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.2025-05-16.174057_2025-05-16.174057_O2IjFa/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.2025-05-16.174057_2025-05-16.174057_O2IjFa/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 ; 11 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; ---mrAAAAATkw ; Alignment reference a 0 0 0 4 4 11 11 11 11 11 0 2 6 c 0 0 0 4 2 0 0 0 0 0 0 2 0 g 0 0 0 2 4 0 0 0 0 0 0 4 2 t 0 0 0 1 1 0 0 0 0 0 11 3 3

MA0052.5_shift3 (MEF2A)
; oligos_6nt_mkv1_m2 versus MA0052.5 (MEF2A); m=1/10; ncol2=10; w=0; offset=0; strand=D; shift=3; score=0.75892; ---cTAAAAATAG ; cor=; Ncor= a 0 0 0 1984.0 627.0 12437.0 13132.0 14680.0 14453.0 14956.0 441.0 15582.0 2566.0 c 0 0 0 10919.0 2974.0 1013.0 253.0 141.0 231.0 173.0 349.0 50.0 1060.0 g 0 0 0 1007.0 236.0 1066.0 610.0 506.0 241.0 202.0 215.0 422.0 11104.0 t 0 0 0 2252.0 12325.0 1646.0 2167.0 835.0 1237.0 831.0 15157.0 108.0 1432.0

MA2124.1_rc_shift3 (Hmga1_rc)
; oligos_6nt_mkv1_m2 versus MA2124.1_rc (Hmga1_rc); m=2/10; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.697897; ---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

MA0497.2_shift3 (MEF2C)
; oligos_6nt_mkv1_m2 versus MA0497.2 (MEF2C); m=3/10; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.694716; ---cyAAAAATAG ; cor=; Ncor= a 0 0 0 382.0 0.0 1616.0 1706.0 2107.0 2131.0 2135.0 56.0 2177.0 389.0 c 0 0 0 1412.0 985.0 256.0 32.0 0.0 0.0 0.0 62.0 0.0 120.0 g 0 0 0 78.0 0.0 74.0 241.0 87.0 2.0 4.0 0.0 32.0 1671.0 t 0 0 0 337.0 1224.0 263.0 230.0 15.0 76.0 70.0 2091.0 0.0 29.0

MA1562.2_shift3 (SOX14)
; oligos_6nt_mkv1_m2 versus MA1562.2 (SOX14); m=4/10; ncol2=9; w=0; offset=0; strand=D; shift=3; score=0.658257; ---CGAACAATg- ; cor=; Ncor= a 0 0 0 68.0 44.0 594.0 594.0 4.0 594.0 594.0 0.0 75.0 0 c 0 0 0 594.0 18.0 8.0 13.0 594.0 0.0 17.0 2.0 67.0 0 g 0 0 0 44.0 594.0 27.0 0.0 10.0 0.0 0.0 16.0 372.0 0 t 0 0 0 99.0 70.0 37.0 19.0 17.0 0.0 5.0 594.0 80.0 0

MA1125.2_shift4 (ZNF384)
; oligos_6nt_mkv1_m2 versus MA1125.2 (ZNF384); m=5/10; ncol2=8; w=0; offset=1; strand=D; shift=4; score=0.626226; ----AAAAAAaa- ; cor=; Ncor= a 0 0 0 0 30354.0 30191.0 30072.0 30252.0 30202.0 30406.0 20322.0 18916.0 0 c 0 0 0 0 7.0 35.0 21.0 13.0 26.0 6.0 2908.0 3963.0 0 g 0 0 0 0 13.0 19.0 26.0 15.0 14.0 0.0 2767.0 2898.0 0 t 0 0 0 0 59.0 188.0 314.0 153.0 191.0 21.0 4436.0 4656.0 0

MA1563.2_shift5 (SOX18)
; oligos_6nt_mkv1_m2 versus MA1563.2 (SOX18); m=6/10; ncol2=8; w=0; offset=2; strand=D; shift=5; score=0.579047; -----aACAATdv ; cor=; Ncor= a 0 0 0 0 0 424.0 424.0 0.0 424.0 424.0 0.0 203.0 382.0 c 0 0 0 0 0 81.0 0.0 424.0 0.0 35.0 0.0 0.0 551.0 g 0 0 0 0 0 170.0 0.0 91.0 0.0 17.0 0.0 221.0 424.0 t 0 0 0 0 0 34.0 0.0 2.0 0.0 0.0 447.0 228.0 0.0

MA0868.3_shift5 (SOX8)
; oligos_6nt_mkv1_m2 versus MA0868.3 (SOX8); m=7/10; ncol2=7; w=0; offset=2; strand=D; shift=5; score=0.521286; -----AACAATr- ; cor=; Ncor= a 0 0 0 0 0 1827.0 1827.0 3.0 1827.0 1827.0 273.0 1356.0 0 c 0 0 0 0 0 151.0 0.0 1827.0 0.0 43.0 36.0 208.0 0 g 0 0 0 0 0 263.0 0.0 35.0 0.0 0.0 20.0 1827.0 0 t 0 0 0 0 0 222.0 45.0 70.0 16.0 36.0 1827.0 287.0 0

