One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/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/apache/2014/10/07/peak-motifs.2014-10-07.093009_2014-10-07.093009_rKpHEN/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_shift2 ; 7 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 |
|---|
| positions_7nt_m5_shift2 (positions_7nt_m5) |
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; positions_7nt_m5; m=0 (reference); ncol1=14; shift=2; ncol=20; --kbCCAGGTCAAGgt----
; Alignment reference
a 0 0 61 53 20 32 253 4 5 4 1 251 198 17 61 63 0 0 0 0
c 0 0 51 75 212 228 5 3 0 5 252 11 18 11 54 65 0 0 0 0
g 0 0 74 67 15 1 3 254 254 5 7 1 33 229 89 50 0 0 0 0
t 0 0 80 71 19 5 5 5 7 252 6 3 17 9 62 88 0 0 0 0
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| MA0071.1_shift2 (RORA_1) |
 |
0.848 |
0.606 |
8.439 |
0.618 |
0.914 |
1.466 |
0.927 |
1 |
1 |
1 |
1 |
1 |
1 |
1 |
1.000 |
1 |
; positions_7nt_m5 versus MA0071.1 (RORA_1); m=1/6; ncol2=10; w=10; offset=0; strand=D; shift=2; score= 1; --wwcwAGGTCA--------
; cor=0.848; Ncor=0.606; logoDP=8.439; NIcor=0.618; NsEucl=0.914; SSD=1.466; NSW=0.927; rcor=1; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.000; match_rank=1
a 0 0 15 9 6 11 21 0 0 0 0 25 0 0 0 0 0 0 0 0
c 0 0 1 1 12 2 0 0 0 0 25 0 0 0 0 0 0 0 0 0
g 0 0 2 0 4 5 4 25 25 0 0 0 0 0 0 0 0 0 0 0
t 0 0 7 15 3 7 0 0 0 25 0 0 0 0 0 0 0 0 0 0
|
| MA0141.1_shift0 (Esrrb) |
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0.847 |
0.529 |
7.537 |
0.531 |
0.913 |
1.502 |
0.925 |
2 |
2 |
3 |
2 |
2 |
2 |
2 |
2.143 |
2 |
; positions_7nt_m5 versus MA0141.1 (Esrrb); m=2/6; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 2.1429; rgsyCAAGGTCA--------
; cor=0.847; Ncor=0.529; logoDP=7.537; NIcor=0.531; NsEucl=0.913; SSD=1.502; NSW=0.925; rcor=2; rNcor=2; rlogoDP=3; rNIcor=2; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.143; match_rank=2
a 1054 673 420 259 310 3326 3567 32 21 182 9 3458 0 0 0 0 0 0 0 0
c 800 829 1211 1250 2664 32 2 5 12 46 3376 20 0 0 0 0 0 0 0 0
g 985 1370 1209 448 627 248 60 3586 3602 244 170 129 0 0 0 0 0 0 0 0
t 793 767 805 1693 52 50 27 31 17 3175 85 27 0 0 0 0 0 0 0 0
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| MA0141.2_shift0 (Esrrb) |
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0.846 |
0.529 |
7.627 |
0.530 |
0.913 |
1.515 |
0.924 |
3 |
3 |
2 |
3 |
3 |
3 |
3 |
2.857 |
3 |
; positions_7nt_m5 versus MA0141.2 (Esrrb); m=3/6; ncol2=12; w=10; offset=-2; strand=D; shift=0; score= 2.8571; rgsyCAAGGTCA--------
; cor=0.846; Ncor=0.529; logoDP=7.627; NIcor=0.530; NsEucl=0.913; SSD=1.515; NSW=0.924; rcor=3; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=3; rSSD=3; rNSW=3; rank_mean=2.857; match_rank=3
