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_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5.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_6nt_mkv4_m5/peak-motifs_oligos_6nt_mkv4_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift0 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=17; shift=0; ncol=17; sTGAGTTCmAGGmCAGC ; Alignment reference a 398 315 375 2863 185 93 41 22 1837 3013 56 53 930 47 2900 328 267 c 1195 290 96 72 94 104 70 2990 873 18 16 13 1363 2847 55 180 2282 g 1245 293 2550 88 2763 99 28 32 277 56 2996 2999 69 49 53 2293 206 t 268 2208 85 83 64 2810 2967 62 119 19 38 41 744 163 98 305 351

MA1540.3_shift3 (NR5A1)
; oligos_6nt_mkv4_m5 versus MA1540.3 (NR5A1); m=1/7; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.659398; ---agtTCAAGGtCA-- ; cor=; Ncor= a 0 0 0 2945.0 708.0 376.0 160.0 72.0 4287.0 4340.0 106.0 87.0 389.0 67.0 4201.0 0 0 c 0 0 0 398.0 558.0 747.0 564.0 4316.0 193.0 86.0 45.0 53.0 964.0 4271.0 144.0 0 0 g 0 0 0 633.0 2825.0 729.0 130.0 189.0 125.0 160.0 4461.0 4440.0 171.0 112.0 154.0 0 0 t 0 0 0 721.0 606.0 2845.0 3843.0 120.0 92.0 111.0 85.0 117.0 3173.0 247.0 198.0 0 0

MA1541.2_shift1 (NR6A1)
; oligos_6nt_mkv4_m5 versus MA1541.2 (NR6A1); m=2/7; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.611578; -cAAGkTCAAGktCR-- ; cor=; Ncor= a 0 124.0 896.0 896.0 13.0 19.0 1.0 7.0 896.0 896.0 21.0 29.0 91.0 39.0 896.0 0 0 c 0 896.0 4.0 91.0 9.0 12.0 74.0 896.0 0.0 96.0 15.0 11.0 185.0 896.0 20.0 0 0 g 0 342.0 44.0 72.0 896.0 443.0 26.0 29.0 2.0 35.0 896.0 524.0 355.0 109.0 359.0 0 0 t 0 132.0 11.0 51.0 62.0 453.0 896.0 40.0 14.0 65.0 62.0 373.0 896.0 254.0 41.0 0 0

MA0505.3_rc_shift6 (Nr5A2_rc)
; oligos_6nt_mkv4_m5 versus MA0505.3_rc (Nr5A2_rc); m=3/7; ncol2=9; w=0; offset=6; strand=R; shift=6; score=0.498201; ------TCAAGGtCA-- ; cor=; Ncor= a 0 0 0 0 0 0 1125.0 322.0 29653.0 29125.0 343.0 237.0 2733.0 483.0 21101.0 0 0 c 0 0 0 0 0 0 2402.0 29010.0 285.0 359.0 166.0 124.0 6736.0 27158.0 2303.0 0 0 g 0 0 0 0 0 0 645.0 870.0 338.0 694.0 29734.0 29854.0 1185.0 869.0 3118.0 0 0 t 0 0 0 0 0 0 26370.0 340.0 266.0 364.0 299.0 327.0 19888.0 2032.0 4020.0 0 0

MA0141.4_shift6 (ESRRB)
; oligos_6nt_mkv4_m5 versus MA0141.4 (ESRRB); m=4/7; ncol2=10; w=0; offset=6; strand=D; shift=6; score=0.489791; ------TCAAGGTCAw- ; cor=; Ncor= a 0 0 0 0 0 0 108.0 9.0 1746.0 1746.0 3.0 1.0 6.0 2.0 1746.0 702.0 0 c 0 0 0 0 0 0 373.0 1746.0 1.0 1.0 2.0 4.0 11.0 1746.0 0.0 256.0 0 g 0 0 0 0 0 0 75.0 255.0 0.0 3.0 1746.0 1746.0 8.0 1.0 56.0 42.0 0 t 0 0 0 0 0 0 1746.0 7.0 4.0 0.0 1.0 3.0 1746.0 15.0 3.0 1045.0 0

