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/positions_7nt_m2/peak-motifs_positions_7nt_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/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift0 ; 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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positions_7nt_m2_shift0 (positions_7nt_m2) |
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; positions_7nt_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; rmAGATTGCACAACTyt
; Alignment reference
a 94 132 262 16 316 0 0 10 2 313 7 332 335 6 35 67 74
c 72 86 4 10 5 0 0 0 332 11 320 3 0 297 15 106 77
g 95 78 9 279 13 1 2 311 1 1 1 1 0 7 2 77 54
t 75 40 61 31 2 335 334 15 1 11 8 0 1 26 284 86 131
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MA0102.3_shift4 (CEBPA) |
|
0.886 |
0.573 |
10.142 |
0.557 |
0.919 |
1.588 |
0.928 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_7nt_m2 versus MA0102.3 (CEBPA); m=1/4; ncol2=11; w=11; offset=4; strand=D; shift=4; score= 1; ----aTTGCAyAAym--
; cor=0.886; Ncor=0.573; logoDP=10.142; NIcor=0.557; NsEucl=0.919; SSD=1.588; NSW=0.928; 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 0 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0
c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0
g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0
t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
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MA0466.1_shift3 (CEBPB) |
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0.875 |
0.566 |
10.055 |
0.546 |
0.916 |
1.708 |
0.922 |
2 |
3 |
2 |
2 |
2 |
2 |
2 |
2.143 |
2 |
; positions_7nt_m2 versus MA0466.1 (CEBPB); m=2/4; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 2.1429; ---kATTGCAymAy---
; cor=0.875; Ncor=0.566; logoDP=10.055; NIcor=0.546; NsEucl=0.916; SSD=1.708; NSW=0.922; rcor=2; rNcor=3; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.143; match_rank=2
a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0
c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0
g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0
t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
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MA0102.1_rc_shift1 (Cebpa_rc) |
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0.811 |
0.572 |
0.356 |
-0.184 |
0.906 |
2.541 |
0.894 |
4 |
2 |
4 |
4 |
3 |
4 |
3 |
3.429 |
3 |
; positions_7nt_m2 versus MA0102.1_rc (Cebpa_rc); m=3/4; ncol2=12; w=12; offset=1; strand=R; shift=1; score= 3.4286; -vrbrTTGcrmaA----
; cor=0.811; Ncor=0.572; logoDP=0.356; NIcor=-0.184; NsEucl=0.906; SSD=2.541; NSW=0.894; rcor=4; rNcor=2; rlogoDP=4; rNIcor=4; rNsEucl=3; rSSD=4; rNSW=3; rank_mean=3.429; match_rank=3
a 0 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 0
c 0 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 0
g 0 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 0
t 0 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0 0
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MA0102.2_rc_shift4 (CEBPA_rc) |
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0.835 |
0.442 |
2.684 |
0.035 |
0.890 |
1.972 |
0.890 |
3 |
4 |
3 |
3 |
4 |
3 |
4 |
3.429 |
4 |
; positions_7nt_m2 versus MA0102.2_rc (CEBPA_rc); m=4/4; ncol2=9; w=9; offset=4; strand=R; shift=4; score= 3.4286; ----rTTGcrmaA----
; cor=0.835; Ncor=0.442; logoDP=2.684; NIcor=0.035; NsEucl=0.890; SSD=1.972; NSW=0.890; rcor=3; rNcor=4; rlogoDP=3; rNIcor=3; rNsEucl=4; rSSD=3; rNSW=4; rank_mean=3.429; match_rank=4
a 0 0 0 0 10 0 0 1 2 5 7 12 15 0 0 0 0
c 0 0 0 0 2 0 0 0 10 2 6 4 0 0 0 0 0
g 0 0 0 0 6 0 0 15 2 9 1 1 0 0 0 0 0
t 0 0 0 0 0 18 18 2 4 2 4 1 3 0 0 0 0
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