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.2026-01-05.125020_2026-01-05.125020_w7RQpp/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.2026-01-05.125020_2026-01-05.125020_w7RQpp/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_shift5 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_7nt_m2_shift5 (positions_7nt_m2)
; positions_7nt_m2; m=0 (reference); ncol1=17; shift=5; ncol=22; -----csGCgGCtGCtGCCkss ; Alignment reference a 0 0 0 0 0 1164 1410 306 370 605 212 212 512 155 257 623 218 276 366 582 815 1138 c 0 0 0 0 0 4709 3157 624 7776 1600 539 8372 1924 705 8326 1838 607 7926 6692 1183 4452 3287 g 0 0 0 0 0 2169 3252 7956 484 6225 8122 395 1984 7995 378 1812 7972 609 1559 2968 2741 3068 t 0 0 0 0 0 1120 1343 276 532 732 289 183 4742 307 201 4889 365 351 545 4429 1154 1669

MA1721.2_rc_shift5 (ZNF93_rc)
; positions_7nt_m2 versus MA1721.2_rc (ZNF93_rc); m=1/5; ncol2=14; w=0; offset=0; strand=R; shift=5; score=0.678061; -----CCGCTGCyGmyrCc--- ; cor=; Ncor= a 0 0 0 0 0 37.0 126.0 44.0 10.0 57.0 44.0 10.0 32.0 50.0 730.0 93.0 940.0 123.0 143.0 0 0 0 c 0 0 0 0 0 2145.0 1784.0 33.0 2328.0 576.0 42.0 2334.0 1263.0 22.0 1483.0 663.0 211.0 1857.0 1499.0 0 0 0 g 0 0 0 0 0 134.0 138.0 2292.0 20.0 96.0 2279.0 26.0 92.0 2278.0 114.0 177.0 1120.0 233.0 279.0 0 0 0 t 0 0 0 0 0 72.0 340.0 19.0 30.0 1659.0 23.0 18.0 1001.0 38.0 61.0 1455.0 117.0 175.0 467.0 0 0 0

MA0816.1_rc_shift6 (Ascl2_rc)
; positions_7nt_m2 versus MA0816.1_rc (Ascl2_rc); m=2/5; ncol2=10; w=0; offset=1; strand=R; shift=6; score=0.429601; ------rrCAGCTGyt------ ; cor=; Ncor= a 0 0 0 0 0 0 199.0 94.0 2.0 300.0 1.0 18.0 15.0 1.0 1.0 16.0 0 0 0 0 0 0 c 0 0 0 0 0 0 28.0 15.0 300.0 0.0 2.0 300.0 0.0 0.0 172.0 63.0 0 0 0 0 0 0 g 0 0 0 0 0 0 101.0 206.0 1.0 0.0 300.0 23.0 0.0 300.0 41.0 36.0 0 0 0 0 0 0 t 0 0 0 0 0 0 34.0 6.0 0.0 4.0 3.0 7.0 300.0 3.0 128.0 237.0 0 0 0 0 0 0

MA1728.2_shift12 (ZNF549)
; positions_7nt_m2 versus MA1728.2 (ZNF549); m=3/5; ncol2=8; w=0; offset=7; strand=D; shift=12; score=0.408656; ------------TGCTGCCC-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 483.0 72.0 50.0 229.0 28.0 55.0 106.0 183.0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 349.0 161.0 4622.0 175.0 80.0 4364.0 4435.0 4133.0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 498.0 4489.0 77.0 128.0 4566.0 177.0 98.0 75.0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 3497.0 105.0 78.0 4295.0 153.0 231.0 188.0 436.0 0 0

MA0048.3_shift6 (NHLH1)
; positions_7nt_m2 versus MA0048.3 (NHLH1); m=4/5; ncol2=9; w=0; offset=1; strand=D; shift=6; score=0.408172; ------cGCAGCTGC------- ; cor=; Ncor= a 0 0 0 0 0 0 788.0 461.0 3.0 2166.0 0.0 96.0 0.0 2.0 296.0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 2166.0 179.0 2166.0 3.0 301.0 2166.0 4.0 4.0 2166.0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 181.0 2166.0 0.0 1.0 2166.0 124.0 4.0 2166.0 102.0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 111.0 142.0 0.0 0.0 114.0 0.0 2166.0 1.0 350.0 0 0 0 0 0 0 0

