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/peak-motifs_motifs_discovered.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_vs_db/peak-motifs_motifs_vs_db_Homer.tab

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

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

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m3_shift0 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m3_shift0 (oligos_6nt_mkv3_m3)
; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; ssCgCCCCGCCCsss ; Alignment reference a 33 30 17 22 8 15 11 8 12 7 13 13 23 35 33 c 124 125 206 45 229 211 218 231 35 242 235 233 84 124 112 g 87 96 46 197 37 47 49 36 228 33 34 30 151 90 96 t 47 40 22 27 17 18 13 16 16 9 9 15 33 42 50

homer_266_Sp1_shift2 (homer_266_Sp1)
; oligos_6nt_mkv3_m3 versus homer_266_Sp1; m=1/7; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.70989; --gGCCCCGCCCCc- ; cor=; Ncor= a 0 0 18.1 5 1.3 3.3 4.9 0.1 2.5 0.1 0.1 0.1 10.3 3.7 0 c 0 0 21.8 0.1 87 81.5 94.9 99.7 0.1 99.7 99.7 88.1 82.4 51.2 0 g 0 0 54.1 94.8 6.1 0.1 0.1 0.1 97.3 0.1 0.1 0.1 0.1 22.1 0 t 0 0 6 0.1 5.6 15.1 0.1 0.1 0.1 0.1 0.1 11.7 7.1 23 0

homer_146_KLF3_shift1 (homer_146_KLF3)
; oligos_6nt_mkv3_m3 versus homer_146_KLF3; m=2/7; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.69435; -yrrCYmCrCCChyb ; cor=; Ncor= a 0 846.28 967.73 1461.08 3.79 3.79 1548.36 3.79 1977.2 3.79 3.79 3.79 1168.86 645.15 751.41 c 0 1001.88 800.75 3.79 3783.61 2717.22 2239.05 3783.61 3.79 3783.61 3783.61 3783.61 1240.97 1240.97 979.11 g 0 823.51 1407.94 2326.34 3.79 3.79 3.79 3.79 1810.21 3.79 3.79 3.79 3.79 823.51 1073.98 t 0 1119.52 618.59 3.79 3.79 1070.19 3.79 3.79 3.79 3.79 3.79 3.79 1381.38 1085.37 990.5

homer_145_KLF14_rc_shift3 (homer_145_KLF14_rc)
; oligos_6nt_mkv3_m3 versus homer_145_KLF14_rc; m=3/7; ncol2=12; w=0; offset=3; strand=R; shift=3; score=0.668116; ---gcCmCgCCCmCy ; cor=; Ncor= a 0 0 0 5089.83 2407.76 1615.33 14995.2 152.39 7009.94 30.48 30.48 30.48 14781.8 1066.73 4724.09 c 0 0 0 5516.52 17860.1 23315.7 15208.5 29502.7 30.48 30386.6 30386.6 29350.3 12800.8 22767.1 12983.6 g 0 0 0 17646.8 3687.84 487.65 182.87 30.48 19140.2 30.48 30.48 274.3 243.82 1493.42 2316.33 t 0 0 0 2224.89 6522.29 5059.35 91.43 792.43 4297.4 30.48 30.48 822.91 2621.11 5150.78 10454

homer_149_Klf9_shift3 (homer_149_Klf9)
; oligos_6nt_mkv3_m3 versus homer_149_Klf9; m=4/7; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.603905; ---GCCACrCCCMCy ; cor=; Ncor= a 0 0 0 12 11.2 0.5 79.4 0.5 42.8 0.2 0.1 0.1 70.1 0.9 12.7 c 0 0 0 2.4 81.9 99 19.1 99 0.1 99.6 99.5 98.2 26.1 90.6 36.2 g 0 0 0 83.3 4.3 0.1 1.2 0.2 52.8 0.1 0.3 0.1 0.1 2 4.7 t 0 0 0 2.3 2.6 0.4 0.3 0.3 4.3 0.1 0.1 1.6 3.7 6.5 46.5

homer_148_KLF5_rc_shift3 (homer_148_KLF5_rc)
; oligos_6nt_mkv3_m3 versus homer_148_KLF5_rc; m=5/7; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.553498; ---GCCmCrCCCw-- ; cor=; Ncor= a 0 0 0 14.8 18.4 2.2 52.6 1.2 49 0.1 0.1 0.1 35.7 0 0 c 0 0 0 1.9 69.4 92.2 40.5 97.2 0.1 99.7 99.7 88.2 22.4 0 0 g 0 0 0 75.6 6 0.1 2.3 0.1 42.8 0.1 0.1 0.1 5.5 0 0 t 0 0 0 7.7 6.2 5.5 4.6 1.5 8.1 0.1 0.1 11.6 36.4 0 0

