One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4.tf -format2 tf -file2 $RSAT/public_html/data/motif_databases/footprintDB/footprintDB.motif.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/2014/09/05/peak-motifs.2014-09-05.202657_2014-09-05.202657_8OTbPR/results/discovered_motifs/dyads_m4/peak-motifs_dyads_m4_vs_db_footprintDB

One-to-n matrix alignment; reference matrix: dyads_m4_shift7 ; 17 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_shift7 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=11; shift=7; ncol=18; -------ymTCCAGAccr ; Alignment reference a 0 0 0 0 0 0 0 5 11 0 0 0 37 0 37 1 9 12 c 0 0 0 0 0 0 0 12 11 0 37 37 0 0 0 22 15 6 g 0 0 0 0 0 0 0 7 6 0 0 0 0 37 0 8 4 12 t 0 0 0 0 0 0 0 13 9 37 0 0 0 0 0 6 9 7

1921_PB0060.1_JASPAR_CORE_2009__shift5 (1921_PB0060.1_JASPAR_CORE_2009_) 0.832 0.538 6.936 0.529 0.921 1.508 0.931 7 5 4 2 1 10 5 4.857 1
; dyads_m4 versus 1921_PB0060.1_JASPAR_CORE_2009_; m=1/16; ncol2=17; w=11; offset=-2; strand=D; shift=5; score= 4.8571; -----mdwatCCAGACrk ; cor=0.832; Ncor=0.538; logoDP=6.936; NIcor=0.529; NsEucl=0.921; SSD=1.508; NSW=0.931; rcor=7; rNcor=5; rlogoDP=4; rNIcor=2; rNsEucl=1; rSSD=10; rNSW=5; rank_mean=4.857; match_rank=1 a 0 0 0 0 0 28 34 40 37 24 3 0 93 1 97 1 67 13 c 0 0 0 0 0 41 14 17 20 18 81 82 6 0 2 98 1 17 g 0 0 0 0 0 11 27 17 21 22 4 4 1 99 0 0 28 33 t 0 0 0 0 0 19 26 26 23 35 13 14 0 0 1 0 4 36

3697_UP00000_UniPROBE_20120919__shift5 (3697_UP00000_UniPROBE_20120919_) 0.832 0.538 6.960 0.529 0.921 1.509 0.931 8 6 3 1 2 11 6 5.286 2
; dyads_m4 versus 3697_UP00000_UniPROBE_20120919_; m=2/16; ncol2=17; w=11; offset=-2; strand=D; shift=5; score= 5.2857; -----mdwawCCAGACrk ; cor=0.832; Ncor=0.538; logoDP=6.960; NIcor=0.529; NsEucl=0.921; SSD=1.509; NSW=0.931; rcor=8; rNcor=6; rlogoDP=3; rNIcor=1; rNsEucl=2; rSSD=11; rNSW=6; rank_mean=5.286; match_rank=2 a 0 0 0 0 0 29 34 40 37 25 3 0 0.93 0.01 0.97 0.01 67 13 c 0 0 0 0 0 41 14 17 20 18 81 0.82 0.06 0 0.02 0.98 1 17 g 0 0 0 0 0 11 26 17 21 22 4 0.04 0.01 0.99 0 0 28 34 t 0 0 0 0 0 19 26 26 22 35 12 0.14 0 0 0.01 0 4 36

2481_MA0092.1_JASPAR_CORE_2009__rc_shift7 (2481_MA0092.1_JASPAR_CORE_2009__rc) 0.846 0.769 3.725 0.338 0.918 1.359 0.932 4 1 10 9 4 9 4 5.857 3
; dyads_m4 versus 2481_MA0092.1_JASPAR_CORE_2009__rc; m=3/16; ncol2=10; w=10; offset=0; strand=R; shift=7; score= 5.8571; -------awkCCAGAys- ; cor=0.846; Ncor=0.769; logoDP=3.725; NIcor=0.338; NsEucl=0.918; SSD=1.359; NSW=0.932; rcor=4; rNcor=1; rlogoDP=10; rNIcor=9; rNsEucl=4; rSSD=9; rNSW=4; rank_mean=5.857; match_rank=3 a 0 0 0 0 0 0 0 16 10 5 1 0 29 1 24 4 7 0 c 0 0 0 0 0 0 0 4 3 1 25 29 0 0 1 15 10 0 g 0 0 0 0 0 0 0 4 0 14 3 0 0 28 2 0 8 0 t 0 0 0 0 0 0 0 5 16 9 0 0 0 0 2 10 4 0

