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_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_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_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift0 ; 6 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_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5) |
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; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=15; shift=0; ncol=15; atGATTGCACAACwy
; Alignment reference
a 1049 667 145 2154 1 1 73 7 2557 96 2699 2698 42 1156 679
c 475 241 158 56 4 1 6 2710 51 2532 26 10 2218 617 807
g 582 485 2173 474 4 10 2440 2 31 16 2 11 95 167 542
t 622 1335 252 44 2719 2716 209 9 89 84 1 9 373 788 700
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MA0102.3_shift3 (CEBPA) |
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0.936 |
0.687 |
9.841 |
0.673 |
0.942 |
0.820 |
0.963 |
1 |
1 |
1 |
1 |
1 |
2 |
1 |
1.143 |
1 |
; oligos_6nt_mkv4_m5 versus MA0102.3 (CEBPA); m=1/5; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 1.1429; ---aTTGCAyAAym-
; cor=0.936; Ncor=0.687; logoDP=9.841; NIcor=0.673; NsEucl=0.942; SSD=0.820; NSW=0.963; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.143; 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
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MA0466.1_shift2 (CEBPB) |
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0.887 |
0.650 |
9.684 |
0.629 |
0.923 |
1.445 |
0.934 |
2 |
2 |
2 |
2 |
2 |
3 |
3 |
2.286 |
2 |
; oligos_6nt_mkv4_m5 versus MA0466.1 (CEBPB); m=2/5; ncol2=11; w=11; offset=2; strand=D; shift=2; score= 2.2857; --kATTGCAymAy--
; cor=0.887; Ncor=0.650; logoDP=9.684; NIcor=0.629; NsEucl=0.923; SSD=1.445; NSW=0.934; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=3; rNSW=3; rank_mean=2.286; 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
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MA0133.1_shift8 (BRCA1) |
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0.871 |
0.406 |
3.107 |
0.410 |
0.910 |
0.791 |
0.943 |
3 |
5 |
3 |
3 |
3 |
1 |
2 |
2.857 |
3 |
; oligos_6nt_mkv4_m5 versus MA0133.1 (BRCA1); m=3/5; ncol2=7; w=7; offset=8; strand=D; shift=8; score= 2.8571; --------mCAAcms
; cor=0.871; Ncor=0.406; logoDP=3.107; NIcor=0.410; NsEucl=0.910; SSD=0.791; NSW=0.943; rcor=3; rNcor=5; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=1; rNSW=2; rank_mean=2.857; 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
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MA0102.2_rc_shift3 (CEBPA_rc) |
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0.843 |
0.506 |
2.640 |
0.048 |
0.895 |
1.771 |
0.902 |
4 |
4 |
4 |
4 |
5 |
4 |
5 |
4.286 |
4 |
; oligos_6nt_mkv4_m5 versus MA0102.2_rc (CEBPA_rc); m=4/5; ncol2=9; w=9; offset=3; strand=R; shift=3; score= 4.2857; ---rTTGcrmaA---
; cor=0.843; Ncor=0.506; logoDP=2.640; NIcor=0.048; NsEucl=0.895; SSD=1.771; NSW=0.902; rcor=4; rNcor=4; rlogoDP=4; rNIcor=4; rNsEucl=5; rSSD=4; rNSW=5; rank_mean=4.286; 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
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MA0102.1_rc_shift0 (Cebpa_rc) |
|
0.802 |
0.641 |
0.297 |
-0.164 |
0.910 |
2.328 |
0.903 |
5 |
3 |
5 |
5 |
4 |
5 |
4 |
4.429 |
5 |
; oligos_6nt_mkv4_m5 versus MA0102.1_rc (Cebpa_rc); m=5/5; ncol2=12; w=12; offset=0; strand=R; shift=0; score= 4.4286; vrbrTTGcrmaA---
; cor=0.802; Ncor=0.641; logoDP=0.297; NIcor=-0.164; NsEucl=0.910; SSD=2.328; NSW=0.903; rcor=5; rNcor=3; rlogoDP=5; rNIcor=5; rNsEucl=4; rSSD=5; rNSW=4; rank_mean=4.429; 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
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