MA0592.4_shift6 (ESRRA)
; oligos_6nt_mkv4_m5 versus MA0592.4 (ESRRA); m=5/7; ncol2=9; w=0; offset=6; strand=D; shift=6; score=0.470455; ------tCAAGGTCA-- ; cor=; Ncor= a 0 0 0 0 0 0 2305.0 972.0 24681.0 24744.0 480.0 223.0 1003.0 293.0 24648.0 0 0 c 0 0 0 0 0 0 6446.0 21854.0 355.0 415.0 340.0 146.0 379.0 23989.0 226.0 0 0 g 0 0 0 0 0 0 1850.0 2323.0 556.0 569.0 24676.0 25332.0 949.0 786.0 781.0 0 0 t 0 0 0 0 0 0 15394.0 846.0 403.0 267.0 499.0 294.0 23664.0 927.0 340.0 0 0

MA0071.1_shift5 (RORA)
; oligos_6nt_mkv4_m5 versus MA0071.1 (RORA); m=6/7; ncol2=10; w=0; offset=5; strand=D; shift=5; score=0.455443; -----wwcwAGGTCA-- ; cor=; Ncor= a 0 0 0 0 0 15.0 9.0 6.0 11.0 21.0 0.0 0.0 0.0 0.0 25.0 0 0 c 0 0 0 0 0 1.0 1.0 12.0 2.0 0.0 0.0 0.0 0.0 25.0 0.0 0 0 g 0 0 0 0 0 2.0 0.0 4.0 5.0 4.0 25.0 25.0 0.0 0.0 0.0 0 0 t 0 0 0 0 0 7.0 15.0 3.0 7.0 0.0 0.0 0.0 25.0 0.0 0.0 0 0

