One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/05/peak-motifs.2026-01-05.115003_2026-01-05.115003_UARk68/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2.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/2026/01/05/peak-motifs.2026-01-05.115003_2026-01-05.115003_UARk68/results/discovered_motifs/oligos_7nt_mkv5_m2/peak-motifs_oligos_7nt_mkv5_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift0 ; 8 matrices ; sort_field=Ncor

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=18; shift=0; ncol=18; GCTGkCCTkGAACTCAsw ; Alignment reference a 323 275 75 152 322 47 29 19 84 102 2865 2782 47 99 105 2224 240 1448 c 181 2247 54 20 62 2833 2859 44 346 39 19 74 2739 67 2365 258 1115 185 g 2258 158 61 2769 1765 31 14 23 781 2804 56 73 41 46 126 254 1256 328 t 207 289 2779 28 820 58 67 2883 1758 24 29 40 142 2757 373 233 358 1008
MA1540.3_rc_shift2 (NR5A1_rc)				; oligos_7nt_mkv5_m2 versus MA1540.3_rc (NR5A1_rc); m=1/7; ncol2=12; w=0; offset=2; strand=R; shift=2; score=0.609664; --TGaCCTTGAact---- ; cor=; Ncor= a 0 0 198.0 247.0 3173.0 117.0 85.0 111.0 92.0 120.0 3843.0 2845.0 606.0 721.0 0 0 0 0 c 0 0 154.0 112.0 171.0 4440.0 4461.0 160.0 125.0 189.0 130.0 729.0 2825.0 633.0 0 0 0 0 g 0 0 144.0 4271.0 964.0 53.0 45.0 86.0 193.0 4316.0 564.0 747.0 558.0 398.0 0 0 0 0 t 0 0 4201.0 67.0 389.0 87.0 106.0 4340.0 4287.0 72.0 160.0 376.0 708.0 2945.0 0 0 0 0
MA1541.2_rc_shift2 (NR6A1_rc)				; oligos_7nt_mkv5_m2 versus MA1541.2_rc (NR6A1_rc); m=2/7; ncol2=14; w=0; offset=2; strand=R; shift=2; score=0.56678; --YGamCTTGAmCTTg-- ; cor=; Ncor= a 0 0 41.0 254.0 896.0 373.0 62.0 65.0 14.0 40.0 896.0 453.0 62.0 51.0 11.0 132.0 0 0 c 0 0 359.0 109.0 355.0 524.0 896.0 35.0 2.0 29.0 26.0 443.0 896.0 72.0 44.0 342.0 0 0 g 0 0 20.0 896.0 185.0 11.0 15.0 96.0 0.0 896.0 74.0 12.0 9.0 91.0 4.0 896.0 0 0 t 0 0 896.0 39.0 91.0 29.0 21.0 896.0 896.0 7.0 1.0 19.0 13.0 896.0 896.0 124.0 0 0
MA0505.3_shift2 (Nr5A2)				; oligos_7nt_mkv5_m2 versus MA0505.3 (Nr5A2); m=3/7; ncol2=9; w=0; offset=2; strand=D; shift=2; score=0.460247; --TGaCCTTGA------- ; cor=; Ncor= a 0 0 4020.0 2032.0 19888.0 327.0 299.0 364.0 266.0 340.0 26370.0 0 0 0 0 0 0 0 c 0 0 3118.0 869.0 1185.0 29854.0 29734.0 694.0 338.0 870.0 645.0 0 0 0 0 0 0 0 g 0 0 2303.0 27158.0 6736.0 124.0 166.0 359.0 285.0 29010.0 2402.0 0 0 0 0 0 0 0 t 0 0 21101.0 483.0 2733.0 237.0 343.0 29125.0 29653.0 322.0 1125.0 0 0 0 0 0 0 0
MA0141.4_rc_shift1 (ESRRB_rc)				; oligos_7nt_mkv5_m2 versus MA0141.4_rc (ESRRB_rc); m=4/7; ncol2=10; w=0; offset=1; strand=R; shift=1; score=0.44421; -wTGACCTTGA------- ; cor=; Ncor= a 0 1045.0 3.0 15.0 1746.0 3.0 1.0 0.0 4.0 7.0 1746.0 0 0 0 0 0 0 0 c 0 42.0 56.0 1.0 8.0 1746.0 1746.0 3.0 0.0 255.0 75.0 0 0 0 0 0 0 0 g 0 256.0 0.0 1746.0 11.0 4.0 2.0 1.0 1.0 1746.0 373.0 0 0 0 0 0 0 0 t 0 702.0 1746.0 2.0 6.0 1.0 3.0 1746.0 1746.0 9.0 108.0 0 0 0 0 0 0 0
MA0592.4_rc_shift2 (ESRRA_rc)				; oligos_7nt_mkv5_m2 versus MA0592.4_rc (ESRRA_rc); m=5/7; ncol2=9; w=0; offset=2; strand=R; shift=2; score=0.428069; --TGACCTTGa------- ; cor=; Ncor= a 0 0 340.0 927.0 23664.0 294.0 499.0 267.0 403.0 846.0 15394.0 0 0 0 0 0 0 0 c 0 0 781.0 786.0 949.0 25332.0 24676.0 569.0 556.0 2323.0 1850.0 0 0 0 0 0 0 0 g 0 0 226.0 23989.0 379.0 146.0 340.0 415.0 355.0 21854.0 6446.0 0 0 0 0 0 0 0 t 0 0 24648.0 293.0 1003.0 223.0 480.0 24744.0 24681.0 972.0 2305.0 0 0 0 0 0 0 0
MA0643.2_rc_shift2 (Esrrg_rc)				; oligos_7nt_mkv5_m2 versus MA0643.2_rc (Esrrg_rc); m=6/7; ncol2=9; w=0; offset=2; strand=R; shift=2; score=0.413915; --TGACCTTsa------- ; cor=; Ncor= a 0 0 60.0 1280.0 14909.0 14.0 298.0 5.0 195.0 490.0 14909.0 0 0 0 0 0 0 0 c 0 0 1561.0 271.0 844.0 14909.0 14909.0 34.0 603.0 4901.0 2800.0 0 0 0 0 0 0 0 g 0 0 34.0 14909.0 41.0 17.0 7.0 12.0 0.0 10009.0 5974.0 0 0 0 0 0 0 0 t 0 0 14909.0 7.0 472.0 0.0 12.0 14909.0 14909.0 705.0 3489.0 0 0 0 0 0 0 0
MA0071.1_rc_shift2 (RORA_rc)				; oligos_7nt_mkv5_m2 versus MA0071.1_rc (RORA_rc); m=7/7; ncol2=10; w=0; offset=2; strand=R; shift=2; score=0.410701; --TGACCTwgww------ ; cor=; Ncor= a 0 0 0.0 0.0 25.0 0.0 0.0 0.0 7.0 3.0 15.0 7.0 0 0 0 0 0 0 c 0 0 0.0 0.0 0.0 25.0 25.0 4.0 5.0 4.0 0.0 2.0 0 0 0 0 0 0 g 0 0 0.0 25.0 0.0 0.0 0.0 0.0 2.0 12.0 1.0 1.0 0 0 0 0 0 0 t 0 0 25.0 0.0 0.0 0.0 0.0 21.0 11.0 6.0 9.0 15.0 0 0 0 0 0 0