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.2025-05-16.175219_2025-05-16.175219_UyZibC/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5.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.2025-05-16.175219_2025-05-16.175219_UyZibC/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift2 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift2 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=11; shift=2; ncol=13; --ryCTAGGCArv ; Alignment reference a 0 0 20 15 2 2 62 4 1 2 59 19 21 c 0 0 16 21 65 1 3 0 3 61 6 18 20 g 0 0 20 17 2 1 4 67 68 4 4 20 21 t 0 0 17 20 4 69 4 2 1 6 4 16 11

MA1979.2_shift1 (ZNF416)
; oligos_7nt_mkv2_m5 versus MA1979.2 (ZNF416); m=1/7; ncol2=10; w=-1; offset=-1; strand=D; shift=1; score=0.57217; -TaTCTGGGCa-- ; cor=; Ncor= a 0 47.0 197.0 48.0 1.0 2.0 1.0 2.0 0.0 4.0 212.0 0 0 c 0 32.0 25.0 28.0 334.0 6.0 7.0 5.0 1.0 320.0 38.0 0 0 g 0 26.0 77.0 15.0 7.0 1.0 335.0 335.0 341.0 3.0 29.0 0 0 t 0 240.0 46.0 254.0 3.0 336.0 2.0 3.0 3.0 18.0 66.0 0 0

MA0161.3_shift4 (NFIC)
; oligos_7nt_mkv2_m5 versus MA0161.3 (NFIC); m=2/7; ncol2=7; w=0; offset=2; strand=D; shift=4; score=0.521491; ----CTTGGCA-- ; cor=; Ncor= a 0 0 0 0 412.0 154.0 352.0 310.0 223.0 264.0 10158.0 0 0 c 0 0 0 0 10542.0 303.0 333.0 129.0 121.0 10725.0 397.0 0 0 g 0 0 0 0 329.0 369.0 177.0 11087.0 10973.0 88.0 478.0 0 0 t 0 0 0 0 324.0 10781.0 10745.0 81.0 290.0 530.0 574.0 0 0

MA1153.2_rc_shift4 (Smad4_rc)
; oligos_7nt_mkv2_m5 versus MA1153.2_rc (Smad4_rc); m=3/7; ncol2=7; w=0; offset=2; strand=R; shift=4; score=0.452493; ----CyAGACr-- ; cor=; Ncor= a 0 0 0 0 0.0 0.0 1000.0 0.0 1000.0 0.0 581.0 0 0 c 0 0 0 0 1000.0 404.0 0.0 0.0 0.0 1000.0 81.0 0 0 g 0 0 0 0 0.0 0.0 0.0 1000.0 0.0 0.0 250.0 0 0 t 0 0 0 0 0.0 596.0 0.0 0.0 0.0 0.0 88.0 0 0

MA1724.2_rc_shift0 (Rfx6_rc)
; oligos_7nt_mkv2_m5 versus MA1724.2_rc (Rfx6_rc); m=4/7; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.434298; GTTGCTAGG---- ; cor=; Ncor= a 635.0 213.0 216.0 339.0 54.0 66.0 6994.0 810.0 272.0 0 0 0 0 c 552.0 339.0 132.0 359.0 8215.0 1205.0 146.0 242.0 232.0 0 0 0 0 g 6811.0 258.0 117.0 7474.0 102.0 64.0 1066.0 6405.0 7859.0 0 0 0 0 t 552.0 7740.0 8085.0 378.0 179.0 7215.0 344.0 1093.0 187.0 0 0 0 0

MA0670.2_rc_shift5 (NFIA_rc)
; oligos_7nt_mkv2_m5 versus MA0670.2_rc (NFIA_rc); m=5/7; ncol2=6; w=0; offset=3; strand=R; shift=5; score=0.429283; -----TTGGCA-- ; cor=; Ncor= a 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 95496.0 0 0 c 0 0 0 0 0 0.0 0.0 0.0 0.0 98253.0 0.0 0 0 g 0 0 0 0 0 0.0 0.0 93394.0 93597.0 0.0 0.0 0 0 t 0 0 0 0 0 89418.0 89071.0 0.0 0.0 0.0 0.0 0 0

MA1730.2_rc_shift6 (ZNF708_rc)
; oligos_7nt_mkv2_m5 versus MA1730.2_rc (ZNF708_rc); m=6/7; ncol2=9; w=0; offset=4; strand=R; shift=6; score=0.424091; ------AGGyACA ; cor=; Ncor= a 0 0 0 0 0 0 800.0 5.0 24.0 6.0 791.0 2.0 780.0 c 0 0 0 0 0 0 13.0 12.0 49.0 436.0 19.0 827.0 8.0 g 0 0 0 0 0 0 31.0 828.0 771.0 4.0 28.0 7.0 54.0 t 0 0 0 0 0 0 5.0 4.0 5.0 403.0 11.0 13.0 7.0

