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_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5.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_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift4 ; 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_m5_shift4 (oligos_7nt_test_vs_ctrl_m5) |
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; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=12; shift=4; ncol=16; ----CrCACACACACr
; Alignment reference
a 0 0 0 0 5 35 0 77 0 80 0 80 0 76 3 27
c 0 0 0 0 73 9 96 0 101 1 102 0 101 2 86 4
g 0 0 0 0 4 54 2 25 1 21 0 22 0 24 4 68
t 0 0 0 0 20 4 4 0 0 0 0 0 1 0 9 3
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| MA0472.1_shift0 (EGR2) |
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0.797 |
0.548 |
7.036 |
0.541 |
0.908 |
2.051 |
0.907 |
2 |
1 |
1 |
1 |
1 |
2 |
1 |
1.286 |
1 |
; oligos_7nt_test_vs_ctrl_m5 versus MA0472.1 (EGR2); m=1/2; ncol2=15; w=11; offset=-4; strand=D; shift=0; score= 1.2857; cmcmCrCCCACrCac-
; cor=0.797; Ncor=0.548; logoDP=7.036; NIcor=0.541; NsEucl=0.908; SSD=2.051; NSW=0.907; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=2; rNSW=1; rank_mean=1.286; match_rank=1
a 169 337 168 387 26 448 0 152 0 1059 0 460 0 558 127 0
c 572 460 572 722 1186 0 1246 1094 1169 187 1246 0 1041 302 617 0
g 291 180 216 65 0 602 0 0 0 0 0 579 114 199 251 0
t 214 269 290 72 34 196 0 0 77 0 0 207 91 187 251 0
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| MA0006.1_rc_shift8 (Arnt::Ahr_rc) |
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0.813 |
0.407 |
2.375 |
-0.002 |
0.865 |
1.310 |
0.891 |
1 |
2 |
2 |
2 |
2 |
1 |
2 |
1.714 |
2 |
; oligos_7nt_test_vs_ctrl_m5 versus MA0006.1_rc (Arnt::Ahr_rc); m=2/2; ncol2=6; w=6; offset=4; strand=R; shift=8; score= 1.7143; --------CACGCr--
; cor=0.813; Ncor=0.407; logoDP=2.375; NIcor=-0.002; NsEucl=0.865; SSD=1.310; NSW=0.891; rcor=1; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=1; rNSW=2; rank_mean=1.714; match_rank=2
a 0 0 0 0 0 0 0 0 0 24 1 1 1 11 0 0
c 0 0 0 0 0 0 0 0 24 0 23 0 23 2 0 0
g 0 0 0 0 0 0 0 0 0 0 0 23 0 8 0 0
t 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0
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