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_6nt_m4/peak-motifs_positions_6nt_m4.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_6nt_m4/peak-motifs_positions_6nt_m4_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_6nt_m4_shift0 ; 4 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_6nt_m4_shift0 (positions_6nt_m4) |
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; positions_6nt_m4; m=0 (reference); ncol1=18; shift=0; ncol=18; wsATGTTGCACAACAGtr
; Alignment reference
a 39 29 88 5 6 0 1 4 2 115 3 118 117 2 106 5 21 32
c 22 32 16 1 4 0 0 0 114 0 110 0 0 110 2 8 25 29
g 27 31 7 0 106 0 0 110 1 0 1 0 0 3 2 99 25 33
t 30 26 7 112 2 118 117 4 1 3 4 0 1 3 8 6 47 24
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MA0102.3_shift4 (CEBPA) |
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0.830 |
0.507 |
9.852 |
0.484 |
0.903 |
2.285 |
0.896 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_6nt_m4 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=4; strand=D; shift=4; score= 1; ----aTTGCAyAAym---
; cor=0.830; Ncor=0.507; logoDP=9.852; NIcor=0.484; NsEucl=0.903; SSD=2.285; NSW=0.896; 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 0
c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0 0
g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0 0
t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0 0
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MA0466.1_shift3 (CEBPB) |
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0.788 |
0.482 |
9.597 |
0.452 |
0.892 |
2.819 |
0.872 |
2 |
3 |
2 |
2 |
3 |
2 |
2 |
2.286 |
2 |
; positions_6nt_m4 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 2.2857; ---kATTGCAymAy----
; cor=0.788; Ncor=0.482; logoDP=9.597; NIcor=0.452; NsEucl=0.892; SSD=2.819; NSW=0.872; rcor=2; rNcor=3; rlogoDP=2; rNIcor=2; rNsEucl=3; rSSD=2; rNSW=2; rank_mean=2.286; match_rank=2
a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0 0
c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0 0
g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0 0
t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0 0
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MA0102.1_rc_shift1 (Cebpa_rc) |
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0.751 |
0.500 |
0.359 |
-0.161 |
0.895 |
3.152 |
0.869 |
3 |
2 |
3 |
3 |
2 |
3 |
3 |
2.714 |
3 |
; positions_6nt_m4 versus MA0102.1_rc (Cebpa_rc); m=3/3; ncol2=12; w=12; offset=1; strand=R; shift=1; score= 2.7143; -vrbrTTGcrmaA-----
; cor=0.751; Ncor=0.500; logoDP=0.359; NIcor=-0.161; NsEucl=0.895; SSD=3.152; NSW=0.869; rcor=3; rNcor=2; rlogoDP=3; rNIcor=3; rNsEucl=2; rSSD=3; rNSW=3; rank_mean=2.714; match_rank=3
a 0 6 8 2 10 0 0 1 2 5 7 12 15 0 0 0 0 0
c 0 5 3 5 2 0 0 0 10 2 6 4 0 0 0 0 0 0
g 0 6 5 6 6 0 0 15 2 9 1 1 0 0 0 0 0 0
t 0 1 2 5 0 18 18 2 4 2 4 1 3 0 0 0 0 0
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