MA0738.2_rc_shift6 (HIC2_rc)
; oligos_7nt_mkv2_m5 versus MA0738.2_rc (HIC2_rc); m=7/7; ncol2=6; w=0; offset=4; strand=R; shift=6; score=0.406495; ------KGGCAy- ; cor=; Ncor= a 0 0 0 0 0 0 0.0 59.0 0.0 151.0 4891.0 367.0 0 c 0 0 0 0 0 0 0.0 0.0 14.0 4891.0 0.0 2285.0 0 g 0 0 0 0 0 0 3425.0 4891.0 4891.0 354.0 117.0 394.0 0 t 0 0 0 0 0 0 1466.0 435.0 23.0 494.0 0.0 2606.0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m5_shift2 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=11; shift=2; ncol=13; --ryCTAGGCArv ; Alignment reference a 0 0 20 15 2 2 62 4 1 2 59 19 21 c 0 0 16 21 65 1 3 0 3 61 6 18 20 g 0 0 20 17 2 1 4 67 68 4 4 20 21 t 0 0 17 20 4 69 4 2 1 6 4 16 11
MA1979.2_shift1 (ZNF416)				; oligos_7nt_mkv2_m5 versus MA1979.2 (ZNF416); m=1/7; ncol2=10; w=-1; offset=-1; strand=D; shift=1; score=0.57217; -TaTCTGGGCa-- ; cor=; Ncor= a 0 47.0 197.0 48.0 1.0 2.0 1.0 2.0 0.0 4.0 212.0 0 0 c 0 32.0 25.0 28.0 334.0 6.0 7.0 5.0 1.0 320.0 38.0 0 0 g 0 26.0 77.0 15.0 7.0 1.0 335.0 335.0 341.0 3.0 29.0 0 0 t 0 240.0 46.0 254.0 3.0 336.0 2.0 3.0 3.0 18.0 66.0 0 0
MA0161.3_shift4 (NFIC)				; oligos_7nt_mkv2_m5 versus MA0161.3 (NFIC); m=2/7; ncol2=7; w=0; offset=2; strand=D; shift=4; score=0.521491; ----CTTGGCA-- ; cor=; Ncor= a 0 0 0 0 412.0 154.0 352.0 310.0 223.0 264.0 10158.0 0 0 c 0 0 0 0 10542.0 303.0 333.0 129.0 121.0 10725.0 397.0 0 0 g 0 0 0 0 329.0 369.0 177.0 11087.0 10973.0 88.0 478.0 0 0 t 0 0 0 0 324.0 10781.0 10745.0 81.0 290.0 530.0 574.0 0 0
MA1153.2_rc_shift4 (Smad4_rc)				; oligos_7nt_mkv2_m5 versus MA1153.2_rc (Smad4_rc); m=3/7; ncol2=7; w=0; offset=2; strand=R; shift=4; score=0.452493; ----CyAGACr-- ; cor=; Ncor= a 0 0 0 0 0.0 0.0 1000.0 0.0 1000.0 0.0 581.0 0 0 c 0 0 0 0 1000.0 404.0 0.0 0.0 0.0 1000.0 81.0 0 0 g 0 0 0 0 0.0 0.0 0.0 1000.0 0.0 0.0 250.0 0 0 t 0 0 0 0 0.0 596.0 0.0 0.0 0.0 0.0 88.0 0 0
MA1724.2_rc_shift0 (Rfx6_rc)				; oligos_7nt_mkv2_m5 versus MA1724.2_rc (Rfx6_rc); m=4/7; ncol2=9; w=-2; offset=-2; strand=R; shift=0; score=0.434298; GTTGCTAGG---- ; cor=; Ncor= a 635.0 213.0 216.0 339.0 54.0 66.0 6994.0 810.0 272.0 0 0 0 0 c 552.0 339.0 132.0 359.0 8215.0 1205.0 146.0 242.0 232.0 0 0 0 0 g 6811.0 258.0 117.0 7474.0 102.0 64.0 1066.0 6405.0 7859.0 0 0 0 0 t 552.0 7740.0 8085.0 378.0 179.0 7215.0 344.0 1093.0 187.0 0 0 0 0
MA0670.2_rc_shift5 (NFIA_rc)				; oligos_7nt_mkv2_m5 versus MA0670.2_rc (NFIA_rc); m=5/7; ncol2=6; w=0; offset=3; strand=R; shift=5; score=0.429283; -----TTGGCA-- ; cor=; Ncor= a 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 95496.0 0 0 c 0 0 0 0 0 0.0 0.0 0.0 0.0 98253.0 0.0 0 0 g 0 0 0 0 0 0.0 0.0 93394.0 93597.0 0.0 0.0 0 0 t 0 0 0 0 0 89418.0 89071.0 0.0 0.0 0.0 0.0 0 0
MA1730.2_rc_shift6 (ZNF708_rc)				; oligos_7nt_mkv2_m5 versus MA1730.2_rc (ZNF708_rc); m=6/7; ncol2=9; w=0; offset=4; strand=R; shift=6; score=0.424091; ------AGGyACA ; cor=; Ncor= a 0 0 0 0 0 0 800.0 5.0 24.0 6.0 791.0 2.0 780.0 c 0 0 0 0 0 0 13.0 12.0 49.0 436.0 19.0 827.0 8.0 g 0 0 0 0 0 0 31.0 828.0 771.0 4.0 28.0 7.0 54.0 t 0 0 0 0 0 0 5.0 4.0 5.0 403.0 11.0 13.0 7.0
MA0738.2_rc_shift6 (HIC2_rc)				; oligos_7nt_mkv2_m5 versus MA0738.2_rc (HIC2_rc); m=7/7; ncol2=6; w=0; offset=4; strand=R; shift=6; score=0.406495; ------KGGCAy- ; cor=; Ncor= a 0 0 0 0 0 0 0.0 59.0 0.0 151.0 4891.0 367.0 0 c 0 0 0 0 0 0 0.0 0.0 14.0 4891.0 0.0 2285.0 0 g 0 0 0 0 0 0 3425.0 4891.0 4891.0 354.0 117.0 394.0 0 t 0 0 0 0 0 0 1466.0 435.0 23.0 494.0 0.0 2606.0 0