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/dyads_m6/peak-motifs_dyads_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/dyads_m6/peak-motifs_dyads_m6_vs_db_FlyFactorSurvey

One-to-n matrix alignment; reference matrix: dyads_m6_shift3 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m6_shift3 (dyads_m6)
; dyads_m6; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ccACCACCAcc ; Alignment reference a 0 0 0 849 627 3918 50 30 4141 38 14 3899 676 705 c 0 0 0 2252 2408 191 4112 4096 103 4058 4126 239 2169 2498 g 0 0 0 690 543 129 102 115 126 110 85 188 692 474 t 0 0 0 681 894 234 208 231 102 266 247 146 935 795

CG31782-F9-11_SOLEXA_FBgn0051782_rc_shift2 (CG31782-F9-11_SOLEXA_FBgn0051782_rc)
; dyads_m6 versus CG31782-F9-11_SOLEXA_FBgn0051782_rc; m=1/7; ncol2=11; w=-1; offset=-1; strand=R; shift=2; score=0.662333; --ctCACCacyaa- ; cor=; Ncor= a 0 0 269 617 42 2023 0 0 1676 407 471 1282 1413 0 c 0 0 1324 287 1979 143 2554 2552 582 1464 954 350 486 0 g 0 0 584 195 25 0 0 0 27 305 289 438 420 0 t 0 0 375 1453 506 386 0 1 269 377 838 482 234 0

lola-PL_SOLEXA_FBgn0005630_shift2 (lola-PL_SOLEXA_FBgn0005630)
; dyads_m6 versus lola-PL_SOLEXA_FBgn0005630; m=2/7; ncol2=14; w=-1; offset=-1; strand=D; shift=2; score=0.576007; --kgmmCCACcgkg ; cor=; Ncor= a 0 0 357 215 944 808 0 0 2061 0 361 407 457 281 c 0 0 322 163 968 793 2061 2061 0 2061 1099 481 334 387 g 0 0 600 1232 0 137 0 0 0 0 123 834 690 939 t 0 0 780 447 148 322 0 0 0 0 476 337 576 452

CG31782_F9-11_SANGER_5_FBgn0051782_shift0 (CG31782_F9-11_SANGER_5_FBgn0051782)
; dyads_m6 versus CG31782_F9-11_SANGER_5_FBgn0051782; m=3/7; ncol2=14; w=-3; offset=-3; strand=D; shift=0; score=0.569271; AssTCWCCAMYAAA ; cor=; Ncor= a 5 0 0 1 0 5 0 0 7 2 0 6 6 5 c 0 2 2 0 7 0 7 7 0 5 5 0 0 0 g 1 4 4 0 0 0 0 0 0 0 0 0 1 0 t 1 1 1 6 0 2 0 0 0 0 2 1 0 1

lola-PL_SANGER_2.5_FBgn0005630_rc_shift2 (lola-PL_SANGER_2.5_FBgn0005630_rc)
; dyads_m6 versus lola-PL_SANGER_2.5_FBgn0005630_rc; m=4/7; ncol2=9; w=-1; offset=-1; strand=R; shift=2; score=0.506519; --TGmcCCACm--- ; cor=; Ncor= a 0 0 2 0 4 2 0 0 11 0 4 0 0 0 c 0 0 0 0 7 5 11 11 0 11 6 0 0 0 g 0 0 0 9 0 2 0 0 0 0 0 0 0 0 t 0 0 8 2 0 2 0 0 0 0 1 0 0 0

Lag1_Cell_FBgn0040918_shift6 (Lag1_Cell_FBgn0040918)
; dyads_m6 versus Lag1_Cell_FBgn0040918; m=5/7; ncol2=10; w=0; offset=3; strand=D; shift=6; score=0.49346; ------CyACyAaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 17 1 0 18 12 10 c 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 1 4 4 t 0 0 0 0 0 0 0 10 0 0 7 0 3 2

Lag1_SOLEXA_FBgn0040918_shift6 (Lag1_SOLEXA_FBgn0040918)
; dyads_m6 versus Lag1_SOLEXA_FBgn0040918; m=6/7; ncol2=10; w=0; offset=3; strand=D; shift=6; score=0.468916; ------CyACyAaw ; cor=; Ncor= a 0 0 0 0 0 0 1 3 186 2 19 206 128 108 c 0 0 0 0 0 0 221 72 32 197 124 0 16 31 g 0 0 0 0 0 0 0 0 5 0 9 9 38 12 t 0 0 0 0 0 0 1 148 0 24 71 8 41 72

