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_m2/peak-motifs_oligos_7nt_mkv4_m2.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_m2/peak-motifs_oligos_7nt_mkv4_m2_vs_db_Homer

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m2_shift3 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2)
; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=13; shift=3; ncol=16; ---ctrGGATTACAgg ; Alignment reference a 0 0 0 28 30 47 6 5 157 2 5 157 3 158 37 33 c 0 0 0 91 16 9 3 6 2 14 4 8 153 5 13 23 g 0 0 0 21 32 94 154 156 5 4 8 3 8 3 85 87 t 0 0 0 33 95 23 10 6 9 153 156 5 9 7 38 30

homer_203_Otx2_rc_shift4 (homer_203_Otx2_rc)
; oligos_7nt_mkv4_m2 versus homer_203_Otx2_rc; m=1/5; ncol2=10; w=0; offset=1; strand=R; shift=4; score=0.595505; ----rrGGATTArs-- ; cor=; Ncor= a 0 0 0 0 2897.13 2888.99 1643.88 553.38 7071.92 8.14 236 7364.89 3385.41 1611.32 0 0 c 0 0 0 0 1920.57 667.32 56.97 8.14 724.28 8.14 8.14 8.14 634.76 2734.37 0 0 g 0 0 0 0 2303.05 3295.89 6355.78 7519.51 8.14 8.14 8.14 8.14 2832.02 2205.4 0 0 t 0 0 0 0 1009.11 1293.94 81.38 56.97 333.66 8113.59 7885.72 756.83 1285.8 1595.05 0 0

homer_225_Pitx1_rc_shift4 (homer_225_Pitx1_rc)
; oligos_7nt_mkv4_m2 versus homer_225_Pitx1_rc; m=2/5; ncol2=8; w=0; offset=1; strand=R; shift=4; score=0.574284; ----mrGgaTTA---- ; cor=; Ncor= a 0 0 0 0 24647.8 24031.6 9771.11 17341.5 53609.1 2200.7 3873.23 67429.4 0 0 0 0 c 0 0 0 0 27640.8 5281.68 528.17 6866.18 18838 352.11 8362.66 2112.67 0 0 0 0 g 0 0 0 0 19278.1 41989.4 73855.5 59066.8 3697.18 176.06 88.03 1408.45 0 0 0 0 t 0 0 0 0 16461.2 16813.3 3873.23 4753.51 11883.8 85299.1 75704.1 17077.4 0 0 0 0

homer_120_GSC_shift5 (homer_120_GSC)
; oligos_7nt_mkv4_m2 versus homer_120_GSC; m=3/5; ncol2=8; w=0; offset=2; strand=D; shift=5; score=0.535452; -----rrGATTAr--- ; cor=; Ncor= a 0 0 0 0 0 28.3 26.1 11.9 90.8 0.2 5.5 94.2 31.6 0 0 0 c 0 0 0 0 0 18.9 3.1 1.6 4.6 0.1 0.1 0.5 13.6 0 0 0 g 0 0 0 0 0 38.3 61.4 83.5 3.3 0.1 0.1 0.8 37.7 0 0 0 t 0 0 0 0 0 14.5 9.4 3 1.3 99.6 94.3 4.5 17.1 0 0 0

homer_42_CRX_rc_shift6 (homer_42_CRX_rc)
; oligos_7nt_mkv4_m2 versus homer_42_CRX_rc; m=4/5; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.473264; ------GGATTArc-- ; cor=; Ncor= a 0 0 0 0 0 0 22.2 0.5 81.1 0.8 8.4 97.3 27.8 16.2 0 0 c 0 0 0 0 0 0 1.3 1.6 18.3 0.6 2.3 0.1 6.2 44.5 0 0 g 0 0 0 0 0 0 75.4 97.8 0.6 1.1 0.3 0.4 52.8 24.5 0 0 t 0 0 0 0 0 0 1.2 0.1 0.1 97.5 89 2.2 13.2 14.8 0 0

