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_6nt_mkv4_m8/peak-motifs_oligos_6nt_mkv4_m8.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_6nt_mkv4_m8/peak-motifs_oligos_6nt_mkv4_m8_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m8_shift3 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m8_shift3 (oligos_6nt_mkv4_m8)
; oligos_6nt_mkv4_m8; m=0 (reference); ncol1=10; shift=3; ncol=13; ---mrCAAAACam ; Alignment reference a 0 0 0 588 575 0 1505 1527 1517 1531 0 700 535 c 0 0 0 401 285 1520 0 0 0 0 1533 288 428 g 0 0 0 275 408 0 3 0 1 0 0 317 327 t 0 0 0 269 265 13 25 6 15 2 0 228 243

Ara_Cell_FBgn0015904_shift4 (Ara_Cell_FBgn0015904)
; oligos_6nt_mkv4_m8 versus Ara_Cell_FBgn0015904; m=1/11; ncol2=8; w=0; offset=1; strand=D; shift=4; score=0.582067; ----raAwwACA- ; cor=; Ncor= a 0 0 0 0 12 16 24 14 23 34 0 34 0 c 0 0 0 0 5 7 1 0 0 0 34 0 0 g 0 0 0 0 10 6 1 5 0 0 0 0 0 t 0 0 0 0 7 5 8 15 11 0 0 0 0

grh_FlyReg_FBgn0259211_rc_shift4 (grh_FlyReg_FBgn0259211_rc)
; oligos_6nt_mkv4_m8 versus grh_FlyReg_FBgn0259211_rc; m=2/11; ncol2=10; w=0; offset=1; strand=R; shift=4; score=0.580747; ----rbwrAACMA ; cor=; Ncor= a 0 0 0 0 4 0 4 4 8 7 1 2 7 c 0 0 0 0 0 3 1 1 0 0 6 6 0 g 0 0 0 0 3 2 1 3 0 1 0 0 1 t 0 0 0 0 1 3 2 0 0 0 1 0 0

pan_FlyReg_FBgn0085432_rc_shift2 (pan_FlyReg_FBgn0085432_rc)
; oligos_6nt_mkv4_m8 versus pan_FlyReg_FBgn0085432_rc; m=3/11; ncol2=8; w=-1; offset=-1; strand=R; shift=2; score=0.502901; --kWTCAAAr--- ; cor=; Ncor= a 0 0 4 17 3 3 23 22 20 8 0 0 0 c 0 0 3 0 5 20 0 1 0 3 0 0 0 g 0 0 11 0 0 2 0 0 3 10 0 0 0 t 0 0 7 8 17 0 2 2 2 4 0 0 0

jim_F1-9_SOLEXA_2.5_FBgn0027339_shift1 (jim_F1-9_SOLEXA_2.5_FBgn0027339)
; oligos_6nt_mkv4_m8 versus jim_F1-9_SOLEXA_2.5_FBgn0027339; m=4/11; ncol2=15; w=-2; offset=-2; strand=D; shift=1; score=0.489351; -rmAAaAAAAmma ; cor=; Ncor= a 0 202 124 372 414 259 411 369 349 412 159 154 240 c 0 60 190 26 6 104 1 52 5 0 222 122 55 g 0 102 43 6 0 0 4 2 64 11 40 74 74 t 0 25 50 19 3 60 7 0 5 0 2 73 54

Exd_Cell_FBgn0000611_rc_shift2 (Exd_Cell_FBgn0000611_rc)
; oligos_6nt_mkv4_m8 versus Exd_Cell_FBgn0000611_rc; m=5/11; ncol2=8; w=-1; offset=-1; strand=R; shift=2; score=0.464969; --yRTCAAAa--- ; cor=; Ncor= a 0 0 0 5 0 0 17 17 14 5 0 0 0 c 0 0 6 0 0 17 0 0 2 4 0 0 0 g 0 0 0 12 0 0 0 0 0 4 0 0 0 t 0 0 11 0 17 0 0 0 1 4 0 0 0

Ara_SOLEXA_FBgn0015904_shift6 (Ara_SOLEXA_FBgn0015904)
; oligos_6nt_mkv4_m8 versus Ara_SOLEXA_FBgn0015904; m=6/11; ncol2=6; w=0; offset=3; strand=D; shift=6; score=0.445715; ------awwACA- ; cor=; Ncor= a 0 0 0 0 0 0 155 97 193 313 0 313 0 c 0 0 0 0 0 0 36 0 0 0 313 0 0 g 0 0 0 0 0 0 44 45 38 0 0 0 0 t 0 0 0 0 0 0 78 171 82 0 0 0 0

exd_FlyReg_FBgn0000611_rc_shift0 (exd_FlyReg_FBgn0000611_rc)
; oligos_6nt_mkv4_m8 versus exd_FlyReg_FBgn0000611_rc; m=7/11; ncol2=10; w=-3; offset=-3; strand=R; shift=0; score=0.433853; twrawyrAAA--- ; cor=; Ncor= a 1 4 3 3 3 1 2 6 5 5 0 0 0 c 1 0 1 1 0 3 1 0 0 1 0 0 0 g 1 0 2 1 0 0 2 0 0 0 0 0 0 t 3 2 0 1 3 2 1 0 1 0 0 0 0

