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_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_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/2025/11/25/peak-motifs.2025-11-25.143236_2025-11-25.143236_C5OFib/results/discovered_motifs/oligos_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift3 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m5_shift3 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=10; shift=3; ncol=13; ---yyCTGTGAkb ; Alignment reference a 0 0 0 1303 1412 86 40 33 69 42 6357 1418 1469 c 0 0 0 1968 1755 6489 683 9 373 50 193 1545 1717 g 0 0 0 1292 1641 151 627 6694 63 6599 60 1972 1779 t 0 0 0 2195 1950 32 5408 22 6253 67 148 1823 1793

MA0038.3_rc_shift3 (GFI1_rc)
; oligos_6nt_mkv4_m5 versus MA0038.3_rc (GFI1_rc); m=1/9; ncol2=11; w=0; offset=0; strand=R; shift=3; score=0.657347; ---tGChGTGATT ; cor=; Ncor= a 0 0 0 4134.0 3702.0 888.0 13996.0 0.0 1594.0 10.0 30161.0 1.0 0.0 c 0 0 0 4079.0 0.0 27514.0 8349.0 3888.0 0.0 0.0 0.0 0.0 0.0 g 0 0 0 5221.0 27891.0 266.0 54.0 27769.0 0.0 30139.0 0.0 0.0 2.0 t 0 0 0 16713.0 292.0 2294.0 7748.0 838.0 29255.0 15.0 0.0 30150.0 30168.0

MA0483.2_rc_shift4 (Gfi1B_rc)
; oligos_6nt_mkv4_m5 versus MA0483.2_rc (Gfi1B_rc); m=2/9; ncol2=10; w=0; offset=1; strand=R; shift=4; score=0.584354; ----GCwGwGATT ; cor=; Ncor= a 0 0 0 0 215.0 27.0 644.0 0.0 707.0 0.0 1395.0 0.0 0.0 c 0 0 0 0 76.0 1676.0 1.0 388.0 0.0 0.0 28.0 2.0 0.0 g 0 0 0 0 1328.0 1.0 0.0 1312.0 21.0 1761.0 338.0 0.0 0.0 t 0 0 0 0 142.0 57.0 1116.0 61.0 1033.0 0.0 0.0 1759.0 1761.0

MA0774.1_rc_shift4 (MEIS2_rc)
; oligos_6nt_mkv4_m5 versus MA0774.1_rc (MEIS2_rc); m=3/9; ncol2=8; w=0; offset=1; strand=R; shift=4; score=0.569126; ----sCTGTCAa- ; cor=; Ncor= a 0 0 0 0 88.0 67.0 0.0 5.0 62.0 0.0 1351.0 1351.0 0 c 0 0 0 0 650.0 1351.0 4.0 0.0 25.0 1351.0 40.0 314.0 0 g 0 0 0 0 701.0 98.0 7.0 1351.0 3.0 0.0 3.0 264.0 0 t 0 0 0 0 157.0 83.0 1351.0 9.0 1351.0 0.0 31.0 408.0 0

MA0769.3_shift5 (TCF7)
; oligos_6nt_mkv4_m5 versus MA0769.3 (TCF7); m=4/9; ncol2=7; w=0; offset=2; strand=D; shift=5; score=0.51927; -----CTTTGAw- ; cor=; Ncor= a 0 0 0 0 0 252.0 246.0 302.0 360.0 266.0 14577.0 4421.0 0 c 0 0 0 0 0 14379.0 125.0 248.0 62.0 278.0 63.0 855.0 0 g 0 0 0 0 0 206.0 67.0 266.0 83.0 13972.0 115.0 1220.0 0 t 0 0 0 0 0 157.0 14556.0 14178.0 14489.0 478.0 239.0 8498.0 0

MA1629.2_rc_shift1 (Zic2_rc)
; oligos_6nt_mkv4_m5 versus MA1629.2_rc (Zic2_rc); m=5/9; ncol2=9; w=-2; offset=-2; strand=R; shift=1; score=0.473084; -CCTGCTGtG--- ; cor=; Ncor= a 0 154.0 410.0 441.0 298.0 67.0 268.0 120.0 2437.0 240.0 0 0 0 c 0 11465.0 11184.0 735.0 269.0 11484.0 186.0 188.0 829.0 585.0 0 0 0 g 0 204.0 133.0 118.0 11272.0 228.0 391.0 11476.0 1765.0 9933.0 0 0 0 t 0 96.0 192.0 10625.0 80.0 140.0 11074.0 135.0 6888.0 1161.0 0 0 0

MA1593.2_rc_shift1 (ZNF317_rc)
; oligos_6nt_mkv4_m5 versus MA1593.2_rc (ZNF317_rc); m=6/9; ncol2=8; w=-2; offset=-2; strand=R; shift=1; score=0.414664; -TCTGCTGT---- ; cor=; Ncor= a 0 224.0 263.0 1601.0 237.0 206.0 717.0 178.0 1245.0 0 0 0 0 c 0 206.0 10730.0 289.0 223.0 10374.0 317.0 183.0 480.0 0 0 0 0 g 0 208.0 186.0 250.0 10608.0 192.0 85.0 10821.0 357.0 0 0 0 0 t 0 10825.0 284.0 9323.0 395.0 691.0 10344.0 281.0 9381.0 0 0 0 0

