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.2026-01-05.125527_2026-01-05.125527_ogDb5d/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/2026/01/05/peak-motifs.2026-01-05.125527_2026-01-05.125527_ogDb5d/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_shift3 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=3; ncol=15; ---ssCGGCtGCGss ; Alignment reference a 0 0 0 3074 2716 794 792 558 414 775 469 594 1166 2755 2976 c 0 0 0 8848 6386 20775 1624 1327 21919 3947 1322 21439 3085 8024 8987 g 0 0 0 8643 11960 1509 20646 21088 1136 5423 21556 1084 18188 10068 8620 t 0 0 0 3174 2677 661 677 766 270 13594 392 622 1300 2892 3156

MA1721.2_shift0 (ZNF93)
; oligos_7nt_mkv5_m4 versus MA1721.2 (ZNF93); m=1/7; ncol2=14; w=-3; offset=-3; strand=D; shift=0; score=0.59329; gGyrkCrGCAGCGG- ; cor=; Ncor= a 467.0 175.0 117.0 1455.0 61.0 38.0 1001.0 18.0 23.0 1659.0 30.0 19.0 340.0 72.0 0 c 279.0 233.0 1120.0 177.0 114.0 2278.0 92.0 26.0 2279.0 96.0 20.0 2292.0 138.0 134.0 0 g 1499.0 1857.0 211.0 663.0 1483.0 22.0 1263.0 2334.0 42.0 576.0 2328.0 33.0 1784.0 2145.0 0 t 143.0 123.0 940.0 93.0 730.0 50.0 32.0 10.0 44.0 57.0 10.0 44.0 126.0 37.0 0

MA0048.3_rc_shift4 (NHLH1_rc)
; oligos_7nt_mkv5_m4 versus MA0048.3_rc (NHLH1_rc); m=2/7; ncol2=9; w=0; offset=1; strand=R; shift=4; score=0.567642; ----GCAGCTGCg-- ; cor=; Ncor= a 0 0 0 0 350.0 1.0 2166.0 0.0 114.0 0.0 0.0 142.0 111.0 0 0 c 0 0 0 0 102.0 2166.0 4.0 124.0 2166.0 1.0 0.0 2166.0 181.0 0 0 g 0 0 0 0 2166.0 4.0 4.0 2166.0 301.0 3.0 2166.0 179.0 2166.0 0 0 t 0 0 0 0 296.0 2.0 0.0 96.0 0.0 2166.0 3.0 461.0 788.0 0 0

MA1529.2_shift0 (NHLH2)
; oligos_7nt_mkv5_m4 versus MA1529.2 (NHLH2); m=3/7; ncol2=16; w=-3; offset=-3; strand=D; shift=0; score=0.551442; gGyMGCAGCTGCGyC ; cor=; Ncor= a 4312.0 3741.0 4921.0 5603.0 2378.0 2.0 21364.0 6.0 525.0 0.0 0.0 693.0 210.0 1184.0 3766.0 c 2219.0 1065.0 6141.0 15451.0 2324.0 21359.0 0.0 2459.0 20268.0 14.0 2.0 20611.0 204.0 7207.0 18351.0 g 13903.0 18450.0 4908.0 671.0 18930.0 2.0 26.0 20096.0 2266.0 3.0 21363.0 275.0 20977.0 1520.0 1183.0 t 5198.0 2763.0 5394.0 151.0 2634.0 5.0 1.0 1054.0 0.0 21358.0 0.0 1230.0 740.0 13503.0 2533.0

MA0500.3_shift4 (MYOG)
; oligos_7nt_mkv5_m4 versus MA0500.3 (MYOG); m=4/7; ncol2=8; w=0; offset=1; strand=D; shift=4; score=0.484246; ----rCAGCTGy--- ; cor=; Ncor= a 0 0 0 0 7159.0 86.0 21782.0 95.0 167.0 163.0 182.0 1667.0 0 0 0 c 0 0 0 0 2730.0 21988.0 176.0 130.0 21964.0 238.0 102.0 10792.0 0 0 0 g 0 0 0 0 10790.0 101.0 236.0 21963.0 131.0 179.0 21985.0 2706.0 0 0 0 t 0 0 0 0 1678.0 182.0 163.0 169.0 95.0 21777.0 88.0 7192.0 0 0 0

