One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5.tf -format2 tf -file2 $RSAT/public_html/motif_databases/Homer/Homer_motifs.tf -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/2026/03/30/peak-motifs.2026-03-30.203840_2026-03-30.203840_4XF5yR/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_vs_db_Homer

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=11; shift=2; ncol=13; --mwAAGTGCTrr ; Alignment reference a 0 0 60 81 182 186 8 6 10 13 14 61 62 c 0 0 56 36 6 8 4 4 3 191 2 28 37 g 0 0 44 27 6 6 197 1 187 2 2 79 62 t 0 0 52 68 18 12 3 201 12 6 194 44 51

homer_185_AAGCACTTAA_rc_shift2 (homer_185_AAGCACTTAA_rc)
; oligos_7nt_mkv4_m5 versus homer_185_AAGCACTTAA_rc; m=1/8; ncol2=10; w=0; offset=0; strand=R; shift=2; score=0.765263; --bTrAGTRcyy- ; cor=; Ncor= a 0 0 4.3 14.1 57.2 95 0.1 0.1 27.7 0.1 0.1 3.8 0 c 0 0 25.6 0.1 3.7 0.1 0.1 0.1 0.1 60.7 27.2 29.7 0 g 0 0 27.4 15 37.8 0.1 98.4 1.2 70.5 22 8.3 11.4 0 t 0 0 42.7 70.8 1.3 4.8 1.4 98.6 1.7 17.2 64.4 55.1 0

homer_18_Bapx1_shift2 (homer_18_Bapx1)
; oligos_7nt_mkv4_m5 versus homer_18_Bapx1; m=2/8; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.713034; --ytrAGTGsyk- ; cor=; Ncor= a 0 0 5.6 17.7 49.7 96.2 0.9 2.4 14 7.9 18.9 18.8 0 c 0 0 33.4 23.1 0.1 0.5 0.1 0.1 0.1 28.9 27.4 12.4 0 g 0 0 10.4 15.6 50.1 1.2 88.2 0.1 85.8 42.5 12.7 28 0 t 0 0 50.6 43.6 0.1 2.1 10.8 97.4 0.1 20.8 41 40.8 0

homer_184_AASCACTCAA_rc_shift2 (homer_184_AASCACTCAA_rc)
; oligos_7nt_mkv4_m5 versus homer_184_AASCACTCAA_rc; m=3/8; ncol2=10; w=0; offset=0; strand=R; shift=2; score=0.660112; --ttrAGwGsyy- ; cor=; Ncor= a 0 0 20.5 11.3 41.1 99.5 1.3 26.3 9.5 1.1 16.9 16.3 0 c 0 0 15.8 19.7 0.6 0.2 0.2 0.2 0.2 38.5 32.7 33.1 0 g 0 0 4 20 56.1 0.2 97.1 8.6 90.1 41.3 15.3 14.9 0 t 0 0 59.8 49.2 2.3 0.2 1.5 65 0.3 19.3 35.3 35.8 0

homer_182_RSCACTYRAG_rc_shift1 (homer_182_RSCACTYRAG_rc)
; oligos_7nt_mkv4_m5 versus homer_182_RSCACTYRAG_rc; m=4/8; ncol2=10; w=-1; offset=-1; strand=R; shift=1; score=0.558547; -sTyrAGWGsy-- ; cor=; Ncor= a 0 6.2 17.3 8.8 48.4 99.7 0.1 27.6 18.9 0.1 14.9 0 0 c 0 44.2 11.4 26.6 0.1 0.1 0.1 0.1 0.1 38.9 37.1 0 0 g 0 25.3 0.1 23.2 51.4 0.1 99.7 0.1 80.9 37.9 11.2 0 0 t 0 24.3 71.2 41.3 0.1 0.1 0.1 72.2 0.1 23.2 36.7 0 0

homer_123_RTACGTGC_shift2 (homer_123_RTACGTGC)
; oligos_7nt_mkv4_m5 versus homer_123_RTACGTGC; m=5/8; ncol2=8; w=0; offset=0; strand=D; shift=2; score=0.528219; --rtACGTGm--- ; cor=; Ncor= a 0 0 38.7 16.2 81.9 0.1 5.2 0.2 0.3 25.1 0 0 0 c 0 0 14.6 14.3 0.6 92.4 0.1 0.7 0.9 59.2 0 0 0 g 0 0 32.1 24.5 16.4 0.1 92.1 0.1 98.3 2.6 0 0 0 t 0 0 14.6 45 1.1 7.4 2.6 99 0.5 13.1 0 0 0