7423_HAND1_si_HOCOMOCO_v9__rc_shift6 (7423_HAND1_si_HOCOMOCO_v9__rc) 0.860 0.717 0.284 -0.134 0.921 1.249 0.938 3 2 15 15 3 6 3 6.714 4
; dyads_m4 versus 7423_HAND1_si_HOCOMOCO_v9__rc; m=4/16; ncol2=11; w=10; offset=-1; strand=R; shift=6; score= 6.7143; ------aawkCCAGAyv- ; cor=0.860; Ncor=0.717; logoDP=0.284; NIcor=-0.134; NsEucl=0.921; SSD=1.249; NSW=0.938; rcor=3; rNcor=2; rlogoDP=15; rNIcor=15; rNsEucl=3; rSSD=6; rNSW=3; rank_mean=6.714; match_rank=4 a 0 0 0 0 0 0 13 14 10 5 1 0 26 0 23 1 7 0 c 0 0 0 0 0 0 4 4 2 1 23 26 0 1 1 15 9 0 g 0 0 0 0 0 0 5 3 1 11 2 0 0 25 2 0 9 0 t 0 0 0 0 0 0 4 5 13 9 0 0 0 0 0 10 1 0

1711_MA0152.1_JASPAR_CORE_2009__shift6 (1711_MA0152.1_JASPAR_CORE_2009_) 0.840 0.420 5.947 0.398 0.879 1.050 0.913 5 12 5 8 10 3 7 7.143 5
; dyads_m4 versus 1711_MA0152.1_JASPAR_CORE_2009_; m=5/16; ncol2=7; w=6; offset=-1; strand=D; shift=6; score= 7.1429; ------TTTTCCA----- ; cor=0.840; Ncor=0.420; logoDP=5.947; NIcor=0.398; NsEucl=0.879; SSD=1.050; NSW=0.913; rcor=5; rNcor=12; rlogoDP=5; rNIcor=8; rNsEucl=10; rSSD=3; rNSW=7; rank_mean=7.143; match_rank=5 a 0 0 0 0 0 0 3 1 1 0 1 0 18 0 0 0 0 0 c 0 0 0 0 0 0 1 2 1 0 25 26 3 0 0 0 0 0 g 0 0 0 0 0 0 2 2 0 0 0 0 1 0 0 0 0 0 t 0 0 0 0 0 0 20 21 24 26 0 0 4 0 0 0 0 0

6130_1imh_C_3D-footprint_20130124__rc_shift8 (6130_1imh_C_3D-footprint_20130124__rc) 0.918 0.417 0.358 -0.024 0.902 0.477 0.952 1 13 14 13 6 2 2 7.286 6
; dyads_m4 versus 6130_1imh_C_3D-footprint_20130124__rc; m=6/16; ncol2=5; w=5; offset=1; strand=R; shift=8; score= 7.2857; --------tTCCa----- ; cor=0.918; Ncor=0.417; logoDP=0.358; NIcor=-0.024; NsEucl=0.902; SSD=0.477; NSW=0.952; rcor=1; rNcor=13; rlogoDP=14; rNIcor=13; rNsEucl=6; rSSD=2; rNSW=2; rank_mean=7.286; match_rank=6 a 0 0 0 0 0 0 0 0 10 10 0 0 64 0 0 0 0 0 c 0 0 0 0 0 0 0 0 12 12 96 96 12 0 0 0 0 0 g 0 0 0 0 0 0 0 0 10 0 0 0 10 0 0 0 0 0 t 0 0 0 0 0 0 0 0 64 74 0 0 10 0 0 0 0 0

6074_1gji_A_3D-footprint_20130124__rc_shift8 (6074_1gji_A_3D-footprint_20130124__rc) 0.918 0.417 0.121 -0.063 0.902 0.477 0.952 2 14 16 14 5 1 1 7.571 7
; dyads_m4 versus 6074_1gji_A_3D-footprint_20130124__rc; m=7/16; ncol2=5; w=5; offset=1; strand=R; shift=8; score= 7.5714; --------kTCCr----- ; cor=0.918; Ncor=0.417; logoDP=0.121; NIcor=-0.063; NsEucl=0.902; SSD=0.477; NSW=0.952; rcor=2; rNcor=14; rlogoDP=16; rNIcor=14; rNsEucl=5; rSSD=1; rNSW=1; rank_mean=7.571; match_rank=7 a 0 0 0 0 0 0 0 0 12 0 0 0 48 0 0 0 0 0 c 0 0 0 0 0 0 0 0 12 0 96 96 12 0 0 0 0 0 g 0 0 0 0 0 0 0 0 24 0 0 0 24 0 0 0 0 0 t 0 0 0 0 0 0 0 0 48 96 0 0 12 0 0 0 0 0

