One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey_2016.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_FlyFactorSurvey
One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_6nt_m3_shift0 (positions_6nt_m3) |
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|
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; positions_6nt_m3; m=0 (reference); ncol1=24; shift=0; ncol=24; gtGtGTGTGTGyGTGTGtkkkkkk
; Alignment reference
a 706 680 497 902 143 113 101 66 117 72 126 244 108 119 146 143 227 472 711 663 797 820 1016 1069
c 591 913 397 618 94 134 36 175 33 117 58 1474 68 153 60 282 133 842 437 698 669 700 902 953
g 3680 646 4351 350 5253 63 5414 32 5399 30 5324 123 5316 75 5255 126 4915 1228 2606 1991 2070 2228 2242 1569
t 625 3363 357 3732 112 5292 51 5329 53 5383 94 3761 110 5255 141 5051 327 3060 1848 2250 2066 1854 1442 2011
|
| klu_SOLEXA_5_FBgn0013469_shift7 (klu_SOLEXA_5_FBgn0013469) |
 |
|
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; positions_6nt_m3 versus klu_SOLEXA_5_FBgn0013469; m=1/1; ncol2=15; w=0; offset=7; strand=D; shift=7; score=0.449315; -------kGyGkGGGTGkkkkk--
; cor=; Ncor=
a 0 0 0 0 0 0 0 75 33 37 7 14 26 10 9 71 3 26 101 95 79 91 0 0
c 0 0 0 0 0 0 0 54 5 230 1 6 0 5 0 48 0 24 64 85 90 82 0 0
g 0 0 0 0 0 0 0 138 360 10 493 168 472 485 491 6 491 298 204 188 168 152 0 0
t 0 0 0 0 0 0 0 156 54 226 2 315 5 3 3 378 9 155 134 135 156 132 0 0
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