homer_157_MafF_rc_shift2 (homer_157_MafF_rc)
; oligos_7nt_mkv4_m5 versus homer_157_MafF_rc; m=6/8; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.523246; --awwwwTGCTGA ; cor=; Ncor= a 0 0 49.1 58.3 62.5 53.6 35 11.4 0.5 15.7 0.8 1.1 98.5 c 0 0 11.1 2.3 0.4 2.6 15.1 4.7 0.4 83.5 0.4 0.1 0.3 g 0 0 20.2 13.3 2.8 2.2 13.7 0.8 99 0.2 0.1 88 0.4 t 0 0 19.6 26.1 34.3 41.6 36.2 83.1 0.1 0.6 98.7 10.8 0.8

homer_16_Bach1_shift3 (homer_16_Bach1)
; oligos_7nt_mkv4_m5 versus homer_16_Bach1; m=7/8; ncol2=15; w=0; offset=1; strand=D; shift=3; score=0.445374; ---wwwwTGCTGA ; cor=; Ncor= a 0 0 0 43.4 48.6 44 26.4 8.4 0.2 6.7 0.5 0.1 95.8 c 0 0 0 8.8 5.9 6.5 24.1 3.7 0.2 92.7 0.5 0.1 0.1 g 0 0 0 22.4 9.4 9.2 19.7 0.8 99.5 0.1 0.1 96.6 0.2 t 0 0 0 25.4 36.1 40.4 29.8 87.1 0.1 0.5 98.9 3.2 3.9