homer_160_Maz_rc_shift4 (homer_160_Maz_rc)
; oligos_6nt_mkv3_m3 versus homer_160_Maz_rc; m=6/7; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.470177; ----CCCCcCCC--- ; cor=; Ncor= a 0 0 0 0 0.1 0.1 0.1 0.1 5.4 8.4 0.1 0.1 0 0 0 c 0 0 0 0 99.7 95.6 89.4 84.8 60.7 70.2 99.7 98.9 0 0 0 g 0 0 0 0 0.1 0.1 5.8 6.1 14.9 8.2 0.1 0.1 0 0 0 t 0 0 0 0 0.1 4.2 4.7 9 19 13.2 0.1 0.9 0 0 0

homer_63_Egr2_rc_shift5 (homer_63_Egr2_rc)
; oligos_6nt_mkv3_m3 versus homer_63_Egr2_rc; m=7/7; ncol2=12; w=0; offset=5; strand=R; shift=5; score=0.425711; -----cmCrCCCACr ; cor=; Ncor= a 0 0 0 0 0 20.4 32.9 1.4 25.3 0.1 0.1 0.1 86.1 0.1 25.5 c 0 0 0 0 0 35.7 51.3 95.3 0.1 99.7 99.7 94.3 13.7 99.7 3.5 g 0 0 0 0 0 19.2 6.6 0.1 58.7 0.1 0.1 0.1 0.1 0.1 55.2 t 0 0 0 0 0 24.8 9.2 3.2 15.9 0.1 0.1 5.5 0.1 0.1 15.8

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m4_shift0 (oligos_6nt_mkv3_m4)
; oligos_6nt_mkv3_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; ssGCGCCGCss ; Alignment reference a 41 47 7 8 8 8 9 13 13 35 35 c 132 113 34 279 46 250 253 21 255 141 114 g 93 100 254 18 243 42 39 261 31 102 109 t 42 48 13 3 11 8 7 13 9 30 50

homer_266_Sp1_shift1 (homer_266_Sp1)
; oligos_6nt_mkv3_m4 versus homer_266_Sp1; m=1/1; ncol2=12; w=0; offset=1; strand=D; shift=1; score=0.611456; -gGCCCCGCCC ; cor=; Ncor= a 0 18.1 5 1.3 3.3 4.9 0.1 2.5 0.1 0.1 0.1 c 0 21.8 0.1 87 81.5 94.9 99.7 0.1 99.7 99.7 88.1 g 0 54.1 94.8 6.1 0.1 0.1 0.1 97.3 0.1 0.1 0.1 t 0 6 0.1 5.6 15.1 0.1 0.1 0.1 0.1 0.1 11.7

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

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m1_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m1_shift1 (oligos_6nt_mkv3_m1)
; oligos_6nt_mkv3_m1; m=0 (reference); ncol1=11; shift=1; ncol=12; -ccgCCTCCCmm ; Alignment reference a 0 62 100 37 6 5 11 12 8 4 131 107 c 0 190 142 66 402 397 7 386 380 375 117 133 g 0 76 90 261 2 8 32 11 15 21 83 101 t 0 89 85 53 7 7 367 8 14 17 86 76

homer_317_Znf263_shift0 (homer_317_Znf263)
; oligos_6nt_mkv3_m1 versus homer_317_Znf263; m=1/2; ncol2=10; w=-1; offset=-1; strand=D; shift=0; score= 0.5594; crsTsCTCCc-- ; cor=; Ncor= a 15.2 33.3 0.5 0.1 0.1 0.1 0.1 0.1 0.1 13.8 0 0 c 41.3 24 33.4 0.1 51.2 99.7 0.1 99.7 99.7 65.8 0 0 g 24.2 30.9 66 0.1 48.6 0.1 0.1 0.1 0.1 0.2 0 0 t 19.3 11.8 0.1 99.7 0.1 0.1 99.7 0.1 0.1 20.3 0 0

homer_63_Egr2_rc_shift3 (homer_63_Egr2_rc)
; oligos_6nt_mkv3_m1 versus homer_63_Egr2_rc; m=2/2; ncol2=12; w=0; offset=2; strand=R; shift=3; score=0.45297; ---cmCrCCCAC ; cor=; Ncor= a 0 0 0 20.4 32.9 1.4 25.3 0.1 0.1 0.1 86.1 0.1 c 0 0 0 35.7 51.3 95.3 0.1 99.7 99.7 94.3 13.7 99.7 g 0 0 0 19.2 6.6 0.1 58.7 0.1 0.1 0.1 0.1 0.1 t 0 0 0 24.8 9.2 3.2 15.9 0.1 0.1 5.5 0.1 0.1

