One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5.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/2014/10/08/peak-motifs.2014-10-08.083939_2014-10-08.083939_hIGyA6/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift1 ; 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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| oligos_6nt_mkv4_m5_shift1 (oligos_6nt_mkv4_m5) |
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; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=11; shift=1; ncol=14; -mkCCTCCCrms--
; Alignment reference
a 0 357 263 13 4 11 9 12 0 347 302 241 0 0
c 0 306 166 1095 1099 6 1103 1089 1113 135 333 357 0 0
g 0 192 312 5 12 52 7 15 7 384 260 336 0 0
t 0 265 379 7 5 1051 1 4 0 254 225 186 0 0
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| MA0154.1_rc_shift5 (EBF1_rc) |
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0.859 |
0.430 |
2.370 |
0.268 |
0.905 |
0.885 |
0.937 |
1 |
3 |
2 |
2 |
1 |
1 |
1 |
1.571 |
1 |
; oligos_6nt_mkv4_m5 versus MA0154.1_rc (EBF1_rc); m=1/3; ncol2=10; w=7; offset=4; strand=R; shift=5; score= 1.5714; -----TCCCtkGrG
; cor=0.859; Ncor=0.430; logoDP=2.370; NIcor=0.268; NsEucl=0.905; SSD=0.885; NSW=0.937; rcor=1; rNcor=3; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.571; match_rank=1
a 0 0 0 0 0 0 0 0 0 3 5 3 7 3
c 0 0 0 0 0 4 25 23 25 5 0 0 1 0
g 0 0 0 0 0 0 0 0 0 1 9 20 16 22
t 0 0 0 0 0 21 0 2 0 16 11 2 1 0
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| MA0079.3_shift0 (SP1) |
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0.750 |
0.625 |
7.812 |
0.635 |
0.894 |
2.249 |
0.888 |
3 |
1 |
1 |
1 |
2 |
3 |
3 |
2.000 |
2 |
; oligos_6nt_mkv4_m5 versus MA0079.3 (SP1); m=2/3; ncol2=11; w=10; offset=-1; strand=D; shift=0; score= 2; gCCCCkCCCCy---
; cor=0.750; Ncor=0.625; logoDP=7.812; NIcor=0.635; NsEucl=0.894; SSD=2.249; NSW=0.888; rcor=3; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=3; rNSW=3; rank_mean=2.000; match_rank=2
a 857 0 99 0 0 1359 0 0 0 1054 652 0 0 0
c 1786 6215 6703 8734 8661 0 8734 8734 6679 6357 4969 0 0 0
g 4271 642 0 0 0 4624 0 0 0 0 734 0 0 0
t 1820 1877 1932 0 73 2751 0 0 2055 1323 2379 0 0 0
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| MA0056.1_rc_shift5 (MZF1_1-4_rc) |
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0.839 |
0.458 |
0.098 |
-0.083 |
0.883 |
0.988 |
0.918 |
2 |
2 |
3 |
3 |
3 |
2 |
2 |
2.429 |
3 |
; oligos_6nt_mkv4_m5 versus MA0056.1_rc (MZF1_1-4_rc); m=3/3; ncol2=6; w=6; offset=4; strand=R; shift=5; score= 2.4286; -----TCCCCr---
; cor=0.839; Ncor=0.458; logoDP=0.098; NIcor=-0.083; NsEucl=0.883; SSD=0.988; NSW=0.918; rcor=2; rNcor=2; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=2; rNSW=2; rank_mean=2.429; match_rank=3
a 0 0 0 0 0 0 0 1 0 1 8 0 0 0
c 0 0 0 0 0 2 20 19 18 19 4 0 0 0
g 0 0 0 0 0 0 0 0 0 0 5 0 0 0
t 0 0 0 0 0 18 0 0 2 0 3 0 0 0
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