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_m4/peak-motifs_oligos_6nt_mkv4_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_6nt_mkv4_m4/peak-motifs_oligos_6nt_mkv4_m4_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m4_shift2 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=11; shift=2; ncol=13; --awACAAAACwa ; Alignment reference a 0 0 2927 2653 4773 373 6440 6317 6430 6605 75 3122 2659 c 0 0 1632 961 652 5642 83 148 64 59 6570 1157 1408 g 0 0 906 1242 592 482 106 88 66 60 19 770 1168 t 0 0 1345 1954 793 313 181 257 250 86 146 1761 1575

MA0084.2_shift2 (SRY)
; oligos_6nt_mkv4_m4 versus MA0084.2 (SRY); m=1/8; ncol2=7; w=0; offset=0; strand=D; shift=2; score=0.514589; --waACAAw---- ; cor=; Ncor= a 0 0 15.0 18.0 25.0 0.0 28.0 27.0 7.0 0 0 0 0 c 0 0 0.0 3.0 0.0 26.0 0.0 0.0 0.0 0 0 0 0 g 0 0 3.0 3.0 0.0 0.0 0.0 1.0 2.0 0 0 0 0 t 0 0 10.0 4.0 3.0 2.0 0.0 0.0 19.0 0 0 0 0

MA0901.3_shift1 (HOXB13)
; oligos_6nt_mkv4_m4 versus MA0901.3 (HOXB13); m=2/8; ncol2=9; w=-1; offset=-1; strand=D; shift=1; score=0.475872; -cCAATAAAA--- ; cor=; Ncor= a 0 11896.0 4212.0 66409.0 73044.0 421.0 73612.0 75997.0 76077.0 70230.0 0 0 0 c 0 47674.0 65312.0 4611.0 726.0 550.0 523.0 599.0 760.0 2465.0 0 0 0 g 0 9096.0 582.0 351.0 1913.0 586.0 1083.0 490.0 625.0 1882.0 0 0 0 t 0 10048.0 8608.0 7343.0 3031.0 77157.0 3496.0 1628.0 1252.0 4137.0 0 0 0

MA1971.2_shift5 (ZBED2)
; oligos_6nt_mkv4_m4 versus MA1971.2 (ZBED2); m=3/8; ncol2=7; w=0; offset=3; strand=D; shift=5; score=0.451928; -----CGAAACC- ; cor=; Ncor= a 0 0 0 0 0 42.0 19.0 1247.0 1264.0 1131.0 17.0 75.0 0 c 0 0 0 0 0 1195.0 21.0 13.0 13.0 94.0 1217.0 962.0 0 g 0 0 0 0 0 42.0 1252.0 29.0 8.0 41.0 43.0 47.0 0 t 0 0 0 0 0 18.0 5.0 8.0 12.0 31.0 20.0 213.0 0

MA0851.2_shift0 (Foxj3)
; oligos_6nt_mkv4_m4 versus MA0851.2 (Foxj3); m=4/8; ncol2=9; w=-2; offset=-2; strand=D; shift=0; score=0.44963; RTAAACAAw---- ; cor=; Ncor= a 30.0 1.0 91.0 96.0 99.0 0.0 99.0 79.0 57.0 0 0 0 0 c 1.0 2.0 8.0 2.0 0.0 81.0 0.0 7.0 9.0 0 0 0 0 g 68.0 0.0 0.0 0.0 0.0 0.0 0.0 6.0 7.0 0 0 0 0 t 0.0 97.0 0.0 3.0 1.0 18.0 1.0 9.0 27.0 0 0 0 0

MA1616.2_shift5 (Prdm15)
; oligos_6nt_mkv4_m4 versus MA1616.2 (Prdm15); m=5/8; ncol2=11; w=0; offset=3; strand=D; shift=5; score=0.430439; -----gAAAACCT ; cor=; Ncor= a 0 0 0 0 0 252.0 2011.0 2121.0 1942.0 1801.0 67.0 222.0 220.0 c 0 0 0 0 0 325.0 60.0 34.0 47.0 138.0 1941.0 1886.0 361.0 g 0 0 0 0 0 1333.0 135.0 58.0 200.0 152.0 101.0 107.0 28.0 t 0 0 0 0 0 327.0 31.0 24.0 48.0 146.0 128.0 22.0 1628.0

