One-to-n alignments
Command: compare-matrices -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/apache/2019/10/25/compare-matrices_2019-10-25.151709_TBOKc6/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -format2 tf -strand DR -lth cor 0.7 -lth Ncor 0.4 -uth match_rank 50 -return cor,Ncor,logoDP,NsEucl,NSW,match_rank,matrix_id,matrix_name,width,strand,offset,consensus,alignments_1ton -o $RSAT/public_html/tmp/apache/2019/10/25/compare-matrices_2019-10-25.151709_TBOKc6/compare-matrices.tab
One-to-n matrix alignment; reference matrix: oligos_5-8nt_m1_shift3 ; 3 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NsEucl |
NSW |
rcor |
rNcor |
rlogoDP |
rNsEucl |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
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| oligos_5-8nt_m1_shift3 (oligos_5-8nt_m1) |
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; oligos_5-8nt_m1; m=0 (reference); ncol1=24; shift=3; ncol=27; ---wwaaAGCCCAAATtttaAAawwyh
; Alignment reference
a 0 0 0 19 22 30 36 47 8 0 2 1 50 42 44 8 13 9 11 32 39 43 30 19 28 13 18
c 0 0 0 13 12 12 6 0 1 54 53 48 1 5 3 4 9 5 7 9 4 4 7 5 4 17 16
g 0 0 0 7 6 5 3 9 42 2 1 1 0 1 5 3 4 7 6 4 3 2 6 9 9 12 8
t 0 0 0 17 16 9 11 0 5 0 0 6 5 8 4 41 30 35 32 11 10 7 13 23 15 14 14
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| TBP3_MA1355.1_JASPAR_shift0 (TBP3:MA1355.1:JASPAR) |
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0.729 |
0.432 |
5.645 |
0.926 |
0.911 |
2 |
1 |
1 |
1 |
2 |
1.400 |
1 |
; oligos_5-8nt_m1 versus TBP3_MA1355.1_JASPAR (TBP3:MA1355.1:JASPAR); m=1/2; ncol2=19; w=16; offset=-3; strand=D; shift=0; score= 1.4; awwwhtwwrCCCTAAwtwy--------
; cor=0.729; Ncor=0.432; logoDP=5.645; NsEucl=0.926; NSW=0.911; rcor=2; rNcor=1; rlogoDP=1; rNsEucl=1; rNSW=2; rank_mean=1.400; match_rank=1
a 266 277 262 237 171 119 302 378 335 42 0 0 0 572 483 191 95 144 140 0 0 0 0 0 0 0 0
c 105 76 91 114 148 80 9 3 0 530 572 572 0 0 0 87 117 137 148 0 0 0 0 0 0 0 0
g 68 68 58 47 43 76 86 1 237 0 0 0 0 0 87 12 25 59 88 0 0 0 0 0 0 0 0
t 133 151 161 174 210 297 175 190 0 0 0 0 572 0 2 282 335 232 196 0 0 0 0 0 0 0 0
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| PK22848.1_M0587_1.02_CISBP_shift10 (PK22848.1:M0587_1.02:CISBP) |
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0.739 |
0.401 |
1.814 |
0.923 |
0.922 |
1 |
2 |
2 |
2 |
1 |
1.600 |
2 |
; oligos_5-8nt_m1 versus PK22848.1_M0587_1.02_CISBP (PK22848.1:M0587_1.02:CISBP); m=2/2; ncol2=13; w=13; offset=7; strand=D; shift=10; score= 1.6; ----------maaAATTTwaawa----
; cor=0.739; Ncor=0.401; logoDP=1.814; NsEucl=0.923; NSW=0.922; rcor=1; rNcor=2; rlogoDP=2; rNsEucl=2; rNSW=1; rank_mean=1.600; match_rank=2
a 0 0 0 0 0 0 0 0 0 0 29 28 67 78 82 0 0 0 26 62 57 39 35 0 0 0 0
c 0 0 0 0 0 0 0 0 0 0 29 24 11 7 4 0 0 0 13 10 15 18 22 0 0 0 0
g 0 0 0 0 0 0 0 0 0 0 21 24 11 7 3 0 0 8 13 18 14 17 21 0 0 0 0
t 0 0 0 0 0 0 0 0 0 0 21 24 11 8 11 100 100 92 48 10 14 26 22 0 0 0 0
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