MA0757.2_shift5 (ONECUT3)
; oligos_6nt_mkv1_m2 versus MA0757.2 (ONECUT3); m=8/10; ncol2=12; w=0; offset=2; strand=D; shift=5; score=0.486351; -----aAAAATCr ; cor=; Ncor= a 0 0 0 0 0 3851.0 6080.0 6080.0 6080.0 6080.0 32.0 23.0 3950.0 c 0 0 0 0 0 379.0 274.0 173.0 28.0 5.0 103.0 6080.0 20.0 g 0 0 0 0 0 1141.0 498.0 112.0 102.0 41.0 14.0 3.0 2130.0 t 0 0 0 0 0 709.0 878.0 1221.0 54.0 11.0 6080.0 5.0 11.0

MA1729.2_shift0 (ZNF680)
; oligos_6nt_mkv1_m2 versus MA1729.2 (ZNF680); m=9/10; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.43642; CCAAGAAGAAT-- ; cor=; Ncor= a 418.0 1120.0 5394.0 4522.0 43.0 5681.0 5479.0 494.0 5661.0 4020.0 202.0 0 0 c 4870.0 4324.0 60.0 17.0 14.0 23.0 13.0 40.0 41.0 808.0 396.0 0 0 g 133.0 69.0 208.0 1116.0 5691.0 44.0 203.0 5144.0 39.0 163.0 213.0 0 0 t 345.0 253.0 104.0 111.0 18.0 18.0 71.0 88.0 25.0 775.0 4955.0 0 0

