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_m9/peak-motifs_oligos_6nt_mkv4_m9.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_m9/peak-motifs_oligos_6nt_mkv4_m9_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m9_shift5 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m9_shift5 (oligos_6nt_mkv4_m9)
; oligos_6nt_mkv4_m9; m=0 (reference); ncol1=11; shift=5; ncol=16; -----mycCCACAGcv ; Alignment reference a 0 0 0 0 0 351 293 194 0 22 1229 47 1193 25 335 370 c 0 0 0 0 0 446 514 929 1366 1252 59 1259 95 36 476 370 g 0 0 0 0 0 285 244 167 14 74 64 49 67 1298 267 380 t 0 0 0 0 0 320 351 112 22 54 50 47 47 43 324 282

lola-PL_SOLEXA_FBgn0005630_shift4 (lola-PL_SOLEXA_FBgn0005630)
; oligos_6nt_mkv4_m9 versus lola-PL_SOLEXA_FBgn0005630; m=1/5; ncol2=14; w=-1; offset=-1; strand=D; shift=4; score=0.598127; ----kgmmCCACcgkg ; cor=; Ncor= a 0 0 0 0 357 215 944 808 0 0 2061 0 361 407 457 281 c 0 0 0 0 322 163 968 793 2061 2061 0 2061 1099 481 334 387 g 0 0 0 0 600 1232 0 137 0 0 0 0 123 834 690 939 t 0 0 0 0 780 447 148 322 0 0 0 0 476 337 576 452

lola-PL_SANGER_2.5_FBgn0005630_rc_shift4 (lola-PL_SANGER_2.5_FBgn0005630_rc)
; oligos_6nt_mkv4_m9 versus lola-PL_SANGER_2.5_FBgn0005630_rc; m=2/5; ncol2=9; w=-1; offset=-1; strand=R; shift=4; score=0.546944; ----TGmcCCACm--- ; cor=; Ncor= a 0 0 0 0 2 0 4 2 0 0 11 0 4 0 0 0 c 0 0 0 0 0 0 7 5 11 11 0 11 6 0 0 0 g 0 0 0 0 0 9 0 2 0 0 0 0 0 0 0 0 t 0 0 0 0 8 2 0 2 0 0 0 0 1 0 0 0

lmd_SOLEXA_5_FBgn0039039_rc_shift0 (lmd_SOLEXA_5_FBgn0039039_rc)
; oligos_6nt_mkv4_m9 versus lmd_SOLEXA_5_FBgn0039039_rc; m=3/5; ncol2=15; w=-5; offset=-5; strand=R; shift=0; score=0.453161; mmgmCCCCCcrCrga- ; cor=; Ncor= a 181 206 90 318 20 45 33 3 14 77 284 3 199 113 143 0 c 196 192 128 182 516 522 516 574 550 384 30 421 130 30 72 0 g 97 85 242 70 0 0 0 0 0 0 249 134 162 339 46 0 t 78 80 117 7 41 10 28 0 13 116 14 19 86 72 56 0

Opa_SANGER_5_FBgn0003002_shift1 (Opa_SANGER_5_FBgn0003002)
; oligos_6nt_mkv4_m9 versus Opa_SANGER_5_FBgn0003002; m=4/5; ncol2=13; w=-4; offset=-4; strand=D; shift=1; score=0.44943; -mkmmMCCCCmCyR-- ; cor=; Ncor= a 0 7 2 4 4 3 1 0 0 0 8 0 0 3 0 0 c 0 3 0 5 7 9 9 12 11 12 3 11 8 0 0 0 g 0 1 5 2 1 0 2 0 1 0 1 1 0 9 0 0 t 0 1 5 1 0 0 0 0 0 0 0 0 4 0 0 0