Mirr_SOLEXA_FBgn0014343_shift6 (Mirr_SOLEXA_FBgn0014343)
; oligos_6nt_mkv4_m8 versus Mirr_SOLEXA_FBgn0014343; m=8/11; ncol2=6; w=0; offset=3; strand=D; shift=6; score=0.425234; ------wwwACA- ; cor=; Ncor= a 0 0 0 0 0 0 550 410 782 1415 0 1415 0 c 0 0 0 0 0 0 158 93 0 0 1415 0 0 g 0 0 0 0 0 0 327 282 204 0 0 0 0 t 0 0 0 0 0 0 380 630 429 0 0 0 0

sage_da_SANGER_5_FBgn0000413_shift6 (sage_da_SANGER_5_FBgn0000413)
; oligos_6nt_mkv4_m8 versus sage_da_SANGER_5_FBgn0000413; m=9/11; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.416231; ------rAAMCAs ; cor=; Ncor= a 0 0 0 0 0 0 12 17 21 16 0 23 0 c 0 0 0 0 0 0 0 3 2 6 23 0 10 g 0 0 0 0 0 0 6 3 0 1 0 0 9 t 0 0 0 0 0 0 5 0 0 0 0 0 4

sage_da_SANGER_5_FBgn0037672_shift6 (sage_da_SANGER_5_FBgn0037672)
; oligos_6nt_mkv4_m8 versus sage_da_SANGER_5_FBgn0037672; m=10/11; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.416231; ------rAAMCAs ; cor=; Ncor= a 0 0 0 0 0 0 12 17 21 16 0 23 0 c 0 0 0 0 0 0 0 3 2 6 23 0 10 g 0 0 0 0 0 0 6 3 0 1 0 0 9 t 0 0 0 0 0 0 5 0 0 0 0 0 4

Side_SANGER_5_FBgn0032741_shift6 (Side_SANGER_5_FBgn0032741)
; oligos_6nt_mkv4_m8 versus Side_SANGER_5_FBgn0032741; m=11/11; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.416231; ------rAAMCAs ; cor=; Ncor= a 0 0 0 0 0 0 12 17 21 16 0 23 0 c 0 0 0 0 0 0 0 3 2 6 23 0 10 g 0 0 0 0 0 0 6 3 0 1 0 0 9 t 0 0 0 0 0 0 5 0 0 0 0 0 4

