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_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3.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_6nt_test_vs_ctrl_m3/peak-motifs_oligos_6nt_test_vs_ctrl_m3_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_shift0 ; 2 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_test_vs_ctrl_m3_shift0 (oligos_6nt_test_vs_ctrl_m3) |
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; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=24; shift=0; ncol=24; wwaaTtTTTATCAGATAAAwAwww
; Alignment reference
a 43 51 73 75 17 31 18 9 17 104 6 14 114 13 107 6 113 101 91 73 88 33 48 42
c 20 21 17 12 13 10 8 5 6 5 12 87 2 7 9 6 4 6 12 14 8 10 21 20
g 18 18 16 20 5 13 10 12 8 7 11 5 2 98 4 4 3 6 8 8 13 7 20 24
t 47 38 22 21 93 74 92 102 97 12 99 22 10 10 8 112 8 15 17 33 19 78 39 42
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| MA0036.2_rc_shift10 (GATA2_rc) |
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0.784 |
0.457 |
1.090 |
-0.022 |
0.929 |
2.003 |
0.928 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_6nt_test_vs_ctrl_m3 versus MA0036.2_rc (GATA2_rc); m=1/1; ncol2=14; w=14; offset=10; strand=R; shift=10; score= 1; ----------dsWGATAAGaayyw
; cor=0.784; Ncor=0.457; logoDP=1.090; NIcor=-0.022; NsEucl=0.929; SSD=2.003; NSW=0.928; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 0 0 0 0 0 0 0 0 0 0 1715 544 3155 0 4380 0 4329 4188 442 2526 2377 876 778 1490
c 0 0 0 0 0 0 0 0 0 0 224 1967 0 0 0 0 0 0 914 765 427 1220 1709 754
g 0 0 0 0 0 0 0 0 0 0 1185 1765 0 4380 0 0 0 192 3015 1057 525 729 768 567
t 0 0 0 0 0 0 0 0 0 0 1256 104 1225 0 0 4380 51 0 9 32 1051 1555 1125 1569
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