One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_6nt_mkv1_m2/peak-motifs_oligos_6nt_mkv1_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/2025/05/16/peak-motifs.2025-05-16.184320_2025-05-16.184320_WEQUPM/results/discovered_motifs/oligos_6nt_mkv1_m2/peak-motifs_oligos_6nt_mkv1_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv1_m2_shift3 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv1_m2_shift3 (oligos_6nt_mkv1_m2)
; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=10; shift=3; ncol=13; ---sbAAATATkw ; Alignment reference a 0 0 0 4 5 21 19 22 1 18 1 4 6 c 0 0 0 9 6 1 1 1 1 2 0 2 3 g 0 0 0 6 6 1 1 0 2 3 1 7 2 t 0 0 0 4 6 0 2 0 19 0 21 10 12

MA0602.2_rc_shift5 (Arid5a_rc)
; oligos_6nt_mkv1_m2 versus MA0602.2_rc (Arid5a_rc); m=1/6; ncol2=8; w=0; offset=2; strand=R; shift=5; score=0.648708; -----cAATATTr ; cor=; Ncor= a 0 0 0 0 0 22.0 83.0 96.0 6.0 93.0 2.0 5.0 48.0 c 0 0 0 0 0 52.0 4.0 1.0 1.0 1.0 1.0 7.0 3.0 g 0 0 0 0 0 3.0 9.0 1.0 1.0 0.0 0.0 3.0 32.0 t 0 0 0 0 0 23.0 4.0 2.0 93.0 6.0 96.0 85.0 16.0

MA2124.1_rc_shift3 (Hmga1_rc)
; oligos_6nt_mkv1_m2 versus MA2124.1_rc (Hmga1_rc); m=2/6; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.56959; ---wTAAAAAT-- ; cor=; Ncor= a 0 0 0 11340.0 542.0 24333.0 24654.0 24779.0 24269.0 24172.0 496.0 0 0 c 0 0 0 2438.0 358.0 294.0 237.0 138.0 303.0 421.0 188.0 0 0 g 0 0 0 2348.0 473.0 409.0 264.0 194.0 200.0 393.0 71.0 0 0 t 0 0 0 9680.0 24433.0 770.0 651.0 695.0 1034.0 820.0 25051.0 0 0

MA0033.2_shift3 (FOXL1)
; oligos_6nt_mkv1_m2 versus MA0033.2 (FOXL1); m=3/6; ncol2=7; w=0; offset=0; strand=D; shift=3; score=0.503211; ---rTAAACA--- ; cor=; Ncor= a 0 0 0 2102.0 10.0 4780.0 4780.0 4780.0 0.0 4780.0 0 0 0 c 0 0 0 13.0 416.0 628.0 38.0 82.0 3723.0 54.0 0 0 0 g 0 0 0 2678.0 0.0 57.0 0.0 50.0 0.0 0.0 0 0 0 t 0 0 0 140.0 4780.0 0.0 15.0 0.0 1057.0 17.0 0 0 0

MA0032.2_shift0 (FOXC1)
; oligos_6nt_mkv1_m2 versus MA0032.2 (FOXC1); m=4/6; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.482354; wAwRTMAAyAw-- ; cor=; Ncor= a 6452.0 14324.0 7893.0 4858.0 2496.0 13117.0 18489.0 18489.0 122.0 18489.0 6702.0 0 0 c 772.0 728.0 2008.0 336.0 1652.0 5372.0 108.0 56.0 8782.0 27.0 1558.0 0 0 g 304.0 4165.0 2422.0 13631.0 390.0 21.0 0.0 141.0 165.0 433.0 1107.0 0 0 t 12038.0 1386.0 10596.0 51.0 18489.0 45.0 57.0 112.0 9708.0 184.0 11787.0 0 0

MA0845.1_shift0 (FOXB1)
; oligos_6nt_mkv1_m2 versus MA0845.1 (FOXB1); m=5/6; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.481092; wAwGTMAAyAt-- ; cor=; Ncor= a 2393.0 5343.0 1983.0 1159.0 180.0 4891.0 6841.0 6841.0 28.0 6841.0 1704.0 0 0 c 272.0 263.0 218.0 54.0 240.0 1950.0 213.0 47.0 2252.0 0.0 573.0 0 0 g 190.0 1498.0 409.0 6841.0 113.0 75.0 0.0 47.0 104.0 157.0 556.0 0 0 t 4448.0 561.0 4858.0 124.0 6841.0 73.0 381.0 216.0 4589.0 147.0 4008.0 0 0

