One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1.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/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/results/discovered_motifs/oligos_7nt_mkv5_m1/peak-motifs_oligos_7nt_mkv5_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_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 |
|---|
| oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1) |
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; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; cvCCACACCcg
; Alignment reference
a 107 133 3 1 463 1 450 0 1 83 110
c 184 124 487 482 4 491 3 495 482 223 112
g 120 154 5 9 25 1 42 0 12 75 152
t 84 84 0 3 3 2 0 0 0 114 121
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| MA0493.1_shift0 (Klf1) |
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0.898 |
0.898 |
8.244 |
0.890 |
0.936 |
1.005 |
0.954 |
2 |
1 |
1 |
1 |
1 |
3 |
2 |
1.571 |
1 |
; oligos_7nt_mkv5_m1 versus MA0493.1 (Klf1); m=1/5; ncol2=11; w=11; offset=0; strand=D; shift=0; score= 1.5714; rrCCACACCCw
; cor=0.898; Ncor=0.898; logoDP=8.244; NIcor=0.890; NsEucl=0.936; SSD=1.005; NSW=0.954; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=3; rNSW=2; rank_mean=1.571; match_rank=1
a 150 167 67 13 404 0 400 0 0 0 280
c 76 40 396 461 118 526 0 526 526 508 35
g 202 305 32 0 0 0 97 0 0 0 0
t 98 14 31 52 4 0 29 0 0 18 211
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| MA0130.1_shift0 (ZNF354C) |
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0.923 |
0.504 |
6.306 |
0.515 |
0.918 |
0.483 |
0.960 |
1 |
4 |
3 |
3 |
2 |
1 |
1 |
2.143 |
2 |
; oligos_7nt_mkv5_m1 versus MA0130.1 (ZNF354C); m=2/5; ncol2=6; w=6; offset=0; strand=D; shift=0; score= 2.1429; mTCCAC-----
; cor=0.923; Ncor=0.504; logoDP=6.306; NIcor=0.515; NsEucl=0.918; SSD=0.483; NSW=0.960; rcor=1; rNcor=4; rlogoDP=3; rNIcor=3; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=2.143; match_rank=2
a 7 3 0 0 16 0 0 0 0 0 0
c 6 2 16 16 0 15 0 0 0 0 0
g 3 0 0 0 0 1 0 0 0 0 0
t 0 11 0 0 0 0 0 0 0 0 0
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| MA0039.2_rc_shift1 (Klf4_rc) |
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0.848 |
0.770 |
0.606 |
-0.220 |
0.914 |
1.463 |
0.927 |
4 |
2 |
5 |
5 |
3 |
4 |
3 |
3.714 |
3 |
; oligos_7nt_mkv5_m1 versus MA0039.2_rc (Klf4_rc); m=3/5; ncol2=10; w=10; offset=1; strand=R; shift=1; score= 3.7143; -gCCmCrCCCw
; cor=0.848; Ncor=0.770; logoDP=0.606; NIcor=-0.220; NsEucl=0.914; SSD=1.463; NSW=0.927; rcor=4; rNcor=2; rlogoDP=5; rNIcor=5; rNsEucl=3; rSSD=4; rNSW=3; rank_mean=3.714; match_rank=3
a 0 932 289 125 2042 34 2139 16 13 6 1765
c 0 280 3789 3902 2179 4273 11 4281 4304 4237 1022
g 0 2858 130 46 80 15 1922 36 13 9 81
t 0 254 123 264 42 22 277 14 14 88 1468
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| MA0599.1_shift1 (KLF5) |
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0.787 |
0.716 |
8.022 |
0.688 |
0.899 |
2.026 |
0.899 |
5 |
3 |
2 |
2 |
4 |
5 |
5 |
3.714 |
4 |
; oligos_7nt_mkv5_m1 versus MA0599.1 (KLF5); m=4/5; ncol2=10; w=10; offset=1; strand=D; shift=1; score= 3.7143; -gCCMCrCCCh
; cor=0.787; Ncor=0.716; logoDP=8.022; NIcor=0.688; NsEucl=0.899; SSD=2.026; NSW=0.899; rcor=5; rNcor=3; rlogoDP=2; rNIcor=2; rNsEucl=4; rSSD=5; rNSW=5; rank_mean=3.714; match_rank=4
a 0 1429 0 0 3477 0 5051 0 0 0 3915
c 0 2023 11900 12008 9569 13611 0 13611 13611 13135 5595
g 0 7572 0 0 0 0 5182 0 0 0 0
t 0 2587 1711 1603 565 0 3378 0 0 476 4101
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| MA0103.1_shift5 (ZEB1) |
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0.852 |
0.465 |
4.866 |
0.450 |
0.889 |
0.895 |
0.925 |
3 |
5 |
4 |
4 |
5 |
2 |
4 |
3.857 |
5 |
; oligos_7nt_mkv5_m1 versus MA0103.1 (ZEB1); m=5/5; ncol2=6; w=6; offset=5; strand=D; shift=5; score= 3.8571; -----CACCTk
; cor=0.852; Ncor=0.465; logoDP=4.866; NIcor=0.450; NsEucl=0.889; SSD=0.895; NSW=0.925; rcor=3; rNcor=5; rlogoDP=4; rNIcor=4; rNsEucl=5; rSSD=2; rNSW=4; rank_mean=3.857; match_rank=5
a 0 0 0 0 0 1 38 0 0 0 10
c 0 0 0 0 0 34 0 40 38 1 1
g 0 0 0 0 0 1 2 1 3 0 16
t 0 0 0 0 0 5 1 0 0 40 14
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