One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/oligos_6nt_mkv4_m22/peak-motifs_oligos_6nt_mkv4_m22.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2020/nonredundant/JASPAR2020_CORE_vertebrates_non-redundant_pfms.tf -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 Myogenin_Rep1_motifs50/results/discovered_motifs/oligos_6nt_mkv4_m22/peak-motifs_oligos_6nt_mkv4_m22_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m22_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m22_shift1 (oligos_6nt_mkv4_m22oligos_6nt_mkv4_m22)
; oligos_6nt_mkv4_m22 (oligos_6nt_mkv4_m22oligos_6nt_mkv4_m22); m=0 (reference); ncol1=10; shift=1; ncol=12; -ssACCGCAgs- ; Alignment reference a 0 478 547 2225 0 0 0 0 2224 309 439 0 c 0 651 863 0 2225 2225 0 2222 0 543 853 0 g 0 645 623 0 0 0 2225 0 1 1136 604 0 t 0 451 192 0 0 0 0 3 0 237 329 0

MA0511.2_shift1 (RUNX2)
; oligos_6nt_mkv4_m22 versus MA0511.2 (RUNX2); m=1/3; ncol2=9; w=9; offset=0; strand=D; shift=1; score=0.786995; -wAACCRCAa-- ; cor=; Ncor= a 0 3872.0 6621.0 6621.0 0.0 0.0 1914.0 0.0 6621.0 4202.0 0 0 c 0 1092.0 556.0 325.0 6621.0 6621.0 36.0 6621.0 476.0 677.0 0 0 g 0 326.0 1215.0 0.0 0.0 0.0 4707.0 0.0 458.0 1134.0 0 0 t 0 2748.0 582.0 0.0 0.0 0.0 120.0 0.0 191.0 607.0 0 0

MA0002.2_rc_shift1 (RUNX1_rc)
; oligos_6nt_mkv4_m22 versus MA0002.2_rc (RUNX1_rc); m=2/3; ncol2=11; w=10; offset=0; strand=R; shift=1; score=0.659569; -waaCCACAram ; cor=; Ncor= a 0 1053.0 1325.0 1339.0 93.0 13.0 1716.0 53.0 1936.0 656.0 814.0 521.0 c 0 289.0 81.0 251.0 1848.0 1987.0 70.0 1872.0 7.0 149.0 467.0 696.0 g 0 158.0 463.0 400.0 42.0 0.0 127.0 75.0 0.0 1072.0 485.0 496.0 t 0 500.0 131.0 10.0 17.0 0.0 87.0 0.0 57.0 123.0 234.0 287.0

MA0684.2_shift0 (RUNX3)
; oligos_6nt_mkv4_m22 versus MA0684.2 (RUNX3); m=3/3; ncol2=12; w=10; offset=-1; strand=D; shift=0; score=0.627384; awAACCTCAawh ; cor=; Ncor= a 7768.0 9558.0 19136.0 26243.0 427.0 495.0 6357.0 611.0 26121.0 16137.0 8778.0 6879.0 c 6083.0 5007.0 2662.0 315.0 26293.0 26208.0 419.0 26015.0 414.0 3077.0 5994.0 6900.0 g 6685.0 3547.0 3500.0 431.0 198.0 385.0 1911.0 390.0 338.0 4696.0 5642.0 6372.0 t 6841.0 9265.0 2079.0 388.0 459.0 289.0 18690.0 361.0 504.0 3467.0 6963.0 7226.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m22_shift1 (oligos_6nt_mkv4_m22oligos_6nt_mkv4_m22)				; oligos_6nt_mkv4_m22 (oligos_6nt_mkv4_m22oligos_6nt_mkv4_m22); m=0 (reference); ncol1=10; shift=1; ncol=12; -ssACCGCAgs- ; Alignment reference a 0 478 547 2225 0 0 0 0 2224 309 439 0 c 0 651 863 0 2225 2225 0 2222 0 543 853 0 g 0 645 623 0 0 0 2225 0 1 1136 604 0 t 0 451 192 0 0 0 0 3 0 237 329 0
MA0511.2_shift1 (RUNX2)				; oligos_6nt_mkv4_m22 versus MA0511.2 (RUNX2); m=1/3; ncol2=9; w=9; offset=0; strand=D; shift=1; score=0.786995; -wAACCRCAa-- ; cor=; Ncor= a 0 3872.0 6621.0 6621.0 0.0 0.0 1914.0 0.0 6621.0 4202.0 0 0 c 0 1092.0 556.0 325.0 6621.0 6621.0 36.0 6621.0 476.0 677.0 0 0 g 0 326.0 1215.0 0.0 0.0 0.0 4707.0 0.0 458.0 1134.0 0 0 t 0 2748.0 582.0 0.0 0.0 0.0 120.0 0.0 191.0 607.0 0 0
MA0002.2_rc_shift1 (RUNX1_rc)				; oligos_6nt_mkv4_m22 versus MA0002.2_rc (RUNX1_rc); m=2/3; ncol2=11; w=10; offset=0; strand=R; shift=1; score=0.659569; -waaCCACAram ; cor=; Ncor= a 0 1053.0 1325.0 1339.0 93.0 13.0 1716.0 53.0 1936.0 656.0 814.0 521.0 c 0 289.0 81.0 251.0 1848.0 1987.0 70.0 1872.0 7.0 149.0 467.0 696.0 g 0 158.0 463.0 400.0 42.0 0.0 127.0 75.0 0.0 1072.0 485.0 496.0 t 0 500.0 131.0 10.0 17.0 0.0 87.0 0.0 57.0 123.0 234.0 287.0
MA0684.2_shift0 (RUNX3)				; oligos_6nt_mkv4_m22 versus MA0684.2 (RUNX3); m=3/3; ncol2=12; w=10; offset=-1; strand=D; shift=0; score=0.627384; awAACCTCAawh ; cor=; Ncor= a 7768.0 9558.0 19136.0 26243.0 427.0 495.0 6357.0 611.0 26121.0 16137.0 8778.0 6879.0 c 6083.0 5007.0 2662.0 315.0 26293.0 26208.0 419.0 26015.0 414.0 3077.0 5994.0 6900.0 g 6685.0 3547.0 3500.0 431.0 198.0 385.0 1911.0 390.0 338.0 4696.0 5642.0 6372.0 t 6841.0 9265.0 2079.0 388.0 459.0 289.0 18690.0 361.0 504.0 3467.0 6963.0 7226.0