7686_UBIP1_f1_HOCOMOCO_v9__shift11 (7686_UBIP1_f1_HOCOMOCO_v9_) 0.809 0.441 5.844 0.468 0.872 1.176 0.902 9 10 6 5 12 5 9 8.000 8
; dyads_m4 versus 7686_UBIP1_f1_HOCOMOCO_v9_; m=8/16; ncol2=6; w=6; offset=4; strand=D; shift=11; score= 8; -----------CAGArA- ; cor=0.809; Ncor=0.441; logoDP=5.844; NIcor=0.468; NsEucl=0.872; SSD=1.176; NSW=0.902; rcor=9; rNcor=10; rlogoDP=6; rNIcor=5; rNsEucl=12; rSSD=5; rNSW=9; rank_mean=8.000; match_rank=8 a 0 0 0 0 0 0 0 0 0 0 0 0 5 0 5 2 4 0 c 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 2 0 0 t 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 1 0

6322_1svc_P_3D-footprint_20130124__shift6 (6322_1svc_P_3D-footprint_20130124_) 0.805 0.402 5.817 0.403 0.877 1.092 0.909 10 16 7 7 11 4 8 9.000 9
; dyads_m4 versus 6322_1svc_P_3D-footprint_20130124_; m=9/16; ncol2=7; w=6; offset=-1; strand=D; shift=6; score= 9; ------gnnTCCc----- ; cor=0.805; Ncor=0.402; logoDP=5.817; NIcor=0.403; NsEucl=0.877; SSD=1.092; NSW=0.909; rcor=10; rNcor=16; rlogoDP=7; rNIcor=7; rNsEucl=11; rSSD=4; rNSW=8; rank_mean=9.000; match_rank=9 a 0 0 0 0 0 0 13 24 24 0 0 0 16 0 0 0 0 0 c 0 0 0 0 0 0 16 24 24 0 96 96 54 0 0 0 0 0 g 0 0 0 0 0 0 54 24 24 0 0 0 13 0 0 0 0 0 t 0 0 0 0 0 0 13 24 24 96 0 0 13 0 0 0 0 0

7623_SMAD4_si_HOCOMOCO_v9__rc_shift8 (7623_SMAD4_si_HOCOMOCO_v9__rc) 0.801 0.582 4.026 0.195 0.885 1.702 0.894 11 4 9 10 9 12 11 9.429 10
; dyads_m4 versus 7623_SMAD4_si_HOCOMOCO_v9__rc; m=10/16; ncol2=8; w=8; offset=1; strand=R; shift=8; score= 9.4286; --------rkmCAGAC-- ; cor=0.801; Ncor=0.582; logoDP=4.026; NIcor=0.195; NsEucl=0.885; SSD=1.702; NSW=0.894; rcor=11; rNcor=4; rlogoDP=9; rNIcor=10; rNsEucl=9; rSSD=12; rNSW=11; rank_mean=9.429; match_rank=10 a 0 0 0 0 0 0 0 0 25 5 22 0 78 0 76 1 0 0 c 0 0 0 0 0 0 0 0 10 9 31 65 0 0 0 71 0 0 g 0 0 0 0 0 0 0 0 33 44 17 0 0 78 2 6 0 0 t 0 0 0 0 0 0 0 0 10 20 8 13 0 0 0 0 0 0

7622_SMAD3_f1_HOCOMOCO_v9__rc_shift8 (7622_SMAD3_f1_HOCOMOCO_v9__rc) 0.782 0.640 2.851 0.185 0.893 1.848 0.897 12 3 11 11 8 13 10 9.714 11
; dyads_m4 versus 7622_SMAD3_f1_HOCOMOCO_v9__rc; m=11/16; ncol2=9; w=9; offset=1; strand=R; shift=8; score= 9.7143; --------rgcCAGACa- ; cor=0.782; Ncor=0.640; logoDP=2.851; NIcor=0.185; NsEucl=0.893; SSD=1.848; NSW=0.897; rcor=12; rNcor=3; rlogoDP=11; rNIcor=11; rNsEucl=8; rSSD=13; rNSW=10; rank_mean=9.714; match_rank=11 a 0 0 0 0 0 0 0 0 25 7 18 5 67 1 66 2 41 0 c 0 0 0 0 0 0 0 0 12 10 32 60 1 0 7 63 7 0 g 0 0 0 0 0 0 0 0 29 40 15 0 2 72 0 7 9 0 t 0 0 0 0 0 0 0 0 7 16 8 8 3 0 0 1 16 0

2553_MA0292.1_JASPAR_CORE_2009__shift8 (2553_MA0292.1_JASPAR_CORE_2009_) 0.765 0.487 6.968 0.500 0.860 1.933 0.862 14 7 2 3 15 14 15 10.000 12
; dyads_m4 versus 2553_MA0292.1_JASPAR_CORE_2009_; m=12/16; ncol2=7; w=7; offset=1; strand=D; shift=8; score= 10; --------hTCCGGA--- ; cor=0.765; Ncor=0.487; logoDP=6.968; NIcor=0.500; NsEucl=0.860; SSD=1.933; NSW=0.862; rcor=14; rNcor=7; rlogoDP=2; rNIcor=3; rNsEucl=15; rSSD=14; rNSW=15; rank_mean=10.000; match_rank=12 a 0 0 0 0 0 0 0 0 28 14 0 0 0 0 93 0 0 0 c 0 0 0 0 0 0 0 0 36 7 100 100 14 0 0 0 0 0 g 0 0 0 0 0 0 0 0 7 7 0 0 86 86 7 0 0 0 t 0 0 0 0 0 0 0 0 28 71 0 0 0 14 0 0 0 0