MA1938.2_rc_shift0 (ERF::NHLH1_rc)
; positions_7nt_m2 versus MA1938.2_rc (ERF::NHLH1_rc); m=5/5; ncol2=16; w=-5; offset=-5; strand=R; shift=0; score=0.401754; ryWTCCGGCAGCTGCt------ ; cor=; Ncor= a 210.0 40.0 84.0 12.0 26.0 7.0 1.0 8.0 15.0 324.0 8.0 28.0 0.0 18.0 21.0 7.0 0 0 0 0 0 0 c 16.0 176.0 11.0 3.0 313.0 325.0 11.0 6.0 317.0 13.0 2.0 288.0 0.0 14.0 290.0 81.0 0 0 0 0 0 0 g 108.0 3.0 0.0 21.0 10.0 0.0 327.0 316.0 12.0 20.0 301.0 11.0 0.0 317.0 14.0 81.0 0 0 0 0 0 0 t 0.0 113.0 241.0 324.0 4.0 27.0 12.0 0.0 1.0 10.0 26.0 1.0 324.0 5.0 0.0 156.0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_7nt_m2_shift5 (positions_7nt_m2)				; positions_7nt_m2; m=0 (reference); ncol1=17; shift=5; ncol=22; -----csGCgGCtGCtGCCkss ; Alignment reference a 0 0 0 0 0 1164 1410 306 370 605 212 212 512 155 257 623 218 276 366 582 815 1138 c 0 0 0 0 0 4709 3157 624 7776 1600 539 8372 1924 705 8326 1838 607 7926 6692 1183 4452 3287 g 0 0 0 0 0 2169 3252 7956 484 6225 8122 395 1984 7995 378 1812 7972 609 1559 2968 2741 3068 t 0 0 0 0 0 1120 1343 276 532 732 289 183 4742 307 201 4889 365 351 545 4429 1154 1669
MA1721.2_rc_shift5 (ZNF93_rc)				; positions_7nt_m2 versus MA1721.2_rc (ZNF93_rc); m=1/5; ncol2=14; w=0; offset=0; strand=R; shift=5; score=0.678061; -----CCGCTGCyGmyrCc--- ; cor=; Ncor= a 0 0 0 0 0 37.0 126.0 44.0 10.0 57.0 44.0 10.0 32.0 50.0 730.0 93.0 940.0 123.0 143.0 0 0 0 c 0 0 0 0 0 2145.0 1784.0 33.0 2328.0 576.0 42.0 2334.0 1263.0 22.0 1483.0 663.0 211.0 1857.0 1499.0 0 0 0 g 0 0 0 0 0 134.0 138.0 2292.0 20.0 96.0 2279.0 26.0 92.0 2278.0 114.0 177.0 1120.0 233.0 279.0 0 0 0 t 0 0 0 0 0 72.0 340.0 19.0 30.0 1659.0 23.0 18.0 1001.0 38.0 61.0 1455.0 117.0 175.0 467.0 0 0 0
MA0816.1_rc_shift6 (Ascl2_rc)				; positions_7nt_m2 versus MA0816.1_rc (Ascl2_rc); m=2/5; ncol2=10; w=0; offset=1; strand=R; shift=6; score=0.429601; ------rrCAGCTGyt------ ; cor=; Ncor= a 0 0 0 0 0 0 199.0 94.0 2.0 300.0 1.0 18.0 15.0 1.0 1.0 16.0 0 0 0 0 0 0 c 0 0 0 0 0 0 28.0 15.0 300.0 0.0 2.0 300.0 0.0 0.0 172.0 63.0 0 0 0 0 0 0 g 0 0 0 0 0 0 101.0 206.0 1.0 0.0 300.0 23.0 0.0 300.0 41.0 36.0 0 0 0 0 0 0 t 0 0 0 0 0 0 34.0 6.0 0.0 4.0 3.0 7.0 300.0 3.0 128.0 237.0 0 0 0 0 0 0
MA1728.2_shift12 (ZNF549)				; positions_7nt_m2 versus MA1728.2 (ZNF549); m=3/5; ncol2=8; w=0; offset=7; strand=D; shift=12; score=0.408656; ------------TGCTGCCC-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 483.0 72.0 50.0 229.0 28.0 55.0 106.0 183.0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 349.0 161.0 4622.0 175.0 80.0 4364.0 4435.0 4133.0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 498.0 4489.0 77.0 128.0 4566.0 177.0 98.0 75.0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 3497.0 105.0 78.0 4295.0 153.0 231.0 188.0 436.0 0 0
MA0048.3_shift6 (NHLH1)				; positions_7nt_m2 versus MA0048.3 (NHLH1); m=4/5; ncol2=9; w=0; offset=1; strand=D; shift=6; score=0.408172; ------cGCAGCTGC------- ; cor=; Ncor= a 0 0 0 0 0 0 788.0 461.0 3.0 2166.0 0.0 96.0 0.0 2.0 296.0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 2166.0 179.0 2166.0 3.0 301.0 2166.0 4.0 4.0 2166.0 0 0 0 0 0 0 0 g 0 0 0 0 0 0 181.0 2166.0 0.0 1.0 2166.0 124.0 4.0 2166.0 102.0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 111.0 142.0 0.0 0.0 114.0 0.0 2166.0 1.0 350.0 0 0 0 0 0 0 0
MA1938.2_rc_shift0 (ERF::NHLH1_rc)				; positions_7nt_m2 versus MA1938.2_rc (ERF::NHLH1_rc); m=5/5; ncol2=16; w=-5; offset=-5; strand=R; shift=0; score=0.401754; ryWTCCGGCAGCTGCt------ ; cor=; Ncor= a 210.0 40.0 84.0 12.0 26.0 7.0 1.0 8.0 15.0 324.0 8.0 28.0 0.0 18.0 21.0 7.0 0 0 0 0 0 0 c 16.0 176.0 11.0 3.0 313.0 325.0 11.0 6.0 317.0 13.0 2.0 288.0 0.0 14.0 290.0 81.0 0 0 0 0 0 0 g 108.0 3.0 0.0 21.0 10.0 0.0 327.0 316.0 12.0 20.0 301.0 11.0 0.0 317.0 14.0 81.0 0 0 0 0 0 0 t 0.0 113.0 241.0 324.0 4.0 27.0 12.0 0.0 1.0 10.0 26.0 1.0 324.0 5.0 0.0 156.0 0 0 0 0 0 0