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_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_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_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift2 ; 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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| oligos_6nt_mkv4_m1_shift2 (oligos_6nt_mkv4_m1) |
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; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=10; shift=2; ncol=18; --waATGTCAkw------
; Alignment reference
a 0 0 562 707 1681 0 0 0 0 1681 394 446 0 0 0 0 0 0
c 0 0 356 407 0 0 0 0 1681 0 401 410 0 0 0 0 0 0
g 0 0 311 290 0 0 1681 0 0 0 434 392 0 0 0 0 0 0
t 0 0 452 277 0 1681 0 1681 0 0 452 433 0 0 0 0 0 0
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| MA0089.1_rc_shift6 (NFE2L1::MafG_rc) |
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0.904 |
0.543 |
0.059 |
-0.127 |
0.911 |
0.575 |
0.952 |
1 |
1 |
4 |
4 |
1 |
1 |
1 |
1.857 |
1 |
; oligos_6nt_mkv4_m1 versus MA0089.1_rc (NFE2L1::MafG_rc); m=1/4; ncol2=6; w=6; offset=4; strand=R; shift=6; score= 1.8571; ------GTCATs------
; cor=0.904; Ncor=0.543; logoDP=0.059; NIcor=-0.127; NsEucl=0.911; SSD=0.575; NSW=0.952; rcor=1; rNcor=1; rlogoDP=4; rNIcor=4; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.857; match_rank=1
a 0 0 0 0 0 0 6 0 1 34 0 6 0 0 0 0 0 0
c 0 0 0 0 0 0 2 0 32 0 3 10 0 0 0 0 0 0
g 0 0 0 0 0 0 26 0 0 0 2 11 0 0 0 0 0 0
t 0 0 0 0 0 0 0 34 1 0 29 7 0 0 0 0 0 0
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| MA0067.1_shift5 (Pax2) |
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0.798 |
0.508 |
3.634 |
0.506 |
0.882 |
1.368 |
0.902 |
2 |
2 |
3 |
2 |
3 |
2 |
2 |
2.286 |
2 |
; oligos_6nt_mkv4_m1 versus MA0067.1 (Pax2); m=2/4; ncol2=8; w=7; offset=3; strand=D; shift=5; score= 2.2857; -----wgTCAykb-----
; cor=0.798; Ncor=0.508; logoDP=3.634; NIcor=0.506; NsEucl=0.882; SSD=1.368; NSW=0.902; rcor=2; rNcor=2; rlogoDP=3; rNIcor=2; rNsEucl=3; rSSD=2; rNSW=2; rank_mean=2.286; match_rank=2
a 0 0 0 0 0 10 7 3 0 26 2 2 1 0 0 0 0 0
c 0 0 0 0 0 7 1 2 28 1 17 0 11 0 0 0 0 0
g 0 0 0 0 0 5 21 0 1 3 1 19 11 0 0 0 0 0
t 0 0 0 0 0 9 2 26 2 1 11 10 8 0 0 0 0 0
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| MA0071.1_shift0 (RORA_1) |
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0.754 |
0.503 |
8.794 |
0.515 |
0.869 |
2.196 |
0.863 |
3 |
3 |
1 |
1 |
4 |
4 |
4 |
2.857 |
3 |
; oligos_6nt_mkv4_m1 versus MA0071.1 (RORA_1); m=3/4; ncol2=10; w=8; offset=-2; strand=D; shift=0; score= 2.8571; wwcwAGGTCA--------
; cor=0.754; Ncor=0.503; logoDP=8.794; NIcor=0.515; NsEucl=0.869; SSD=2.196; NSW=0.863; rcor=3; rNcor=3; rlogoDP=1; rNIcor=1; rNsEucl=4; rSSD=4; rNSW=4; rank_mean=2.857; match_rank=3
a 15 9 6 11 21 0 0 0 0 25 0 0 0 0 0 0 0 0
c 1 1 12 2 0 0 0 0 25 0 0 0 0 0 0 0 0 0
g 2 0 4 5 4 25 25 0 0 0 0 0 0 0 0 0 0 0
t 7 15 3 7 0 0 0 25 0 0 0 0 0 0 0 0 0 0
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| MA0258.1_shift2 (ESR2) |
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0.754 |
0.419 |
5.998 |
0.417 |
0.900 |
1.992 |
0.900 |
4 |
4 |
2 |
3 |
2 |
3 |
3 |
3.000 |
4 |
; oligos_6nt_mkv4_m1 versus MA0258.1 (ESR2); m=4/4; ncol2=18; w=10; offset=0; strand=D; shift=2; score= 3; --cwrGGTCAsgkTGmCC
; cor=0.754; Ncor=0.419; logoDP=5.998; NIcor=0.417; NsEucl=0.900; SSD=1.992; NSW=0.900; rcor=4; rNcor=4; rlogoDP=2; rNIcor=3; rNsEucl=2; rSSD=3; rNSW=3; rank_mean=3.000; match_rank=4
a 0 0 78 158 186 27 18 13 0 337 49 64 52 21 63 178 34 46
c 0 0 161 51 15 0 20 19 357 1 123 63 61 33 25 99 268 289
g 0 0 63 41 154 275 319 33 0 0 113 149 147 24 265 19 2 0
t 0 0 55 107 2 55 0 292 0 19 72 81 97 279 4 61 53 22
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