MA1100.3_shift4 (ASCL1)
; oligos_7nt_mkv5_m4 versus MA1100.3 (ASCL1); m=5/7; ncol2=8; w=0; offset=1; strand=D; shift=4; score=0.46788; ----rCAGCTGc--- ; cor=; Ncor= a 0 0 0 0 1334.0 0.0 4413.0 107.0 729.0 118.0 52.0 177.0 0 0 0 c 0 0 0 0 521.0 4413.0 157.0 1288.0 4413.0 24.0 0.0 3065.0 0 0 0 g 0 0 0 0 3079.0 0.0 60.0 4413.0 1320.0 121.0 4413.0 814.0 0 0 0 t 0 0 0 0 354.0 14.0 218.0 625.0 20.0 4413.0 29.0 1349.0 0 0 0

MA1713.2_rc_shift1 (ZNF610_rc)
; oligos_7nt_mkv5_m4 versus MA1713.2_rc (ZNF610_rc); m=6/7; ncol2=10; w=-2; offset=-2; strand=R; shift=1; score=0.43223; -GGAGCGGCgs---- ; cor=; Ncor= a 0 101.0 3.0 2289.0 4.0 11.0 15.0 20.0 79.0 293.0 250.0 0 0 0 0 c 0 186.0 62.0 45.0 21.0 2312.0 41.0 84.0 2118.0 392.0 738.0 0 0 0 0 g 0 1976.0 2315.0 34.0 2357.0 45.0 2312.0 2245.0 121.0 1347.0 1222.0 0 0 0 0 t 0 123.0 6.0 18.0 4.0 18.0 18.0 37.0 68.0 354.0 176.0 0 0 0 0

