One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_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/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_vs_db_jaspar_core_vertebrates

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift1 ; 7 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_m1_shift1 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -wkATTGCACAAywh ; Alignment reference a 0 1173 857 3161 3 5 52 3 4369 17 4506 4512 149 1831 1226 c 0 816 719 307 3 4 3 4509 16 4467 9 3 2623 988 1193 g 0 861 1532 915 4 3 4418 2 107 5 4 3 337 502 930 t 0 1671 1413 138 4511 4509 48 7 29 32 2 3 1412 1200 1172

MA0102.3_shift3 (CEBPA) 0.947 0.744 10.183 0.730 0.946 0.701 0.968 1 1 1 1 1 1 1 1.000 1
; oligos_7nt_mkv5_m1 versus MA0102.3 (CEBPA); m=1/6; ncol2=11; w=11; offset=2; strand=D; shift=3; score= 1; ---aTTGCAyAAym- ; cor=0.947; Ncor=0.744; logoDP=10.183; NIcor=0.730; NsEucl=0.946; SSD=0.701; NSW=0.968; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0

MA0466.1_shift2 (CEBPB) 0.919 0.722 9.948 0.704 0.936 0.995 0.955 2 2 2 2 2 3 2 2.143 2
; oligos_7nt_mkv5_m1 versus MA0466.1 (CEBPB); m=2/6; ncol2=11; w=11; offset=1; strand=D; shift=2; score= 2.1429; --kATTGCAymAy-- ; cor=0.919; Ncor=0.722; logoDP=9.948; NIcor=0.704; NsEucl=0.936; SSD=0.995; NSW=0.955; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=3; rNSW=2; rank_mean=2.143; match_rank=2 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0

MA0133.1_shift8 (BRCA1) 0.841 0.421 3.257 0.425 0.903 0.920 0.934 3 5 3 3 4 2 3 3.286 3
; oligos_7nt_mkv5_m1 versus MA0133.1 (BRCA1); m=3/6; ncol2=7; w=7; offset=7; strand=D; shift=8; score= 3.2857; --------mCAAcms ; cor=0.841; Ncor=0.421; logoDP=3.257; NIcor=0.425; NsEucl=0.903; SSD=0.920; NSW=0.934; rcor=3; rNcor=5; rlogoDP=3; rNIcor=3; rNsEucl=4; rSSD=2; rNSW=3; rank_mean=3.286; match_rank=3 a 0 0 0 0 0 0 0 0 15 4 41 36 7 19 3 c 0 0 0 0 0 0 0 0 11 35 1 2 29 14 22 g 0 0 0 0 0 0 0 0 10 2 1 4 6 7 15 t 0 0 0 0 0 0 0 0 7 2 0 1 1 3 3

MA0102.2_rc_shift3 (CEBPA_rc) 0.838 0.539 2.636 0.051 0.891 1.910 0.894 4 4 4 5 5 5 5 4.571 4
; oligos_7nt_mkv5_m1 versus MA0102.2_rc (CEBPA_rc); m=4/6; ncol2=9; w=9; offset=2; strand=R; shift=3; score= 4.5714; ---rTTGcrmaA--- ; cor=0.838; Ncor=0.539; logoDP=2.636; NIcor=0.051; NsEucl=0.891; SSD=1.910; NSW=0.894; rcor=4; rNcor=4; rlogoDP=4; rNIcor=5; rNsEucl=5; rSSD=5; rNSW=5; rank_mean=4.571; match_rank=4 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0

MA0102.1_rc_shift0 (Cebpa_rc) 0.824 0.604 0.206 -0.158 0.908 2.040 0.907 5 3 6 6 3 6 4 4.714 5
; oligos_7nt_mkv5_m1 versus MA0102.1_rc (Cebpa_rc); m=5/6; ncol2=12; w=11; offset=-1; strand=R; shift=0; score= 4.7143; vrbrTTGcrmaA--- ; cor=0.824; Ncor=0.604; logoDP=0.206; NIcor=-0.158; NsEucl=0.908; SSD=2.040; NSW=0.907; rcor=5; rNcor=3; rlogoDP=6; rNIcor=6; rNsEucl=3; rSSD=6; rNSW=4; rank_mean=4.714; match_rank=5 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0

MA0078.1_rc_shift7 (Sox17_rc) 0.758 0.405 2.129 0.068 0.879 1.876 0.883 6 6 5 4 6 4 6 5.286 6
; oligos_7nt_mkv5_m1 versus MA0078.1_rc (Sox17_rc); m=6/6; ncol2=9; w=8; offset=6; strand=R; shift=7; score= 5.2857; -------sACAATrd ; cor=0.758; Ncor=0.405; logoDP=2.129; NIcor=0.068; NsEucl=0.879; SSD=1.876; NSW=0.883; rcor=6; rNcor=6; rlogoDP=5; rNIcor=4; rNsEucl=6; rSSD=4; rNSW=6; rank_mean=5.286; match_rank=6 a 0 0 0 0 0 0 0 4 29 0 31 30 1 9 11 c 0 0 0 0 0 0 0 10 2 31 0 0 0 1 4 g 0 0 0 0 0 0 0 17 0 0 0 1 0 18 8 t 0 0 0 0 0 0 0 0 0 0 0 0 30 3 8