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv3_m5_shift3 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv3_m5_shift3 (oligos_6nt_mkv3_m5)
; oligos_6nt_mkv3_m5; m=0 (reference); ncol1=10; shift=3; ncol=13; ---svCGaGCGss ; Alignment reference a 0 0 0 55 62 14 11 160 7 9 11 52 54 c 0 0 0 66 69 208 13 26 5 216 11 78 73 g 0 0 0 81 70 8 219 45 233 13 216 72 77 t 0 0 0 45 46 17 4 16 2 9 9 45 43

homer_326_ZNF519_shift0 (homer_326_ZNF519)
; oligos_6nt_mkv3_m5 versus homer_326_ZNF519; m=1/1; ncol2=10; w=-3; offset=-3; strand=D; shift=0; score=0.482002; GAGsCCGAGC--- ; cor=; Ncor= a 0.45 443.67 0.45 8.9 4.89 9.35 0.45 424.97 0.45 0.45 0 0 0 c 0.45 0.45 0.45 214.94 432.99 411.62 29.37 11.12 0.45 432.09 0 0 0 g 443.67 0.45 443.67 150.86 4.45 0.45 414.74 7.12 441.88 0.45 0 0 0 t 0.45 0.45 0.45 70.31 2.67 23.59 0.45 1.78 2.23 12.02 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m4_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m4_shift3 (oligos_7nt_mkv4_m4)
; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=11; shift=3; ncol=14; ---dtAAAGGCAyr ; Alignment reference a 0 0 0 52 44 181 150 181 3 16 4 187 39 66 c 0 0 0 30 30 3 25 3 3 2 179 0 50 33 g 0 0 0 49 30 1 4 2 179 162 3 3 38 49 t 0 0 0 63 90 9 15 8 9 14 8 4 67 46

homer_289_Tcf4_shift0 (homer_289_Tcf4)
; oligos_7nt_mkv4_m4 versus homer_289_Tcf4; m=1/3; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.453389; AsWTCAAAGgva-- ; cor=; Ncor= a 83.2 0.5 73.7 2.2 0.1 99.7 98.9 99.5 5.8 20.3 28 44.5 0 0 c 1.3 50.1 0.2 0.2 90.1 0.1 0.5 0.1 0.1 13.5 30.7 19.7 0 0 g 9.7 48.5 0.1 0.1 9.5 0.1 0.5 0.3 94 59.2 35.6 16.5 0 0 t 5.8 0.9 26 97.5 0.3 0.1 0.1 0.1 0.1 7 5.7 19.3 0 0

homer_262_Sox3_rc_shift2 (homer_262_Sox3_rc)
; oligos_7nt_mkv4_m4 versus homer_262_Sox3_rc; m=2/3; ncol2=8; w=-1; offset=-1; strand=R; shift=2; score=0.414101; --rACAAwRG---- ; cor=; Ncor= a 0 0 40.9 83 12.3 99.7 99.7 51.7 26 13.9 0 0 0 0 c 0 0 18.5 11.3 84.3 0.1 0.1 0.1 0.3 14.7 0 0 0 0 g 0 0 33 0.1 2.7 0.1 0.1 0.1 70.5 69.5 0 0 0 0 t 0 0 7.6 5.6 0.7 0.1 0.1 48.1 3.2 1.9 0 0 0 0

homer_290_TCFL2_shift0 (homer_290_TCFL2)
; oligos_7nt_mkv4_m4 versus homer_290_TCFL2; m=3/3; ncol2=10; w=-3; offset=-3; strand=D; shift=0; score=0.400889; ASwTCAAAGG---- ; cor=; Ncor= a 506.48 0.51 252.48 0.51 0.51 506.48 506.48 506.48 9.65 0.51 0 0 0 0 c 0.51 350.52 0.51 0.51 506.48 0.51 0.51 0.51 0.51 100.08 0 0 0 0 g 0.51 156.46 0.51 0.51 0.51 0.51 0.51 0.51 497.33 406.91 0 0 0 0 t 0.51 0.51 254.51 506.48 0.51 0.51 0.51 0.51 0.51 0.51 0 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

