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_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2.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_m2/peak-motifs_oligos_6nt_test_vs_ctrl_m2_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_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_m2_shift0 (oligos_6nt_test_vs_ctrl_m2) |
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; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=24; shift=0; ncol=24; watAgAGATAAAaAttaaaawhww
; Alignment reference
a 58 80 42 181 36 194 26 197 12 184 187 162 138 151 50 43 140 134 139 139 53 64 80 73
c 43 40 32 1 13 3 6 6 6 6 7 18 19 11 11 26 16 18 21 17 18 55 40 42
g 40 43 32 14 144 4 167 5 6 10 8 9 21 24 16 19 23 20 18 24 22 38 28 35
t 71 49 106 16 19 11 13 4 188 12 10 23 34 26 135 124 33 40 34 32 119 55 64 62
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| MA0036.2_rc_shift3 (GATA2_rc) |
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0.785 |
0.458 |
1.215 |
-0.018 |
0.925 |
2.209 |
0.921 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_6nt_test_vs_ctrl_m2 versus MA0036.2_rc (GATA2_rc); m=1/1; ncol2=14; w=14; offset=3; strand=R; shift=3; score= 1; ---dsWGATAAGaayyw-------
; cor=0.785; Ncor=0.458; logoDP=1.215; NIcor=-0.018; NsEucl=0.925; SSD=2.209; NSW=0.921; 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 1715 544 3155 0 4380 0 4329 4188 442 2526 2377 876 778 1490 0 0 0 0 0 0 0
c 0 0 0 224 1967 0 0 0 0 0 0 914 765 427 1220 1709 754 0 0 0 0 0 0 0
g 0 0 0 1185 1765 0 4380 0 0 0 192 3015 1057 525 729 768 567 0 0 0 0 0 0 0
t 0 0 0 1256 104 1225 0 0 4380 51 0 9 32 1051 1555 1125 1569 0 0 0 0 0 0 0
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