lmd_SANGER_5_FBgn0039039_rc_shift0 (lmd_SANGER_5_FBgn0039039_rc)
; oligos_6nt_mkv4_m9 versus lmd_SANGER_5_FBgn0039039_rc; m=5/5; ncol2=14; w=-5; offset=-5; strand=R; shift=0; score=0.419373; mmkaCCCCCCrCmG-- ; cor=; Ncor= a 10 8 1 13 0 0 0 0 0 1 11 0 9 3 0 0 c 8 9 3 5 20 22 22 22 22 16 1 18 7 1 0 0 g 2 3 11 4 0 0 0 0 0 0 10 4 3 15 0 0 t 1 2 7 0 2 0 0 0 0 5 0 0 3 2 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m9_shift5 (oligos_6nt_mkv4_m9)				; oligos_6nt_mkv4_m9; m=0 (reference); ncol1=11; shift=5; ncol=16; -----mycCCACAGcv ; Alignment reference a 0 0 0 0 0 351 293 194 0 22 1229 47 1193 25 335 370 c 0 0 0 0 0 446 514 929 1366 1252 59 1259 95 36 476 370 g 0 0 0 0 0 285 244 167 14 74 64 49 67 1298 267 380 t 0 0 0 0 0 320 351 112 22 54 50 47 47 43 324 282
lola-PL_SOLEXA_FBgn0005630_shift4 (lola-PL_SOLEXA_FBgn0005630)				; oligos_6nt_mkv4_m9 versus lola-PL_SOLEXA_FBgn0005630; m=1/5; ncol2=14; w=-1; offset=-1; strand=D; shift=4; score=0.598127; ----kgmmCCACcgkg ; cor=; Ncor= a 0 0 0 0 357 215 944 808 0 0 2061 0 361 407 457 281 c 0 0 0 0 322 163 968 793 2061 2061 0 2061 1099 481 334 387 g 0 0 0 0 600 1232 0 137 0 0 0 0 123 834 690 939 t 0 0 0 0 780 447 148 322 0 0 0 0 476 337 576 452
lola-PL_SANGER_2.5_FBgn0005630_rc_shift4 (lola-PL_SANGER_2.5_FBgn0005630_rc)				; oligos_6nt_mkv4_m9 versus lola-PL_SANGER_2.5_FBgn0005630_rc; m=2/5; ncol2=9; w=-1; offset=-1; strand=R; shift=4; score=0.546944; ----TGmcCCACm--- ; cor=; Ncor= a 0 0 0 0 2 0 4 2 0 0 11 0 4 0 0 0 c 0 0 0 0 0 0 7 5 11 11 0 11 6 0 0 0 g 0 0 0 0 0 9 0 2 0 0 0 0 0 0 0 0 t 0 0 0 0 8 2 0 2 0 0 0 0 1 0 0 0
lmd_SOLEXA_5_FBgn0039039_rc_shift0 (lmd_SOLEXA_5_FBgn0039039_rc)				; oligos_6nt_mkv4_m9 versus lmd_SOLEXA_5_FBgn0039039_rc; m=3/5; ncol2=15; w=-5; offset=-5; strand=R; shift=0; score=0.453161; mmgmCCCCCcrCrga- ; cor=; Ncor= a 181 206 90 318 20 45 33 3 14 77 284 3 199 113 143 0 c 196 192 128 182 516 522 516 574 550 384 30 421 130 30 72 0 g 97 85 242 70 0 0 0 0 0 0 249 134 162 339 46 0 t 78 80 117 7 41 10 28 0 13 116 14 19 86 72 56 0
Opa_SANGER_5_FBgn0003002_shift1 (Opa_SANGER_5_FBgn0003002)				; oligos_6nt_mkv4_m9 versus Opa_SANGER_5_FBgn0003002; m=4/5; ncol2=13; w=-4; offset=-4; strand=D; shift=1; score=0.44943; -mkmmMCCCCmCyR-- ; cor=; Ncor= a 0 7 2 4 4 3 1 0 0 0 8 0 0 3 0 0 c 0 3 0 5 7 9 9 12 11 12 3 11 8 0 0 0 g 0 1 5 2 1 0 2 0 1 0 1 1 0 9 0 0 t 0 1 5 1 0 0 0 0 0 0 0 0 4 0 0 0
lmd_SANGER_5_FBgn0039039_rc_shift0 (lmd_SANGER_5_FBgn0039039_rc)				; oligos_6nt_mkv4_m9 versus lmd_SANGER_5_FBgn0039039_rc; m=5/5; ncol2=14; w=-5; offset=-5; strand=R; shift=0; score=0.419373; mmkaCCCCCCrCmG-- ; cor=; Ncor= a 10 8 1 13 0 0 0 0 0 1 11 0 9 3 0 0 c 8 9 3 5 20 22 22 22 22 16 1 18 7 1 0 0 g 2 3 11 4 0 0 0 0 0 0 10 4 3 15 0 0 t 1 2 7 0 2 0 0 0 0 5 0 0 3 2 0 0