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_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_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_6nt_mkv3_m2/peak-motifs_oligos_6nt_mkv3_m2_vs_db_Homer

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m2_shift9 ; 10 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m2_shift9 (oligos_6nt_mkv3_m2)
; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=11; shift=9; ncol=20; ---------amwCCCAGChm ; Alignment reference a 0 0 0 0 0 0 0 0 0 135 92 158 7 12 3 314 4 11 116 95 c 0 0 0 0 0 0 0 0 0 71 97 46 342 325 339 22 5 329 94 121 g 0 0 0 0 0 0 0 0 0 88 82 54 5 10 7 15 346 5 53 69 t 0 0 0 0 0 0 0 0 0 65 88 101 5 12 10 8 4 14 96 74

homer_323_ZNF416_rc_shift10 (homer_323_ZNF416_rc)
; oligos_6nt_mkv3_m2 versus homer_323_ZNF416_rc; m=1/9; ncol2=10; w=0; offset=1; strand=R; shift=10; score=0.714343; ----------TKCCCAGkcw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 309.5 85.87 1.79 71.56 84.08 1438.36 32.2 427.57 400.74 733.49 c 0 0 0 0 0 0 0 0 0 0 85.87 1.79 1592.21 1561.8 1701.34 159.22 1.79 359.59 615.42 164.59 g 0 0 0 0 0 0 0 0 0 0 168.17 1227.25 1.79 1.79 1.79 16.1 1753.22 518.81 327.39 313.07 t 0 0 0 0 0 0 0 0 0 0 1225.47 474.09 193.21 153.85 1.79 175.32 1.79 483.03 445.46 579.64

homer_312_Zic_rc_shift11 (homer_312_Zic_rc)
; oligos_6nt_mkv3_m2 versus homer_312_Zic_rc; m=2/9; ncol2=10; w=0; offset=2; strand=R; shift=11; score=0.56982; -----------dMwCAGCrk ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 28 31 28.9 0.1 83.6 0.1 0.1 61.5 0.1 c 0 0 0 0 0 0 0 0 0 0 0 3.3 68.8 16 99.7 6 0.1 87.1 0.1 0.1 g 0 0 0 0 0 0 0 0 0 0 0 34.3 0.1 6.7 0.1 0.1 99.7 0.1 38.3 60.2 t 0 0 0 0 0 0 0 0 0 0 0 34.4 0.1 48.4 0.1 10.3 0.1 12.7 0.1 39.6

homer_272_ATTTCCCAGVAKSCY_shift8 (homer_272_ATTTCCCAGVAKSCY)
; oligos_6nt_mkv3_m2 versus homer_272_ATTTCCCAGVAKSCY; m=3/9; ncol2=15; w=-1; offset=-1; strand=D; shift=8; score=0.546964; --------awyTCCCAkvAk ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1812.22 889.2 213 615.34 3.38 3.38 3.38 3164.62 142 1240.83 2718.32 263.72 c 0 0 0 0 0 0 0 0 608.58 598.44 1149.54 175.81 3370.86 3370.86 3370.86 3.38 385.43 1037.97 152.14 74.38 g 0 0 0 0 0 0 0 0 500.39 456.44 294.15 37.19 3.38 3.38 3.38 199.48 1781.79 1058.25 500.39 1386.21 t 0 0 0 0 0 0 0 0 459.82 1436.92 1724.31 2552.66 3.38 3.38 3.38 13.52 1071.78 43.95 10.14 1656.69

homer_245_Ronin_shift2 (homer_245_Ronin)
; oligos_6nt_mkv3_m2 versus homer_245_Ronin; m=4/9; ncol2=20; w=-7; offset=-7; strand=D; shift=2; score=0.420099; --rACTACAwyTCCCAgmAk ; cor=; Ncor= a 0 0 42.6 99.7 0.1 0.1 97.1 0.1 85.9 62.7 10 8.5 0.1 0.1 0.1 78.3 7.1 37.2 74.5 11.3 c 0 0 7.1 0.1 99.7 3.1 0.1 99.7 1.4 4.3 47.1 5.7 97.1 99.7 98.5 0.1 13.1 33 5.7 5.7 g 0 0 47.5 0.1 0.1 0.1 0.1 0.1 11.3 7.1 15.6 1.4 0.1 0.1 0.1 21.5 64.2 24.1 18.4 45.7 t 0 0 2.8 0.1 0.1 96.7 2.7 0.1 1.4 25.9 27.4 84.4 2.7 0.1 1.3 0.1 15.6 5.7 1.4 37.3

