One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/25/peak-motifs.2025-11-25.143236_2025-11-25.143236_C5OFib/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4.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/2025/11/25/peak-motifs.2025-11-25.143236_2025-11-25.143236_C5OFib/results/discovered_motifs/oligos_7nt_mkv5_m4/peak-motifs_oligos_7nt_mkv5_m4_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m4_shift0 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; gwCGAAATCac ; Alignment reference a 552 1095 226 81 2231 2217 2068 103 67 1103 566 c 479 364 1994 31 41 62 199 75 2173 447 858 g 851 268 75 2055 58 60 62 96 97 283 524 t 534 689 121 249 86 77 87 2142 79 583 468

MA1971.2_shift2 (ZBED2)
; oligos_7nt_mkv5_m4 versus MA1971.2 (ZBED2); m=1/5; ncol2=7; w=0; offset=2; strand=D; shift=2; score=0.501812; --CGAAACC-- ; cor=; Ncor= a 0 0 42.0 19.0 1247.0 1264.0 1131.0 17.0 75.0 0 0 c 0 0 1195.0 21.0 13.0 13.0 94.0 1217.0 962.0 0 0 g 0 0 42.0 1252.0 29.0 8.0 41.0 43.0 47.0 0 0 t 0 0 18.0 5.0 8.0 12.0 31.0 20.0 213.0 0 0

MA2339.1_shift3 (Nanog)
; oligos_7nt_mkv5_m4 versus MA2339.1 (Nanog); m=2/5; ncol2=7; w=0; offset=3; strand=D; shift=3; score=0.471615; ---GCAATCA- ; cor=; Ncor= a 0 0 0 480.0 143.0 6992.0 7959.0 235.0 348.0 8076.0 0 c 0 0 0 164.0 7298.0 400.0 206.0 96.0 7421.0 131.0 0 g 0 0 0 7830.0 93.0 365.0 196.0 124.0 149.0 180.0 0 t 0 0 0 190.0 1130.0 907.0 303.0 8209.0 746.0 277.0 0

MA0483.2_shift4 (Gfi1B)
; oligos_7nt_mkv5_m4 versus MA0483.2 (Gfi1B); m=3/5; ncol2=10; w=0; offset=4; strand=D; shift=4; score=0.459748; ----aAATCwC ; cor=; Ncor= a 0 0 0 0 1124.0 1761.0 1759.0 0.0 0.0 1033.0 61.0 c 0 0 0 0 438.0 0.0 0.0 338.0 1761.0 21.0 1312.0 g 0 0 0 0 104.0 0.0 2.0 28.0 0.0 0.0 388.0 t 0 0 0 0 95.0 0.0 0.0 1395.0 0.0 707.0 0.0

MA0679.3_shift4 (ONECUT1)
; oligos_7nt_mkv5_m4 versus MA0679.3 (ONECUT1); m=4/5; ncol2=9; w=0; offset=4; strand=D; shift=4; score=0.446264; ----aAATCAA ; cor=; Ncor= a 0 0 0 0 37926.0 52146.0 60015.0 482.0 1345.0 59595.0 60870.0 c 0 0 0 0 7555.0 1011.0 358.0 294.0 60181.0 438.0 247.0 g 0 0 0 0 6149.0 7794.0 1166.0 241.0 278.0 1226.0 366.0 t 0 0 0 0 10589.0 1268.0 680.0 61202.0 415.0 960.0 736.0