Matrix name	cor	Ncor	logoDP	NIcor	NsEucl	SSD	NSW	rcor	rNcor	rlogoDP	rNIcor	rNsEucl	rSSD	rNSW	rank_mean	match_rank	Aligned matrices
oligos_7nt_mkv5_m1_shift1 (oligos_7nt_mkv5_m1)																	; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=14; shift=1; ncol=15; -wkATTGCACAAywh ; Alignment reference a 0 1173 857 3161 3 5 52 3 4369 17 4506 4512 149 1831 1226 c 0 816 719 307 3 4 3 4509 16 4467 9 3 2623 988 1193 g 0 861 1532 915 4 3 4418 2 107 5 4 3 337 502 930 t 0 1671 1413 138 4511 4509 48 7 29 32 2 3 1412 1200 1172
MA0102.3_shift3 (CEBPA)	0.947	0.744	10.183	0.730	0.946	0.701	0.968	1	1	1	1	1	1	1	1.000	1	; oligos_7nt_mkv5_m1 versus MA0102.3 (CEBPA); m=1/6; ncol2=11; w=11; offset=2; strand=D; shift=3; score= 1; ---aTTGCAyAAym- ; cor=0.947; Ncor=0.744; logoDP=10.183; NIcor=0.730; NsEucl=0.946; SSD=0.701; NSW=0.968; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1 a 0 0 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0
MA0466.1_shift2 (CEBPB)	0.919	0.722	9.948	0.704	0.936	0.995	0.955	2	2	2	2	2	3	2	2.143	2	; oligos_7nt_mkv5_m1 versus MA0466.1 (CEBPB); m=2/6; ncol2=11; w=11; offset=1; strand=D; shift=2; score= 2.1429; --kATTGCAymAy-- ; cor=0.919; Ncor=0.722; logoDP=9.948; NIcor=0.704; NsEucl=0.936; SSD=0.995; NSW=0.955; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=3; rNSW=2; rank_mean=2.143; match_rank=2 a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0
MA0133.1_shift8 (BRCA1)	0.841	0.421	3.257	0.425	0.903	0.920	0.934	3	5	3	3	4	2	3	3.286	3	; oligos_7nt_mkv5_m1 versus MA0133.1 (BRCA1); m=3/6; ncol2=7; w=7; offset=7; strand=D; shift=8; score= 3.2857; --------mCAAcms ; cor=0.841; Ncor=0.421; logoDP=3.257; NIcor=0.425; NsEucl=0.903; SSD=0.920; NSW=0.934; rcor=3; rNcor=5; rlogoDP=3; rNIcor=3; rNsEucl=4; rSSD=2; rNSW=3; rank_mean=3.286; match_rank=3 a 0 0 0 0 0 0 0 0 15 4 41 36 7 19 3 c 0 0 0 0 0 0 0 0 11 35 1 2 29 14 22 g 0 0 0 0 0 0 0 0 10 2 1 4 6 7 15 t 0 0 0 0 0 0 0 0 7 2 0 1 1 3 3
MA0102.2_rc_shift3 (CEBPA_rc)	0.838	0.539	2.636	0.051	0.891	1.910	0.894	4	4	4	5	5	5	5	4.571	4	; oligos_7nt_mkv5_m1 versus MA0102.2_rc (CEBPA_rc); m=4/6; ncol2=9; w=9; offset=2; strand=R; shift=3; score= 4.5714; ---rTTGcrmaA--- ; cor=0.838; Ncor=0.539; logoDP=2.636; NIcor=0.051; NsEucl=0.891; SSD=1.910; NSW=0.894; rcor=4; rNcor=4; rlogoDP=4; rNIcor=5; rNsEucl=5; rSSD=5; rNSW=5; rank_mean=4.571; match_rank=4 a 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 c 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 g 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 t 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0
MA0102.1_rc_shift0 (Cebpa_rc)	0.824	0.604	0.206	-0.158	0.908	2.040	0.907	5	3	6	6	3	6	4	4.714	5	; oligos_7nt_mkv5_m1 versus MA0102.1_rc (Cebpa_rc); m=5/6; ncol2=12; w=11; offset=-1; strand=R; shift=0; score= 4.7143; vrbrTTGcrmaA--- ; cor=0.824; Ncor=0.604; logoDP=0.206; NIcor=-0.158; NsEucl=0.908; SSD=2.040; NSW=0.907; rcor=5; rNcor=3; rlogoDP=6; rNIcor=6; rNsEucl=3; rSSD=6; rNSW=4; rank_mean=4.714; match_rank=5 a 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 c 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 g 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 t 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0
MA0078.1_rc_shift7 (Sox17_rc)	0.758	0.405	2.129	0.068	0.879	1.876	0.883	6	6	5	4	6	4	6	5.286	6	; oligos_7nt_mkv5_m1 versus MA0078.1_rc (Sox17_rc); m=6/6; ncol2=9; w=8; offset=6; strand=R; shift=7; score= 5.2857; -------sACAATrd ; cor=0.758; Ncor=0.405; logoDP=2.129; NIcor=0.068; NsEucl=0.879; SSD=1.876; NSW=0.883; rcor=6; rNcor=6; rlogoDP=5; rNIcor=4; rNsEucl=6; rSSD=4; rNSW=6; rank_mean=5.286; match_rank=6 a 0 0 0 0 0 0 0 4 29 0 31 30 1 9 11 c 0 0 0 0 0 0 0 10 2 31 0 0 0 1 4 g 0 0 0 0 0 0 0 17 0 0 0 1 0 18 8 t 0 0 0 0 0 0 0 0 0 0 0 0 30 3 8