One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_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/wwwrun/2014/09/03/peak-motifs.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_7nt_m4/peak-motifs_positions_7nt_m4_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_7nt_m4_shift0 ; 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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| positions_7nt_m4_shift0 (positions_7nt_m4) |
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; positions_7nt_m4; m=0 (reference); ncol1=16; shift=0; ncol=16; arATGATGCAACCAkw
; Alignment reference
a 134 112 325 0 1 338 15 1 14 362 355 10 36 327 85 104
c 69 68 14 0 2 1 5 1 342 0 1 269 315 12 84 72
g 90 100 20 0 336 10 10 356 0 0 6 10 3 6 99 69
t 69 82 3 362 23 13 332 4 6 0 0 73 8 17 94 117
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| MA0466.1_rc_shift2 (CEBPB_rc) |
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0.804 |
0.553 |
1.196 |
-0.168 |
0.900 |
2.425 |
0.890 |
1 |
1 |
2 |
2 |
1 |
1 |
1 |
1.286 |
1 |
; positions_7nt_m4 versus MA0466.1_rc (CEBPB_rc); m=1/2; ncol2=11; w=11; offset=2; strand=R; shift=2; score= 1.2857; --rTkrTGCAATm---
; cor=0.804; Ncor=0.553; logoDP=1.196; NIcor=-0.168; NsEucl=0.900; SSD=2.425; NSW=0.890; rcor=1; rNcor=1; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
a 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 0
c 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 0
g 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 0
t 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0 0
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| MA0102.3_rc_shift1 (CEBPA_rc) |
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0.776 |
0.534 |
4.707 |
0.144 |
0.897 |
2.567 |
0.883 |
2 |
2 |
1 |
1 |
2 |
2 |
2 |
1.714 |
2 |
; positions_7nt_m4 versus MA0102.3_rc (CEBPA_rc); m=2/2; ncol2=11; w=11; offset=1; strand=R; shift=1; score= 1.7143; -krTTrTGCAAt----
; cor=0.776; Ncor=0.534; logoDP=4.707; NIcor=0.144; NsEucl=0.897; SSD=2.567; NSW=0.883; rcor=2; rNcor=2; rlogoDP=1; rNIcor=1; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=1.714; match_rank=2
a 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 0
c 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 0
g 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 0
t 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0 0
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