One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5.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.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/oligos_7nt_mkv5_m5/peak-motifs_oligos_7nt_mkv5_m5_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift2 ; 5 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 |
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oligos_7nt_mkv5_m5_shift2 (oligos_7nt_mkv5_m5) |
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; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=12; shift=2; ncol=14; --wrTTGCTCAAya
; Alignment reference
a 0 0 798 1165 0 0 0 0 5 0 2811 2811 291 989
c 0 0 484 563 0 1 0 2811 0 2811 0 0 857 675
g 0 0 602 755 0 0 2811 0 6 0 0 0 492 465
t 0 0 927 328 2811 2810 0 0 2800 0 0 0 1171 682
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MA0102.3_shift3 (CEBPA) |
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0.803 |
0.736 |
9.717 |
0.722 |
0.904 |
2.210 |
0.900 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_7nt_mkv5_m5 versus MA0102.3 (CEBPA); m=1/4; ncol2=11; w=11; offset=1; strand=D; shift=3; score= 1; ---aTTGCAyAAym
; cor=0.803; Ncor=0.736; logoDP=9.717; NIcor=0.722; NsEucl=0.904; SSD=2.210; NSW=0.900; 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
c 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963
g 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890
t 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661
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MA0466.1_shift2 (CEBPB) |
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0.779 |
0.714 |
9.501 |
0.691 |
0.899 |
2.478 |
0.887 |
3 |
2 |
2 |
2 |
2 |
4 |
2 |
2.429 |
2 |
; oligos_7nt_mkv5_m5 versus MA0466.1 (CEBPB); m=2/4; ncol2=11; w=11; offset=0; strand=D; shift=2; score= 2.4286; --kATTGCAymAy-
; cor=0.779; Ncor=0.714; logoDP=9.501; NIcor=0.691; NsEucl=0.899; SSD=2.478; NSW=0.887; rcor=3; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=4; rNSW=2; rank_mean=2.429; match_rank=2
a 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0
c 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0
g 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0
t 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0
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MA0102.2_rc_shift3 (CEBPA_rc) |
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0.784 |
0.588 |
2.577 |
0.065 |
0.880 |
2.350 |
0.869 |
2 |
3 |
3 |
3 |
4 |
2 |
4 |
3.000 |
3 |
; oligos_7nt_mkv5_m5 versus MA0102.2_rc (CEBPA_rc); m=3/4; ncol2=9; w=9; offset=1; strand=R; shift=3; score= 3; ---rTTGcrmaA--
; cor=0.784; Ncor=0.588; logoDP=2.577; NIcor=0.065; NsEucl=0.880; SSD=2.350; NSW=0.869; rcor=2; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=4; rSSD=2; rNSW=4; rank_mean=3.000; match_rank=3
a 0 0 0 10 0 0 1 2 5 7 12 15 0 0
c 0 0 0 2 0 0 0 10 2 6 4 0 0 0
g 0 0 0 6 0 0 15 2 9 1 1 0 0 0
t 0 0 0 0 18 18 2 4 2 4 1 3 0 0
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MA0102.1_rc_shift0 (Cebpa_rc) |
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0.778 |
0.556 |
0.504 |
-0.105 |
0.890 |
2.408 |
0.880 |
4 |
4 |
4 |
4 |
3 |
3 |
3 |
3.571 |
4 |
; oligos_7nt_mkv5_m5 versus MA0102.1_rc (Cebpa_rc); m=4/4; ncol2=12; w=10; offset=-2; strand=R; shift=0; score= 3.5714; vrbrTTGcrmaA--
; cor=0.778; Ncor=0.556; logoDP=0.504; NIcor=-0.105; NsEucl=0.890; SSD=2.408; NSW=0.880; rcor=4; rNcor=4; rlogoDP=4; rNIcor=4; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=3.571; match_rank=4
a 6 8 2 10 0 0 1 2 5 7 12 15 0 0
c 5 3 5 2 0 0 0 10 2 6 4 0 0 0
g 6 5 6 6 0 0 15 2 9 1 1 0 0 0
t 1 2 5 0 18 18 2 4 2 4 1 3 0 0
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