One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_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/wwwrun/2014/09/03/peak-motifs.2014-09-03.182940_2014-09-03.182940_LkVj4M/results/discovered_motifs/positions_8nt_m5/peak-motifs_positions_8nt_m5_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_8nt_m5_shift0 ; 4 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_8nt_m5_shift0 (positions_8nt_m5) |
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; positions_8nt_m5; m=0 (reference); ncol1=17; shift=0; ncol=17; rwATGTTGCAATCATtw
; Alignment reference
a 51 42 154 1 0 17 1 1 7 163 165 3 8 146 9 41 46
c 33 31 4 1 2 3 4 1 152 2 0 3 152 7 13 38 40
g 45 38 7 0 155 2 5 164 1 0 0 3 2 3 10 36 34
t 37 55 1 164 9 144 156 0 6 1 1 157 4 10 134 51 46
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MA0102.3_rc_shift1 (CEBPA_rc) |
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0.798 |
0.516 |
4.406 |
0.116 |
0.900 |
2.401 |
0.891 |
2 |
2 |
2 |
2 |
1 |
1 |
1 |
1.571 |
1 |
; positions_8nt_m5 versus MA0102.3_rc (CEBPA_rc); m=1/3; ncol2=11; w=11; offset=1; strand=R; shift=1; score= 1.5714; -krTTrTGCAAt-----
; cor=0.798; Ncor=0.516; logoDP=4.406; NIcor=0.116; NsEucl=0.900; SSD=2.401; NSW=0.891; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.571; match_rank=1
a 0 3661 7826 0 0 5004 1022 0 3309 15318 15318 0 0 0 0 0 0
c 0 890 1804 0 0 0 1066 0 11304 0 0 3635 0 0 0 0 0
g 0 4963 5688 0 3092 7654 1274 15318 0 0 0 1332 0 0 0 0 0
t 0 5804 0 15318 12226 2660 11956 0 705 0 0 10351 0 0 0 0 0
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MA0466.1_rc_shift2 (CEBPB_rc) |
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0.814 |
0.526 |
2.312 |
-0.065 |
0.900 |
2.409 |
0.891 |
1 |
1 |
3 |
3 |
2 |
2 |
2 |
2.000 |
2 |
; positions_8nt_m5 versus MA0466.1_rc (CEBPB_rc); m=2/3; ncol2=11; w=11; offset=2; strand=R; shift=2; score= 2; --rTkrTGCAATm----
; cor=0.814; Ncor=0.526; logoDP=2.312; NIcor=-0.065; NsEucl=0.900; SSD=2.409; NSW=0.891; rcor=1; rNcor=1; rlogoDP=3; rNIcor=3; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.000; match_rank=2
a 0 0 61413 0 0 38886 9286 0 19407 99494 99494 0 42845 0 0 0 0
c 0 0 2043 0 0 0 10015 0 75531 0 0 18428 33617 0 0 0 0
g 0 0 36038 0 39343 51954 5478 99494 0 0 0 5868 10026 0 0 0 0
t 0 0 0 99494 60151 8654 74715 0 4556 0 0 75198 13006 0 0 0 0
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MA0102.2_shift3 (CEBPA) |
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0.761 |
0.403 |
5.949 |
0.375 |
0.876 |
2.497 |
0.861 |
3 |
3 |
1 |
1 |
3 |
3 |
3 |
2.429 |
3 |
; positions_8nt_m5 versus MA0102.2 (CEBPA); m=3/3; ncol2=9; w=9; offset=3; strand=D; shift=3; score= 2.4286; ---TtkygCAAy-----
; cor=0.761; Ncor=0.403; logoDP=5.949; NIcor=0.375; NsEucl=0.876; SSD=2.497; NSW=0.861; rcor=3; rNcor=3; rlogoDP=1; rNIcor=1; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.429; match_rank=3
a 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0 0 0
c 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0 0 0
g 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0 0 0
t 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0 0 0
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