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.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.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.2025-11-26.205219_2025-11-26.205219_vuDZlG/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_FlyFactorSurvey
One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_6nt_m2_shift0 (positions_6nt_m2) |
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; positions_6nt_m2; m=0 (reference); ncol1=24; shift=0; ncol=24; mmmmmmaCACACrCACACACaCac
; Alignment reference
a 1976 1421 1813 2043 2202 1829 3002 319 4970 139 5172 110 3697 93 5299 53 5244 49 5209 111 3668 354 3315 615
c 1544 2207 2209 2024 1977 2553 1221 4839 124 5173 74 5231 121 5239 30 5314 32 5331 63 5169 347 4284 638 3623
g 937 884 682 659 682 428 830 133 280 56 151 67 1466 57 113 33 173 34 132 91 609 386 904 586
t 1057 1002 810 788 653 704 461 223 140 146 117 106 230 125 72 114 65 100 110 143 890 490 657 690
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| klu_SOLEXA_5_FBgn0013469_rc_shift2 (klu_SOLEXA_5_FBgn0013469_rc) |
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; positions_6nt_m2 versus klu_SOLEXA_5_FBgn0013469_rc; m=1/1; ncol2=15; w=0; offset=2; strand=R; shift=2; score=0.449377; --mmmmmCACCCmCrCm-------
; cor=; Ncor=
a 0 0 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 0 0 0 0 0 0
c 0 0 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 0 0 0 0 0 0
g 0 0 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 0 0 0 0 0 0
t 0 0 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0 0 0 0 0 0 0
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