2742_PF0055.1_JASPAR_CORE_2009__rc_shift7 (2742_PF0055.1_JASPAR_CORE_2009__rc) 0.836 0.456 1.961 0.003 0.863 1.356 0.887 6 9 12 12 14 8 14 10.714 13
; dyads_m4 versus 2742_PF0055.1_JASPAR_CORE_2009__rc; m=13/16; ncol2=6; w=6; offset=0; strand=R; shift=7; score=10.7143; -------TTTCCA----- ; cor=0.836; Ncor=0.456; logoDP=1.961; NIcor=0.003; NsEucl=0.863; SSD=1.356; NSW=0.887; rcor=6; rNcor=9; rlogoDP=12; rNIcor=12; rNsEucl=14; rSSD=8; rNSW=14; rank_mean=10.714; match_rank=13 a 0 0 0 0 0 0 0 0 0 0 0 0 6612 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 6612 6612 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 6612 6612 6612 0 0 0 0 0 0 0 0

2532_MA0266.1_JASPAR_CORE_2009__shift8 (2532_MA0266.1_JASPAR_CORE_2009_) 0.757 0.482 7.967 0.486 0.854 2.095 0.850 16 8 1 4 16 15 16 10.857 14
; dyads_m4 versus 2532_MA0266.1_JASPAR_CORE_2009_; m=14/16; ncol2=7; w=7; offset=1; strand=D; shift=8; score=10.8571; --------sTCTAGA--- ; cor=0.757; Ncor=0.482; logoDP=7.967; NIcor=0.486; NsEucl=0.854; SSD=2.095; NSW=0.850; rcor=16; rNcor=8; rlogoDP=1; rNIcor=4; rNsEucl=16; rSSD=15; rNSW=16; rank_mean=10.857; match_rank=14 a 0 0 0 0 0 0 0 0 18 9 0 0 100 0 95 0 0 0 c 0 0 0 0 0 0 0 0 39 9 100 0 0 0 2 0 0 0 g 0 0 0 0 0 0 0 0 25 2 0 0 0 100 2 0 0 0 t 0 0 0 0 0 0 0 0 18 80 0 100 0 0 2 0 0 0

2487_MA0098.1_JASPAR_CORE_2009__shift7 (2487_MA0098.1_JASPAR_CORE_2009_) 0.761 0.415 5.191 0.426 0.863 1.355 0.887 15 15 8 6 13 7 13 11.000 15
; dyads_m4 versus 2487_MA0098.1_JASPAR_CORE_2009_; m=15/16; ncol2=6; w=6; offset=0; strand=D; shift=7; score= 11; -------ywTCCk----- ; cor=0.761; Ncor=0.415; logoDP=5.191; NIcor=0.426; NsEucl=0.863; SSD=1.355; NSW=0.887; rcor=15; rNcor=15; rlogoDP=8; rNIcor=6; rNsEucl=13; rSSD=7; rNSW=13; rank_mean=11.000; match_rank=15 a 0 0 0 0 0 0 0 4 17 0 0 0 5 0 0 0 0 0 c 0 0 0 0 0 0 0 16 0 1 39 39 3 0 0 0 0 0 g 0 0 0 0 0 0 0 4 0 0 1 0 17 0 0 0 0 0 t 0 0 0 0 0 0 0 16 23 39 0 1 15 0 0 0 0 0

2362_CN0199.1_JASPAR_CORE_2009__rc_shift0 (2362_CN0199.1_JASPAR_CORE_2009__rc) 0.775 0.431 0.369 -0.146 0.896 2.173 0.891 13 11 13 16 7 16 12 12.571 16
; dyads_m4 versus 2362_CN0199.1_JASPAR_CORE_2009__rc; m=16/16; ncol2=17; w=10; offset=-7; strand=R; shift=0; score=12.5714; CTGGAAATTTCCAgAGC- ; cor=0.775; Ncor=0.431; logoDP=0.369; NIcor=-0.146; NsEucl=0.896; SSD=2.173; NSW=0.891; rcor=13; rNcor=11; rlogoDP=13; rNIcor=16; rNsEucl=7; rSSD=16; rNSW=12; rank_mean=12.571; match_rank=16 a 8 11 1 6 77 77 68 14 1 0 0 3 71 19 68 2 7 0 c 64 2 0 1 0 2 2 4 2 5 81 77 0 10 3 1 66 0 g 9 0 80 70 4 2 7 0 4 3 0 1 0 45 5 63 7 0 t 0 68 0 4 0 0 4 63 74 73 0 0 10 7 5 15 1 0

