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/positions_8nt_m3/peak-motifs_positions_8nt_m3.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/positions_8nt_m3/peak-motifs_positions_8nt_m3_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_8nt_m3_shift1 ; 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 |
|---|
| positions_8nt_m3_shift1 (positions_8nt_m3) |
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; positions_8nt_m3; m=0 (reference); ncol1=14; shift=1; ncol=15; -wtATTGCCCAATaw
; Alignment reference
a 0 331 246 842 1 1 12 2 34 5 1110 1118 50 412 284
c 0 229 210 94 0 1 0 1116 933 1097 4 0 179 259 273
g 0 247 258 141 0 1 1104 0 142 4 3 0 80 183 202
t 0 311 404 41 1117 1115 2 0 9 12 1 0 809 264 359
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| MA0102.3_shift3 (CEBPA) |
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0.844 |
0.663 |
9.783 |
0.657 |
0.913 |
1.814 |
0.918 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_8nt_m3 versus MA0102.3 (CEBPA); m=1/4; ncol2=11; w=11; offset=2; strand=D; shift=3; score= 1; ---aTTGCAyAAym-
; cor=0.844; Ncor=0.663; logoDP=9.783; NIcor=0.657; NsEucl=0.913; SSD=1.814; NSW=0.918; 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
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| MA0466.1_shift2 (CEBPB) |
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0.829 |
0.651 |
9.663 |
0.649 |
0.909 |
1.986 |
0.910 |
2 |
2 |
2 |
2 |
2 |
3 |
2 |
2.143 |
2 |
; positions_8nt_m3 versus MA0466.1 (CEBPB); m=2/4; ncol2=11; w=11; offset=1; strand=D; shift=2; score= 2.1429; --kATTGCAymAy--
; cor=0.829; Ncor=0.651; logoDP=9.663; NIcor=0.649; NsEucl=0.909; SSD=1.986; NSW=0.910; 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
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| MA0102.2_rc_shift3 (CEBPA_rc) |
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0.826 |
0.531 |
2.985 |
0.143 |
0.890 |
1.956 |
0.891 |
3 |
4 |
3 |
3 |
4 |
2 |
4 |
3.286 |
3 |
; positions_8nt_m3 versus MA0102.2_rc (CEBPA_rc); m=3/4; ncol2=9; w=9; offset=2; strand=R; shift=3; score= 3.2857; ---rTTGcrmaA---
; cor=0.826; Ncor=0.531; logoDP=2.985; NIcor=0.143; NsEucl=0.890; SSD=1.956; NSW=0.891; rcor=3; rNcor=4; rlogoDP=3; rNIcor=3; rNsEucl=4; rSSD=2; rNSW=4; rank_mean=3.286; match_rank=3
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) |
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0.815 |
0.598 |
0.310 |
-0.156 |
0.908 |
2.048 |
0.907 |
4 |
3 |
4 |
4 |
3 |
4 |
3 |
3.571 |
4 |
; positions_8nt_m3 versus MA0102.1_rc (Cebpa_rc); m=4/4; ncol2=12; w=11; offset=-1; strand=R; shift=0; score= 3.5714; vrbrTTGcrmaA---
; cor=0.815; Ncor=0.598; logoDP=0.310; NIcor=-0.156; NsEucl=0.908; SSD=2.048; NSW=0.907; rcor=4; rNcor=3; rlogoDP=4; rNIcor=4; rNsEucl=3; rSSD=4; rNSW=3; rank_mean=3.571; match_rank=4
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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