MA1125.2_shift6 (ZNF384)
; oligos_6nt_mkv4_m4 versus MA1125.2 (ZNF384); m=6/8; ncol2=8; w=0; offset=4; strand=D; shift=6; score=0.413755; ------AAAAAAa ; cor=; Ncor= a 0 0 0 0 0 0 30354.0 30191.0 30072.0 30252.0 30202.0 30406.0 20322.0 c 0 0 0 0 0 0 7.0 35.0 21.0 13.0 26.0 6.0 2908.0 g 0 0 0 0 0 0 13.0 19.0 26.0 15.0 14.0 0.0 2767.0 t 0 0 0 0 0 0 59.0 188.0 314.0 153.0 191.0 21.0 4436.0

MA1489.1_shift0 (FOXN3)
; oligos_6nt_mkv4_m4 versus MA1489.1 (FOXN3); m=7/8; ncol2=8; w=-2; offset=-2; strand=D; shift=0; score=0.412421; GTAAACAA----- ; cor=; Ncor= a 9.0 9.0 971.0 971.0 971.0 9.0 971.0 971.0 0 0 0 0 0 c 9.0 9.0 9.0 9.0 9.0 971.0 9.0 9.0 0 0 0 0 0 g 971.0 9.0 9.0 9.0 9.0 9.0 9.0 9.0 0 0 0 0 0 t 9.0 971.0 9.0 9.0 9.0 9.0 9.0 9.0 0 0 0 0 0

