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_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_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_6nt_test_vs_ctrl_m4/peak-motifs_oligos_6nt_test_vs_ctrl_m4_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m4_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_m4_shift0 (oligos_6nt_test_vs_ctrl_m4) |
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; oligos_6nt_test_vs_ctrl_m4; m=0 (reference); ncol1=24; shift=0; ncol=24; sssssscgCGCCCCGCCCvsssss
; Alignment reference
a 153 137 120 109 106 88 107 81 62 81 55 67 55 60 59 61 55 35 327 68 105 94 162 157
c 514 510 621 396 680 723 734 305 887 202 918 840 880 853 158 886 882 934 392 311 313 340 535 476
g 386 435 329 600 332 316 276 744 207 850 190 239 239 218 941 226 244 200 376 776 732 699 373 418
t 171 142 154 119 106 97 107 94 68 91 61 78 50 93 66 51 43 55 129 69 74 91 154 173
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| MA0516.1_shift9 (SP2) |
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0.772 |
0.482 |
2.970 |
0.488 |
0.933 |
2.046 |
0.932 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; oligos_6nt_test_vs_ctrl_m4 versus MA0516.1 (SP2); m=1/1; ncol2=15; w=15; offset=9; strand=D; shift=9; score= 1; ---------gyCCCGCCyCyyccs
; cor=0.772; Ncor=0.482; logoDP=2.970; NIcor=0.488; NsEucl=0.933; SSD=2.046; NSW=0.932; 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 0 160 39 52 0 0 174 0 0 0 206 115 187 226 228 203
c 0 0 0 0 0 0 0 0 0 253 811 1386 1679 1643 0 1686 1656 1108 1196 971 554 717 794 745
g 0 0 0 0 0 0 0 0 0 1028 257 1 7 0 1280 0 0 0 0 99 325 401 408 422
t 0 0 0 0 0 0 0 0 0 245 579 247 0 43 232 0 30 578 284 501 620 342 256 316
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