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
dyads_m4_shift7 (dyads_m4)																	; dyads_m4; m=0 (reference); ncol1=11; shift=7; ncol=18; -------ymTCCAGAccr ; Alignment reference a 0 0 0 0 0 0 0 5 11 0 0 0 37 0 37 1 9 12 c 0 0 0 0 0 0 0 12 11 0 37 37 0 0 0 22 15 6 g 0 0 0 0 0 0 0 7 6 0 0 0 0 37 0 8 4 12 t 0 0 0 0 0 0 0 13 9 37 0 0 0 0 0 6 9 7
1921_PB0060.1_JASPAR_CORE_2009__shift5 (1921_PB0060.1_JASPAR_CORE_2009_)	0.832	0.538	6.936	0.529	0.921	1.508	0.931	7	5	4	2	1	10	5	4.857	1	; dyads_m4 versus 1921_PB0060.1_JASPAR_CORE_2009_; m=1/16; ncol2=17; w=11; offset=-2; strand=D; shift=5; score= 4.8571; -----mdwatCCAGACrk ; cor=0.832; Ncor=0.538; logoDP=6.936; NIcor=0.529; NsEucl=0.921; SSD=1.508; NSW=0.931; rcor=7; rNcor=5; rlogoDP=4; rNIcor=2; rNsEucl=1; rSSD=10; rNSW=5; rank_mean=4.857; match_rank=1 a 0 0 0 0 0 28 34 40 37 24 3 0 93 1 97 1 67 13 c 0 0 0 0 0 41 14 17 20 18 81 82 6 0 2 98 1 17 g 0 0 0 0 0 11 27 17 21 22 4 4 1 99 0 0 28 33 t 0 0 0 0 0 19 26 26 23 35 13 14 0 0 1 0 4 36
3697_UP00000_UniPROBE_20120919__shift5 (3697_UP00000_UniPROBE_20120919_)	0.832	0.538	6.960	0.529	0.921	1.509	0.931	8	6	3	1	2	11	6	5.286	2	; dyads_m4 versus 3697_UP00000_UniPROBE_20120919_; m=2/16; ncol2=17; w=11; offset=-2; strand=D; shift=5; score= 5.2857; -----mdwawCCAGACrk ; cor=0.832; Ncor=0.538; logoDP=6.960; NIcor=0.529; NsEucl=0.921; SSD=1.509; NSW=0.931; rcor=8; rNcor=6; rlogoDP=3; rNIcor=1; rNsEucl=2; rSSD=11; rNSW=6; rank_mean=5.286; match_rank=2 a 0 0 0 0 0 29 34 40 37 25 3 0 0.93 0.01 0.97 0.01 67 13 c 0 0 0 0 0 41 14 17 20 18 81 0.82 0.06 0 0.02 0.98 1 17 g 0 0 0 0 0 11 26 17 21 22 4 0.04 0.01 0.99 0 0 28 34 t 0 0 0 0 0 19 26 26 22 35 12 0.14 0 0 0.01 0 4 36
2481_MA0092.1_JASPAR_CORE_2009__rc_shift7 (2481_MA0092.1_JASPAR_CORE_2009__rc)	0.846	0.769	3.725	0.338	0.918	1.359	0.932	4	1	10	9	4	9	4	5.857	3	; dyads_m4 versus 2481_MA0092.1_JASPAR_CORE_2009__rc; m=3/16; ncol2=10; w=10; offset=0; strand=R; shift=7; score= 5.8571; -------awkCCAGAys- ; cor=0.846; Ncor=0.769; logoDP=3.725; NIcor=0.338; NsEucl=0.918; SSD=1.359; NSW=0.932; rcor=4; rNcor=1; rlogoDP=10; rNIcor=9; rNsEucl=4; rSSD=9; rNSW=4; rank_mean=5.857; match_rank=3 a 0 0 0 0 0 0 0 16 10 5 1 0 29 1 24 4 7 0 c 0 0 0 0 0 0 0 4 3 1 25 29 0 0 1 15 10 0 g 0 0 0 0 0 0 0 4 0 14 3 0 0 28 2 0 8 0 t 0 0 0 0 0 0 0 5 16 9 0 0 0 0 2 10 4 0
7423_HAND1_si_HOCOMOCO_v9__rc_shift6 (7423_HAND1_si_HOCOMOCO_v9__rc)	0.860	0.717	0.284	-0.134	0.921	1.249	0.938	3	2	15	15	3	6	3	6.714	4	; dyads_m4 versus 7423_HAND1_si_HOCOMOCO_v9__rc; m=4/16; ncol2=11; w=10; offset=-1; strand=R; shift=6; score= 6.7143; ------aawkCCAGAyv- ; cor=0.860; Ncor=0.717; logoDP=0.284; NIcor=-0.134; NsEucl=0.921; SSD=1.249; NSW=0.938; rcor=3; rNcor=2; rlogoDP=15; rNIcor=15; rNsEucl=3; rSSD=6; rNSW=3; rank_mean=6.714; match_rank=4 a 0 0 0 0 0 0 13 14 10 5 1 0 26 0 23 1 7 0 c 0 0 0 0 0 0 4 4 2 1 23 26 0 1 1 15 9 0 g 0 0 0 0 0 0 5 3 1 11 2 0 0 25 2 0 9 0 t 0 0 0 0 0 0 4 5 13 9 0 0 0 0 0 10 1 0