MA0442.3_shift4 (SOX10)
; oligos_6nt_mkv4_m4 versus MA0442.3 (SOX10); m=8/8; ncol2=6; w=0; offset=2; strand=D; shift=4; score=0.401423; ----ACAAAG--- ; cor=; Ncor= a 0 0 0 0 2023.0 3.0 2029.0 1968.0 1959.0 10.0 0 0 0 c 0 0 0 0 4.0 1989.0 7.0 28.0 23.0 13.0 0 0 0 g 0 0 0 0 3.0 11.0 7.0 20.0 12.0 2012.0 0 0 0 t 0 0 0 0 25.0 52.0 12.0 39.0 61.0 20.0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m4_shift2 (oligos_6nt_mkv4_m4)				; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=11; shift=2; ncol=13; --awACAAAACwa ; Alignment reference a 0 0 2927 2653 4773 373 6440 6317 6430 6605 75 3122 2659 c 0 0 1632 961 652 5642 83 148 64 59 6570 1157 1408 g 0 0 906 1242 592 482 106 88 66 60 19 770 1168 t 0 0 1345 1954 793 313 181 257 250 86 146 1761 1575
MA0084.2_shift2 (SRY)				; oligos_6nt_mkv4_m4 versus MA0084.2 (SRY); m=1/8; ncol2=7; w=0; offset=0; strand=D; shift=2; score=0.514589; --waACAAw---- ; cor=; Ncor= a 0 0 15.0 18.0 25.0 0.0 28.0 27.0 7.0 0 0 0 0 c 0 0 0.0 3.0 0.0 26.0 0.0 0.0 0.0 0 0 0 0 g 0 0 3.0 3.0 0.0 0.0 0.0 1.0 2.0 0 0 0 0 t 0 0 10.0 4.0 3.0 2.0 0.0 0.0 19.0 0 0 0 0
MA0901.3_shift1 (HOXB13)				; oligos_6nt_mkv4_m4 versus MA0901.3 (HOXB13); m=2/8; ncol2=9; w=-1; offset=-1; strand=D; shift=1; score=0.475872; -cCAATAAAA--- ; cor=; Ncor= a 0 11896.0 4212.0 66409.0 73044.0 421.0 73612.0 75997.0 76077.0 70230.0 0 0 0 c 0 47674.0 65312.0 4611.0 726.0 550.0 523.0 599.0 760.0 2465.0 0 0 0 g 0 9096.0 582.0 351.0 1913.0 586.0 1083.0 490.0 625.0 1882.0 0 0 0 t 0 10048.0 8608.0 7343.0 3031.0 77157.0 3496.0 1628.0 1252.0 4137.0 0 0 0
MA1971.2_shift5 (ZBED2)				; oligos_6nt_mkv4_m4 versus MA1971.2 (ZBED2); m=3/8; ncol2=7; w=0; offset=3; strand=D; shift=5; score=0.451928; -----CGAAACC- ; cor=; Ncor= a 0 0 0 0 0 42.0 19.0 1247.0 1264.0 1131.0 17.0 75.0 0 c 0 0 0 0 0 1195.0 21.0 13.0 13.0 94.0 1217.0 962.0 0 g 0 0 0 0 0 42.0 1252.0 29.0 8.0 41.0 43.0 47.0 0 t 0 0 0 0 0 18.0 5.0 8.0 12.0 31.0 20.0 213.0 0
MA0851.2_shift0 (Foxj3)				; oligos_6nt_mkv4_m4 versus MA0851.2 (Foxj3); m=4/8; ncol2=9; w=-2; offset=-2; strand=D; shift=0; score=0.44963; RTAAACAAw---- ; cor=; Ncor= a 30.0 1.0 91.0 96.0 99.0 0.0 99.0 79.0 57.0 0 0 0 0 c 1.0 2.0 8.0 2.0 0.0 81.0 0.0 7.0 9.0 0 0 0 0 g 68.0 0.0 0.0 0.0 0.0 0.0 0.0 6.0 7.0 0 0 0 0 t 0.0 97.0 0.0 3.0 1.0 18.0 1.0 9.0 27.0 0 0 0 0
MA1616.2_shift5 (Prdm15)				; oligos_6nt_mkv4_m4 versus MA1616.2 (Prdm15); m=5/8; ncol2=11; w=0; offset=3; strand=D; shift=5; score=0.430439; -----gAAAACCT ; cor=; Ncor= a 0 0 0 0 0 252.0 2011.0 2121.0 1942.0 1801.0 67.0 222.0 220.0 c 0 0 0 0 0 325.0 60.0 34.0 47.0 138.0 1941.0 1886.0 361.0 g 0 0 0 0 0 1333.0 135.0 58.0 200.0 152.0 101.0 107.0 28.0 t 0 0 0 0 0 327.0 31.0 24.0 48.0 146.0 128.0 22.0 1628.0
MA1125.2_shift6 (ZNF384)				; oligos_6nt_mkv4_m4 versus MA1125.2 (ZNF384); m=6/8; ncol2=8; w=0; offset=4; strand=D; shift=6; score=0.413755; ------AAAAAAa ; cor=; Ncor= a 0 0 0 0 0 0 30354.0 30191.0 30072.0 30252.0 30202.0 30406.0 20322.0 c 0 0 0 0 0 0 7.0 35.0 21.0 13.0 26.0 6.0 2908.0 g 0 0 0 0 0 0 13.0 19.0 26.0 15.0 14.0 0.0 2767.0 t 0 0 0 0 0 0 59.0 188.0 314.0 153.0 191.0 21.0 4436.0
MA1489.1_shift0 (FOXN3)				; oligos_6nt_mkv4_m4 versus MA1489.1 (FOXN3); m=7/8; ncol2=8; w=-2; offset=-2; strand=D; shift=0; score=0.412421; GTAAACAA----- ; cor=; Ncor= a 9.0 9.0 971.0 971.0 971.0 9.0 971.0 971.0 0 0 0 0 0 c 9.0 9.0 9.0 9.0 9.0 971.0 9.0 9.0 0 0 0 0 0 g 971.0 9.0 9.0 9.0 9.0 9.0 9.0 9.0 0 0 0 0 0 t 9.0 971.0 9.0 9.0 9.0 9.0 9.0 9.0 0 0 0 0 0
MA0442.3_shift4 (SOX10)				; oligos_6nt_mkv4_m4 versus MA0442.3 (SOX10); m=8/8; ncol2=6; w=0; offset=2; strand=D; shift=4; score=0.401423; ----ACAAAG--- ; cor=; Ncor= a 0 0 0 0 2023.0 3.0 2029.0 1968.0 1959.0 10.0 0 0 0 c 0 0 0 0 4.0 1989.0 7.0 28.0 23.0 13.0 0 0 0 g 0 0 0 0 3.0 11.0 7.0 20.0 12.0 2012.0 0 0 0 t 0 0 0 0 25.0 52.0 12.0 39.0 61.0 20.0 0 0 0