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_m5/peak-motifs_positions_7nt_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.2014-09-03.094519_2014-09-03.094519_gM9GBj/results/discovered_motifs/positions_7nt_m5/peak-motifs_positions_7nt_m5_vs_db_jaspar_core_vertebrates
One-to-n matrix alignment; reference matrix: positions_7nt_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_7nt_m5_shift0 (positions_7nt_m5) |
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; positions_7nt_m5; m=0 (reference); ncol1=17; shift=0; ncol=17; wyCTCTTGCACAACTbh
; Alignment reference
a 53 47 13 1 20 0 1 2 0 181 11 196 198 3 6 36 50
c 42 60 160 8 161 0 0 0 199 8 186 2 1 179 15 54 54
g 46 38 9 0 18 0 1 190 1 3 1 1 0 3 4 54 25
t 59 55 18 191 1 200 198 8 0 8 2 1 1 15 175 56 71
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MA0102.3_shift4 (CEBPA) |
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0.811 |
0.525 |
9.745 |
0.510 |
0.900 |
2.402 |
0.891 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_7nt_m5 versus MA0102.3 (CEBPA); m=1/3; ncol2=11; w=11; offset=4; strand=D; shift=4; score= 1; ----aTTGCAyAAym--
; cor=0.811; Ncor=0.525; logoDP=9.745; NIcor=0.510; NsEucl=0.900; SSD=2.402; NSW=0.891; 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 10351 0 0 705 0 11956 2660 12226 15318 0 5804 0 0
c 0 0 0 0 1332 0 0 0 15318 1274 7654 3092 0 5688 4963 0 0
g 0 0 0 0 3635 0 0 11304 0 1066 0 0 0 1804 890 0 0
t 0 0 0 0 0 15318 15318 3309 0 1022 5004 0 0 7826 3661 0 0
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MA0466.1_shift3 (CEBPB) |
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0.791 |
0.512 |
9.578 |
0.490 |
0.895 |
2.681 |
0.878 |
2 |
2 |
2 |
2 |
2 |
3 |
2 |
2.143 |
2 |
; positions_7nt_m5 versus MA0466.1 (CEBPB); m=2/3; ncol2=11; w=11; offset=3; strand=D; shift=3; score= 2.1429; ---kATTGCAymAy---
; cor=0.791; Ncor=0.512; logoDP=9.578; NIcor=0.490; NsEucl=0.895; SSD=2.681; NSW=0.878; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=2; rSSD=3; rNSW=2; rank_mean=2.143; match_rank=2
a 0 0 0 13006 75198 0 0 4556 0 74715 8654 60151 99494 0 0 0 0
c 0 0 0 10026 5868 0 0 0 99494 5478 51954 39343 0 36038 0 0 0
g 0 0 0 33617 18428 0 0 75531 0 10015 0 0 0 2043 0 0 0
t 0 0 0 42845 0 99494 99494 19407 0 9286 38886 0 0 61413 0 0 0
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MA0102.2_shift5 (CEBPA) |
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0.774 |
0.410 |
6.119 |
0.384 |
0.877 |
2.449 |
0.864 |
3 |
3 |
3 |
3 |
3 |
2 |
3 |
2.857 |
3 |
; positions_7nt_m5 versus MA0102.2 (CEBPA); m=3/3; ncol2=9; w=9; offset=5; strand=D; shift=5; score= 2.8571; -----TtkygCAAy---
; cor=0.774; Ncor=0.410; logoDP=6.119; NIcor=0.384; NsEucl=0.877; SSD=2.449; NSW=0.864; rcor=3; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=3; rSSD=2; rNSW=3; rank_mean=2.857; match_rank=3
a 0 0 0 0 0 3 1 4 2 4 2 18 18 0 0 0 0
c 0 0 0 0 0 0 1 1 9 2 15 0 0 6 0 0 0
g 0 0 0 0 0 0 4 6 2 10 0 0 0 2 0 0 0
t 0 0 0 0 0 15 12 7 5 2 1 0 0 10 0 0 0
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