One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184343_2025-05-16.184343_1fYTf9/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_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/2025/05/16/peak-motifs.2025-05-16.184343_2025-05-16.184343_1fYTf9/results/discovered_motifs/oligos_7nt_mkv2_m5/peak-motifs_oligos_7nt_mkv2_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m5_shift6 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m5_shift6 (oligos_7nt_mkv2_m5)
; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=12; shift=6; ncol=18; ------kmAGCCAAGAws ; Alignment reference a 0 0 0 0 0 0 18 27 58 4 6 2 71 77 5 72 22 18 c 0 0 0 0 0 0 15 25 6 3 69 73 3 1 2 3 13 24 g 0 0 0 0 0 0 24 15 7 68 4 2 5 0 70 4 17 21 t 0 0 0 0 0 0 23 13 9 5 1 3 1 2 3 1 28 17

MA1979.2_rc_shift8 (ZNF416_rc)
; oligos_7nt_mkv2_m5 versus MA1979.2_rc (ZNF416_rc); m=1/7; ncol2=10; w=0; offset=2; strand=R; shift=8; score=0.593718; --------tGCCCAGAtA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 66.0 18.0 3.0 3.0 2.0 336.0 3.0 254.0 46.0 240.0 c 0 0 0 0 0 0 0 0 29.0 3.0 341.0 335.0 335.0 1.0 7.0 15.0 77.0 26.0 g 0 0 0 0 0 0 0 0 38.0 320.0 1.0 5.0 7.0 6.0 334.0 28.0 25.0 32.0 t 0 0 0 0 0 0 0 0 212.0 4.0 0.0 2.0 1.0 2.0 1.0 48.0 197.0 47.0

MA1588.1_rc_shift5 (ZNF136_rc)
; oligos_7nt_mkv2_m5 versus MA1588.1_rc (ZNF136_rc); m=2/7; ncol2=15; w=-1; offset=-1; strand=R; shift=5; score=0.575603; -----gyCAACCaAGAAT ; cor=; Ncor= a 0 0 0 0 0 571.0 144.0 92.0 2956.0 2339.0 48.0 98.0 2164.0 3033.0 203.0 3078.0 3095.0 25.0 c 0 0 0 0 0 82.0 1048.0 2904.0 102.0 33.0 2995.0 2799.0 511.0 46.0 31.0 27.0 34.0 69.0 g 0 0 0 0 0 1973.0 120.0 40.0 60.0 672.0 48.0 17.0 93.0 83.0 2910.0 69.0 34.0 29.0 t 0 0 0 0 0 575.0 1889.0 165.0 83.0 157.0 110.0 287.0 433.0 39.0 57.0 27.0 38.0 3078.0

MA0161.3_rc_shift8 (NFIC_rc)
; oligos_7nt_mkv2_m5 versus MA0161.3_rc (NFIC_rc); m=3/7; ncol2=7; w=0; offset=2; strand=R; shift=8; score=0.505305; --------TGCCAAG--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 574.0 530.0 290.0 81.0 10745.0 10781.0 324.0 0 0 0 c 0 0 0 0 0 0 0 0 478.0 88.0 10973.0 11087.0 177.0 369.0 329.0 0 0 0 g 0 0 0 0 0 0 0 0 397.0 10725.0 121.0 129.0 333.0 303.0 10542.0 0 0 0 t 0 0 0 0 0 0 0 0 10158.0 264.0 223.0 310.0 352.0 154.0 412.0 0 0 0

MA1729.2_shift10 (ZNF680)
; oligos_7nt_mkv2_m5 versus MA1729.2 (ZNF680); m=4/7; ncol2=11; w=0; offset=4; strand=D; shift=10; score=0.448295; ----------CCAAGAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 418.0 1120.0 5394.0 4522.0 43.0 5681.0 5479.0 494.0 c 0 0 0 0 0 0 0 0 0 0 4870.0 4324.0 60.0 17.0 14.0 23.0 13.0 40.0 g 0 0 0 0 0 0 0 0 0 0 133.0 69.0 208.0 1116.0 5691.0 44.0 203.0 5144.0 t 0 0 0 0 0 0 0 0 0 0 345.0 253.0 104.0 111.0 18.0 18.0 71.0 88.0