MA1583.2_rc_shift3 (ZFP57_rc)
; oligos_7nt_mkv5_m4 versus MA1583.2_rc (ZFP57_rc); m=7/7; ncol2=7; w=0; offset=0; strand=R; shift=3; score=0.414406; ---TGCGGCA----- ; cor=; Ncor= a 0 0 0 156.0 187.0 59.0 7.0 36.0 24.0 6143.0 0 0 0 0 0 c 0 0 0 729.0 279.0 6166.0 719.0 16.0 6213.0 140.0 0 0 0 0 0 g 0 0 0 331.0 5828.0 16.0 5595.0 6254.0 71.0 37.0 0 0 0 0 0 t 0 0 0 5116.0 38.0 91.0 11.0 26.0 24.0 12.0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=12; shift=3; ncol=15; ---ssCGGCtGCGss ; Alignment reference a 0 0 0 3074 2716 794 792 558 414 775 469 594 1166 2755 2976 c 0 0 0 8848 6386 20775 1624 1327 21919 3947 1322 21439 3085 8024 8987 g 0 0 0 8643 11960 1509 20646 21088 1136 5423 21556 1084 18188 10068 8620 t 0 0 0 3174 2677 661 677 766 270 13594 392 622 1300 2892 3156
MA1721.2_shift0 (ZNF93)				; oligos_7nt_mkv5_m4 versus MA1721.2 (ZNF93); m=1/7; ncol2=14; w=-3; offset=-3; strand=D; shift=0; score=0.59329; gGyrkCrGCAGCGG- ; cor=; Ncor= a 467.0 175.0 117.0 1455.0 61.0 38.0 1001.0 18.0 23.0 1659.0 30.0 19.0 340.0 72.0 0 c 279.0 233.0 1120.0 177.0 114.0 2278.0 92.0 26.0 2279.0 96.0 20.0 2292.0 138.0 134.0 0 g 1499.0 1857.0 211.0 663.0 1483.0 22.0 1263.0 2334.0 42.0 576.0 2328.0 33.0 1784.0 2145.0 0 t 143.0 123.0 940.0 93.0 730.0 50.0 32.0 10.0 44.0 57.0 10.0 44.0 126.0 37.0 0
MA0048.3_rc_shift4 (NHLH1_rc)				; oligos_7nt_mkv5_m4 versus MA0048.3_rc (NHLH1_rc); m=2/7; ncol2=9; w=0; offset=1; strand=R; shift=4; score=0.567642; ----GCAGCTGCg-- ; cor=; Ncor= a 0 0 0 0 350.0 1.0 2166.0 0.0 114.0 0.0 0.0 142.0 111.0 0 0 c 0 0 0 0 102.0 2166.0 4.0 124.0 2166.0 1.0 0.0 2166.0 181.0 0 0 g 0 0 0 0 2166.0 4.0 4.0 2166.0 301.0 3.0 2166.0 179.0 2166.0 0 0 t 0 0 0 0 296.0 2.0 0.0 96.0 0.0 2166.0 3.0 461.0 788.0 0 0
MA1529.2_shift0 (NHLH2)				; oligos_7nt_mkv5_m4 versus MA1529.2 (NHLH2); m=3/7; ncol2=16; w=-3; offset=-3; strand=D; shift=0; score=0.551442; gGyMGCAGCTGCGyC ; cor=; Ncor= a 4312.0 3741.0 4921.0 5603.0 2378.0 2.0 21364.0 6.0 525.0 0.0 0.0 693.0 210.0 1184.0 3766.0 c 2219.0 1065.0 6141.0 15451.0 2324.0 21359.0 0.0 2459.0 20268.0 14.0 2.0 20611.0 204.0 7207.0 18351.0 g 13903.0 18450.0 4908.0 671.0 18930.0 2.0 26.0 20096.0 2266.0 3.0 21363.0 275.0 20977.0 1520.0 1183.0 t 5198.0 2763.0 5394.0 151.0 2634.0 5.0 1.0 1054.0 0.0 21358.0 0.0 1230.0 740.0 13503.0 2533.0
MA0500.3_shift4 (MYOG)				; oligos_7nt_mkv5_m4 versus MA0500.3 (MYOG); m=4/7; ncol2=8; w=0; offset=1; strand=D; shift=4; score=0.484246; ----rCAGCTGy--- ; cor=; Ncor= a 0 0 0 0 7159.0 86.0 21782.0 95.0 167.0 163.0 182.0 1667.0 0 0 0 c 0 0 0 0 2730.0 21988.0 176.0 130.0 21964.0 238.0 102.0 10792.0 0 0 0 g 0 0 0 0 10790.0 101.0 236.0 21963.0 131.0 179.0 21985.0 2706.0 0 0 0 t 0 0 0 0 1678.0 182.0 163.0 169.0 95.0 21777.0 88.0 7192.0 0 0 0
MA1100.3_shift4 (ASCL1)				; oligos_7nt_mkv5_m4 versus MA1100.3 (ASCL1); m=5/7; ncol2=8; w=0; offset=1; strand=D; shift=4; score=0.46788; ----rCAGCTGc--- ; cor=; Ncor= a 0 0 0 0 1334.0 0.0 4413.0 107.0 729.0 118.0 52.0 177.0 0 0 0 c 0 0 0 0 521.0 4413.0 157.0 1288.0 4413.0 24.0 0.0 3065.0 0 0 0 g 0 0 0 0 3079.0 0.0 60.0 4413.0 1320.0 121.0 4413.0 814.0 0 0 0 t 0 0 0 0 354.0 14.0 218.0 625.0 20.0 4413.0 29.0 1349.0 0 0 0
MA1713.2_rc_shift1 (ZNF610_rc)				; oligos_7nt_mkv5_m4 versus MA1713.2_rc (ZNF610_rc); m=6/7; ncol2=10; w=-2; offset=-2; strand=R; shift=1; score=0.43223; -GGAGCGGCgs---- ; cor=; Ncor= a 0 101.0 3.0 2289.0 4.0 11.0 15.0 20.0 79.0 293.0 250.0 0 0 0 0 c 0 186.0 62.0 45.0 21.0 2312.0 41.0 84.0 2118.0 392.0 738.0 0 0 0 0 g 0 1976.0 2315.0 34.0 2357.0 45.0 2312.0 2245.0 121.0 1347.0 1222.0 0 0 0 0 t 0 123.0 6.0 18.0 4.0 18.0 18.0 37.0 68.0 354.0 176.0 0 0 0 0
MA1583.2_rc_shift3 (ZFP57_rc)				; oligos_7nt_mkv5_m4 versus MA1583.2_rc (ZFP57_rc); m=7/7; ncol2=7; w=0; offset=0; strand=R; shift=3; score=0.414406; ---TGCGGCA----- ; cor=; Ncor= a 0 0 0 156.0 187.0 59.0 7.0 36.0 24.0 6143.0 0 0 0 0 0 c 0 0 0 729.0 279.0 6166.0 719.0 16.0 6213.0 140.0 0 0 0 0 0 g 0 0 0 331.0 5828.0 16.0 5595.0 6254.0 71.0 37.0 0 0 0 0 0 t 0 0 0 5116.0 38.0 91.0 11.0 26.0 24.0 12.0 0 0 0 0 0