One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/01/04/peak-motifs.2026-01-04.175405_2026-01-04.175405_YulKOI/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_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/2026/01/04/peak-motifs.2026-01-04.175405_2026-01-04.175405_YulKOI/results/discovered_motifs/oligos_7nt_test_vs_ctrl_m5/peak-motifs_oligos_7nt_test_vs_ctrl_m5_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_m5_shift1 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)
; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=12; shift=1; ncol=13; -wmATGCTCATtw ; Alignment reference a 0 1630 1325 4022 173 271 194 241 170 4388 199 1086 1334 c 0 935 1371 254 71 214 4243 127 4243 164 180 1000 1048 g 0 901 979 192 158 4023 120 70 247 66 242 1202 871 t 0 1378 1169 376 4442 336 287 4406 184 226 4223 1556 1591

MA0787.1_shift1 (POU3F2)
; oligos_7nt_test_vs_ctrl_m5 versus MA0787.1 (POU3F2); m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.710208; -wTATGCwAATka ; cor=; Ncor= a 0 591.0 163.0 1292.0 28.0 19.0 68.0 688.0 1292.0 1292.0 63.0 137.0 1292.0 c 0 61.0 65.0 16.0 30.0 9.0 1292.0 4.0 16.0 6.0 19.0 165.0 262.0 g 0 171.0 40.0 25.0 12.0 1292.0 153.0 1.0 32.0 0.0 28.0 452.0 261.0 t 0 700.0 1292.0 0.0 1292.0 60.0 372.0 604.0 45.0 13.0 1292.0 840.0 562.0

MA0788.1_shift0 (POU3F3)
; oligos_7nt_test_vs_ctrl_m5 versus MA0788.1 (POU3F3); m=2/5; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.668631; wwTATGCwAATtw ; cor=; Ncor= a 576.0 440.0 129.0 1078.0 25.0 22.0 28.0 506.0 1078.0 1078.0 53.0 240.0 536.0 c 75.0 41.0 57.0 11.0 33.0 10.0 1078.0 4.0 11.0 6.0 20.0 141.0 85.0 g 137.0 131.0 64.0 12.0 49.0 1078.0 118.0 1.0 77.0 15.0 12.0 237.0 115.0 t 290.0 637.0 1078.0 30.0 1078.0 86.0 343.0 572.0 79.0 14.0 1078.0 1078.0 542.0

MA0786.2_shift1 (POU3F1)
; oligos_7nt_test_vs_ctrl_m5 versus MA0786.2 (POU3F1); m=3/5; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.597241; -wTATGywAAT-- ; cor=; Ncor= a 0 1034.0 505.0 2471.0 44.0 37.0 170.0 1423.0 2471.0 2471.0 259.0 0 0 c 0 126.0 186.0 7.0 53.0 13.0 2471.0 1.0 103.0 20.0 95.0 0 0 g 0 322.0 128.0 26.0 21.0 2471.0 413.0 21.0 130.0 25.0 128.0 0 0 t 0 1437.0 2471.0 21.0 2471.0 232.0 1119.0 1048.0 284.0 63.0 2471.0 0 0

MA0789.1_shift2 (POU3F4)
; oligos_7nt_test_vs_ctrl_m5 versus MA0789.1 (POU3F4); m=4/5; ncol2=9; w=0; offset=1; strand=D; shift=2; score=0.54222; --TATGCwAAT-- ; cor=; Ncor= a 0 0 941.0 11117.0 59.0 53.0 136.0 6447.0 11117.0 11117.0 705.0 0 0 c 0 0 349.0 23.0 59.0 19.0 11117.0 10.0 332.0 47.0 247.0 0 0 g 0 0 136.0 68.0 24.0 11117.0 602.0 56.0 315.0 88.0 292.0 0 0 t 0 0 11117.0 26.0 11117.0 245.0 2565.0 4670.0 885.0 168.0 11117.0 0 0