1711_MA0152.1_JASPAR_CORE_2009__shift6 (1711_MA0152.1_JASPAR_CORE_2009_)	0.840	0.420	5.947	0.398	0.879	1.050	0.913	5	12	5	8	10	3	7	7.143	5	; dyads_m4 versus 1711_MA0152.1_JASPAR_CORE_2009_; m=5/16; ncol2=7; w=6; offset=-1; strand=D; shift=6; score= 7.1429; ------TTTTCCA----- ; cor=0.840; Ncor=0.420; logoDP=5.947; NIcor=0.398; NsEucl=0.879; SSD=1.050; NSW=0.913; rcor=5; rNcor=12; rlogoDP=5; rNIcor=8; rNsEucl=10; rSSD=3; rNSW=7; rank_mean=7.143; match_rank=5 a 0 0 0 0 0 0 3 1 1 0 1 0 18 0 0 0 0 0 c 0 0 0 0 0 0 1 2 1 0 25 26 3 0 0 0 0 0 g 0 0 0 0 0 0 2 2 0 0 0 0 1 0 0 0 0 0 t 0 0 0 0 0 0 20 21 24 26 0 0 4 0 0 0 0 0
6130_1imh_C_3D-footprint_20130124__rc_shift8 (6130_1imh_C_3D-footprint_20130124__rc)	0.918	0.417	0.358	-0.024	0.902	0.477	0.952	1	13	14	13	6	2	2	7.286	6	; dyads_m4 versus 6130_1imh_C_3D-footprint_20130124__rc; m=6/16; ncol2=5; w=5; offset=1; strand=R; shift=8; score= 7.2857; --------tTCCa----- ; cor=0.918; Ncor=0.417; logoDP=0.358; NIcor=-0.024; NsEucl=0.902; SSD=0.477; NSW=0.952; rcor=1; rNcor=13; rlogoDP=14; rNIcor=13; rNsEucl=6; rSSD=2; rNSW=2; rank_mean=7.286; match_rank=6 a 0 0 0 0 0 0 0 0 10 10 0 0 64 0 0 0 0 0 c 0 0 0 0 0 0 0 0 12 12 96 96 12 0 0 0 0 0 g 0 0 0 0 0 0 0 0 10 0 0 0 10 0 0 0 0 0 t 0 0 0 0 0 0 0 0 64 74 0 0 10 0 0 0 0 0
6074_1gji_A_3D-footprint_20130124__rc_shift8 (6074_1gji_A_3D-footprint_20130124__rc)	0.918	0.417	0.121	-0.063	0.902	0.477	0.952	2	14	16	14	5	1	1	7.571	7	; dyads_m4 versus 6074_1gji_A_3D-footprint_20130124__rc; m=7/16; ncol2=5; w=5; offset=1; strand=R; shift=8; score= 7.5714; --------kTCCr----- ; cor=0.918; Ncor=0.417; logoDP=0.121; NIcor=-0.063; NsEucl=0.902; SSD=0.477; NSW=0.952; rcor=2; rNcor=14; rlogoDP=16; rNIcor=14; rNsEucl=5; rSSD=1; rNSW=1; rank_mean=7.571; match_rank=7 a 0 0 0 0 0 0 0 0 12 0 0 0 48 0 0 0 0 0 c 0 0 0 0 0 0 0 0 12 0 96 96 12 0 0 0 0 0 g 0 0 0 0 0 0 0 0 24 0 0 0 24 0 0 0 0 0 t 0 0 0 0 0 0 0 0 48 96 0 0 12 0 0 0 0 0
7686_UBIP1_f1_HOCOMOCO_v9__shift11 (7686_UBIP1_f1_HOCOMOCO_v9_)	0.809	0.441	5.844	0.468	0.872	1.176	0.902	9	10	6	5	12	5	9	8.000	8	; dyads_m4 versus 7686_UBIP1_f1_HOCOMOCO_v9_; m=8/16; ncol2=6; w=6; offset=4; strand=D; shift=11; score= 8; -----------CAGArA- ; cor=0.809; Ncor=0.441; logoDP=5.844; NIcor=0.468; NsEucl=0.872; SSD=1.176; NSW=0.902; rcor=9; rNcor=10; rlogoDP=6; rNIcor=5; rNsEucl=12; rSSD=5; rNSW=9; rank_mean=8.000; match_rank=8 a 0 0 0 0 0 0 0 0 0 0 0 0 5 0 5 2 4 0 c 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 2 0 0 t 0 0 0 0 0 0 0 0 0 0 0 1 0 1 0 1 1 0
