One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -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/2026/01/05/peak-motifs.2026-01-05.125020_2026-01-05.125020_w7RQpp/results/discovered_motifs/positions_6nt_m2/peak-motifs_positions_6nt_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: positions_6nt_m2_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)
; positions_6nt_m2; m=0 (reference); ncol1=19; shift=0; ncol=19; wwTTAAAAATAAwAwAAww ; Alignment reference a 2672 2970 1245 1203 6314 6426 6472 6485 6583 1534 6431 6166 2090 6267 2064 6133 6149 3291 2951 c 1240 1182 763 370 394 426 344 374 319 436 413 694 447 374 582 483 424 1112 1285 g 1132 1118 458 464 399 404 348 322 407 412 421 356 405 497 481 420 447 1138 1146 t 2995 2769 5573 6002 932 783 875 858 730 5657 774 823 5097 901 4912 1003 1019 2498 2657

MA0497.2_shift2 (MEF2C)
; positions_6nt_m2 versus MA0497.2 (MEF2C); m=1/3; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.430936; --cyAAAAATAGm------ ; cor=; Ncor= a 0 0 382.0 0.0 1616.0 1706.0 2107.0 2131.0 2135.0 56.0 2177.0 389.0 975.0 0 0 0 0 0 0 c 0 0 1412.0 985.0 256.0 32.0 0.0 0.0 0.0 62.0 0.0 120.0 836.0 0 0 0 0 0 0 g 0 0 78.0 0.0 74.0 241.0 87.0 2.0 4.0 0.0 32.0 1671.0 148.0 0 0 0 0 0 0 t 0 0 337.0 1224.0 263.0 230.0 15.0 76.0 70.0 2091.0 0.0 29.0 250.0 0 0 0 0 0 0

MA0052.5_shift2 (MEF2A)
; positions_6nt_m2 versus MA0052.5 (MEF2A); m=2/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.427612; --cTAAAAATAG------- ; cor=; Ncor= a 0 0 1984.0 627.0 12437.0 13132.0 14680.0 14453.0 14956.0 441.0 15582.0 2566.0 0 0 0 0 0 0 0 c 0 0 10919.0 2974.0 1013.0 253.0 141.0 231.0 173.0 349.0 50.0 1060.0 0 0 0 0 0 0 0 g 0 0 1007.0 236.0 1066.0 610.0 506.0 241.0 202.0 215.0 422.0 11104.0 0 0 0 0 0 0 0 t 0 0 2252.0 12325.0 1646.0 2167.0 835.0 1237.0 831.0 15157.0 108.0 1432.0 0 0 0 0 0 0 0

MA2124.1_rc_shift2 (Hmga1_rc)
; positions_6nt_m2 versus MA2124.1_rc (Hmga1_rc); m=3/3; ncol2=8; w=0; offset=2; strand=R; shift=2; score=0.404534; --wTAAAAAT--------- ; cor=; Ncor= a 0 0 11340.0 542.0 24333.0 24654.0 24779.0 24269.0 24172.0 496.0 0 0 0 0 0 0 0 0 0 c 0 0 2438.0 358.0 294.0 237.0 138.0 303.0 421.0 188.0 0 0 0 0 0 0 0 0 0 g 0 0 2348.0 473.0 409.0 264.0 194.0 200.0 393.0 71.0 0 0 0 0 0 0 0 0 0 t 0 0 9680.0 24433.0 770.0 651.0 695.0 1034.0 820.0 25051.0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m2_shift0 (positions_6nt_m2)				; positions_6nt_m2; m=0 (reference); ncol1=19; shift=0; ncol=19; wwTTAAAAATAAwAwAAww ; Alignment reference a 2672 2970 1245 1203 6314 6426 6472 6485 6583 1534 6431 6166 2090 6267 2064 6133 6149 3291 2951 c 1240 1182 763 370 394 426 344 374 319 436 413 694 447 374 582 483 424 1112 1285 g 1132 1118 458 464 399 404 348 322 407 412 421 356 405 497 481 420 447 1138 1146 t 2995 2769 5573 6002 932 783 875 858 730 5657 774 823 5097 901 4912 1003 1019 2498 2657
MA0497.2_shift2 (MEF2C)				; positions_6nt_m2 versus MA0497.2 (MEF2C); m=1/3; ncol2=11; w=0; offset=2; strand=D; shift=2; score=0.430936; --cyAAAAATAGm------ ; cor=; Ncor= a 0 0 382.0 0.0 1616.0 1706.0 2107.0 2131.0 2135.0 56.0 2177.0 389.0 975.0 0 0 0 0 0 0 c 0 0 1412.0 985.0 256.0 32.0 0.0 0.0 0.0 62.0 0.0 120.0 836.0 0 0 0 0 0 0 g 0 0 78.0 0.0 74.0 241.0 87.0 2.0 4.0 0.0 32.0 1671.0 148.0 0 0 0 0 0 0 t 0 0 337.0 1224.0 263.0 230.0 15.0 76.0 70.0 2091.0 0.0 29.0 250.0 0 0 0 0 0 0
MA0052.5_shift2 (MEF2A)				; positions_6nt_m2 versus MA0052.5 (MEF2A); m=2/3; ncol2=10; w=0; offset=2; strand=D; shift=2; score=0.427612; --cTAAAAATAG------- ; cor=; Ncor= a 0 0 1984.0 627.0 12437.0 13132.0 14680.0 14453.0 14956.0 441.0 15582.0 2566.0 0 0 0 0 0 0 0 c 0 0 10919.0 2974.0 1013.0 253.0 141.0 231.0 173.0 349.0 50.0 1060.0 0 0 0 0 0 0 0 g 0 0 1007.0 236.0 1066.0 610.0 506.0 241.0 202.0 215.0 422.0 11104.0 0 0 0 0 0 0 0 t 0 0 2252.0 12325.0 1646.0 2167.0 835.0 1237.0 831.0 15157.0 108.0 1432.0 0 0 0 0 0 0 0
MA2124.1_rc_shift2 (Hmga1_rc)				; positions_6nt_m2 versus MA2124.1_rc (Hmga1_rc); m=3/3; ncol2=8; w=0; offset=2; strand=R; shift=2; score=0.404534; --wTAAAAAT--------- ; cor=; Ncor= a 0 0 11340.0 542.0 24333.0 24654.0 24779.0 24269.0 24172.0 496.0 0 0 0 0 0 0 0 0 0 c 0 0 2438.0 358.0 294.0 237.0 138.0 303.0 421.0 188.0 0 0 0 0 0 0 0 0 0 g 0 0 2348.0 473.0 409.0 264.0 194.0 200.0 393.0 71.0 0 0 0 0 0 0 0 0 0 t 0 0 9680.0 24433.0 770.0 651.0 695.0 1034.0 820.0 25051.0 0 0 0 0 0 0 0 0 0