homer_124_HIF2a_rc_shift0 (homer_124_HIF2a_rc)
; oligos_7nt_mkv4_m5 versus homer_124_HIF2a_rc; m=8/8; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.432921; rgvtACGTGm--- ; cor=; Ncor= a 25.9 18.2 26 14.7 95 0.1 0.1 0.1 0.1 34.2 0 0 0 c 9.8 22.1 25.8 1.7 0.3 99.5 0.5 1 0.1 52.3 0 0 0 g 42.5 40.3 44 23.6 3.4 0.3 98.3 0.1 99.7 5.4 0 0 0 t 21.7 19.4 4.2 60 1.3 0.1 1.1 98.8 0.1 8.1 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m5_shift2 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=11; shift=2; ncol=13; --mwAAGTGCTrr ; Alignment reference a 0 0 60 81 182 186 8 6 10 13 14 61 62 c 0 0 56 36 6 8 4 4 3 191 2 28 37 g 0 0 44 27 6 6 197 1 187 2 2 79 62 t 0 0 52 68 18 12 3 201 12 6 194 44 51
homer_185_AAGCACTTAA_rc_shift2 (homer_185_AAGCACTTAA_rc)				; oligos_7nt_mkv4_m5 versus homer_185_AAGCACTTAA_rc; m=1/8; ncol2=10; w=0; offset=0; strand=R; shift=2; score=0.765263; --bTrAGTRcyy- ; cor=; Ncor= a 0 0 4.3 14.1 57.2 95 0.1 0.1 27.7 0.1 0.1 3.8 0 c 0 0 25.6 0.1 3.7 0.1 0.1 0.1 0.1 60.7 27.2 29.7 0 g 0 0 27.4 15 37.8 0.1 98.4 1.2 70.5 22 8.3 11.4 0 t 0 0 42.7 70.8 1.3 4.8 1.4 98.6 1.7 17.2 64.4 55.1 0
homer_18_Bapx1_shift2 (homer_18_Bapx1)				; oligos_7nt_mkv4_m5 versus homer_18_Bapx1; m=2/8; ncol2=10; w=0; offset=0; strand=D; shift=2; score=0.713034; --ytrAGTGsyk- ; cor=; Ncor= a 0 0 5.6 17.7 49.7 96.2 0.9 2.4 14 7.9 18.9 18.8 0 c 0 0 33.4 23.1 0.1 0.5 0.1 0.1 0.1 28.9 27.4 12.4 0 g 0 0 10.4 15.6 50.1 1.2 88.2 0.1 85.8 42.5 12.7 28 0 t 0 0 50.6 43.6 0.1 2.1 10.8 97.4 0.1 20.8 41 40.8 0
homer_184_AASCACTCAA_rc_shift2 (homer_184_AASCACTCAA_rc)				; oligos_7nt_mkv4_m5 versus homer_184_AASCACTCAA_rc; m=3/8; ncol2=10; w=0; offset=0; strand=R; shift=2; score=0.660112; --ttrAGwGsyy- ; cor=; Ncor= a 0 0 20.5 11.3 41.1 99.5 1.3 26.3 9.5 1.1 16.9 16.3 0 c 0 0 15.8 19.7 0.6 0.2 0.2 0.2 0.2 38.5 32.7 33.1 0 g 0 0 4 20 56.1 0.2 97.1 8.6 90.1 41.3 15.3 14.9 0 t 0 0 59.8 49.2 2.3 0.2 1.5 65 0.3 19.3 35.3 35.8 0
homer_182_RSCACTYRAG_rc_shift1 (homer_182_RSCACTYRAG_rc)				; oligos_7nt_mkv4_m5 versus homer_182_RSCACTYRAG_rc; m=4/8; ncol2=10; w=-1; offset=-1; strand=R; shift=1; score=0.558547; -sTyrAGWGsy-- ; cor=; Ncor= a 0 6.2 17.3 8.8 48.4 99.7 0.1 27.6 18.9 0.1 14.9 0 0 c 0 44.2 11.4 26.6 0.1 0.1 0.1 0.1 0.1 38.9 37.1 0 0 g 0 25.3 0.1 23.2 51.4 0.1 99.7 0.1 80.9 37.9 11.2 0 0 t 0 24.3 71.2 41.3 0.1 0.1 0.1 72.2 0.1 23.2 36.7 0 0
homer_123_RTACGTGC_shift2 (homer_123_RTACGTGC)				; oligos_7nt_mkv4_m5 versus homer_123_RTACGTGC; m=5/8; ncol2=8; w=0; offset=0; strand=D; shift=2; score=0.528219; --rtACGTGm--- ; cor=; Ncor= a 0 0 38.7 16.2 81.9 0.1 5.2 0.2 0.3 25.1 0 0 0 c 0 0 14.6 14.3 0.6 92.4 0.1 0.7 0.9 59.2 0 0 0 g 0 0 32.1 24.5 16.4 0.1 92.1 0.1 98.3 2.6 0 0 0 t 0 0 14.6 45 1.1 7.4 2.6 99 0.5 13.1 0 0 0
homer_157_MafF_rc_shift2 (homer_157_MafF_rc)				; oligos_7nt_mkv4_m5 versus homer_157_MafF_rc; m=6/8; ncol2=15; w=0; offset=0; strand=R; shift=2; score=0.523246; --awwwwTGCTGA ; cor=; Ncor= a 0 0 49.1 58.3 62.5 53.6 35 11.4 0.5 15.7 0.8 1.1 98.5 c 0 0 11.1 2.3 0.4 2.6 15.1 4.7 0.4 83.5 0.4 0.1 0.3 g 0 0 20.2 13.3 2.8 2.2 13.7 0.8 99 0.2 0.1 88 0.4 t 0 0 19.6 26.1 34.3 41.6 36.2 83.1 0.1 0.6 98.7 10.8 0.8
homer_16_Bach1_shift3 (homer_16_Bach1)				; oligos_7nt_mkv4_m5 versus homer_16_Bach1; m=7/8; ncol2=15; w=0; offset=1; strand=D; shift=3; score=0.445374; ---wwwwTGCTGA ; cor=; Ncor= a 0 0 0 43.4 48.6 44 26.4 8.4 0.2 6.7 0.5 0.1 95.8 c 0 0 0 8.8 5.9 6.5 24.1 3.7 0.2 92.7 0.5 0.1 0.1 g 0 0 0 22.4 9.4 9.2 19.7 0.8 99.5 0.1 0.1 96.6 0.2 t 0 0 0 25.4 36.1 40.4 29.8 87.1 0.1 0.5 98.9 3.2 3.9
homer_124_HIF2a_rc_shift0 (homer_124_HIF2a_rc)				; oligos_7nt_mkv4_m5 versus homer_124_HIF2a_rc; m=8/8; ncol2=10; w=-2; offset=-2; strand=R; shift=0; score=0.432921; rgvtACGTGm--- ; cor=; Ncor= a 25.9 18.2 26 14.7 95 0.1 0.1 0.1 0.1 34.2 0 0 0 c 9.8 22.1 25.8 1.7 0.3 99.5 0.5 1 0.1 52.3 0 0 0 g 42.5 40.3 44 23.6 3.4 0.3 98.3 0.1 99.7 5.4 0 0 0 t 21.7 19.4 4.2 60 1.3 0.1 1.1 98.8 0.1 8.1 0 0 0