MA0038.3_shift4 (GFI1)
; oligos_7nt_mkv5_m4 versus MA0038.3 (GFI1); m=5/5; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.416627; ----mAATCAC ; cor=; Ncor= a 0 0 0 0 19146.0 30168.0 30150.0 0.0 15.0 29255.0 838.0 c 0 0 0 0 10155.0 2.0 0.0 0.0 30139.0 0.0 27769.0 g 0 0 0 0 812.0 0.0 0.0 0.0 0.0 0.0 3888.0 t 0 0 0 0 565.0 0.0 1.0 30161.0 10.0 1594.0 0.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m4_shift0 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; gwCGAAATCac ; Alignment reference a 552 1095 226 81 2231 2217 2068 103 67 1103 566 c 479 364 1994 31 41 62 199 75 2173 447 858 g 851 268 75 2055 58 60 62 96 97 283 524 t 534 689 121 249 86 77 87 2142 79 583 468
MA1971.2_shift2 (ZBED2)				; oligos_7nt_mkv5_m4 versus MA1971.2 (ZBED2); m=1/5; ncol2=7; w=0; offset=2; strand=D; shift=2; score=0.501812; --CGAAACC-- ; cor=; Ncor= a 0 0 42.0 19.0 1247.0 1264.0 1131.0 17.0 75.0 0 0 c 0 0 1195.0 21.0 13.0 13.0 94.0 1217.0 962.0 0 0 g 0 0 42.0 1252.0 29.0 8.0 41.0 43.0 47.0 0 0 t 0 0 18.0 5.0 8.0 12.0 31.0 20.0 213.0 0 0
MA2339.1_shift3 (Nanog)				; oligos_7nt_mkv5_m4 versus MA2339.1 (Nanog); m=2/5; ncol2=7; w=0; offset=3; strand=D; shift=3; score=0.471615; ---GCAATCA- ; cor=; Ncor= a 0 0 0 480.0 143.0 6992.0 7959.0 235.0 348.0 8076.0 0 c 0 0 0 164.0 7298.0 400.0 206.0 96.0 7421.0 131.0 0 g 0 0 0 7830.0 93.0 365.0 196.0 124.0 149.0 180.0 0 t 0 0 0 190.0 1130.0 907.0 303.0 8209.0 746.0 277.0 0
MA0483.2_shift4 (Gfi1B)				; oligos_7nt_mkv5_m4 versus MA0483.2 (Gfi1B); m=3/5; ncol2=10; w=0; offset=4; strand=D; shift=4; score=0.459748; ----aAATCwC ; cor=; Ncor= a 0 0 0 0 1124.0 1761.0 1759.0 0.0 0.0 1033.0 61.0 c 0 0 0 0 438.0 0.0 0.0 338.0 1761.0 21.0 1312.0 g 0 0 0 0 104.0 0.0 2.0 28.0 0.0 0.0 388.0 t 0 0 0 0 95.0 0.0 0.0 1395.0 0.0 707.0 0.0
MA0679.3_shift4 (ONECUT1)				; oligos_7nt_mkv5_m4 versus MA0679.3 (ONECUT1); m=4/5; ncol2=9; w=0; offset=4; strand=D; shift=4; score=0.446264; ----aAATCAA ; cor=; Ncor= a 0 0 0 0 37926.0 52146.0 60015.0 482.0 1345.0 59595.0 60870.0 c 0 0 0 0 7555.0 1011.0 358.0 294.0 60181.0 438.0 247.0 g 0 0 0 0 6149.0 7794.0 1166.0 241.0 278.0 1226.0 366.0 t 0 0 0 0 10589.0 1268.0 680.0 61202.0 415.0 960.0 736.0
MA0038.3_shift4 (GFI1)				; oligos_7nt_mkv5_m4 versus MA0038.3 (GFI1); m=5/5; ncol2=11; w=0; offset=4; strand=D; shift=4; score=0.416627; ----mAATCAC ; cor=; Ncor= a 0 0 0 0 19146.0 30168.0 30150.0 0.0 15.0 29255.0 838.0 c 0 0 0 0 10155.0 2.0 0.0 0.0 30139.0 0.0 27769.0 g 0 0 0 0 812.0 0.0 0.0 0.0 0.0 0.0 3888.0 t 0 0 0 0 565.0 0.0 1.0 30161.0 10.0 1594.0 0.0