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_m3_shift0 (oligos_6nt_mkv3_m3)				; oligos_6nt_mkv3_m3; m=0 (reference); ncol1=15; shift=0; ncol=15; ssCgCCCCGCCCsss ; Alignment reference a 33 30 17 22 8 15 11 8 12 7 13 13 23 35 33 c 124 125 206 45 229 211 218 231 35 242 235 233 84 124 112 g 87 96 46 197 37 47 49 36 228 33 34 30 151 90 96 t 47 40 22 27 17 18 13 16 16 9 9 15 33 42 50
homer_266_Sp1_shift2 (homer_266_Sp1)				; oligos_6nt_mkv3_m3 versus homer_266_Sp1; m=1/7; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.70989; --gGCCCCGCCCCc- ; cor=; Ncor= a 0 0 18.1 5 1.3 3.3 4.9 0.1 2.5 0.1 0.1 0.1 10.3 3.7 0 c 0 0 21.8 0.1 87 81.5 94.9 99.7 0.1 99.7 99.7 88.1 82.4 51.2 0 g 0 0 54.1 94.8 6.1 0.1 0.1 0.1 97.3 0.1 0.1 0.1 0.1 22.1 0 t 0 0 6 0.1 5.6 15.1 0.1 0.1 0.1 0.1 0.1 11.7 7.1 23 0
homer_146_KLF3_shift1 (homer_146_KLF3)				; oligos_6nt_mkv3_m3 versus homer_146_KLF3; m=2/7; ncol2=15; w=0; offset=1; strand=D; shift=1; score=0.69435; -yrrCYmCrCCChyb ; cor=; Ncor= a 0 846.28 967.73 1461.08 3.79 3.79 1548.36 3.79 1977.2 3.79 3.79 3.79 1168.86 645.15 751.41 c 0 1001.88 800.75 3.79 3783.61 2717.22 2239.05 3783.61 3.79 3783.61 3783.61 3783.61 1240.97 1240.97 979.11 g 0 823.51 1407.94 2326.34 3.79 3.79 3.79 3.79 1810.21 3.79 3.79 3.79 3.79 823.51 1073.98 t 0 1119.52 618.59 3.79 3.79 1070.19 3.79 3.79 3.79 3.79 3.79 3.79 1381.38 1085.37 990.5
homer_145_KLF14_rc_shift3 (homer_145_KLF14_rc)				; oligos_6nt_mkv3_m3 versus homer_145_KLF14_rc; m=3/7; ncol2=12; w=0; offset=3; strand=R; shift=3; score=0.668116; ---gcCmCgCCCmCy ; cor=; Ncor= a 0 0 0 5089.83 2407.76 1615.33 14995.2 152.39 7009.94 30.48 30.48 30.48 14781.8 1066.73 4724.09 c 0 0 0 5516.52 17860.1 23315.7 15208.5 29502.7 30.48 30386.6 30386.6 29350.3 12800.8 22767.1 12983.6 g 0 0 0 17646.8 3687.84 487.65 182.87 30.48 19140.2 30.48 30.48 274.3 243.82 1493.42 2316.33 t 0 0 0 2224.89 6522.29 5059.35 91.43 792.43 4297.4 30.48 30.48 822.91 2621.11 5150.78 10454
homer_149_Klf9_shift3 (homer_149_Klf9)				; oligos_6nt_mkv3_m3 versus homer_149_Klf9; m=4/7; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.603905; ---GCCACrCCCMCy ; cor=; Ncor= a 0 0 0 12 11.2 0.5 79.4 0.5 42.8 0.2 0.1 0.1 70.1 0.9 12.7 c 0 0 0 2.4 81.9 99 19.1 99 0.1 99.6 99.5 98.2 26.1 90.6 36.2 g 0 0 0 83.3 4.3 0.1 1.2 0.2 52.8 0.1 0.3 0.1 0.1 2 4.7 t 0 0 0 2.3 2.6 0.4 0.3 0.3 4.3 0.1 0.1 1.6 3.7 6.5 46.5
homer_148_KLF5_rc_shift3 (homer_148_KLF5_rc)				; oligos_6nt_mkv3_m3 versus homer_148_KLF5_rc; m=5/7; ncol2=10; w=0; offset=3; strand=R; shift=3; score=0.553498; ---GCCmCrCCCw-- ; cor=; Ncor= a 0 0 0 14.8 18.4 2.2 52.6 1.2 49 0.1 0.1 0.1 35.7 0 0 c 0 0 0 1.9 69.4 92.2 40.5 97.2 0.1 99.7 99.7 88.2 22.4 0 0 g 0 0 0 75.6 6 0.1 2.3 0.1 42.8 0.1 0.1 0.1 5.5 0 0 t 0 0 0 7.7 6.2 5.5 4.6 1.5 8.1 0.1 0.1 11.6 36.4 0 0
homer_160_Maz_rc_shift4 (homer_160_Maz_rc)				; oligos_6nt_mkv3_m3 versus homer_160_Maz_rc; m=6/7; ncol2=8; w=0; offset=4; strand=R; shift=4; score=0.470177; ----CCCCcCCC--- ; cor=; Ncor= a 0 0 0 0 0.1 0.1 0.1 0.1 5.4 8.4 0.1 0.1 0 0 0 c 0 0 0 0 99.7 95.6 89.4 84.8 60.7 70.2 99.7 98.9 0 0 0 g 0 0 0 0 0.1 0.1 5.8 6.1 14.9 8.2 0.1 0.1 0 0 0 t 0 0 0 0 0.1 4.2 4.7 9 19 13.2 0.1 0.9 0 0 0
homer_63_Egr2_rc_shift5 (homer_63_Egr2_rc)				; oligos_6nt_mkv3_m3 versus homer_63_Egr2_rc; m=7/7; ncol2=12; w=0; offset=5; strand=R; shift=5; score=0.425711; -----cmCrCCCACr ; cor=; Ncor= a 0 0 0 0 0 20.4 32.9 1.4 25.3 0.1 0.1 0.1 86.1 0.1 25.5 c 0 0 0 0 0 35.7 51.3 95.3 0.1 99.7 99.7 94.3 13.7 99.7 3.5 g 0 0 0 0 0 19.2 6.6 0.1 58.7 0.1 0.1 0.1 0.1 0.1 55.2 t 0 0 0 0 0 24.8 9.2 3.2 15.9 0.1 0.1 5.5 0.1 0.1 15.8

