rNsEucl=7; rSSD=6; rNSW=7; rank_mean=5.429; match_rank=7 a 0 0 0 0 0 0 3 11 10 0 0 13 9 0 0 c 0 0 0 0 0 0 11 0 7 0 0 0 1 0 0 g 0 0 0 0 0 0 1 2 0 0 0 4 0 0 0 t 0 0 0 0 0 0 2 4 0 17 17 0 7 0 0