MA1646.2_rc_shift1 (OSR2_rc)
; oligos_6nt_mkv4_m5 versus MA1646.2_rc (OSR2_rc); m=7/9; ncol2=8; w=-2; offset=-2; strand=R; shift=1; score=0.409683; -GCTTCTGt---- ; cor=; Ncor= a 0 1192.0 240.0 279.0 1526.0 157.0 275.0 211.0 1950.0 0 0 0 0 c 0 841.0 13982.0 516.0 901.0 14206.0 737.0 406.0 2117.0 0 0 0 0 g 0 12109.0 170.0 288.0 703.0 229.0 197.0 13937.0 2221.0 0 0 0 0 t 0 666.0 416.0 13725.0 11678.0 216.0 13599.0 254.0 8520.0 0 0 0 0

MA1523.2_rc_shift7 (MSANTD3_rc)
; oligos_6nt_mkv4_m5 versus MA1523.2_rc (MSANTD3_rc); m=8/9; ncol2=7; w=0; offset=4; strand=R; shift=7; score=0.401453; -------kTGAGT ; cor=; Ncor= a 0 0 0 0 0 0 0 96.0 59.0 60.0 954.0 45.0 16.0 c 0 0 0 0 0 0 0 63.0 24.0 29.0 0.0 27.0 2.0 g 0 0 0 0 0 0 0 568.0 140.0 862.0 7.0 896.0 0.0 t 0 0 0 0 0 0 0 271.0 775.0 47.0 37.0 31.0 980.0

