One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_7nt_mkv4_m38/peak-motifs_oligos_7nt_mkv4_m38.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_Rep2_motifs50/results/discovered_motifs/oligos_7nt_mkv4_m38/peak-motifs_oligos_7nt_mkv4_m38_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m38_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m38_shift2 (oligos_7nt_mkv4_m38oligos_7nt_mkv4_m38)
; oligos_7nt_mkv4_m38 (oligos_7nt_mkv4_m38oligos_7nt_mkv4_m38); m=0 (reference); ncol1=12; shift=2; ncol=14; --ssGCGCtCGCss ; Alignment reference a 0 0 37 33 6 4 3 6 16 0 1 4 46 31 c 0 0 113 129 12 264 11 259 41 270 12 255 73 106 g 0 0 91 71 241 8 260 6 66 4 254 13 97 96 t 0 0 36 44 18 1 3 6 154 3 10 5 61 44

MA0506.1_rc_shift3 (NRF1_rc)
; oligos_7nt_mkv4_m38 versus MA0506.1_rc (NRF1_rc); m=1/3; ncol2=11; w=11; offset=1; strand=R; shift=3; score=0.684957; ---yGCGCAkGCGC ; cor=; Ncor= a 0 0 0 0.0 0.0 0.0 286.0 0.0 3693.0 313.0 140.0 0.0 0.0 0.0 c 0 0 0 1575.0 0.0 4275.0 0.0 4624.0 528.0 935.0 468.0 4239.0 0.0 3647.0 g 0 0 0 804.0 4550.0 349.0 4338.0 0.0 403.0 1862.0 4016.0 189.0 4001.0 375.0 t 0 0 0 2245.0 74.0 0.0 0.0 0.0 0.0 1514.0 0.0 196.0 623.0 602.0

MA0632.2_shift4 (TCFL5)
; oligos_7nt_mkv4_m38 versus MA0632.2 (TCFL5); m=2/3; ncol2=10; w=10; offset=2; strand=D; shift=4; score=0.587505; ----kCrCGCGCmc ; cor=; Ncor= a 0 0 0 0 2810.0 0.0 72543.0 0.0 1566.0 1765.0 3520.0 1593.0 72543.0 10588.0 c 0 0 0 0 10582.0 72543.0 0.0 72543.0 0.0 57092.0 657.0 72543.0 44394.0 47538.0 g 0 0 0 0 22297.0 0.0 29710.0 0.0 72543.0 0.0 72543.0 4594.0 19096.0 5747.0 t 0 0 0 0 36854.0 0.0 9359.0 1643.0 0.0 15451.0 0.0 635.0 25921.0 8670.0

MA1650.1_shift0 (ZBTB14)
; oligos_7nt_mkv4_m38 versus MA1650.1 (ZBTB14); m=3/3; ncol2=12; w=10; offset=-2; strand=D; shift=0; score=0.514381; ssCCGCGCACss-- ; cor=; Ncor= a 570.0 501.0 335.0 41.0 93.0 68.0 132.0 56.0 4500.0 99.0 970.0 442.0 0 0 c 1779.0 1972.0 3525.0 4292.0 294.0 4078.0 305.0 4178.0 37.0 3674.0 1618.0 2260.0 0 0 g 1668.0 1555.0 614.0 155.0 4098.0 319.0 4043.0 261.0 10.0 651.0 1451.0 1239.0 0 0 t 530.0 519.0 73.0 59.0 62.0 82.0 67.0 52.0 0.0 123.0 508.0 606.0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m38_shift2 (oligos_7nt_mkv4_m38oligos_7nt_mkv4_m38)				; oligos_7nt_mkv4_m38 (oligos_7nt_mkv4_m38oligos_7nt_mkv4_m38); m=0 (reference); ncol1=12; shift=2; ncol=14; --ssGCGCtCGCss ; Alignment reference a 0 0 37 33 6 4 3 6 16 0 1 4 46 31 c 0 0 113 129 12 264 11 259 41 270 12 255 73 106 g 0 0 91 71 241 8 260 6 66 4 254 13 97 96 t 0 0 36 44 18 1 3 6 154 3 10 5 61 44
MA0506.1_rc_shift3 (NRF1_rc)				; oligos_7nt_mkv4_m38 versus MA0506.1_rc (NRF1_rc); m=1/3; ncol2=11; w=11; offset=1; strand=R; shift=3; score=0.684957; ---yGCGCAkGCGC ; cor=; Ncor= a 0 0 0 0.0 0.0 0.0 286.0 0.0 3693.0 313.0 140.0 0.0 0.0 0.0 c 0 0 0 1575.0 0.0 4275.0 0.0 4624.0 528.0 935.0 468.0 4239.0 0.0 3647.0 g 0 0 0 804.0 4550.0 349.0 4338.0 0.0 403.0 1862.0 4016.0 189.0 4001.0 375.0 t 0 0 0 2245.0 74.0 0.0 0.0 0.0 0.0 1514.0 0.0 196.0 623.0 602.0
MA0632.2_shift4 (TCFL5)				; oligos_7nt_mkv4_m38 versus MA0632.2 (TCFL5); m=2/3; ncol2=10; w=10; offset=2; strand=D; shift=4; score=0.587505; ----kCrCGCGCmc ; cor=; Ncor= a 0 0 0 0 2810.0 0.0 72543.0 0.0 1566.0 1765.0 3520.0 1593.0 72543.0 10588.0 c 0 0 0 0 10582.0 72543.0 0.0 72543.0 0.0 57092.0 657.0 72543.0 44394.0 47538.0 g 0 0 0 0 22297.0 0.0 29710.0 0.0 72543.0 0.0 72543.0 4594.0 19096.0 5747.0 t 0 0 0 0 36854.0 0.0 9359.0 1643.0 0.0 15451.0 0.0 635.0 25921.0 8670.0
MA1650.1_shift0 (ZBTB14)				; oligos_7nt_mkv4_m38 versus MA1650.1 (ZBTB14); m=3/3; ncol2=12; w=10; offset=-2; strand=D; shift=0; score=0.514381; ssCCGCGCACss-- ; cor=; Ncor= a 570.0 501.0 335.0 41.0 93.0 68.0 132.0 56.0 4500.0 99.0 970.0 442.0 0 0 c 1779.0 1972.0 3525.0 4292.0 294.0 4078.0 305.0 4178.0 37.0 3674.0 1618.0 2260.0 0 0 g 1668.0 1555.0 614.0 155.0 4098.0 319.0 4043.0 261.0 10.0 651.0 1451.0 1239.0 0 0 t 530.0 519.0 73.0 59.0 62.0 82.0 67.0 52.0 0.0 123.0 508.0 606.0 0 0