One-to-n alignments
Command: compare-matrices -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/04/09/compare-matrices_2026-04-09.121224_cmDgyc/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/www-data/2026/04/09/compare-matrices_2026-04-09.121224_cmDgyc/compare-matrices.tab
One-to-n matrix alignment; reference matrix: positions_7nt_m5_shift0 ; 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 |
|---|
| positions_7nt_m5_shift0 (positions_7nt_m5) |
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; positions_7nt_m5; m=0 (reference); ncol1=15; shift=0; ncol=15; rwcGGAGAAGAGArr
; Alignment reference
a 803 784 380 300 323 2025 105 2051 2050 125 2113 372 1693 813 804
c 334 415 1529 113 53 159 43 90 101 53 92 154 152 408 393
g 735 562 189 1794 1925 72 2171 176 106 2138 70 1633 305 654 633
t 501 612 275 166 72 117 54 56 116 57 98 214 223 498 543
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| ONAC127_UN0430.2_JASPAR_shift7 (ONAC127:UN0430.2:JASPAR) |
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0.762 |
0.406 |
3.608 |
0.878 |
0.881 |
1 |
1 |
2 |
1 |
1 |
1.200 |
1 |
; positions_7nt_m5 versus ONAC127_UN0430.2_JASPAR (ONAC127:UN0430.2:JASPAR); m=1/2; ncol2=8; w=0; offset=7; strand=D; shift=7; score= 1.2; -------AAGAAAAG
; cor=0.762; Ncor=0.406; logoDP=3.608; NsEucl=0.878; NSW=0.881; rcor=1; rNcor=1; rlogoDP=2; rNsEucl=1; rNSW=1; rank_mean=1.200; match_rank=1
a 0 0 0 0 0 0 0 65 67 4 57 61 63 58 3
c 0 0 0 0 0 0 0 0 0 0 2 5 0 1 7
g 0 0 0 0 0 0 0 0 0 62 7 1 5 3 56
t 0 0 0 0 0 0 0 3 1 2 2 1 0 6 2
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| NTL8_MA1678.3_JASPAR_shift6 (NTL8:MA1678.3:JASPAR) |
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0.755 |
0.402 |
3.879 |
0.875 |
0.875 |
2 |
2 |
1 |
2 |
2 |
1.800 |
2 |
; positions_7nt_m5 versus NTL8_MA1678.3_JASPAR (NTL8:MA1678.3:JASPAR); m=2/2; ncol2=8; w=0; offset=6; strand=D; shift=6; score= 1.8; ------GAAGAAAC-
; cor=0.755; Ncor=0.402; logoDP=3.879; NsEucl=0.875; NSW=0.875; rcor=2; rNcor=2; rlogoDP=1; rNsEucl=2; rNSW=2; rank_mean=1.800; match_rank=2
a 0 0 0 0 0 0 64 958 912 8 795 957 933 45 0
c 0 0 0 0 0 0 171 5 12 6 79 4 10 850 0
g 0 0 0 0 0 0 669 10 42 956 35 3 16 40 0
t 0 0 0 0 0 0 78 9 16 12 73 18 23 47 0
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