One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/oligos_8nt_mkv2_m19/peak-motifs_oligos_8nt_mkv2_m19.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_Rep3_motifs50/results/discovered_motifs/oligos_8nt_mkv2_m19/peak-motifs_oligos_8nt_mkv2_m19_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: oligos_8nt_mkv2_m19_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_8nt_mkv2_m19_shift2 (oligos_8nt_mkv2_m19oligos_8nt_mkv2_m19)
; oligos_8nt_mkv2_m19 (oligos_8nt_mkv2_m19oligos_8nt_mkv2_m19); m=0 (reference); ncol1=12; shift=2; ncol=14; --TMACTCACTCAy ; Alignment reference a 0 0 3 17 23 0 1 0 23 0 1 0 23 1 c 0 0 3 6 0 24 0 24 0 24 0 24 0 6 g 0 0 0 0 0 0 0 0 1 0 1 0 0 1 t 0 0 18 1 1 0 23 0 0 0 22 0 1 16

MA1523.1_shift0 (MSANTD3)
; oligos_8nt_mkv2_m19 versus MA1523.1 (MSANTD3); m=1/3; ncol2=10; w=8; offset=-2; strand=D; shift=0; score=0.474851; stmCACTCAm---- ; cor=; Ncor= a 98.0 111.0 332.0 64.0 980.0 31.0 37.0 47.0 775.0 271.0 0 0 0 0 c 269.0 211.0 272.0 723.0 0.0 896.0 7.0 862.0 140.0 568.0 0 0 0 0 g 515.0 220.0 249.0 31.0 2.0 27.0 0.0 29.0 24.0 63.0 0 0 0 0 t 117.0 456.0 145.0 180.0 16.0 45.0 954.0 60.0 59.0 96.0 0 0 0 0

MA0063.2_shift5 (NKX2-5)
; oligos_8nt_mkv2_m19 versus MA0063.2 (NKX2-5); m=2/3; ncol2=11; w=9; offset=3; strand=D; shift=5; score=0.457423; -----rmCACTCAA ; cor=; Ncor= a 0 0 0 0 0 1723.0 1526.0 96.0 5246.0 144.0 135.0 222.0 4819.0 4931.0 c 0 0 0 0 0 1024.0 1646.0 5002.0 48.0 5098.0 82.0 4319.0 120.0 165.0 g 0 0 0 0 0 1687.0 1318.0 24.0 76.0 49.0 61.0 62.0 217.0 98.0 t 0 0 0 0 0 1010.0 954.0 322.0 74.0 153.0 5166.0 841.0 288.0 250.0

MA0099.3_rc_shift0 (FOS::JUN_rc)
; oligos_8nt_mkv2_m19 versus MA0099.3_rc (FOS::JUN_rc); m=3/3; ncol2=10; w=8; offset=-2; strand=R; shift=0; score=0.40201; krTGACTCAy---- ; cor=; Ncor= a 162.0 568.0 4.0 4.0 991.0 54.0 45.0 168.0 990.0 40.0 0 0 0 0 c 164.0 95.0 2.0 3.0 2.0 688.0 4.0 824.0 2.0 257.0 0 0 0 0 g 397.0 313.0 2.0 963.0 2.0 180.0 131.0 1.0 5.0 111.0 0 0 0 0 t 277.0 24.0 992.0 30.0 5.0 78.0 820.0 7.0 3.0 592.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_8nt_mkv2_m19_shift2 (oligos_8nt_mkv2_m19oligos_8nt_mkv2_m19)				; oligos_8nt_mkv2_m19 (oligos_8nt_mkv2_m19oligos_8nt_mkv2_m19); m=0 (reference); ncol1=12; shift=2; ncol=14; --TMACTCACTCAy ; Alignment reference a 0 0 3 17 23 0 1 0 23 0 1 0 23 1 c 0 0 3 6 0 24 0 24 0 24 0 24 0 6 g 0 0 0 0 0 0 0 0 1 0 1 0 0 1 t 0 0 18 1 1 0 23 0 0 0 22 0 1 16
MA1523.1_shift0 (MSANTD3)				; oligos_8nt_mkv2_m19 versus MA1523.1 (MSANTD3); m=1/3; ncol2=10; w=8; offset=-2; strand=D; shift=0; score=0.474851; stmCACTCAm---- ; cor=; Ncor= a 98.0 111.0 332.0 64.0 980.0 31.0 37.0 47.0 775.0 271.0 0 0 0 0 c 269.0 211.0 272.0 723.0 0.0 896.0 7.0 862.0 140.0 568.0 0 0 0 0 g 515.0 220.0 249.0 31.0 2.0 27.0 0.0 29.0 24.0 63.0 0 0 0 0 t 117.0 456.0 145.0 180.0 16.0 45.0 954.0 60.0 59.0 96.0 0 0 0 0
MA0063.2_shift5 (NKX2-5)				; oligos_8nt_mkv2_m19 versus MA0063.2 (NKX2-5); m=2/3; ncol2=11; w=9; offset=3; strand=D; shift=5; score=0.457423; -----rmCACTCAA ; cor=; Ncor= a 0 0 0 0 0 1723.0 1526.0 96.0 5246.0 144.0 135.0 222.0 4819.0 4931.0 c 0 0 0 0 0 1024.0 1646.0 5002.0 48.0 5098.0 82.0 4319.0 120.0 165.0 g 0 0 0 0 0 1687.0 1318.0 24.0 76.0 49.0 61.0 62.0 217.0 98.0 t 0 0 0 0 0 1010.0 954.0 322.0 74.0 153.0 5166.0 841.0 288.0 250.0
MA0099.3_rc_shift0 (FOS::JUN_rc)				; oligos_8nt_mkv2_m19 versus MA0099.3_rc (FOS::JUN_rc); m=3/3; ncol2=10; w=8; offset=-2; strand=R; shift=0; score=0.40201; krTGACTCAy---- ; cor=; Ncor= a 162.0 568.0 4.0 4.0 991.0 54.0 45.0 168.0 990.0 40.0 0 0 0 0 c 164.0 95.0 2.0 3.0 2.0 688.0 4.0 824.0 2.0 257.0 0 0 0 0 g 397.0 313.0 2.0 963.0 2.0 180.0 131.0 1.0 5.0 111.0 0 0 0 0 t 277.0 24.0 992.0 30.0 5.0 78.0 820.0 7.0 3.0 592.0 0 0 0 0