MA0671.2_shift8 (NFIX)
; oligos_7nt_mkv2_m5 versus MA0671.2 (NFIX); m=5/7; ncol2=6; w=0; offset=2; strand=D; shift=8; score=0.444162; --------tGCCAr---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 11279.0 132.0 3.0 0.0 32864.0 32864.0 0 0 0 0 c 0 0 0 0 0 0 0 0 9695.0 186.0 32864.0 32864.0 2230.0 1356.0 0 0 0 0 g 0 0 0 0 0 0 0 0 5911.0 32864.0 3257.0 0.0 180.0 12688.0 0 0 0 0 t 0 0 0 0 0 0 0 0 32864.0 2539.0 29.0 0.0 110.0 2399.0 0 0 0 0

MA0670.2_shift8 (NFIA)
; oligos_7nt_mkv2_m5 versus MA0670.2 (NFIA); m=6/7; ncol2=6; w=0; offset=2; strand=D; shift=8; score=0.414012; --------TGCCAA---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 89071.0 89418.0 0 0 0 0 c 0 0 0 0 0 0 0 0 0.0 0.0 93597.0 93394.0 0.0 0.0 0 0 0 0 g 0 0 0 0 0 0 0 0 0.0 98253.0 0.0 0.0 0.0 0.0 0 0 0 0 t 0 0 0 0 0 0 0 0 95496.0 0.0 0.0 0.0 0.0 0.0 0 0 0 0