homer_147_Klf4_shift6 (homer_147_Klf4)
; oligos_6nt_mkv3_m2 versus homer_147_Klf4; m=5/9; ncol2=10; w=-3; offset=-3; strand=D; shift=6; score=0.417329; ------GCCACACCCA---- ; cor=; Ncor= a 0 0 0 0 0 0 16.3 6.1 0.1 85.9 0.1 85.5 0.1 0.1 0.1 76.4 0 0 0 0 c 0 0 0 0 0 0 0.4 90.7 99.4 13.2 99.7 0.1 99.7 99.7 99.7 8.3 0 0 0 0 g 0 0 0 0 0 0 82.7 1.4 0.1 0.8 0.1 14.3 0.1 0.1 0.1 0.6 0 0 0 0 t 0 0 0 0 0 0 0.6 1.7 0.4 0.1 0.1 0.1 0.1 0.1 0.1 14.7 0 0 0 0

homer_310_Zfp809_rc_shift11 (homer_310_Zfp809_rc)
; oligos_6nt_mkv3_m2 versus homer_310_Zfp809_rc; m=6/9; ncol2=15; w=0; offset=2; strand=R; shift=11; score=0.41156; -----------TCCCaGmCr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 125.02 3.38 3.38 3.38 2233.52 479.82 1351.6 30.41 1523.93 c 0 0 0 0 0 0 0 0 0 0 0 564.29 3368.86 3368.86 3368.86 10.14 185.84 1240.09 3118.82 520.37 g 0 0 0 0 0 0 0 0 0 0 0 300.73 3.38 3.38 3.38 706.21 2649.14 645.39 3.38 1327.95 t 0 0 0 0 0 0 0 0 0 0 0 2388.95 3.38 3.38 3.38 429.13 64.2 141.92 226.39 3.38

homer_74_CACAGCAGGGGG_shift12 (homer_74_CACAGCAGGGGG)
; oligos_6nt_mkv3_m2 versus homer_74_CACAGCAGGGGG; m=7/9; ncol2=12; w=0; offset=3; strand=D; shift=12; score=0.40881; ------------CwCAGCAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 12 48.1 1.4 92 2 0.8 87.5 2.8 c 0 0 0 0 0 0 0 0 0 0 0 0 83.7 23.2 98.2 0.3 1.8 94.2 0.1 0.1 g 0 0 0 0 0 0 0 0 0 0 0 0 3.4 1.4 0.2 1.1 95.3 0.5 4.2 92 t 0 0 0 0 0 0 0 0 0 0 0 0 0.9 27.3 0.1 6.6 0.9 4.4 8.2 5

homer_111_CGGCTGCNGNNNNCAGATAA_rc_shift0 (homer_111_CGGCTGCNGNNNNCAGATAA_rc)
; oligos_6nt_mkv3_m2 versus homer_111_CGGCTGCNGNNNNCAGATAA_rc; m=8/9; ncol2=20; w=-9; offset=-9; strand=R; shift=0; score=0.408323; tTATCwsyssscmvCAGvyg ; cor=; Ncor= a 5.6 1.5 95.7 0.1 0.1 30.4 8.2 20.2 18.7 19.3 21.9 20.8 25.4 26.3 0.9 95.1 0.3 25.1 21.9 18.4 c 22.5 0.3 0.1 0.1 99.7 0.6 36.8 29.5 26.9 34.5 31.3 40.4 32.7 34.8 98.9 0.1 12 45 37.4 19 g 4.4 0.1 4.1 0.1 0.1 1.5 43.3 19.3 33.6 28.7 27.2 24.9 19.9 35.7 0.1 0.1 84.2 25.1 8.5 43.3 t 67.5 98.1 0.1 99.7 0.1 67.5 11.7 31 20.8 17.5 19.6 14 21.9 3.2 0.1 4.7 3.5 4.7 32.2 19.3

homer_115_AACTACAATTCCCAGAATGC_shift2 (homer_115_AACTACAATTCCCAGAATGC)
; oligos_6nt_mkv3_m2 versus homer_115_AACTACAATTCCCAGAATGC; m=9/9; ncol2=20; w=-7; offset=-7; strand=D; shift=2; score=0.401738; --rACTACAwyTCCCAGmAk ; cor=; Ncor= a 0 0 54.3 99.7 0.1 0.1 99.7 0.1 89.8 51.8 9.7 3.5 0.1 0.1 0.1 94.2 11.3 52.7 83 7.1 c 0 0 0.5 0.1 99.7 0.7 0.1 99.7 2.6 9.2 25.9 0.1 96.3 99.7 99.7 0.1 9.6 26.6 0.7 1.6 g 0 0 45.2 0.1 0.1 0.1 0.1 0.1 7.5 8 8 0.1 0.1 0.1 0.1 5.6 71.3 18.1 16.2 42.6 t 0 0 0.1 0.1 0.1 99.1 0.1 0.1 0.1 31.1 56.4 96.3 3.5 0.1 0.1 0.1 7.8 2.6 0.1 48.7

