One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/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/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/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_shift0 ; 3 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_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4) |
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; oligos_7nt_test_vs_ctrl_m4; m=0 (reference); ncol1=12; shift=0; ncol=15; wwGATTAATCww---
; Alignment reference
a 62 78 13 184 6 7 185 185 8 29 60 59 0 0 0
c 35 32 0 4 5 2 6 4 4 158 30 44 0 0 0
g 44 30 158 4 4 6 2 5 4 0 32 35 0 0 0
t 59 60 29 8 185 185 7 6 184 13 78 62 0 0 0
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| MA0151.1_rc_shift3 (ARID3A_rc) |
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0.834 |
0.417 |
5.853 |
0.398 |
0.871 |
1.203 |
0.900 |
1 |
2 |
1 |
1 |
2 |
1 |
2 |
1.429 |
1 |
; oligos_7nt_test_vs_ctrl_m4 versus MA0151.1_rc (ARID3A_rc); m=1/2; ncol2=6; w=6; offset=3; strand=R; shift=3; score= 1.4286; ---TTTrAT------
; cor=0.834; Ncor=0.417; logoDP=5.853; NIcor=0.398; NsEucl=0.871; SSD=1.203; NSW=0.900; rcor=1; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=1; rNSW=2; rank_mean=1.429; match_rank=1
a 0 0 0 6 0 0 17 27 0 0 0 0 0 0 0
c 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
g 0 0 0 0 0 0 9 0 0 0 0 0 0 0 0
t 0 0 0 20 27 27 1 0 27 0 0 0 0 0 0
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| MA0467.1_rc_shift4 (Crx_rc) |
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0.792 |
0.422 |
0.344 |
-0.094 |
0.889 |
1.570 |
0.902 |
2 |
1 |
2 |
2 |
1 |
2 |
1 |
1.571 |
2 |
; oligos_7nt_test_vs_ctrl_m4 versus MA0467.1_rc (Crx_rc); m=2/2; ncol2=11; w=8; offset=4; strand=R; shift=4; score= 1.5714; ----yTAATCCyCTt
; cor=0.792; Ncor=0.422; logoDP=0.344; NIcor=-0.094; NsEucl=0.889; SSD=1.570; NSW=0.902; rcor=2; rNcor=1; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.571; match_rank=2
a 0 0 0 0 175 102 2068 2097 0 0 8 109 225 183 135
c 0 0 0 0 1326 0 0 0 0 2097 1574 823 1470 417 458
g 0 0 0 0 52 0 29 0 465 0 0 222 55 43 297
t 0 0 0 0 544 1995 0 0 1632 0 515 943 347 1454 1207
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