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_m1/peak-motifs_oligos_6nt_test_vs_ctrl_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/2014/10/08/peak-motifs.2014-10-08.082435_2014-10-08.082435_N0FUYh/results/discovered_motifs/oligos_6nt_test_vs_ctrl_m1/peak-motifs_oligos_6nt_test_vs_ctrl_m1_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m1_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_m1_shift0 (oligos_6nt_test_vs_ctrl_m1) |
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; oligos_6nt_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; aaTgAGATAAAaAttaaAaTcTww
; Alignment reference
a 44 41 8 20 101 16 108 7 99 112 97 82 83 24 23 80 81 90 80 16 21 16 40 45
c 24 29 1 12 3 12 2 3 6 0 4 13 6 19 16 7 17 7 13 2 67 7 19 25
g 25 22 8 77 6 86 5 4 8 3 8 9 9 11 16 12 6 8 9 11 10 3 25 13
t 28 29 104 12 11 7 6 107 8 6 12 17 23 67 66 22 17 16 19 92 23 95 37 38
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| MA0036.2_rc_shift2 (GATA2_rc) |
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0.769 |
0.448 |
1.262 |
-0.016 |
0.924 |
2.271 |
0.919 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_6nt_test_vs_ctrl_m1 versus MA0036.2_rc (GATA2_rc); m=1/1; ncol2=14; w=14; offset=2; strand=R; shift=2; score= 1; --dsWGATAAGaayyw--------
; cor=0.769; Ncor=0.448; logoDP=1.262; NIcor=-0.016; NsEucl=0.924; SSD=2.271; NSW=0.919; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 0 0 1715 544 3155 0 4380 0 4329 4188 442 2526 2377 876 778 1490 0 0 0 0 0 0 0 0
c 0 0 224 1967 0 0 0 0 0 0 914 765 427 1220 1709 754 0 0 0 0 0 0 0 0
g 0 0 1185 1765 0 4380 0 0 0 192 3015 1057 525 729 768 567 0 0 0 0 0 0 0 0
t 0 0 1256 104 1225 0 0 4380 51 0 9 32 1051 1555 1125 1569 0 0 0 0 0 0 0 0
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