homer_214_Pax7_rc_shift0 (homer_214_Pax7_rc)
; oligos_7nt_mkv4_m2 versus homer_214_Pax7_rc; m=5/5; ncol2=12; w=-3; offset=-3; strand=R; shift=0; score=0.411828; kTAATykGATTA---- ; cor=; Ncor= a 15.7 2.8 98.4 99.6 5.5 5.1 24.2 17.2 96.7 0.1 0.8 98.3 0 0 0 0 c 6.9 0.3 0.6 0.1 1.2 63.3 5.3 9.9 0.6 0.2 1.2 0.3 0 0 0 0 g 49.7 1.8 0.6 0.2 0.4 5.9 38.2 71.3 1.5 0.4 0.6 0.4 0 0 0 0 t 27.7 95.1 0.4 0.1 92.9 25.7 32.3 1.6 1.2 99.3 97.4 1 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m2_shift3 (oligos_7nt_mkv4_m2)				; oligos_7nt_mkv4_m2; m=0 (reference); ncol1=13; shift=3; ncol=16; ---ctrGGATTACAgg ; Alignment reference a 0 0 0 28 30 47 6 5 157 2 5 157 3 158 37 33 c 0 0 0 91 16 9 3 6 2 14 4 8 153 5 13 23 g 0 0 0 21 32 94 154 156 5 4 8 3 8 3 85 87 t 0 0 0 33 95 23 10 6 9 153 156 5 9 7 38 30
homer_203_Otx2_rc_shift4 (homer_203_Otx2_rc)				; oligos_7nt_mkv4_m2 versus homer_203_Otx2_rc; m=1/5; ncol2=10; w=0; offset=1; strand=R; shift=4; score=0.595505; ----rrGGATTArs-- ; cor=; Ncor= a 0 0 0 0 2897.13 2888.99 1643.88 553.38 7071.92 8.14 236 7364.89 3385.41 1611.32 0 0 c 0 0 0 0 1920.57 667.32 56.97 8.14 724.28 8.14 8.14 8.14 634.76 2734.37 0 0 g 0 0 0 0 2303.05 3295.89 6355.78 7519.51 8.14 8.14 8.14 8.14 2832.02 2205.4 0 0 t 0 0 0 0 1009.11 1293.94 81.38 56.97 333.66 8113.59 7885.72 756.83 1285.8 1595.05 0 0
homer_225_Pitx1_rc_shift4 (homer_225_Pitx1_rc)				; oligos_7nt_mkv4_m2 versus homer_225_Pitx1_rc; m=2/5; ncol2=8; w=0; offset=1; strand=R; shift=4; score=0.574284; ----mrGgaTTA---- ; cor=; Ncor= a 0 0 0 0 24647.8 24031.6 9771.11 17341.5 53609.1 2200.7 3873.23 67429.4 0 0 0 0 c 0 0 0 0 27640.8 5281.68 528.17 6866.18 18838 352.11 8362.66 2112.67 0 0 0 0 g 0 0 0 0 19278.1 41989.4 73855.5 59066.8 3697.18 176.06 88.03 1408.45 0 0 0 0 t 0 0 0 0 16461.2 16813.3 3873.23 4753.51 11883.8 85299.1 75704.1 17077.4 0 0 0 0
homer_120_GSC_shift5 (homer_120_GSC)				; oligos_7nt_mkv4_m2 versus homer_120_GSC; m=3/5; ncol2=8; w=0; offset=2; strand=D; shift=5; score=0.535452; -----rrGATTAr--- ; cor=; Ncor= a 0 0 0 0 0 28.3 26.1 11.9 90.8 0.2 5.5 94.2 31.6 0 0 0 c 0 0 0 0 0 18.9 3.1 1.6 4.6 0.1 0.1 0.5 13.6 0 0 0 g 0 0 0 0 0 38.3 61.4 83.5 3.3 0.1 0.1 0.8 37.7 0 0 0 t 0 0 0 0 0 14.5 9.4 3 1.3 99.6 94.3 4.5 17.1 0 0 0
homer_42_CRX_rc_shift6 (homer_42_CRX_rc)				; oligos_7nt_mkv4_m2 versus homer_42_CRX_rc; m=4/5; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.473264; ------GGATTArc-- ; cor=; Ncor= a 0 0 0 0 0 0 22.2 0.5 81.1 0.8 8.4 97.3 27.8 16.2 0 0 c 0 0 0 0 0 0 1.3 1.6 18.3 0.6 2.3 0.1 6.2 44.5 0 0 g 0 0 0 0 0 0 75.4 97.8 0.6 1.1 0.3 0.4 52.8 24.5 0 0 t 0 0 0 0 0 0 1.2 0.1 0.1 97.5 89 2.2 13.2 14.8 0 0
homer_214_Pax7_rc_shift0 (homer_214_Pax7_rc)				; oligos_7nt_mkv4_m2 versus homer_214_Pax7_rc; m=5/5; ncol2=12; w=-3; offset=-3; strand=R; shift=0; score=0.411828; kTAATykGATTA---- ; cor=; Ncor= a 15.7 2.8 98.4 99.6 5.5 5.1 24.2 17.2 96.7 0.1 0.8 98.3 0 0 0 0 c 6.9 0.3 0.6 0.1 1.2 63.3 5.3 9.9 0.6 0.2 1.2 0.3 0 0 0 0 g 49.7 1.8 0.6 0.2 0.4 5.9 38.2 71.3 1.5 0.4 0.6 0.4 0 0 0 0 t 27.7 95.1 0.4 0.1 92.9 25.7 32.3 1.6 1.2 99.3 97.4 1 0 0 0 0