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/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_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.2026-01-05.052000_2026-01-05.052000_2qIqyX/results/discovered_motifs/oligos_7nt_mkv4_m5/peak-motifs_oligos_7nt_mkv4_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m5_shift7 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m5_shift7 (oligos_7nt_mkv4_m5)
; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=12; shift=7; ncol=19; -------srGACwTGCCyr ; Alignment reference a 0 0 0 0 0 0 0 117 200 23 523 5 200 15 5 5 15 89 208 c 0 0 0 0 0 0 0 189 43 11 12 577 26 10 11 528 549 272 84 g 0 0 0 0 0 0 0 178 229 555 45 14 16 12 573 14 14 34 194 t 0 0 0 0 0 0 0 113 125 8 17 1 355 560 8 50 19 202 111

MA0738.2_shift12 (HIC2)
; oligos_7nt_mkv4_m5 versus MA0738.2 (HIC2); m=1/4; ncol2=6; w=0; offset=5; strand=D; shift=12; score=0.439613; ------------rTGCCM- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 2606.0 0.0 494.0 23.0 435.0 1466.0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 394.0 117.0 354.0 4891.0 4891.0 3425.0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 2285.0 0.0 4891.0 14.0 0.0 0.0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 367.0 4891.0 151.0 0.0 59.0 0.0 0

MA0739.2_shift12 (Hic1)
; oligos_7nt_mkv4_m5 versus MA0739.2 (Hic1); m=2/4; ncol2=8; w=0; offset=5; strand=D; shift=12; score=0.438066; ------------rTGCCAa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 6337.0 62.0 950.0 50.0 88.0 9008.0 6140.0 c 0 0 0 0 0 0 0 0 0 0 0 0 719.0 422.0 588.0 11007.0 11007.0 1999.0 1986.0 g 0 0 0 0 0 0 0 0 0 0 0 0 4670.0 73.0 11007.0 121.0 31.0 3.0 2267.0 t 0 0 0 0 0 0 0 0 0 0 0 0 666.0 11007.0 183.0 0.0 68.0 317.0 614.0

MA0106.3_shift9 (TP53)
; oligos_7nt_mkv4_m5 versus MA0106.3 (TP53); m=3/4; ncol2=18; w=0; offset=2; strand=D; shift=9; score=0.41856; ---------rACATGyCcg ; 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 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 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 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

MA0861.2_rc_shift0 (TP73_rc)
; oligos_7nt_mkv4_m5 versus MA0861.2_rc (TP73_rc); m=4/4; ncol2=16; w=-7; offset=-7; strand=R; shift=0; score=0.405925; 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 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 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 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

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m5_shift7 (oligos_7nt_mkv4_m5)				; oligos_7nt_mkv4_m5; m=0 (reference); ncol1=12; shift=7; ncol=19; -------srGACwTGCCyr ; Alignment reference a 0 0 0 0 0 0 0 117 200 23 523 5 200 15 5 5 15 89 208 c 0 0 0 0 0 0 0 189 43 11 12 577 26 10 11 528 549 272 84 g 0 0 0 0 0 0 0 178 229 555 45 14 16 12 573 14 14 34 194 t 0 0 0 0 0 0 0 113 125 8 17 1 355 560 8 50 19 202 111
MA0738.2_shift12 (HIC2)				; oligos_7nt_mkv4_m5 versus MA0738.2 (HIC2); m=1/4; ncol2=6; w=0; offset=5; strand=D; shift=12; score=0.439613; ------------rTGCCM- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 2606.0 0.0 494.0 23.0 435.0 1466.0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 394.0 117.0 354.0 4891.0 4891.0 3425.0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 2285.0 0.0 4891.0 14.0 0.0 0.0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 367.0 4891.0 151.0 0.0 59.0 0.0 0
MA0739.2_shift12 (Hic1)				; oligos_7nt_mkv4_m5 versus MA0739.2 (Hic1); m=2/4; ncol2=8; w=0; offset=5; strand=D; shift=12; score=0.438066; ------------rTGCCAa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 6337.0 62.0 950.0 50.0 88.0 9008.0 6140.0 c 0 0 0 0 0 0 0 0 0 0 0 0 719.0 422.0 588.0 11007.0 11007.0 1999.0 1986.0 g 0 0 0 0 0 0 0 0 0 0 0 0 4670.0 73.0 11007.0 121.0 31.0 3.0 2267.0 t 0 0 0 0 0 0 0 0 0 0 0 0 666.0 11007.0 183.0 0.0 68.0 317.0 614.0
MA0106.3_shift9 (TP53)				; oligos_7nt_mkv4_m5 versus MA0106.3 (TP53); m=3/4; ncol2=18; w=0; offset=2; strand=D; shift=9; score=0.41856; ---------rACATGyCcg ; 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 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 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 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
MA0861.2_rc_shift0 (TP73_rc)				; oligos_7nt_mkv4_m5 versus MA0861.2_rc (TP73_rc); m=4/4; ncol2=16; w=-7; offset=-7; strand=R; shift=0; score=0.405925; 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 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 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 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