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/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_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/oligos_7nt_mkv5_m3/peak-motifs_oligos_7nt_mkv5_m3_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift5 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m3_shift5 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=5; ncol=17; -----caCCAmCACCac ; Alignment reference a 0 0 0 0 0 537 1591 66 86 2670 1679 63 2659 69 354 1474 675 c 0 0 0 0 0 1526 481 2678 2677 71 919 2713 103 2669 2209 633 1190 g 0 0 0 0 0 300 368 59 42 43 104 15 52 63 104 430 431 t 0 0 0 0 0 489 412 49 47 68 150 61 38 51 185 315 556

CG10267_SANGER_5_FBgn0037446_shift6 (CG10267_SANGER_5_FBgn0037446)
; oligos_7nt_mkv5_m3 versus CG10267_SANGER_5_FBgn0037446; m=1/4; ncol2=10; w=0; offset=1; strand=D; shift=6; score=0.601382; ------whyAACACTR- ; cor=; Ncor= a 0 0 0 0 0 0 8 6 1 16 16 1 16 0 0 11 0 c 0 0 0 0 0 0 0 6 10 0 0 14 0 16 0 0 0 g 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 5 0 t 0 0 0 0 0 0 7 4 5 0 0 1 0 0 16 0 0

Aef1_FlyReg_FBgn0005694_shift8 (Aef1_FlyReg_FBgn0005694)
; oligos_7nt_mkv5_m3 versus Aef1_FlyReg_FBgn0005694; m=2/4; ncol2=8; w=0; offset=3; strand=D; shift=8; score=0.48462; --------CAACwACw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 3 3 0 2 3 0 2 0 c 0 0 0 0 0 0 0 0 3 0 0 3 0 0 3 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0

CG31782-F9-11_SOLEXA_FBgn0051782_rc_shift3 (CG31782-F9-11_SOLEXA_FBgn0051782_rc)
; oligos_7nt_mkv5_m3 versus CG31782-F9-11_SOLEXA_FBgn0051782_rc; m=3/4; ncol2=11; w=-2; offset=-2; strand=R; shift=3; score=0.457205; ---ctCACCacyaa--- ; cor=; Ncor= a 0 0 0 269 617 42 2023 0 0 1676 407 471 1282 1413 0 0 0 c 0 0 0 1324 287 1979 143 2554 2552 582 1464 954 350 486 0 0 0 g 0 0 0 584 195 25 0 0 0 27 305 289 438 420 0 0 0 t 0 0 0 375 1453 506 386 0 1 269 377 838 482 234 0 0 0

klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)
; oligos_7nt_mkv5_m3 versus klu_SOLEXA_5_FBgn0013469_rc; m=4/4; ncol2=15; w=-5; offset=-5; strand=R; shift=0; score=0.412172; mmmmmCACCCmCrCm-- ; cor=; Ncor= a 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 0 c 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 0 g 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 0 t 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m3_shift5 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=5; ncol=17; -----caCCAmCACCac ; Alignment reference a 0 0 0 0 0 537 1591 66 86 2670 1679 63 2659 69 354 1474 675 c 0 0 0 0 0 1526 481 2678 2677 71 919 2713 103 2669 2209 633 1190 g 0 0 0 0 0 300 368 59 42 43 104 15 52 63 104 430 431 t 0 0 0 0 0 489 412 49 47 68 150 61 38 51 185 315 556
CG10267_SANGER_5_FBgn0037446_shift6 (CG10267_SANGER_5_FBgn0037446)				; oligos_7nt_mkv5_m3 versus CG10267_SANGER_5_FBgn0037446; m=1/4; ncol2=10; w=0; offset=1; strand=D; shift=6; score=0.601382; ------whyAACACTR- ; cor=; Ncor= a 0 0 0 0 0 0 8 6 1 16 16 1 16 0 0 11 0 c 0 0 0 0 0 0 0 6 10 0 0 14 0 16 0 0 0 g 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 5 0 t 0 0 0 0 0 0 7 4 5 0 0 1 0 0 16 0 0
Aef1_FlyReg_FBgn0005694_shift8 (Aef1_FlyReg_FBgn0005694)				; oligos_7nt_mkv5_m3 versus Aef1_FlyReg_FBgn0005694; m=2/4; ncol2=8; w=0; offset=3; strand=D; shift=8; score=0.48462; --------CAACwACw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 3 3 0 2 3 0 2 0 c 0 0 0 0 0 0 0 0 3 0 0 3 0 0 3 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0
CG31782-F9-11_SOLEXA_FBgn0051782_rc_shift3 (CG31782-F9-11_SOLEXA_FBgn0051782_rc)				; oligos_7nt_mkv5_m3 versus CG31782-F9-11_SOLEXA_FBgn0051782_rc; m=3/4; ncol2=11; w=-2; offset=-2; strand=R; shift=3; score=0.457205; ---ctCACCacyaa--- ; cor=; Ncor= a 0 0 0 269 617 42 2023 0 0 1676 407 471 1282 1413 0 0 0 c 0 0 0 1324 287 1979 143 2554 2552 582 1464 954 350 486 0 0 0 g 0 0 0 584 195 25 0 0 0 27 305 289 438 420 0 0 0 t 0 0 0 375 1453 506 386 0 1 269 377 838 482 234 0 0 0
klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)				; oligos_7nt_mkv5_m3 versus klu_SOLEXA_5_FBgn0013469_rc; m=4/4; ncol2=15; w=-5; offset=-5; strand=R; shift=0; score=0.412172; mmmmmCACCCmCrCm-- ; cor=; Ncor= a 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 0 c 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 0 g 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 0 t 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0 0