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.2026-01-05.125527_2026-01-05.125527_ogDb5d/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_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.2026-01-05.125527_2026-01-05.125527_ogDb5d/results/discovered_motifs/positions_7nt_m2/peak-motifs_positions_7nt_m2_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: positions_7nt_m2_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift1 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=17; shift=1; ncol=18; -ssgCttGGCaGCCGCss ; Alignment reference a 0 968 1100 537 189 305 269 242 149 216 3768 178 232 444 327 194 956 789 c 0 2073 1848 1200 5220 978 1354 731 357 5186 1012 400 5210 4544 386 5171 1987 1792 g 0 1986 2022 3541 349 1161 992 4753 5311 446 829 5231 392 534 4923 406 1943 2440 t 0 953 1010 702 222 3536 3365 254 163 132 371 171 146 458 344 209 1094 959

MA0048.3_rc_shift8 (NHLH1_rc)
; positions_7nt_m2 versus MA0048.3_rc (NHLH1_rc); m=1/3; ncol2=9; w=0; offset=7; strand=R; shift=8; score=0.411905; --------GCAGCTGCg- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 350.0 1.0 2166.0 0.0 114.0 0.0 0.0 142.0 111.0 0 c 0 0 0 0 0 0 0 0 102.0 2166.0 4.0 124.0 2166.0 1.0 0.0 2166.0 181.0 0 g 0 0 0 0 0 0 0 0 2166.0 4.0 4.0 2166.0 301.0 3.0 2166.0 179.0 2166.0 0 t 0 0 0 0 0 0 0 0 296.0 2.0 0.0 96.0 0.0 2166.0 3.0 461.0 788.0 0

MA1599.2_rc_shift0 (ZNF682_rc)
; positions_7nt_m2 versus MA1599.2_rc (ZNF682_rc); m=2/3; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.404945; GGGGCTTrGCC------- ; cor=; Ncor= a 64.0 7.0 11.0 33.0 7.0 6.0 13.0 358.0 58.0 36.0 89.0 0 0 0 0 0 0 0 c 32.0 10.0 9.0 13.0 1038.0 22.0 20.0 55.0 105.0 877.0 774.0 0 0 0 0 0 0 0 g 896.0 1034.0 1033.0 999.0 7.0 31.0 72.0 597.0 795.0 42.0 85.0 0 0 0 0 0 0 0 t 66.0 7.0 5.0 13.0 6.0 999.0 953.0 48.0 100.0 103.0 110.0 0 0 0 0 0 0 0

MA1721.2_shift7 (ZNF93)
; positions_7nt_m2 versus MA1721.2 (ZNF93); m=3/3; ncol2=14; w=0; offset=6; strand=D; shift=7; score=0.401757; -------gGyrkCrGCAG ; cor=; Ncor= a 0 0 0 0 0 0 0 467.0 175.0 117.0 1455.0 61.0 38.0 1001.0 18.0 23.0 1659.0 30.0 c 0 0 0 0 0 0 0 279.0 233.0 1120.0 177.0 114.0 2278.0 92.0 26.0 2279.0 96.0 20.0 g 0 0 0 0 0 0 0 1499.0 1857.0 211.0 663.0 1483.0 22.0 1263.0 2334.0 42.0 576.0 2328.0 t 0 0 0 0 0 0 0 143.0 123.0 940.0 93.0 730.0 50.0 32.0 10.0 44.0 57.0 10.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift1 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=17; shift=1; ncol=18; -ssgCttGGCaGCCGCss ; Alignment reference a 0 968 1100 537 189 305 269 242 149 216 3768 178 232 444 327 194 956 789 c 0 2073 1848 1200 5220 978 1354 731 357 5186 1012 400 5210 4544 386 5171 1987 1792 g 0 1986 2022 3541 349 1161 992 4753 5311 446 829 5231 392 534 4923 406 1943 2440 t 0 953 1010 702 222 3536 3365 254 163 132 371 171 146 458 344 209 1094 959
MA0048.3_rc_shift8 (NHLH1_rc)				; positions_7nt_m2 versus MA0048.3_rc (NHLH1_rc); m=1/3; ncol2=9; w=0; offset=7; strand=R; shift=8; score=0.411905; --------GCAGCTGCg- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 350.0 1.0 2166.0 0.0 114.0 0.0 0.0 142.0 111.0 0 c 0 0 0 0 0 0 0 0 102.0 2166.0 4.0 124.0 2166.0 1.0 0.0 2166.0 181.0 0 g 0 0 0 0 0 0 0 0 2166.0 4.0 4.0 2166.0 301.0 3.0 2166.0 179.0 2166.0 0 t 0 0 0 0 0 0 0 0 296.0 2.0 0.0 96.0 0.0 2166.0 3.0 461.0 788.0 0
MA1599.2_rc_shift0 (ZNF682_rc)				; positions_7nt_m2 versus MA1599.2_rc (ZNF682_rc); m=2/3; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.404945; GGGGCTTrGCC------- ; cor=; Ncor= a 64.0 7.0 11.0 33.0 7.0 6.0 13.0 358.0 58.0 36.0 89.0 0 0 0 0 0 0 0 c 32.0 10.0 9.0 13.0 1038.0 22.0 20.0 55.0 105.0 877.0 774.0 0 0 0 0 0 0 0 g 896.0 1034.0 1033.0 999.0 7.0 31.0 72.0 597.0 795.0 42.0 85.0 0 0 0 0 0 0 0 t 66.0 7.0 5.0 13.0 6.0 999.0 953.0 48.0 100.0 103.0 110.0 0 0 0 0 0 0 0
MA1721.2_shift7 (ZNF93)				; positions_7nt_m2 versus MA1721.2 (ZNF93); m=3/3; ncol2=14; w=0; offset=6; strand=D; shift=7; score=0.401757; -------gGyrkCrGCAG ; cor=; Ncor= a 0 0 0 0 0 0 0 467.0 175.0 117.0 1455.0 61.0 38.0 1001.0 18.0 23.0 1659.0 30.0 c 0 0 0 0 0 0 0 279.0 233.0 1120.0 177.0 114.0 2278.0 92.0 26.0 2279.0 96.0 20.0 g 0 0 0 0 0 0 0 1499.0 1857.0 211.0 663.0 1483.0 22.0 1263.0 2334.0 42.0 576.0 2328.0 t 0 0 0 0 0 0 0 143.0 123.0 940.0 93.0 730.0 50.0 32.0 10.0 44.0 57.0 10.0