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m8_shift3 (oligos_6nt_mkv4_m8)				; oligos_6nt_mkv4_m8; m=0 (reference); ncol1=10; shift=3; ncol=13; ---mrCAAAACam ; Alignment reference a 0 0 0 588 575 0 1505 1527 1517 1531 0 700 535 c 0 0 0 401 285 1520 0 0 0 0 1533 288 428 g 0 0 0 275 408 0 3 0 1 0 0 317 327 t 0 0 0 269 265 13 25 6 15 2 0 228 243
Ara_Cell_FBgn0015904_shift4 (Ara_Cell_FBgn0015904)				; oligos_6nt_mkv4_m8 versus Ara_Cell_FBgn0015904; m=1/11; ncol2=8; w=0; offset=1; strand=D; shift=4; score=0.582067; ----raAwwACA- ; cor=; Ncor= a 0 0 0 0 12 16 24 14 23 34 0 34 0 c 0 0 0 0 5 7 1 0 0 0 34 0 0 g 0 0 0 0 10 6 1 5 0 0 0 0 0 t 0 0 0 0 7 5 8 15 11 0 0 0 0
grh_FlyReg_FBgn0259211_rc_shift4 (grh_FlyReg_FBgn0259211_rc)				; oligos_6nt_mkv4_m8 versus grh_FlyReg_FBgn0259211_rc; m=2/11; ncol2=10; w=0; offset=1; strand=R; shift=4; score=0.580747; ----rbwrAACMA ; cor=; Ncor= a 0 0 0 0 4 0 4 4 8 7 1 2 7 c 0 0 0 0 0 3 1 1 0 0 6 6 0 g 0 0 0 0 3 2 1 3 0 1 0 0 1 t 0 0 0 0 1 3 2 0 0 0 1 0 0
pan_FlyReg_FBgn0085432_rc_shift2 (pan_FlyReg_FBgn0085432_rc)				; oligos_6nt_mkv4_m8 versus pan_FlyReg_FBgn0085432_rc; m=3/11; ncol2=8; w=-1; offset=-1; strand=R; shift=2; score=0.502901; --kWTCAAAr--- ; cor=; Ncor= a 0 0 4 17 3 3 23 22 20 8 0 0 0 c 0 0 3 0 5 20 0 1 0 3 0 0 0 g 0 0 11 0 0 2 0 0 3 10 0 0 0 t 0 0 7 8 17 0 2 2 2 4 0 0 0
jim_F1-9_SOLEXA_2.5_FBgn0027339_shift1 (jim_F1-9_SOLEXA_2.5_FBgn0027339)				; oligos_6nt_mkv4_m8 versus jim_F1-9_SOLEXA_2.5_FBgn0027339; m=4/11; ncol2=15; w=-2; offset=-2; strand=D; shift=1; score=0.489351; -rmAAaAAAAmma ; cor=; Ncor= a 0 202 124 372 414 259 411 369 349 412 159 154 240 c 0 60 190 26 6 104 1 52 5 0 222 122 55 g 0 102 43 6 0 0 4 2 64 11 40 74 74 t 0 25 50 19 3 60 7 0 5 0 2 73 54
Exd_Cell_FBgn0000611_rc_shift2 (Exd_Cell_FBgn0000611_rc)				; oligos_6nt_mkv4_m8 versus Exd_Cell_FBgn0000611_rc; m=5/11; ncol2=8; w=-1; offset=-1; strand=R; shift=2; score=0.464969; --yRTCAAAa--- ; cor=; Ncor= a 0 0 0 5 0 0 17 17 14 5 0 0 0 c 0 0 6 0 0 17 0 0 2 4 0 0 0 g 0 0 0 12 0 0 0 0 0 4 0 0 0 t 0 0 11 0 17 0 0 0 1 4 0 0 0
Ara_SOLEXA_FBgn0015904_shift6 (Ara_SOLEXA_FBgn0015904)				; oligos_6nt_mkv4_m8 versus Ara_SOLEXA_FBgn0015904; m=6/11; ncol2=6; w=0; offset=3; strand=D; shift=6; score=0.445715; ------awwACA- ; cor=; Ncor= a 0 0 0 0 0 0 155 97 193 313 0 313 0 c 0 0 0 0 0 0 36 0 0 0 313 0 0 g 0 0 0 0 0 0 44 45 38 0 0 0 0 t 0 0 0 0 0 0 78 171 82 0 0 0 0
exd_FlyReg_FBgn0000611_rc_shift0 (exd_FlyReg_FBgn0000611_rc)				; oligos_6nt_mkv4_m8 versus exd_FlyReg_FBgn0000611_rc; m=7/11; ncol2=10; w=-3; offset=-3; strand=R; shift=0; score=0.433853; twrawyrAAA--- ; cor=; Ncor= a 1 4 3 3 3 1 2 6 5 5 0 0 0 c 1 0 1 1 0 3 1 0 0 1 0 0 0 g 1 0 2 1 0 0 2 0 0 0 0 0 0 t 3 2 0 1 3 2 1 0 1 0 0 0 0
Mirr_SOLEXA_FBgn0014343_shift6 (Mirr_SOLEXA_FBgn0014343)				; oligos_6nt_mkv4_m8 versus Mirr_SOLEXA_FBgn0014343; m=8/11; ncol2=6; w=0; offset=3; strand=D; shift=6; score=0.425234; ------wwwACA- ; cor=; Ncor= a 0 0 0 0 0 0 550 410 782 1415 0 1415 0 c 0 0 0 0 0 0 158 93 0 0 1415 0 0 g 0 0 0 0 0 0 327 282 204 0 0 0 0 t 0 0 0 0 0 0 380 630 429 0 0 0 0
sage_da_SANGER_5_FBgn0000413_shift6 (sage_da_SANGER_5_FBgn0000413)				; oligos_6nt_mkv4_m8 versus sage_da_SANGER_5_FBgn0000413; m=9/11; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.416231; ------rAAMCAs ; cor=; Ncor= a 0 0 0 0 0 0 12 17 21 16 0 23 0 c 0 0 0 0 0 0 0 3 2 6 23 0 10 g 0 0 0 0 0 0 6 3 0 1 0 0 9 t 0 0 0 0 0 0 5 0 0 0 0 0 4
sage_da_SANGER_5_FBgn0037672_shift6 (sage_da_SANGER_5_FBgn0037672)				; oligos_6nt_mkv4_m8 versus sage_da_SANGER_5_FBgn0037672; m=10/11; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.416231; ------rAAMCAs ; cor=; Ncor= a 0 0 0 0 0 0 12 17 21 16 0 23 0 c 0 0 0 0 0 0 0 3 2 6 23 0 10 g 0 0 0 0 0 0 6 3 0 1 0 0 9 t 0 0 0 0 0 0 5 0 0 0 0 0 4
Side_SANGER_5_FBgn0032741_shift6 (Side_SANGER_5_FBgn0032741)				; oligos_6nt_mkv4_m8 versus Side_SANGER_5_FBgn0032741; m=11/11; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.416231; ------rAAMCAs ; cor=; Ncor= a 0 0 0 0 0 0 12 17 21 16 0 23 0 c 0 0 0 0 0 0 0 3 2 6 23 0 10 g 0 0 0 0 0 0 6 3 0 1 0 0 9 t 0 0 0 0 0 0 5 0 0 0 0 0 4