MA0606.3_shift1 (Nfat5)
; oligos_6nt_mkv1_m2 versus MA0606.3 (Nfat5); m=10/10; ncol2=8; w=-2; offset=-2; strand=D; shift=1; score=0.406343; -ATGGAAAA---- ; cor=; Ncor= a 0 279.0 35.0 13.0 16.0 328.0 336.0 334.0 315.0 0 0 0 0 c 0 17.0 10.0 0.0 8.0 8.0 1.0 4.0 8.0 0 0 0 0 g 0 47.0 9.0 332.0 325.0 15.0 10.0 8.0 19.0 0 0 0 0 t 0 13.0 302.0 11.0 7.0 5.0 9.0 10.0 14.0 0 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; ---mrAAAAATkw ; Alignment reference a 0 0 0 4 4 11 11 11 11 11 0 2 6 c 0 0 0 4 2 0 0 0 0 0 0 2 0 g 0 0 0 2 4 0 0 0 0 0 0 4 2 t 0 0 0 1 1 0 0 0 0 0 11 3 3
MA0052.5_shift3 (MEF2A)				; oligos_6nt_mkv1_m2 versus MA0052.5 (MEF2A); m=1/10; ncol2=10; w=0; offset=0; strand=D; shift=3; score=0.75892; ---cTAAAAATAG ; cor=; Ncor= a 0 0 0 1984.0 627.0 12437.0 13132.0 14680.0 14453.0 14956.0 441.0 15582.0 2566.0 c 0 0 0 10919.0 2974.0 1013.0 253.0 141.0 231.0 173.0 349.0 50.0 1060.0 g 0 0 0 1007.0 236.0 1066.0 610.0 506.0 241.0 202.0 215.0 422.0 11104.0 t 0 0 0 2252.0 12325.0 1646.0 2167.0 835.0 1237.0 831.0 15157.0 108.0 1432.0
MA2124.1_rc_shift3 (Hmga1_rc)				; oligos_6nt_mkv1_m2 versus MA2124.1_rc (Hmga1_rc); m=2/10; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.697897; ---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
MA0497.2_shift3 (MEF2C)				; oligos_6nt_mkv1_m2 versus MA0497.2 (MEF2C); m=3/10; ncol2=11; w=0; offset=0; strand=D; shift=3; score=0.694716; ---cyAAAAATAG ; cor=; Ncor= a 0 0 0 382.0 0.0 1616.0 1706.0 2107.0 2131.0 2135.0 56.0 2177.0 389.0 c 0 0 0 1412.0 985.0 256.0 32.0 0.0 0.0 0.0 62.0 0.0 120.0 g 0 0 0 78.0 0.0 74.0 241.0 87.0 2.0 4.0 0.0 32.0 1671.0 t 0 0 0 337.0 1224.0 263.0 230.0 15.0 76.0 70.0 2091.0 0.0 29.0
MA1562.2_shift3 (SOX14)				; oligos_6nt_mkv1_m2 versus MA1562.2 (SOX14); m=4/10; ncol2=9; w=0; offset=0; strand=D; shift=3; score=0.658257; ---CGAACAATg- ; cor=; Ncor= a 0 0 0 68.0 44.0 594.0 594.0 4.0 594.0 594.0 0.0 75.0 0 c 0 0 0 594.0 18.0 8.0 13.0 594.0 0.0 17.0 2.0 67.0 0 g 0 0 0 44.0 594.0 27.0 0.0 10.0 0.0 0.0 16.0 372.0 0 t 0 0 0 99.0 70.0 37.0 19.0 17.0 0.0 5.0 594.0 80.0 0
MA1125.2_shift4 (ZNF384)				; oligos_6nt_mkv1_m2 versus MA1125.2 (ZNF384); m=5/10; ncol2=8; w=0; offset=1; strand=D; shift=4; score=0.626226; ----AAAAAAaa- ; cor=; Ncor= a 0 0 0 0 30354.0 30191.0 30072.0 30252.0 30202.0 30406.0 20322.0 18916.0 0 c 0 0 0 0 7.0 35.0 21.0 13.0 26.0 6.0 2908.0 3963.0 0 g 0 0 0 0 13.0 19.0 26.0 15.0 14.0 0.0 2767.0 2898.0 0 t 0 0 0 0 59.0 188.0 314.0 153.0 191.0 21.0 4436.0 4656.0 0
MA1563.2_shift5 (SOX18)				; oligos_6nt_mkv1_m2 versus MA1563.2 (SOX18); m=6/10; ncol2=8; w=0; offset=2; strand=D; shift=5; score=0.579047; -----aACAATdv ; cor=; Ncor= a 0 0 0 0 0 424.0 424.0 0.0 424.0 424.0 0.0 203.0 382.0 c 0 0 0 0 0 81.0 0.0 424.0 0.0 35.0 0.0 0.0 551.0 g 0 0 0 0 0 170.0 0.0 91.0 0.0 17.0 0.0 221.0 424.0 t 0 0 0 0 0 34.0 0.0 2.0 0.0 0.0 447.0 228.0 0.0
MA0868.3_shift5 (SOX8)				; oligos_6nt_mkv1_m2 versus MA0868.3 (SOX8); m=7/10; ncol2=7; w=0; offset=2; strand=D; shift=5; score=0.521286; -----AACAATr- ; cor=; Ncor= a 0 0 0 0 0 1827.0 1827.0 3.0 1827.0 1827.0 273.0 1356.0 0 c 0 0 0 0 0 151.0 0.0 1827.0 0.0 43.0 36.0 208.0 0 g 0 0 0 0 0 263.0 0.0 35.0 0.0 0.0 20.0 1827.0 0 t 0 0 0 0 0 222.0 45.0 70.0 16.0 36.0 1827.0 287.0 0
MA0757.2_shift5 (ONECUT3)				; oligos_6nt_mkv1_m2 versus MA0757.2 (ONECUT3); m=8/10; ncol2=12; w=0; offset=2; strand=D; shift=5; score=0.486351; -----aAAAATCr ; cor=; Ncor= a 0 0 0 0 0 3851.0 6080.0 6080.0 6080.0 6080.0 32.0 23.0 3950.0 c 0 0 0 0 0 379.0 274.0 173.0 28.0 5.0 103.0 6080.0 20.0 g 0 0 0 0 0 1141.0 498.0 112.0 102.0 41.0 14.0 3.0 2130.0 t 0 0 0 0 0 709.0 878.0 1221.0 54.0 11.0 6080.0 5.0 11.0
MA1729.2_shift0 (ZNF680)				; oligos_6nt_mkv1_m2 versus MA1729.2 (ZNF680); m=9/10; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.43642; CCAAGAAGAAT-- ; cor=; Ncor= a 418.0 1120.0 5394.0 4522.0 43.0 5681.0 5479.0 494.0 5661.0 4020.0 202.0 0 0 c 4870.0 4324.0 60.0 17.0 14.0 23.0 13.0 40.0 41.0 808.0 396.0 0 0 g 133.0 69.0 208.0 1116.0 5691.0 44.0 203.0 5144.0 39.0 163.0 213.0 0 0 t 345.0 253.0 104.0 111.0 18.0 18.0 71.0 88.0 25.0 775.0 4955.0 0 0
MA0606.3_shift1 (Nfat5)				; oligos_6nt_mkv1_m2 versus MA0606.3 (Nfat5); m=10/10; ncol2=8; w=-2; offset=-2; strand=D; shift=1; score=0.406343; -ATGGAAAA---- ; cor=; Ncor= a 0 279.0 35.0 13.0 16.0 328.0 336.0 334.0 315.0 0 0 0 0 c 0 17.0 10.0 0.0 8.0 8.0 1.0 4.0 8.0 0 0 0 0 g 0 47.0 9.0 332.0 325.0 15.0 10.0 8.0 19.0 0 0 0 0 t 0 13.0 302.0 11.0 7.0 5.0 9.0 10.0 14.0 0 0 0 0