One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.150329_2014-10-07.150329_sPZtpE/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_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/apache/2014/10/07/peak-motifs.2014-10-07.150329_2014-10-07.150329_sPZtpE/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m4/peak-motifs_oligos_7nt_test_vs_ctrl_m4_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m4_shift6 ; 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 |
|---|
| oligos_7nt_test_vs_ctrl_m4_shift6 (oligos_7nt_test_vs_ctrl_m4) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=12; shift=6; ncol=18; ------ssGmGGGmGGcG
; Alignment reference
a 0 0 0 0 0 0 9 5 1 45 0 1 1 50 0 1 7 4
c 0 0 0 0 0 0 39 46 8 24 12 12 0 26 6 1 51 6
g 0 0 0 0 0 0 22 23 66 6 63 63 75 0 70 73 10 52
t 0 0 0 0 0 0 6 2 1 1 1 0 0 0 0 1 8 14
|
| MA0469.1_rc_shift0 (E2F3_rc) |
 |
0.807 |
0.403 |
0.591 |
0.030 |
0.897 |
1.705 |
0.905 |
1 |
4 |
4 |
1 |
2 |
1 |
1 |
2.000 |
1 |
; oligos_7nt_test_vs_ctrl_m4 versus MA0469.1_rc (E2F3_rc); m=1/4; ncol2=15; w=9; offset=-6; strand=R; shift=0; score= 2; srsygsggGCGGGAr---
; cor=0.807; Ncor=0.403; logoDP=0.591; NIcor=0.030; NsEucl=0.897; SSD=1.705; NSW=0.905; rcor=1; rNcor=4; rlogoDP=4; rNIcor=1; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=2.000; match_rank=1
a 259 645 160 274 302 629 460 239 0 309 0 0 0 2549 1149 0 0 0
c 644 200 582 512 556 742 397 607 0 2240 0 80 0 0 0 0 0 0
g 718 640 1075 329 1495 903 1327 1703 2549 0 2549 2469 2549 0 1400 0 0 0
t 305 441 109 811 196 275 365 0 0 0 0 0 0 0 0 0 0 0
|
| MA0162.2_rc_shift5 (EGR1_rc) |
 |
0.761 |
0.652 |
0.942 |
-0.120 |
0.910 |
2.332 |
0.903 |
4 |
1 |
2 |
3 |
1 |
4 |
2 |
2.429 |
2 |
; oligos_7nt_test_vs_ctrl_m4 versus MA0162.2_rc (EGR1_rc); m=2/4; ncol2=14; w=12; offset=-1; strand=R; shift=5; score= 2.4286; -----gGmGKGGGcGGgg
; cor=0.761; Ncor=0.652; logoDP=0.942; NIcor=-0.120; NsEucl=0.910; SSD=2.332; NSW=0.903; rcor=4; rNcor=1; rlogoDP=2; rNIcor=3; rNsEucl=1; rSSD=4; rNSW=2; rank_mean=2.429; match_rank=2
a 0 0 0 0 0 1722 987 3289 304 243 1491 404 0 2505 449 490 2797 2544
c 0 0 0 0 0 1913 1420 6599 0 0 611 0 0 6840 0 0 2250 1359
g 0 0 0 0 0 5595 9849 0 11952 8361 10154 11852 12256 0 11574 10431 6049 6847
t 0 0 0 0 0 3026 0 2368 0 3652 0 0 0 2911 233 1335 1160 1506
|
| MA0599.1_rc_shift9 (KLF5_rc) |
 |
0.762 |
0.528 |
1.176 |
-0.082 |
0.888 |
2.022 |
0.888 |
3 |
3 |
1 |
2 |
4 |
2 |
4 |
2.714 |
3 |
; oligos_7nt_test_vs_ctrl_m4 versus MA0599.1_rc (KLF5_rc); m=3/4; ncol2=10; w=9; offset=3; strand=R; shift=9; score= 2.7143; ---------dGGGyGKGG
; cor=0.762; Ncor=0.528; logoDP=1.176; NIcor=-0.082; NsEucl=0.888; SSD=2.022; NSW=0.888; rcor=3; rNcor=3; rlogoDP=1; rNIcor=2; rNsEucl=4; rSSD=2; rNSW=4; rank_mean=2.714; match_rank=3
a 0 0 0 0 0 0 0 0 0 4101 476 0 0 3378 0 565 1603 1711
c 0 0 0 0 0 0 0 0 0 0 0 0 0 5182 0 0 0 0
g 0 0 0 0 0 0 0 0 0 5595 13135 13611 13611 0 13611 9569 12008 11900
t 0 0 0 0 0 0 0 0 0 3915 0 0 0 5051 0 3477 0 0
|
| MA0079.3_rc_shift8 (SP1_rc) |
 |
0.764 |
0.588 |
0.789 |
-0.121 |
0.896 |
2.158 |
0.892 |
2 |
2 |
3 |
4 |
3 |
3 |
3 |
2.857 |
4 |
; oligos_7nt_test_vs_ctrl_m4 versus MA0079.3_rc (SP1_rc); m=4/4; ncol2=11; w=10; offset=2; strand=R; shift=8; score= 2.8571; --------rGGGGmGGGG
; cor=0.764; Ncor=0.588; logoDP=0.789; NIcor=-0.121; NsEucl=0.896; SSD=2.158; NSW=0.892; rcor=2; rNcor=2; rlogoDP=3; rNIcor=4; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.857; match_rank=4
a 0 0 0 0 0 0 0 0 2379 1323 2055 0 0 2751 73 0 1932 1877
c 0 0 0 0 0 0 0 0 734 0 0 0 0 4624 0 0 0 642
g 0 0 0 0 0 0 0 0 4969 6357 6679 8734 8734 0 8661 8734 6703 6215
t 0 0 0 0 0 0 0 0 652 1054 0 0 0 1359 0 0 99 0
|