MA2327.1_shift0 (PGR)
; oligos_6nt_mkv4_m5 versus MA2327.1 (PGR); m=9/9; ncol2=9; w=-3; offset=-3; strand=D; shift=0; score=0.400103; ACAkwmTGT---- ; cor=; Ncor= a 29390.0 299.0 27485.0 5276.0 8275.0 8527.0 328.0 765.0 173.0 0 0 0 0 c 121.0 28612.0 363.0 6470.0 6654.0 9602.0 1695.0 185.0 190.0 0 0 0 0 g 189.0 185.0 1689.0 9598.0 6656.0 6465.0 364.0 28617.0 122.0 0 0 0 0 t 164.0 768.0 327.0 8520.0 8279.0 5270.0 27477.0 297.0 29379.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m5_shift3 (oligos_6nt_mkv4_m5)				; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=10; shift=3; ncol=13; ---yyCTGTGAkb ; Alignment reference a 0 0 0 1303 1412 86 40 33 69 42 6357 1418 1469 c 0 0 0 1968 1755 6489 683 9 373 50 193 1545 1717 g 0 0 0 1292 1641 151 627 6694 63 6599 60 1972 1779 t 0 0 0 2195 1950 32 5408 22 6253 67 148 1823 1793
MA0038.3_rc_shift3 (GFI1_rc)				; oligos_6nt_mkv4_m5 versus MA0038.3_rc (GFI1_rc); m=1/9; ncol2=11; w=0; offset=0; strand=R; shift=3; score=0.657347; ---tGChGTGATT ; cor=; Ncor= a 0 0 0 4134.0 3702.0 888.0 13996.0 0.0 1594.0 10.0 30161.0 1.0 0.0 c 0 0 0 4079.0 0.0 27514.0 8349.0 3888.0 0.0 0.0 0.0 0.0 0.0 g 0 0 0 5221.0 27891.0 266.0 54.0 27769.0 0.0 30139.0 0.0 0.0 2.0 t 0 0 0 16713.0 292.0 2294.0 7748.0 838.0 29255.0 15.0 0.0 30150.0 30168.0
MA0483.2_rc_shift4 (Gfi1B_rc)				; oligos_6nt_mkv4_m5 versus MA0483.2_rc (Gfi1B_rc); m=2/9; ncol2=10; w=0; offset=1; strand=R; shift=4; score=0.584354; ----GCwGwGATT ; cor=; Ncor= a 0 0 0 0 215.0 27.0 644.0 0.0 707.0 0.0 1395.0 0.0 0.0 c 0 0 0 0 76.0 1676.0 1.0 388.0 0.0 0.0 28.0 2.0 0.0 g 0 0 0 0 1328.0 1.0 0.0 1312.0 21.0 1761.0 338.0 0.0 0.0 t 0 0 0 0 142.0 57.0 1116.0 61.0 1033.0 0.0 0.0 1759.0 1761.0
MA0774.1_rc_shift4 (MEIS2_rc)				; oligos_6nt_mkv4_m5 versus MA0774.1_rc (MEIS2_rc); m=3/9; ncol2=8; w=0; offset=1; strand=R; shift=4; score=0.569126; ----sCTGTCAa- ; cor=; Ncor= a 0 0 0 0 88.0 67.0 0.0 5.0 62.0 0.0 1351.0 1351.0 0 c 0 0 0 0 650.0 1351.0 4.0 0.0 25.0 1351.0 40.0 314.0 0 g 0 0 0 0 701.0 98.0 7.0 1351.0 3.0 0.0 3.0 264.0 0 t 0 0 0 0 157.0 83.0 1351.0 9.0 1351.0 0.0 31.0 408.0 0
MA0769.3_shift5 (TCF7)				; oligos_6nt_mkv4_m5 versus MA0769.3 (TCF7); m=4/9; ncol2=7; w=0; offset=2; strand=D; shift=5; score=0.51927; -----CTTTGAw- ; cor=; Ncor= a 0 0 0 0 0 252.0 246.0 302.0 360.0 266.0 14577.0 4421.0 0 c 0 0 0 0 0 14379.0 125.0 248.0 62.0 278.0 63.0 855.0 0 g 0 0 0 0 0 206.0 67.0 266.0 83.0 13972.0 115.0 1220.0 0 t 0 0 0 0 0 157.0 14556.0 14178.0 14489.0 478.0 239.0 8498.0 0
MA1629.2_rc_shift1 (Zic2_rc)				; oligos_6nt_mkv4_m5 versus MA1629.2_rc (Zic2_rc); m=5/9; ncol2=9; w=-2; offset=-2; strand=R; shift=1; score=0.473084; -CCTGCTGtG--- ; cor=; Ncor= a 0 154.0 410.0 441.0 298.0 67.0 268.0 120.0 2437.0 240.0 0 0 0 c 0 11465.0 11184.0 735.0 269.0 11484.0 186.0 188.0 829.0 585.0 0 0 0 g 0 204.0 133.0 118.0 11272.0 228.0 391.0 11476.0 1765.0 9933.0 0 0 0 t 0 96.0 192.0 10625.0 80.0 140.0 11074.0 135.0 6888.0 1161.0 0 0 0
MA1593.2_rc_shift1 (ZNF317_rc)				; oligos_6nt_mkv4_m5 versus MA1593.2_rc (ZNF317_rc); m=6/9; ncol2=8; w=-2; offset=-2; strand=R; shift=1; score=0.414664; -TCTGCTGT---- ; cor=; Ncor= a 0 224.0 263.0 1601.0 237.0 206.0 717.0 178.0 1245.0 0 0 0 0 c 0 206.0 10730.0 289.0 223.0 10374.0 317.0 183.0 480.0 0 0 0 0 g 0 208.0 186.0 250.0 10608.0 192.0 85.0 10821.0 357.0 0 0 0 0 t 0 10825.0 284.0 9323.0 395.0 691.0 10344.0 281.0 9381.0 0 0 0 0
MA1646.2_rc_shift1 (OSR2_rc)				; oligos_6nt_mkv4_m5 versus MA1646.2_rc (OSR2_rc); m=7/9; ncol2=8; w=-2; offset=-2; strand=R; shift=1; score=0.409683; -GCTTCTGt---- ; cor=; Ncor= a 0 1192.0 240.0 279.0 1526.0 157.0 275.0 211.0 1950.0 0 0 0 0 c 0 841.0 13982.0 516.0 901.0 14206.0 737.0 406.0 2117.0 0 0 0 0 g 0 12109.0 170.0 288.0 703.0 229.0 197.0 13937.0 2221.0 0 0 0 0 t 0 666.0 416.0 13725.0 11678.0 216.0 13599.0 254.0 8520.0 0 0 0 0
MA1523.2_rc_shift7 (MSANTD3_rc)				; oligos_6nt_mkv4_m5 versus MA1523.2_rc (MSANTD3_rc); m=8/9; ncol2=7; w=0; offset=4; strand=R; shift=7; score=0.401453; -------kTGAGT ; cor=; Ncor= a 0 0 0 0 0 0 0 96.0 59.0 60.0 954.0 45.0 16.0 c 0 0 0 0 0 0 0 63.0 24.0 29.0 0.0 27.0 2.0 g 0 0 0 0 0 0 0 568.0 140.0 862.0 7.0 896.0 0.0 t 0 0 0 0 0 0 0 271.0 775.0 47.0 37.0 31.0 980.0
MA2327.1_shift0 (PGR)				; oligos_6nt_mkv4_m5 versus MA2327.1 (PGR); m=9/9; ncol2=9; w=-3; offset=-3; strand=D; shift=0; score=0.400103; ACAkwmTGT---- ; cor=; Ncor= a 29390.0 299.0 27485.0 5276.0 8275.0 8527.0 328.0 765.0 173.0 0 0 0 0 c 121.0 28612.0 363.0 6470.0 6654.0 9602.0 1695.0 185.0 190.0 0 0 0 0 g 189.0 185.0 1689.0 9598.0 6656.0 6465.0 364.0 28617.0 122.0 0 0 0 0 t 164.0 768.0 327.0 8520.0 8279.0 5270.0 27477.0 297.0 29379.0 0 0 0 0