6322_1svc_P_3D-footprint_20130124__shift6 (6322_1svc_P_3D-footprint_20130124_)	0.805	0.402	5.817	0.403	0.877	1.092	0.909	10	16	7	7	11	4	8	9.000	9	; dyads_m4 versus 6322_1svc_P_3D-footprint_20130124_; m=9/16; ncol2=7; w=6; offset=-1; strand=D; shift=6; score= 9; ------gnnTCCc----- ; cor=0.805; Ncor=0.402; logoDP=5.817; NIcor=0.403; NsEucl=0.877; SSD=1.092; NSW=0.909; rcor=10; rNcor=16; rlogoDP=7; rNIcor=7; rNsEucl=11; rSSD=4; rNSW=8; rank_mean=9.000; match_rank=9 a 0 0 0 0 0 0 13 24 24 0 0 0 16 0 0 0 0 0 c 0 0 0 0 0 0 16 24 24 0 96 96 54 0 0 0 0 0 g 0 0 0 0 0 0 54 24 24 0 0 0 13 0 0 0 0 0 t 0 0 0 0 0 0 13 24 24 96 0 0 13 0 0 0 0 0
7623_SMAD4_si_HOCOMOCO_v9__rc_shift8 (7623_SMAD4_si_HOCOMOCO_v9__rc)	0.801	0.582	4.026	0.195	0.885	1.702	0.894	11	4	9	10	9	12	11	9.429	10	; dyads_m4 versus 7623_SMAD4_si_HOCOMOCO_v9__rc; m=10/16; ncol2=8; w=8; offset=1; strand=R; shift=8; score= 9.4286; --------rkmCAGAC-- ; cor=0.801; Ncor=0.582; logoDP=4.026; NIcor=0.195; NsEucl=0.885; SSD=1.702; NSW=0.894; rcor=11; rNcor=4; rlogoDP=9; rNIcor=10; rNsEucl=9; rSSD=12; rNSW=11; rank_mean=9.429; match_rank=10 a 0 0 0 0 0 0 0 0 25 5 22 0 78 0 76 1 0 0 c 0 0 0 0 0 0 0 0 10 9 31 65 0 0 0 71 0 0 g 0 0 0 0 0 0 0 0 33 44 17 0 0 78 2 6 0 0 t 0 0 0 0 0 0 0 0 10 20 8 13 0 0 0 0 0 0
7622_SMAD3_f1_HOCOMOCO_v9__rc_shift8 (7622_SMAD3_f1_HOCOMOCO_v9__rc)	0.782	0.640	2.851	0.185	0.893	1.848	0.897	12	3	11	11	8	13	10	9.714	11	; dyads_m4 versus 7622_SMAD3_f1_HOCOMOCO_v9__rc; m=11/16; ncol2=9; w=9; offset=1; strand=R; shift=8; score= 9.7143; --------rgcCAGACa- ; cor=0.782; Ncor=0.640; logoDP=2.851; NIcor=0.185; NsEucl=0.893; SSD=1.848; NSW=0.897; rcor=12; rNcor=3; rlogoDP=11; rNIcor=11; rNsEucl=8; rSSD=13; rNSW=10; rank_mean=9.714; match_rank=11 a 0 0 0 0 0 0 0 0 25 7 18 5 67 1 66 2 41 0 c 0 0 0 0 0 0 0 0 12 10 32 60 1 0 7 63 7 0 g 0 0 0 0 0 0 0 0 29 40 15 0 2 72 0 7 9 0 t 0 0 0 0 0 0 0 0 7 16 8 8 3 0 0 1 16 0
2553_MA0292.1_JASPAR_CORE_2009__shift8 (2553_MA0292.1_JASPAR_CORE_2009_)	0.765	0.487	6.968	0.500	0.860	1.933	0.862	14	7	2	3	15	14	15	10.000	12	; dyads_m4 versus 2553_MA0292.1_JASPAR_CORE_2009_; m=12/16; ncol2=7; w=7; offset=1; strand=D; shift=8; score= 10; --------hTCCGGA--- ; cor=0.765; Ncor=0.487; logoDP=6.968; NIcor=0.500; NsEucl=0.860; SSD=1.933; NSW=0.862; rcor=14; rNcor=7; rlogoDP=2; rNIcor=3; rNsEucl=15; rSSD=14; rNSW=15; rank_mean=10.000; match_rank=12 a 0 0 0 0 0 0 0 0 28 14 0 0 0 0 93 0 0 0 c 0 0 0 0 0 0 0 0 36 7 100 100 14 0 0 0 0 0 g 0 0 0 0 0 0 0 0 7 7 0 0 86 86 7 0 0 0 t 0 0 0 0 0 0 0 0 28 71 0 0 0 14 0 0 0 0