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_m4_shift3 (oligos_7nt_mkv4_m4)				; oligos_7nt_mkv4_m4; m=0 (reference); ncol1=11; shift=3; ncol=14; ---dtAAAGGCAyr ; Alignment reference a 0 0 0 52 44 181 150 181 3 16 4 187 39 66 c 0 0 0 30 30 3 25 3 3 2 179 0 50 33 g 0 0 0 49 30 1 4 2 179 162 3 3 38 49 t 0 0 0 63 90 9 15 8 9 14 8 4 67 46
homer_289_Tcf4_shift0 (homer_289_Tcf4)				; oligos_7nt_mkv4_m4 versus homer_289_Tcf4; m=1/3; ncol2=12; w=-3; offset=-3; strand=D; shift=0; score=0.453389; AsWTCAAAGgva-- ; cor=; Ncor= a 83.2 0.5 73.7 2.2 0.1 99.7 98.9 99.5 5.8 20.3 28 44.5 0 0 c 1.3 50.1 0.2 0.2 90.1 0.1 0.5 0.1 0.1 13.5 30.7 19.7 0 0 g 9.7 48.5 0.1 0.1 9.5 0.1 0.5 0.3 94 59.2 35.6 16.5 0 0 t 5.8 0.9 26 97.5 0.3 0.1 0.1 0.1 0.1 7 5.7 19.3 0 0
homer_262_Sox3_rc_shift2 (homer_262_Sox3_rc)				; oligos_7nt_mkv4_m4 versus homer_262_Sox3_rc; m=2/3; ncol2=8; w=-1; offset=-1; strand=R; shift=2; score=0.414101; --rACAAwRG---- ; cor=; Ncor= a 0 0 40.9 83 12.3 99.7 99.7 51.7 26 13.9 0 0 0 0 c 0 0 18.5 11.3 84.3 0.1 0.1 0.1 0.3 14.7 0 0 0 0 g 0 0 33 0.1 2.7 0.1 0.1 0.1 70.5 69.5 0 0 0 0 t 0 0 7.6 5.6 0.7 0.1 0.1 48.1 3.2 1.9 0 0 0 0
homer_290_TCFL2_shift0 (homer_290_TCFL2)				; oligos_7nt_mkv4_m4 versus homer_290_TCFL2; m=3/3; ncol2=10; w=-3; offset=-3; strand=D; shift=0; score=0.400889; ASwTCAAAGG---- ; cor=; Ncor= a 506.48 0.51 252.48 0.51 0.51 506.48 506.48 506.48 9.65 0.51 0 0 0 0 c 0.51 350.52 0.51 0.51 506.48 0.51 0.51 0.51 0.51 100.08 0 0 0 0 g 0.51 156.46 0.51 0.51 0.51 0.51 0.51 0.51 497.33 406.91 0 0 0 0 t 0.51 0.51 254.51 506.48 0.51 0.51 0.51 0.51 0.51 0.51 0 0 0 0