MA1549.2_rc_shift6 (POU6F1_rc)
; oligos_7nt_test_vs_ctrl_m5 versus MA1549.2_rc (POU6F1_rc); m=5/5; ncol2=7; w=0; offset=5; strand=R; shift=6; score=0.489507; ------CTCATTA ; cor=; Ncor= a 0 0 0 0 0 0 1855.0 411.0 615.0 6413.0 0.0 0.0 6413.0 c 0 0 0 0 0 0 6413.0 0.0 5799.0 298.0 0.0 255.0 10.0 g 0 0 0 0 0 0 851.0 96.0 206.0 0.0 0.0 179.0 273.0 t 0 0 0 0 0 0 314.0 6413.0 67.0 0.0 6413.0 6413.0 164.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_test_vs_ctrl_m5_shift1 (oligos_7nt_test_vs_ctrl_m5)				; oligos_7nt_test_vs_ctrl_m5; m=0 (reference); ncol1=12; shift=1; ncol=13; -wmATGCTCATtw ; Alignment reference a 0 1630 1325 4022 173 271 194 241 170 4388 199 1086 1334 c 0 935 1371 254 71 214 4243 127 4243 164 180 1000 1048 g 0 901 979 192 158 4023 120 70 247 66 242 1202 871 t 0 1378 1169 376 4442 336 287 4406 184 226 4223 1556 1591
MA0787.1_shift1 (POU3F2)				; oligos_7nt_test_vs_ctrl_m5 versus MA0787.1 (POU3F2); m=1/5; ncol2=12; w=0; offset=0; strand=D; shift=1; score=0.710208; -wTATGCwAATka ; cor=; Ncor= a 0 591.0 163.0 1292.0 28.0 19.0 68.0 688.0 1292.0 1292.0 63.0 137.0 1292.0 c 0 61.0 65.0 16.0 30.0 9.0 1292.0 4.0 16.0 6.0 19.0 165.0 262.0 g 0 171.0 40.0 25.0 12.0 1292.0 153.0 1.0 32.0 0.0 28.0 452.0 261.0 t 0 700.0 1292.0 0.0 1292.0 60.0 372.0 604.0 45.0 13.0 1292.0 840.0 562.0
MA0788.1_shift0 (POU3F3)				; oligos_7nt_test_vs_ctrl_m5 versus MA0788.1 (POU3F3); m=2/5; ncol2=13; w=-1; offset=-1; strand=D; shift=0; score=0.668631; wwTATGCwAATtw ; cor=; Ncor= a 576.0 440.0 129.0 1078.0 25.0 22.0 28.0 506.0 1078.0 1078.0 53.0 240.0 536.0 c 75.0 41.0 57.0 11.0 33.0 10.0 1078.0 4.0 11.0 6.0 20.0 141.0 85.0 g 137.0 131.0 64.0 12.0 49.0 1078.0 118.0 1.0 77.0 15.0 12.0 237.0 115.0 t 290.0 637.0 1078.0 30.0 1078.0 86.0 343.0 572.0 79.0 14.0 1078.0 1078.0 542.0
MA0786.2_shift1 (POU3F1)				; oligos_7nt_test_vs_ctrl_m5 versus MA0786.2 (POU3F1); m=3/5; ncol2=10; w=0; offset=0; strand=D; shift=1; score=0.597241; -wTATGywAAT-- ; cor=; Ncor= a 0 1034.0 505.0 2471.0 44.0 37.0 170.0 1423.0 2471.0 2471.0 259.0 0 0 c 0 126.0 186.0 7.0 53.0 13.0 2471.0 1.0 103.0 20.0 95.0 0 0 g 0 322.0 128.0 26.0 21.0 2471.0 413.0 21.0 130.0 25.0 128.0 0 0 t 0 1437.0 2471.0 21.0 2471.0 232.0 1119.0 1048.0 284.0 63.0 2471.0 0 0
MA0789.1_shift2 (POU3F4)				; oligos_7nt_test_vs_ctrl_m5 versus MA0789.1 (POU3F4); m=4/5; ncol2=9; w=0; offset=1; strand=D; shift=2; score=0.54222; --TATGCwAAT-- ; cor=; Ncor= a 0 0 941.0 11117.0 59.0 53.0 136.0 6447.0 11117.0 11117.0 705.0 0 0 c 0 0 349.0 23.0 59.0 19.0 11117.0 10.0 332.0 47.0 247.0 0 0 g 0 0 136.0 68.0 24.0 11117.0 602.0 56.0 315.0 88.0 292.0 0 0 t 0 0 11117.0 26.0 11117.0 245.0 2565.0 4670.0 885.0 168.0 11117.0 0 0
MA1549.2_rc_shift6 (POU6F1_rc)				; oligos_7nt_test_vs_ctrl_m5 versus MA1549.2_rc (POU6F1_rc); m=5/5; ncol2=7; w=0; offset=5; strand=R; shift=6; score=0.489507; ------CTCATTA ; cor=; Ncor= a 0 0 0 0 0 0 1855.0 411.0 615.0 6413.0 0.0 0.0 6413.0 c 0 0 0 0 0 0 6413.0 0.0 5799.0 298.0 0.0 255.0 10.0 g 0 0 0 0 0 0 851.0 96.0 206.0 0.0 0.0 179.0 273.0 t 0 0 0 0 0 0 314.0 6413.0 67.0 0.0 6413.0 6413.0 164.0