MA0052.5_shift1 (MEF2A)
; oligos_6nt_mkv1_m2 versus MA0052.5 (MEF2A); m=6/6; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.470205; -cTAAAAATAG-- ; cor=; Ncor= a 0 1984.0 627.0 12437.0 13132.0 14680.0 14453.0 14956.0 441.0 15582.0 2566.0 0 0 c 0 10919.0 2974.0 1013.0 253.0 141.0 231.0 173.0 349.0 50.0 1060.0 0 0 g 0 1007.0 236.0 1066.0 610.0 506.0 241.0 202.0 215.0 422.0 11104.0 0 0 t 0 2252.0 12325.0 1646.0 2167.0 835.0 1237.0 831.0 15157.0 108.0 1432.0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv1_m2_shift3 (oligos_6nt_mkv1_m2)				; oligos_6nt_mkv1_m2; m=0 (reference); ncol1=10; shift=3; ncol=13; ---sbAAATATkw ; Alignment reference a 0 0 0 4 5 21 19 22 1 18 1 4 6 c 0 0 0 9 6 1 1 1 1 2 0 2 3 g 0 0 0 6 6 1 1 0 2 3 1 7 2 t 0 0 0 4 6 0 2 0 19 0 21 10 12
MA0602.2_rc_shift5 (Arid5a_rc)				; oligos_6nt_mkv1_m2 versus MA0602.2_rc (Arid5a_rc); m=1/6; ncol2=8; w=0; offset=2; strand=R; shift=5; score=0.648708; -----cAATATTr ; cor=; Ncor= a 0 0 0 0 0 22.0 83.0 96.0 6.0 93.0 2.0 5.0 48.0 c 0 0 0 0 0 52.0 4.0 1.0 1.0 1.0 1.0 7.0 3.0 g 0 0 0 0 0 3.0 9.0 1.0 1.0 0.0 0.0 3.0 32.0 t 0 0 0 0 0 23.0 4.0 2.0 93.0 6.0 96.0 85.0 16.0
MA2124.1_rc_shift3 (Hmga1_rc)				; oligos_6nt_mkv1_m2 versus MA2124.1_rc (Hmga1_rc); m=2/6; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.56959; ---wTAAAAAT-- ; cor=; Ncor= a 0 0 0 11340.0 542.0 24333.0 24654.0 24779.0 24269.0 24172.0 496.0 0 0 c 0 0 0 2438.0 358.0 294.0 237.0 138.0 303.0 421.0 188.0 0 0 g 0 0 0 2348.0 473.0 409.0 264.0 194.0 200.0 393.0 71.0 0 0 t 0 0 0 9680.0 24433.0 770.0 651.0 695.0 1034.0 820.0 25051.0 0 0
MA0033.2_shift3 (FOXL1)				; oligos_6nt_mkv1_m2 versus MA0033.2 (FOXL1); m=3/6; ncol2=7; w=0; offset=0; strand=D; shift=3; score=0.503211; ---rTAAACA--- ; cor=; Ncor= a 0 0 0 2102.0 10.0 4780.0 4780.0 4780.0 0.0 4780.0 0 0 0 c 0 0 0 13.0 416.0 628.0 38.0 82.0 3723.0 54.0 0 0 0 g 0 0 0 2678.0 0.0 57.0 0.0 50.0 0.0 0.0 0 0 0 t 0 0 0 140.0 4780.0 0.0 15.0 0.0 1057.0 17.0 0 0 0
MA0032.2_shift0 (FOXC1)				; oligos_6nt_mkv1_m2 versus MA0032.2 (FOXC1); m=4/6; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.482354; wAwRTMAAyAw-- ; cor=; Ncor= a 6452.0 14324.0 7893.0 4858.0 2496.0 13117.0 18489.0 18489.0 122.0 18489.0 6702.0 0 0 c 772.0 728.0 2008.0 336.0 1652.0 5372.0 108.0 56.0 8782.0 27.0 1558.0 0 0 g 304.0 4165.0 2422.0 13631.0 390.0 21.0 0.0 141.0 165.0 433.0 1107.0 0 0 t 12038.0 1386.0 10596.0 51.0 18489.0 45.0 57.0 112.0 9708.0 184.0 11787.0 0 0
MA0845.1_shift0 (FOXB1)				; oligos_6nt_mkv1_m2 versus MA0845.1 (FOXB1); m=5/6; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.481092; wAwGTMAAyAt-- ; cor=; Ncor= a 2393.0 5343.0 1983.0 1159.0 180.0 4891.0 6841.0 6841.0 28.0 6841.0 1704.0 0 0 c 272.0 263.0 218.0 54.0 240.0 1950.0 213.0 47.0 2252.0 0.0 573.0 0 0 g 190.0 1498.0 409.0 6841.0 113.0 75.0 0.0 47.0 104.0 157.0 556.0 0 0 t 4448.0 561.0 4858.0 124.0 6841.0 73.0 381.0 216.0 4589.0 147.0 4008.0 0 0
MA0052.5_shift1 (MEF2A)				; oligos_6nt_mkv1_m2 versus MA0052.5 (MEF2A); m=6/6; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.470205; -cTAAAAATAG-- ; cor=; Ncor= a 0 1984.0 627.0 12437.0 13132.0 14680.0 14453.0 14956.0 441.0 15582.0 2566.0 0 0 c 0 10919.0 2974.0 1013.0 253.0 141.0 231.0 173.0 349.0 50.0 1060.0 0 0 g 0 1007.0 236.0 1066.0 610.0 506.0 241.0 202.0 215.0 422.0 11104.0 0 0 t 0 2252.0 12325.0 1646.0 2167.0 835.0 1237.0 831.0 15157.0 108.0 1432.0 0 0