MA0119.1_shift0 (NFIC::TLX1)
; oligos_7nt_mkv2_m5 versus MA0119.1 (NFIC::TLX1); m=7/7; ncol2=14; w=-6; offset=-6; strand=D; shift=0; score=0.402818; TGGCAssrwGCCAA---- ; cor=; Ncor= a 0.0 0.0 0.0 0.0 14.0 2.0 2.0 7.0 4.0 0.0 0.0 0.0 16.0 14.0 0 0 0 0 c 0.0 0.0 0.0 16.0 1.0 8.0 8.0 1.0 3.0 0.0 16.0 16.0 0.0 0.0 0 0 0 0 g 0.0 16.0 16.0 0.0 0.0 5.0 4.0 5.0 2.0 16.0 0.0 0.0 0.0 1.0 0 0 0 0 t 16.0 0.0 0.0 0.0 1.0 1.0 2.0 3.0 7.0 0.0 0.0 0.0 0.0 1.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m5_shift6 (oligos_7nt_mkv2_m5)				; oligos_7nt_mkv2_m5; m=0 (reference); ncol1=12; shift=6; ncol=18; ------kmAGCCAAGAws ; Alignment reference a 0 0 0 0 0 0 18 27 58 4 6 2 71 77 5 72 22 18 c 0 0 0 0 0 0 15 25 6 3 69 73 3 1 2 3 13 24 g 0 0 0 0 0 0 24 15 7 68 4 2 5 0 70 4 17 21 t 0 0 0 0 0 0 23 13 9 5 1 3 1 2 3 1 28 17
MA1979.2_rc_shift8 (ZNF416_rc)				; oligos_7nt_mkv2_m5 versus MA1979.2_rc (ZNF416_rc); m=1/7; ncol2=10; w=0; offset=2; strand=R; shift=8; score=0.593718; --------tGCCCAGAtA ; cor=; Ncor= a 0 0 0 0 0 0 0 0 66.0 18.0 3.0 3.0 2.0 336.0 3.0 254.0 46.0 240.0 c 0 0 0 0 0 0 0 0 29.0 3.0 341.0 335.0 335.0 1.0 7.0 15.0 77.0 26.0 g 0 0 0 0 0 0 0 0 38.0 320.0 1.0 5.0 7.0 6.0 334.0 28.0 25.0 32.0 t 0 0 0 0 0 0 0 0 212.0 4.0 0.0 2.0 1.0 2.0 1.0 48.0 197.0 47.0
MA1588.1_rc_shift5 (ZNF136_rc)				; oligos_7nt_mkv2_m5 versus MA1588.1_rc (ZNF136_rc); m=2/7; ncol2=15; w=-1; offset=-1; strand=R; shift=5; score=0.575603; -----gyCAACCaAGAAT ; cor=; Ncor= a 0 0 0 0 0 571.0 144.0 92.0 2956.0 2339.0 48.0 98.0 2164.0 3033.0 203.0 3078.0 3095.0 25.0 c 0 0 0 0 0 82.0 1048.0 2904.0 102.0 33.0 2995.0 2799.0 511.0 46.0 31.0 27.0 34.0 69.0 g 0 0 0 0 0 1973.0 120.0 40.0 60.0 672.0 48.0 17.0 93.0 83.0 2910.0 69.0 34.0 29.0 t 0 0 0 0 0 575.0 1889.0 165.0 83.0 157.0 110.0 287.0 433.0 39.0 57.0 27.0 38.0 3078.0
MA0161.3_rc_shift8 (NFIC_rc)				; oligos_7nt_mkv2_m5 versus MA0161.3_rc (NFIC_rc); m=3/7; ncol2=7; w=0; offset=2; strand=R; shift=8; score=0.505305; --------TGCCAAG--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 574.0 530.0 290.0 81.0 10745.0 10781.0 324.0 0 0 0 c 0 0 0 0 0 0 0 0 478.0 88.0 10973.0 11087.0 177.0 369.0 329.0 0 0 0 g 0 0 0 0 0 0 0 0 397.0 10725.0 121.0 129.0 333.0 303.0 10542.0 0 0 0 t 0 0 0 0 0 0 0 0 10158.0 264.0 223.0 310.0 352.0 154.0 412.0 0 0 0
MA1729.2_shift10 (ZNF680)				; oligos_7nt_mkv2_m5 versus MA1729.2 (ZNF680); m=4/7; ncol2=11; w=0; offset=4; strand=D; shift=10; score=0.448295; ----------CCAAGAAG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 418.0 1120.0 5394.0 4522.0 43.0 5681.0 5479.0 494.0 c 0 0 0 0 0 0 0 0 0 0 4870.0 4324.0 60.0 17.0 14.0 23.0 13.0 40.0 g 0 0 0 0 0 0 0 0 0 0 133.0 69.0 208.0 1116.0 5691.0 44.0 203.0 5144.0 t 0 0 0 0 0 0 0 0 0 0 345.0 253.0 104.0 111.0 18.0 18.0 71.0 88.0
MA0671.2_shift8 (NFIX)				; oligos_7nt_mkv2_m5 versus MA0671.2 (NFIX); m=5/7; ncol2=6; w=0; offset=2; strand=D; shift=8; score=0.444162; --------tGCCAr---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 11279.0 132.0 3.0 0.0 32864.0 32864.0 0 0 0 0 c 0 0 0 0 0 0 0 0 9695.0 186.0 32864.0 32864.0 2230.0 1356.0 0 0 0 0 g 0 0 0 0 0 0 0 0 5911.0 32864.0 3257.0 0.0 180.0 12688.0 0 0 0 0 t 0 0 0 0 0 0 0 0 32864.0 2539.0 29.0 0.0 110.0 2399.0 0 0 0 0
MA0670.2_shift8 (NFIA)				; oligos_7nt_mkv2_m5 versus MA0670.2 (NFIA); m=6/7; ncol2=6; w=0; offset=2; strand=D; shift=8; score=0.414012; --------TGCCAA---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 89071.0 89418.0 0 0 0 0 c 0 0 0 0 0 0 0 0 0.0 0.0 93597.0 93394.0 0.0 0.0 0 0 0 0 g 0 0 0 0 0 0 0 0 0.0 98253.0 0.0 0.0 0.0 0.0 0 0 0 0 t 0 0 0 0 0 0 0 0 95496.0 0.0 0.0 0.0 0.0 0.0 0 0 0 0
MA0119.1_shift0 (NFIC::TLX1)				; oligos_7nt_mkv2_m5 versus MA0119.1 (NFIC::TLX1); m=7/7; ncol2=14; w=-6; offset=-6; strand=D; shift=0; score=0.402818; TGGCAssrwGCCAA---- ; cor=; Ncor= a 0.0 0.0 0.0 0.0 14.0 2.0 2.0 7.0 4.0 0.0 0.0 0.0 16.0 14.0 0 0 0 0 c 0.0 0.0 0.0 16.0 1.0 8.0 8.0 1.0 3.0 0.0 16.0 16.0 0.0 0.0 0 0 0 0 g 0.0 16.0 16.0 0.0 0.0 5.0 4.0 5.0 2.0 16.0 0.0 0.0 0.0 1.0 0 0 0 0 t 16.0 0.0 0.0 0.0 1.0 1.0 2.0 3.0 7.0 0.0 0.0 0.0 0.0 1.0 0 0 0 0