2742_PF0055.1_JASPAR_CORE_2009__rc_shift7 (2742_PF0055.1_JASPAR_CORE_2009__rc)	0.836	0.456	1.961	0.003	0.863	1.356	0.887	6	9	12	12	14	8	14	10.714	13	; dyads_m4 versus 2742_PF0055.1_JASPAR_CORE_2009__rc; m=13/16; ncol2=6; w=6; offset=0; strand=R; shift=7; score=10.7143; -------TTTCCA----- ; cor=0.836; Ncor=0.456; logoDP=1.961; NIcor=0.003; NsEucl=0.863; SSD=1.356; NSW=0.887; rcor=6; rNcor=9; rlogoDP=12; rNIcor=12; rNsEucl=14; rSSD=8; rNSW=14; rank_mean=10.714; match_rank=13 a 0 0 0 0 0 0 0 0 0 0 0 0 6612 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 6612 6612 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 6612 6612 6612 0 0 0 0 0 0 0 0
2532_MA0266.1_JASPAR_CORE_2009__shift8 (2532_MA0266.1_JASPAR_CORE_2009_)	0.757	0.482	7.967	0.486	0.854	2.095	0.850	16	8	1	4	16	15	16	10.857	14	; dyads_m4 versus 2532_MA0266.1_JASPAR_CORE_2009_; m=14/16; ncol2=7; w=7; offset=1; strand=D; shift=8; score=10.8571; --------sTCTAGA--- ; cor=0.757; Ncor=0.482; logoDP=7.967; NIcor=0.486; NsEucl=0.854; SSD=2.095; NSW=0.850; rcor=16; rNcor=8; rlogoDP=1; rNIcor=4; rNsEucl=16; rSSD=15; rNSW=16; rank_mean=10.857; match_rank=14 a 0 0 0 0 0 0 0 0 18 9 0 0 100 0 95 0 0 0 c 0 0 0 0 0 0 0 0 39 9 100 0 0 0 2 0 0 0 g 0 0 0 0 0 0 0 0 25 2 0 0 0 100 2 0 0 0 t 0 0 0 0 0 0 0 0 18 80 0 100 0 0 2 0 0 0
2487_MA0098.1_JASPAR_CORE_2009__shift7 (2487_MA0098.1_JASPAR_CORE_2009_)	0.761	0.415	5.191	0.426	0.863	1.355	0.887	15	15	8	6	13	7	13	11.000	15	; dyads_m4 versus 2487_MA0098.1_JASPAR_CORE_2009_; m=15/16; ncol2=6; w=6; offset=0; strand=D; shift=7; score= 11; -------ywTCCk----- ; cor=0.761; Ncor=0.415; logoDP=5.191; NIcor=0.426; NsEucl=0.863; SSD=1.355; NSW=0.887; rcor=15; rNcor=15; rlogoDP=8; rNIcor=6; rNsEucl=13; rSSD=7; rNSW=13; rank_mean=11.000; match_rank=15 a 0 0 0 0 0 0 0 4 17 0 0 0 5 0 0 0 0 0 c 0 0 0 0 0 0 0 16 0 1 39 39 3 0 0 0 0 0 g 0 0 0 0 0 0 0 4 0 0 1 0 17 0 0 0 0 0 t 0 0 0 0 0 0 0 16 23 39 0 1 15 0 0 0 0 0
2362_CN0199.1_JASPAR_CORE_2009__rc_shift0 (2362_CN0199.1_JASPAR_CORE_2009__rc)	0.775	0.431	0.369	-0.146	0.896	2.173	0.891	13	11	13	16	7	16	12	12.571	16	; dyads_m4 versus 2362_CN0199.1_JASPAR_CORE_2009__rc; m=16/16; ncol2=17; w=10; offset=-7; strand=R; shift=0; score=12.5714; CTGGAAATTTCCAgAGC- ; cor=0.775; Ncor=0.431; logoDP=0.369; NIcor=-0.146; NsEucl=0.896; SSD=2.173; NSW=0.891; rcor=13; rNcor=11; rlogoDP=13; rNIcor=16; rNsEucl=7; rSSD=16; rNSW=12; rank_mean=12.571; match_rank=16 a 8 11 1 6 77 77 68 14 1 0 0 3 71 19 68 2 7 0 c 64 2 0 1 0 2 2 4 2 5 81 77 0 10 3 1 66 0 g 9 0 80 70 4 2 7 0 4 3 0 1 0 45 5 63 7 0 t 0 68 0 4 0 0 4 63 74 73 0 0 10 7 5 15 1 0