klu_SANGER_10_FBgn0013469_rc_shift6 (klu_SANGER_10_FBgn0013469_rc)
; dyads_m6 versus klu_SANGER_10_FBgn0013469_rc; m=7/7; ncol2=11; w=0; offset=3; strand=R; shift=6; score=0.40692; ------mCACCCmC ; cor=; Ncor= a 0 0 0 0 0 0 7 0 18 0 0 0 13 0 c 0 0 0 0 0 0 11 20 0 20 20 19 7 20 g 0 0 0 0 0 0 2 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 2 0 0 1 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m6_shift3 (dyads_m6)				; dyads_m6; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ccACCACCAcc ; Alignment reference a 0 0 0 849 627 3918 50 30 4141 38 14 3899 676 705 c 0 0 0 2252 2408 191 4112 4096 103 4058 4126 239 2169 2498 g 0 0 0 690 543 129 102 115 126 110 85 188 692 474 t 0 0 0 681 894 234 208 231 102 266 247 146 935 795
CG31782-F9-11_SOLEXA_FBgn0051782_rc_shift2 (CG31782-F9-11_SOLEXA_FBgn0051782_rc)				; dyads_m6 versus CG31782-F9-11_SOLEXA_FBgn0051782_rc; m=1/7; ncol2=11; w=-1; offset=-1; strand=R; shift=2; score=0.662333; --ctCACCacyaa- ; cor=; Ncor= a 0 0 269 617 42 2023 0 0 1676 407 471 1282 1413 0 c 0 0 1324 287 1979 143 2554 2552 582 1464 954 350 486 0 g 0 0 584 195 25 0 0 0 27 305 289 438 420 0 t 0 0 375 1453 506 386 0 1 269 377 838 482 234 0
lola-PL_SOLEXA_FBgn0005630_shift2 (lola-PL_SOLEXA_FBgn0005630)				; dyads_m6 versus lola-PL_SOLEXA_FBgn0005630; m=2/7; ncol2=14; w=-1; offset=-1; strand=D; shift=2; score=0.576007; --kgmmCCACcgkg ; cor=; Ncor= a 0 0 357 215 944 808 0 0 2061 0 361 407 457 281 c 0 0 322 163 968 793 2061 2061 0 2061 1099 481 334 387 g 0 0 600 1232 0 137 0 0 0 0 123 834 690 939 t 0 0 780 447 148 322 0 0 0 0 476 337 576 452
CG31782_F9-11_SANGER_5_FBgn0051782_shift0 (CG31782_F9-11_SANGER_5_FBgn0051782)				; dyads_m6 versus CG31782_F9-11_SANGER_5_FBgn0051782; m=3/7; ncol2=14; w=-3; offset=-3; strand=D; shift=0; score=0.569271; AssTCWCCAMYAAA ; cor=; Ncor= a 5 0 0 1 0 5 0 0 7 2 0 6 6 5 c 0 2 2 0 7 0 7 7 0 5 5 0 0 0 g 1 4 4 0 0 0 0 0 0 0 0 0 1 0 t 1 1 1 6 0 2 0 0 0 0 2 1 0 1
lola-PL_SANGER_2.5_FBgn0005630_rc_shift2 (lola-PL_SANGER_2.5_FBgn0005630_rc)				; dyads_m6 versus lola-PL_SANGER_2.5_FBgn0005630_rc; m=4/7; ncol2=9; w=-1; offset=-1; strand=R; shift=2; score=0.506519; --TGmcCCACm--- ; cor=; Ncor= a 0 0 2 0 4 2 0 0 11 0 4 0 0 0 c 0 0 0 0 7 5 11 11 0 11 6 0 0 0 g 0 0 0 9 0 2 0 0 0 0 0 0 0 0 t 0 0 8 2 0 2 0 0 0 0 1 0 0 0
Lag1_Cell_FBgn0040918_shift6 (Lag1_Cell_FBgn0040918)				; dyads_m6 versus Lag1_Cell_FBgn0040918; m=5/7; ncol2=10; w=0; offset=3; strand=D; shift=6; score=0.49346; ------CyACyAaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 17 1 0 18 12 10 c 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 1 4 4 t 0 0 0 0 0 0 0 10 0 0 7 0 3 2
Lag1_SOLEXA_FBgn0040918_shift6 (Lag1_SOLEXA_FBgn0040918)				; dyads_m6 versus Lag1_SOLEXA_FBgn0040918; m=6/7; ncol2=10; w=0; offset=3; strand=D; shift=6; score=0.468916; ------CyACyAaw ; cor=; Ncor= a 0 0 0 0 0 0 1 3 186 2 19 206 128 108 c 0 0 0 0 0 0 221 72 32 197 124 0 16 31 g 0 0 0 0 0 0 0 0 5 0 9 9 38 12 t 0 0 0 0 0 0 1 148 0 24 71 8 41 72
klu_SANGER_10_FBgn0013469_rc_shift6 (klu_SANGER_10_FBgn0013469_rc)				; dyads_m6 versus klu_SANGER_10_FBgn0013469_rc; m=7/7; ncol2=11; w=0; offset=3; strand=R; shift=6; score=0.40692; ------mCACCCmC ; cor=; Ncor= a 0 0 0 0 0 0 7 0 18 0 0 0 13 0 c 0 0 0 0 0 0 11 20 0 20 20 19 7 20 g 0 0 0 0 0 0 2 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 2 0 0 1 0 0