MA0643.2_shift6 (Esrrg)
; oligos_6nt_mkv4_m5 versus MA0643.2 (Esrrg); m=7/7; ncol2=9; w=0; offset=6; strand=D; shift=6; score=0.455387; ------tsAAGGTCA-- ; cor=; Ncor= a 0 0 0 0 0 0 3489.0 705.0 14909.0 14909.0 12.0 0.0 472.0 7.0 14909.0 0 0 c 0 0 0 0 0 0 5974.0 10009.0 0.0 12.0 7.0 17.0 41.0 14909.0 34.0 0 0 g 0 0 0 0 0 0 2800.0 4901.0 603.0 34.0 14909.0 14909.0 844.0 271.0 1561.0 0 0 t 0 0 0 0 0 0 14909.0 490.0 195.0 5.0 298.0 14.0 14909.0 1280.0 60.0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)				; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=17; shift=0; ncol=17; sTGAGTTCmAGGmCAGC ; Alignment reference a 398 315 375 2863 185 93 41 22 1837 3013 56 53 930 47 2900 328 267 c 1195 290 96 72 94 104 70 2990 873 18 16 13 1363 2847 55 180 2282 g 1245 293 2550 88 2763 99 28 32 277 56 2996 2999 69 49 53 2293 206 t 268 2208 85 83 64 2810 2967 62 119 19 38 41 744 163 98 305 351
MA1540.3_shift3 (NR5A1)				; oligos_6nt_mkv4_m5 versus MA1540.3 (NR5A1); m=1/7; ncol2=12; w=0; offset=3; strand=D; shift=3; score=0.659398; ---agtTCAAGGtCA-- ; cor=; Ncor= a 0 0 0 2945.0 708.0 376.0 160.0 72.0 4287.0 4340.0 106.0 87.0 389.0 67.0 4201.0 0 0 c 0 0 0 398.0 558.0 747.0 564.0 4316.0 193.0 86.0 45.0 53.0 964.0 4271.0 144.0 0 0 g 0 0 0 633.0 2825.0 729.0 130.0 189.0 125.0 160.0 4461.0 4440.0 171.0 112.0 154.0 0 0 t 0 0 0 721.0 606.0 2845.0 3843.0 120.0 92.0 111.0 85.0 117.0 3173.0 247.0 198.0 0 0
MA1541.2_shift1 (NR6A1)				; oligos_6nt_mkv4_m5 versus MA1541.2 (NR6A1); m=2/7; ncol2=14; w=0; offset=1; strand=D; shift=1; score=0.611578; -cAAGkTCAAGktCR-- ; cor=; Ncor= a 0 124.0 896.0 896.0 13.0 19.0 1.0 7.0 896.0 896.0 21.0 29.0 91.0 39.0 896.0 0 0 c 0 896.0 4.0 91.0 9.0 12.0 74.0 896.0 0.0 96.0 15.0 11.0 185.0 896.0 20.0 0 0 g 0 342.0 44.0 72.0 896.0 443.0 26.0 29.0 2.0 35.0 896.0 524.0 355.0 109.0 359.0 0 0 t 0 132.0 11.0 51.0 62.0 453.0 896.0 40.0 14.0 65.0 62.0 373.0 896.0 254.0 41.0 0 0
MA0505.3_rc_shift6 (Nr5A2_rc)				; oligos_6nt_mkv4_m5 versus MA0505.3_rc (Nr5A2_rc); m=3/7; ncol2=9; w=0; offset=6; strand=R; shift=6; score=0.498201; ------TCAAGGtCA-- ; cor=; Ncor= a 0 0 0 0 0 0 1125.0 322.0 29653.0 29125.0 343.0 237.0 2733.0 483.0 21101.0 0 0 c 0 0 0 0 0 0 2402.0 29010.0 285.0 359.0 166.0 124.0 6736.0 27158.0 2303.0 0 0 g 0 0 0 0 0 0 645.0 870.0 338.0 694.0 29734.0 29854.0 1185.0 869.0 3118.0 0 0 t 0 0 0 0 0 0 26370.0 340.0 266.0 364.0 299.0 327.0 19888.0 2032.0 4020.0 0 0
MA0141.4_shift6 (ESRRB)				; oligos_6nt_mkv4_m5 versus MA0141.4 (ESRRB); m=4/7; ncol2=10; w=0; offset=6; strand=D; shift=6; score=0.489791; ------TCAAGGTCAw- ; cor=; Ncor= a 0 0 0 0 0 0 108.0 9.0 1746.0 1746.0 3.0 1.0 6.0 2.0 1746.0 702.0 0 c 0 0 0 0 0 0 373.0 1746.0 1.0 1.0 2.0 4.0 11.0 1746.0 0.0 256.0 0 g 0 0 0 0 0 0 75.0 255.0 0.0 3.0 1746.0 1746.0 8.0 1.0 56.0 42.0 0 t 0 0 0 0 0 0 1746.0 7.0 4.0 0.0 1.0 3.0 1746.0 15.0 3.0 1045.0 0
MA0592.4_shift6 (ESRRA)				; oligos_6nt_mkv4_m5 versus MA0592.4 (ESRRA); m=5/7; ncol2=9; w=0; offset=6; strand=D; shift=6; score=0.470455; ------tCAAGGTCA-- ; cor=; Ncor= a 0 0 0 0 0 0 2305.0 972.0 24681.0 24744.0 480.0 223.0 1003.0 293.0 24648.0 0 0 c 0 0 0 0 0 0 6446.0 21854.0 355.0 415.0 340.0 146.0 379.0 23989.0 226.0 0 0 g 0 0 0 0 0 0 1850.0 2323.0 556.0 569.0 24676.0 25332.0 949.0 786.0 781.0 0 0 t 0 0 0 0 0 0 15394.0 846.0 403.0 267.0 499.0 294.0 23664.0 927.0 340.0 0 0
MA0071.1_shift5 (RORA)				; oligos_6nt_mkv4_m5 versus MA0071.1 (RORA); m=6/7; ncol2=10; w=0; offset=5; strand=D; shift=5; score=0.455443; -----wwcwAGGTCA-- ; cor=; Ncor= a 0 0 0 0 0 15.0 9.0 6.0 11.0 21.0 0.0 0.0 0.0 0.0 25.0 0 0 c 0 0 0 0 0 1.0 1.0 12.0 2.0 0.0 0.0 0.0 0.0 25.0 0.0 0 0 g 0 0 0 0 0 2.0 0.0 4.0 5.0 4.0 25.0 25.0 0.0 0.0 0.0 0 0 t 0 0 0 0 0 7.0 15.0 3.0 7.0 0.0 0.0 0.0 25.0 0.0 0.0 0 0
MA0643.2_shift6 (Esrrg)				; oligos_6nt_mkv4_m5 versus MA0643.2 (Esrrg); m=7/7; ncol2=9; w=0; offset=6; strand=D; shift=6; score=0.455387; ------tsAAGGTCA-- ; cor=; Ncor= a 0 0 0 0 0 0 3489.0 705.0 14909.0 14909.0 12.0 0.0 472.0 7.0 14909.0 0 0 c 0 0 0 0 0 0 5974.0 10009.0 0.0 12.0 7.0 17.0 41.0 14909.0 34.0 0 0 g 0 0 0 0 0 0 2800.0 4901.0 603.0 34.0 14909.0 14909.0 844.0 271.0 1561.0 0 0 t 0 0 0 0 0 0 14909.0 490.0 195.0 5.0 298.0 14.0 14909.0 1280.0 60.0 0 0