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_m6/peak-motifs_positions_6nt_m6.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_m6/peak-motifs_positions_6nt_m6_vs_db_FlyFactorSurvey
One-to-n matrix alignment; reference matrix: positions_6nt_m6_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| positions_6nt_m6_shift0 (positions_6nt_m6) |
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; positions_6nt_m6; m=0 (reference); ncol1=24; shift=0; ncol=24; acaCacACACACACACACACACac
; Alignment reference
a 5382 1628 6496 1163 6198 1950 6965 341 9355 152 9447 127 9572 127 7544 82 9553 64 9347 116 7140 653 6251 1014
c 1768 5987 1310 7182 1877 6536 1286 9166 169 9522 71 9641 64 9499 131 9623 49 9636 85 9519 511 7825 1066 6677
g 1480 953 1117 718 1014 540 1076 151 256 61 300 49 195 105 1952 60 217 54 337 129 1051 660 1499 1023
t 1328 1390 1035 895 869 932 631 300 178 223 140 141 127 227 331 193 139 204 189 194 1256 820 1142 1244
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| klu_SOLEXA_5_FBgn0013469_rc_shift2 (klu_SOLEXA_5_FBgn0013469_rc) |
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; positions_6nt_m6 versus klu_SOLEXA_5_FBgn0013469_rc; m=1/1; ncol2=15; w=0; offset=2; strand=R; shift=2; score=0.443304; --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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