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv3_m2_shift9 (oligos_6nt_mkv3_m2)				; oligos_6nt_mkv3_m2; m=0 (reference); ncol1=11; shift=9; ncol=20; ---------amwCCCAGChm ; Alignment reference a 0 0 0 0 0 0 0 0 0 135 92 158 7 12 3 314 4 11 116 95 c 0 0 0 0 0 0 0 0 0 71 97 46 342 325 339 22 5 329 94 121 g 0 0 0 0 0 0 0 0 0 88 82 54 5 10 7 15 346 5 53 69 t 0 0 0 0 0 0 0 0 0 65 88 101 5 12 10 8 4 14 96 74
homer_323_ZNF416_rc_shift10 (homer_323_ZNF416_rc)				; oligos_6nt_mkv3_m2 versus homer_323_ZNF416_rc; m=1/9; ncol2=10; w=0; offset=1; strand=R; shift=10; score=0.714343; ----------TKCCCAGkcw ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 309.5 85.87 1.79 71.56 84.08 1438.36 32.2 427.57 400.74 733.49 c 0 0 0 0 0 0 0 0 0 0 85.87 1.79 1592.21 1561.8 1701.34 159.22 1.79 359.59 615.42 164.59 g 0 0 0 0 0 0 0 0 0 0 168.17 1227.25 1.79 1.79 1.79 16.1 1753.22 518.81 327.39 313.07 t 0 0 0 0 0 0 0 0 0 0 1225.47 474.09 193.21 153.85 1.79 175.32 1.79 483.03 445.46 579.64
homer_312_Zic_rc_shift11 (homer_312_Zic_rc)				; oligos_6nt_mkv3_m2 versus homer_312_Zic_rc; m=2/9; ncol2=10; w=0; offset=2; strand=R; shift=11; score=0.56982; -----------dMwCAGCrk ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 28 31 28.9 0.1 83.6 0.1 0.1 61.5 0.1 c 0 0 0 0 0 0 0 0 0 0 0 3.3 68.8 16 99.7 6 0.1 87.1 0.1 0.1 g 0 0 0 0 0 0 0 0 0 0 0 34.3 0.1 6.7 0.1 0.1 99.7 0.1 38.3 60.2 t 0 0 0 0 0 0 0 0 0 0 0 34.4 0.1 48.4 0.1 10.3 0.1 12.7 0.1 39.6
homer_272_ATTTCCCAGVAKSCY_shift8 (homer_272_ATTTCCCAGVAKSCY)				; oligos_6nt_mkv3_m2 versus homer_272_ATTTCCCAGVAKSCY; m=3/9; ncol2=15; w=-1; offset=-1; strand=D; shift=8; score=0.546964; --------awyTCCCAkvAk ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1812.22 889.2 213 615.34 3.38 3.38 3.38 3164.62 142 1240.83 2718.32 263.72 c 0 0 0 0 0 0 0 0 608.58 598.44 1149.54 175.81 3370.86 3370.86 3370.86 3.38 385.43 1037.97 152.14 74.38 g 0 0 0 0 0 0 0 0 500.39 456.44 294.15 37.19 3.38 3.38 3.38 199.48 1781.79 1058.25 500.39 1386.21 t 0 0 0 0 0 0 0 0 459.82 1436.92 1724.31 2552.66 3.38 3.38 3.38 13.52 1071.78 43.95 10.14 1656.69
homer_245_Ronin_shift2 (homer_245_Ronin)				; oligos_6nt_mkv3_m2 versus homer_245_Ronin; m=4/9; ncol2=20; w=-7; offset=-7; strand=D; shift=2; score=0.420099; --rACTACAwyTCCCAgmAk ; cor=; Ncor= a 0 0 42.6 99.7 0.1 0.1 97.1 0.1 85.9 62.7 10 8.5 0.1 0.1 0.1 78.3 7.1 37.2 74.5 11.3 c 0 0 7.1 0.1 99.7 3.1 0.1 99.7 1.4 4.3 47.1 5.7 97.1 99.7 98.5 0.1 13.1 33 5.7 5.7 g 0 0 47.5 0.1 0.1 0.1 0.1 0.1 11.3 7.1 15.6 1.4 0.1 0.1 0.1 21.5 64.2 24.1 18.4 45.7 t 0 0 2.8 0.1 0.1 96.7 2.7 0.1 1.4 25.9 27.4 84.4 2.7 0.1 1.3 0.1 15.6 5.7 1.4 37.3