a 1055 673 403 260 312 3347 3590 33 12 180 9 3478 0 0 0 0 0 0 0 0
c 801 832 1212 1230 2653 32 2 2 11 43 3394 21 0 0 0 0 0 0 0 0
g 984 1352 1212 449 630 248 60 3597 3622 243 167 128 0 0 0 0 0 0 0 0
t 773 767 807 1702 51 27 6 29 16 3192 85 26 0 0 0 0 0 0 0 0
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| MA0160.1_shift5 (NR4A2) |
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0.811 |
0.464 |
6.218 |
0.462 |
0.887 |
1.649 |
0.897 |
4 |
4 |
4 |
4 |
6 |
4 |
6 |
4.571 |
4 |
; positions_7nt_m5 versus MA0160.1 (NR4A2); m=4/6; ncol2=8; w=8; offset=3; strand=D; shift=5; score= 4.5714; -----aAGGTCAc-------
; cor=0.811; Ncor=0.464; logoDP=6.218; NIcor=0.462; NsEucl=0.887; SSD=1.649; NSW=0.897; rcor=4; rNcor=4; rlogoDP=4; rNIcor=4; rNsEucl=6; rSSD=4; rNSW=6; rank_mean=4.571; match_rank=4
a 0 0 0 0 0 8 13 0 3 2 0 14 3 0 0 0 0 0 0 0
c 0 0 0 0 0 1 0 0 0 2 13 0 8 0 0 0 0 0 0 0
g 0 0 0 0 0 3 1 13 11 0 0 0 2 0 0 0 0 0 0 0
t 0 0 0 0 0 1 0 1 0 10 1 0 0 0 0 0 0 0 0 0
|
| MA0258.2_shift6 (ESR2) |
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0.811 |
0.427 |
6.029 |
0.437 |
0.909 |
1.659 |
0.917 |
5 |
6 |
5 |
6 |
5 |
5 |
4 |
5.143 |
5 |
; positions_7nt_m5 versus MA0258.2 (ESR2); m=5/6; ncol2=15; w=10; offset=4; strand=D; shift=6; score= 5.1429; ------rGGTCAsmstGaCC
; cor=0.811; Ncor=0.427; logoDP=6.029; NIcor=0.437; NsEucl=0.909; SSD=1.659; NSW=0.917; rcor=5; rNcor=6; rlogoDP=5; rNIcor=6; rNsEucl=5; rSSD=5; rNSW=4; rank_mean=5.143; match_rank=5
a 0 0 0 0 0 0 5410 429 59 74 0 8098 502 2092 1808 1602 1121 3278 434 1111
c 0 0 0 0 0 0 96 0 0 147 7621 1 4202 3235 2510 975 398 2056 6469 5854
g 0 0 0 0 0 0 2563 7170 8143 989 533 57 2738 1688 2173 533 6658 1391 363 0
t 0 0 0 0 0 0 174 644 41 7033 89 87 801 1228 1752 5133 66 1518 977 1278
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| MA0258.1_shift4 (ESR2) |
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0.762 |
0.457 |
5.240 |
0.449 |
0.909 |
2.380 |
0.901 |
6 |
5 |
6 |
5 |
4 |
6 |
5 |
5.286 |
6 |
; positions_7nt_m5 versus MA0258.1 (ESR2); m=6/6; ncol2=18; w=12; offset=2; strand=D; shift=4; score= 5.2857; ----cwrGGTCAsgkTGmCC
; cor=0.762; Ncor=0.457; logoDP=5.240; NIcor=0.449; NsEucl=0.909; SSD=2.380; NSW=0.901; rcor=6; rNcor=5; rlogoDP=6; rNIcor=5; rNsEucl=4; rSSD=6; rNSW=5; rank_mean=5.286; match_rank=6
a 0 0 0 0 78 158 186 27 18 13 0 337 49 64 52 21 63 178 34 46
c 0 0 0 0 161 51 15 0 20 19 357 1 123 63 61 33 25 99 268 289
g 0 0 0 0 63 41 154 275 319 33 0 0 113 149 147 24 265 19 2 0
t 0 0 0 0 55 107 2 55 0 292 0 19 72 81 97 279 4 61 53 22
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