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.2026-01-05.052000_2026-01-05.052000_2qIqyX/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3.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.2026-01-05.052000_2026-01-05.052000_2qIqyX/results/discovered_motifs/positions_6nt_m3/peak-motifs_positions_6nt_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift4 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=18; shift=4; ncol=22; ----gyccrGACATGCCCagrc ; Alignment reference a 0 0 0 0 92 120 129 132 443 72 682 10 746 51 10 15 44 44 481 120 344 186 c 0 0 0 0 187 394 435 399 54 56 19 837 36 17 8 728 769 662 82 175 117 430 g 0 0 0 0 472 91 160 149 270 714 157 14 19 23 847 10 23 27 196 504 312 159 t 0 0 0 0 119 265 146 190 103 28 12 9 69 779 5 117 34 137 111 71 97 95

MA0106.3_shift9 (TP53)
; positions_6nt_m3 versus MA0106.3 (TP53); m=1/3; ncol2=18; w=0; offset=5; strand=D; shift=9; score=0.501161; ---------rACATGyCcgGrC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 7544.0 10514.0 45.0 11931.0 1710.0 8.0 244.0 1228.0 1145.0 3851.0 3584.0 7104.0 0.0 c 0 0 0 0 0 0 0 0 0 1037.0 116.0 19689.0 204.0 374.0 2.0 12014.0 17286.0 11875.0 1474.0 756.0 26.0 19350.0 g 0 0 0 0 0 0 0 0 0 6563.0 2433.0 13.0 653.0 137.0 20393.0 109.0 417.0 2151.0 9954.0 17846.0 8821.0 4.0 t 0 0 0 0 0 0 0 0 0 2268.0 735.0 837.0 739.0 18893.0 0.0 7106.0 2642.0 3774.0 2118.0 1546.0 190.0 1.0

MA0861.2_rc_shift0 (TP73_rc)
; positions_6nt_m3 versus MA0861.2_rc (TP73_rc); m=2/3; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.458156; rCrTGTyyrgACATGy------ ; cor=; Ncor= a 6995.0 39.0 8476.0 2302.0 0.0 442.0 1002.0 2457.0 4242.0 2749.0 11892.0 1.0 11480.0 198.0 0.0 208.0 0 0 0 0 0 0 c 181.0 13026.0 130.0 279.0 0.0 1414.0 7797.0 3558.0 2230.0 783.0 91.0 11787.0 806.0 557.0 0.0 3304.0 0 0 0 0 0 0 g 6944.0 170.0 5965.0 143.0 11703.0 145.0 441.0 2418.0 2940.0 8161.0 2591.0 28.0 293.0 124.0 10829.0 429.0 0 0 0 0 0 0 t 993.0 16.0 256.0 10125.0 0.0 9639.0 3988.0 3488.0 2166.0 1377.0 130.0 8.0 3837.0 8760.0 0.0 6206.0 0 0 0 0 0 0

MA1979.2_rc_shift13 (ZNF416_rc)
; positions_6nt_m3 versus MA1979.2_rc (ZNF416_rc); m=3/3; ncol2=10; w=0; offset=9; strand=R; shift=13; score=0.411503; -------------tGCCCAGAt ; cor=; Ncor= a 0 0 0 0 0 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 c 0 0 0 0 0 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 g 0 0 0 0 0 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 t 0 0 0 0 0 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

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m3_shift4 (positions_6nt_m3)				; positions_6nt_m3; m=0 (reference); ncol1=18; shift=4; ncol=22; ----gyccrGACATGCCCagrc ; Alignment reference a 0 0 0 0 92 120 129 132 443 72 682 10 746 51 10 15 44 44 481 120 344 186 c 0 0 0 0 187 394 435 399 54 56 19 837 36 17 8 728 769 662 82 175 117 430 g 0 0 0 0 472 91 160 149 270 714 157 14 19 23 847 10 23 27 196 504 312 159 t 0 0 0 0 119 265 146 190 103 28 12 9 69 779 5 117 34 137 111 71 97 95
MA0106.3_shift9 (TP53)				; positions_6nt_m3 versus MA0106.3 (TP53); m=1/3; ncol2=18; w=0; offset=5; strand=D; shift=9; score=0.501161; ---------rACATGyCcgGrC ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 7544.0 10514.0 45.0 11931.0 1710.0 8.0 244.0 1228.0 1145.0 3851.0 3584.0 7104.0 0.0 c 0 0 0 0 0 0 0 0 0 1037.0 116.0 19689.0 204.0 374.0 2.0 12014.0 17286.0 11875.0 1474.0 756.0 26.0 19350.0 g 0 0 0 0 0 0 0 0 0 6563.0 2433.0 13.0 653.0 137.0 20393.0 109.0 417.0 2151.0 9954.0 17846.0 8821.0 4.0 t 0 0 0 0 0 0 0 0 0 2268.0 735.0 837.0 739.0 18893.0 0.0 7106.0 2642.0 3774.0 2118.0 1546.0 190.0 1.0
MA0861.2_rc_shift0 (TP73_rc)				; positions_6nt_m3 versus MA0861.2_rc (TP73_rc); m=2/3; ncol2=16; w=-4; offset=-4; strand=R; shift=0; score=0.458156; rCrTGTyyrgACATGy------ ; cor=; Ncor= a 6995.0 39.0 8476.0 2302.0 0.0 442.0 1002.0 2457.0 4242.0 2749.0 11892.0 1.0 11480.0 198.0 0.0 208.0 0 0 0 0 0 0 c 181.0 13026.0 130.0 279.0 0.0 1414.0 7797.0 3558.0 2230.0 783.0 91.0 11787.0 806.0 557.0 0.0 3304.0 0 0 0 0 0 0 g 6944.0 170.0 5965.0 143.0 11703.0 145.0 441.0 2418.0 2940.0 8161.0 2591.0 28.0 293.0 124.0 10829.0 429.0 0 0 0 0 0 0 t 993.0 16.0 256.0 10125.0 0.0 9639.0 3988.0 3488.0 2166.0 1377.0 130.0 8.0 3837.0 8760.0 0.0 6206.0 0 0 0 0 0 0
MA1979.2_rc_shift13 (ZNF416_rc)				; positions_6nt_m3 versus MA1979.2_rc (ZNF416_rc); m=3/3; ncol2=10; w=0; offset=9; strand=R; shift=13; score=0.411503; -------------tGCCCAGAt ; cor=; Ncor= a 0 0 0 0 0 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 c 0 0 0 0 0 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 g 0 0 0 0 0 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 t 0 0 0 0 0 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