homer_147_Klf4_shift6 (homer_147_Klf4)				; oligos_6nt_mkv3_m2 versus homer_147_Klf4; m=5/9; ncol2=10; w=-3; offset=-3; strand=D; shift=6; score=0.417329; ------GCCACACCCA---- ; cor=; Ncor= a 0 0 0 0 0 0 16.3 6.1 0.1 85.9 0.1 85.5 0.1 0.1 0.1 76.4 0 0 0 0 c 0 0 0 0 0 0 0.4 90.7 99.4 13.2 99.7 0.1 99.7 99.7 99.7 8.3 0 0 0 0 g 0 0 0 0 0 0 82.7 1.4 0.1 0.8 0.1 14.3 0.1 0.1 0.1 0.6 0 0 0 0 t 0 0 0 0 0 0 0.6 1.7 0.4 0.1 0.1 0.1 0.1 0.1 0.1 14.7 0 0 0 0
homer_310_Zfp809_rc_shift11 (homer_310_Zfp809_rc)				; oligos_6nt_mkv3_m2 versus homer_310_Zfp809_rc; m=6/9; ncol2=15; w=0; offset=2; strand=R; shift=11; score=0.41156; -----------TCCCaGmCr ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 125.02 3.38 3.38 3.38 2233.52 479.82 1351.6 30.41 1523.93 c 0 0 0 0 0 0 0 0 0 0 0 564.29 3368.86 3368.86 3368.86 10.14 185.84 1240.09 3118.82 520.37 g 0 0 0 0 0 0 0 0 0 0 0 300.73 3.38 3.38 3.38 706.21 2649.14 645.39 3.38 1327.95 t 0 0 0 0 0 0 0 0 0 0 0 2388.95 3.38 3.38 3.38 429.13 64.2 141.92 226.39 3.38
homer_74_CACAGCAGGGGG_shift12 (homer_74_CACAGCAGGGGG)				; oligos_6nt_mkv3_m2 versus homer_74_CACAGCAGGGGG; m=7/9; ncol2=12; w=0; offset=3; strand=D; shift=12; score=0.40881; ------------CwCAGCAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 12 48.1 1.4 92 2 0.8 87.5 2.8 c 0 0 0 0 0 0 0 0 0 0 0 0 83.7 23.2 98.2 0.3 1.8 94.2 0.1 0.1 g 0 0 0 0 0 0 0 0 0 0 0 0 3.4 1.4 0.2 1.1 95.3 0.5 4.2 92 t 0 0 0 0 0 0 0 0 0 0 0 0 0.9 27.3 0.1 6.6 0.9 4.4 8.2 5
homer_111_CGGCTGCNGNNNNCAGATAA_rc_shift0 (homer_111_CGGCTGCNGNNNNCAGATAA_rc)				; oligos_6nt_mkv3_m2 versus homer_111_CGGCTGCNGNNNNCAGATAA_rc; m=8/9; ncol2=20; w=-9; offset=-9; strand=R; shift=0; score=0.408323; tTATCwsyssscmvCAGvyg ; cor=; Ncor= a 5.6 1.5 95.7 0.1 0.1 30.4 8.2 20.2 18.7 19.3 21.9 20.8 25.4 26.3 0.9 95.1 0.3 25.1 21.9 18.4 c 22.5 0.3 0.1 0.1 99.7 0.6 36.8 29.5 26.9 34.5 31.3 40.4 32.7 34.8 98.9 0.1 12 45 37.4 19 g 4.4 0.1 4.1 0.1 0.1 1.5 43.3 19.3 33.6 28.7 27.2 24.9 19.9 35.7 0.1 0.1 84.2 25.1 8.5 43.3 t 67.5 98.1 0.1 99.7 0.1 67.5 11.7 31 20.8 17.5 19.6 14 21.9 3.2 0.1 4.7 3.5 4.7 32.2 19.3
homer_115_AACTACAATTCCCAGAATGC_shift2 (homer_115_AACTACAATTCCCAGAATGC)				; oligos_6nt_mkv3_m2 versus homer_115_AACTACAATTCCCAGAATGC; m=9/9; ncol2=20; w=-7; offset=-7; strand=D; shift=2; score=0.401738; --rACTACAwyTCCCAGmAk ; cor=; Ncor= a 0 0 54.3 99.7 0.1 0.1 99.7 0.1 89.8 51.8 9.7 3.5 0.1 0.1 0.1 94.2 11.3 52.7 83 7.1 c 0 0 0.5 0.1 99.7 0.7 0.1 99.7 2.6 9.2 25.9 0.1 96.3 99.7 99.7 0.1 9.6 26.6 0.7 1.6 g 0 0 45.2 0.1 0.1 0.1 0.1 0.1 7.5 8 8 0.1 0.1 0.1 0.1 5.6 71.3 18.1 16.2 42.6 t 0 0 0.1 0.1 0.1 99.1 0.1 0.1 0.1 31.1 56.4 96.3 3.5 0.1 0.1 0.1 7.8 2.6 0.1 48.7