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/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1.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/oligos_6nt_mkv4_m1/peak-motifs_oligos_6nt_mkv4_m1_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift6 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m1_shift6 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=11; shift=6; ncol=17; ------cycCCACAAmm ; Alignment reference a 0 0 0 0 0 0 354 335 306 0 2 1250 50 1267 1364 427 379 c 0 0 0 0 0 0 516 530 804 1437 1382 94 1304 72 17 444 541 g 0 0 0 0 0 0 254 207 179 0 16 42 44 36 33 264 277 t 0 0 0 0 0 0 320 372 155 7 44 58 46 69 30 309 247

lola-PL_SOLEXA_FBgn0005630_shift5 (lola-PL_SOLEXA_FBgn0005630)
; oligos_6nt_mkv4_m1 versus lola-PL_SOLEXA_FBgn0005630; m=1/4; ncol2=14; w=-1; offset=-1; strand=D; shift=5; score=0.555117; -----kgmmCCACcgkg ; cor=; Ncor= a 0 0 0 0 0 357 215 944 808 0 0 2061 0 361 407 457 281 c 0 0 0 0 0 322 163 968 793 2061 2061 0 2061 1099 481 334 387 g 0 0 0 0 0 600 1232 0 137 0 0 0 0 123 834 690 939 t 0 0 0 0 0 780 447 148 322 0 0 0 0 476 337 576 452

lola-PL_SANGER_2.5_FBgn0005630_rc_shift5 (lola-PL_SANGER_2.5_FBgn0005630_rc)
; oligos_6nt_mkv4_m1 versus lola-PL_SANGER_2.5_FBgn0005630_rc; m=2/4; ncol2=9; w=-1; offset=-1; strand=R; shift=5; score=0.544368; -----TGmcCCACm--- ; cor=; Ncor= a 0 0 0 0 0 2 0 4 2 0 0 11 0 4 0 0 0 c 0 0 0 0 0 0 0 7 5 11 11 0 11 6 0 0 0 g 0 0 0 0 0 0 9 0 2 0 0 0 0 0 0 0 0 t 0 0 0 0 0 8 2 0 2 0 0 0 0 1 0 0 0

Lag1_Cell_FBgn0040918_shift9 (Lag1_Cell_FBgn0040918)
; oligos_6nt_mkv4_m1 versus Lag1_Cell_FBgn0040918; m=3/4; ncol2=10; w=0; offset=3; strand=D; shift=9; score=0.440737; ---------CyACyAaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 17 1 0 18 12 10 c 0 0 0 0 0 0 0 0 0 19 9 2 18 12 0 0 3 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 4 t 0 0 0 0 0 0 0 0 0 0 10 0 0 7 0 3 2

CG7368_SOLEXA_2.5_FBgn0036179_rc_shift0 (CG7368_SOLEXA_2.5_FBgn0036179_rc)
; oligos_6nt_mkv4_m1 versus CG7368_SOLEXA_2.5_FBgn0036179_rc; m=4/4; ncol2=15; w=-6; offset=-6; strand=R; shift=0; score=0.400001; yyCCCCChCCCmChm-- ; cor=; Ncor= a 38 51 27 3 8 1 34 90 44 3 8 97 14 64 95 0 0 c 111 95 203 230 227 235 200 84 170 230 224 133 199 66 65 0 0 g 16 22 1 0 0 0 0 0 1 0 0 0 0 19 13 0 0 t 67 68 5 3 1 0 2 62 21 3 4 6 23 81 26 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m1_shift6 (oligos_6nt_mkv4_m1)				; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=11; shift=6; ncol=17; ------cycCCACAAmm ; Alignment reference a 0 0 0 0 0 0 354 335 306 0 2 1250 50 1267 1364 427 379 c 0 0 0 0 0 0 516 530 804 1437 1382 94 1304 72 17 444 541 g 0 0 0 0 0 0 254 207 179 0 16 42 44 36 33 264 277 t 0 0 0 0 0 0 320 372 155 7 44 58 46 69 30 309 247
lola-PL_SOLEXA_FBgn0005630_shift5 (lola-PL_SOLEXA_FBgn0005630)				; oligos_6nt_mkv4_m1 versus lola-PL_SOLEXA_FBgn0005630; m=1/4; ncol2=14; w=-1; offset=-1; strand=D; shift=5; score=0.555117; -----kgmmCCACcgkg ; cor=; Ncor= a 0 0 0 0 0 357 215 944 808 0 0 2061 0 361 407 457 281 c 0 0 0 0 0 322 163 968 793 2061 2061 0 2061 1099 481 334 387 g 0 0 0 0 0 600 1232 0 137 0 0 0 0 123 834 690 939 t 0 0 0 0 0 780 447 148 322 0 0 0 0 476 337 576 452
lola-PL_SANGER_2.5_FBgn0005630_rc_shift5 (lola-PL_SANGER_2.5_FBgn0005630_rc)				; oligos_6nt_mkv4_m1 versus lola-PL_SANGER_2.5_FBgn0005630_rc; m=2/4; ncol2=9; w=-1; offset=-1; strand=R; shift=5; score=0.544368; -----TGmcCCACm--- ; cor=; Ncor= a 0 0 0 0 0 2 0 4 2 0 0 11 0 4 0 0 0 c 0 0 0 0 0 0 0 7 5 11 11 0 11 6 0 0 0 g 0 0 0 0 0 0 9 0 2 0 0 0 0 0 0 0 0 t 0 0 0 0 0 8 2 0 2 0 0 0 0 1 0 0 0
Lag1_Cell_FBgn0040918_shift9 (Lag1_Cell_FBgn0040918)				; oligos_6nt_mkv4_m1 versus Lag1_Cell_FBgn0040918; m=3/4; ncol2=10; w=0; offset=3; strand=D; shift=9; score=0.440737; ---------CyACyAaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 17 1 0 18 12 10 c 0 0 0 0 0 0 0 0 0 19 9 2 18 12 0 0 3 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 4 t 0 0 0 0 0 0 0 0 0 0 10 0 0 7 0 3 2
CG7368_SOLEXA_2.5_FBgn0036179_rc_shift0 (CG7368_SOLEXA_2.5_FBgn0036179_rc)				; oligos_6nt_mkv4_m1 versus CG7368_SOLEXA_2.5_FBgn0036179_rc; m=4/4; ncol2=15; w=-6; offset=-6; strand=R; shift=0; score=0.400001; yyCCCCChCCCmChm-- ; cor=; Ncor= a 38 51 27 3 8 1 34 90 44 3 8 97 14 64 95 0 0 c 111 95 203 230 227 235 200 84 170 230 224 133 199 66 65 0 0 g 16 22 1 0 0 0 0 0 1 0 0 0 0 19 13 0 0 t 67 68 5 3 1 0 2 62 21 3 4 6 23 81 26 0 0