One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/positions_6nt_m8/peak-motifs_positions_6nt_m8.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/positions_6nt_m8/peak-motifs_positions_6nt_m8_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: positions_6nt_m8_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m8_shift0 (positions_6nt_m8positions_6nt_m8)
; positions_6nt_m8 (positions_6nt_m8positions_6nt_m8); m=0 (reference); ncol1=23; shift=0; ncol=24; vsAGCTGGCAGCTGCACCTGcbm- ; Alignment reference a 11 8 30 1 3 2 2 4 2 35 3 1 1 0 5 30 0 0 0 0 1 5 12 0 c 10 17 2 6 31 4 3 4 36 0 0 38 0 0 31 1 33 36 2 2 24 10 15 0 g 10 10 4 30 2 2 34 28 1 1 36 0 0 39 1 2 4 0 0 35 8 14 9 0 t 8 4 3 2 3 31 0 3 0 3 0 0 38 0 2 6 2 3 37 2 6 10 3 0

MA0500.2_shift5 (MYOG)
; positions_6nt_m8 versus MA0500.2 (MYOG); m=1/3; ncol2=12; w=12; offset=5; strand=D; shift=5; score=0.423123; -----sarCAGCTGyts------- ; cor=; Ncor= a 0 0 0 0 0 5310.0 8428.0 7159.0 86.0 21782.0 95.0 167.0 163.0 182.0 1667.0 4667.0 5018.0 0 0 0 0 0 0 0 c 0 0 0 0 0 6381.0 3754.0 2730.0 21988.0 176.0 130.0 21964.0 238.0 102.0 10792.0 5497.0 5660.0 0 0 0 0 0 0 0 g 0 0 0 0 0 5596.0 5483.0 10790.0 101.0 236.0 21963.0 131.0 179.0 21985.0 2706.0 3718.0 6369.0 0 0 0 0 0 0 0 t 0 0 0 0 0 5070.0 4692.0 1678.0 182.0 163.0 169.0 95.0 21777.0 88.0 7192.0 8475.0 5310.0 0 0 0 0 0 0 0

MA0830.2_shift11 (TCF4)
; positions_6nt_m8 versus MA0830.2 (TCF4); m=2/3; ncol2=13; w=12; offset=11; strand=D; shift=11; score=0.417322; -----------cggCACCTGccss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 6048.0 7034.0 4168.0 243.0 27023.0 216.0 356.0 372.0 251.0 1694.0 5534.0 6413.0 5133.0 c 0 0 0 0 0 0 0 0 0 0 0 10052.0 6754.0 5062.0 28686.0 635.0 26765.0 27724.0 1016.0 540.0 18935.0 12872.0 8658.0 9843.0 g 0 0 0 0 0 0 0 0 0 0 0 7140.0 8618.0 18498.0 321.0 1295.0 1733.0 1197.0 679.0 28432.0 5281.0 4933.0 7964.0 7662.0 t 0 0 0 0 0 0 0 0 0 0 0 6225.0 7059.0 1737.0 215.0 512.0 751.0 188.0 27398.0 242.0 3555.0 6126.0 6430.0 6827.0

MA1631.1_shift11 (ASCL1(var.2))
; positions_6nt_m8 versus MA1631.1 (ASCL1(var.2)); m=3/3; ncol2=13; w=12; offset=11; strand=D; shift=11; score=0.408534; -----------cdgCACCTGCysc ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 6833.0 8952.0 5836.0 184.0 32315.0 163.0 196.0 368.0 251.0 399.0 4490.0 7083.0 5972.0 c 0 0 0 0 0 0 0 0 0 0 0 11805.0 7998.0 6654.0 33562.0 563.0 30169.0 33402.0 740.0 445.0 28844.0 17883.0 10555.0 11996.0 g 0 0 0 0 0 0 0 0 0 0 0 8371.0 8601.0 18576.0 321.0 860.0 3209.0 607.0 492.0 33411.0 2719.0 2966.0 8939.0 8356.0 t 0 0 0 0 0 0 0 0 0 0 0 7347.0 8805.0 3290.0 289.0 618.0 815.0 151.0 32756.0 249.0 2394.0 9017.0 7779.0 8032.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m8_shift0 (positions_6nt_m8positions_6nt_m8)				; positions_6nt_m8 (positions_6nt_m8positions_6nt_m8); m=0 (reference); ncol1=23; shift=0; ncol=24; vsAGCTGGCAGCTGCACCTGcbm- ; Alignment reference a 11 8 30 1 3 2 2 4 2 35 3 1 1 0 5 30 0 0 0 0 1 5 12 0 c 10 17 2 6 31 4 3 4 36 0 0 38 0 0 31 1 33 36 2 2 24 10 15 0 g 10 10 4 30 2 2 34 28 1 1 36 0 0 39 1 2 4 0 0 35 8 14 9 0 t 8 4 3 2 3 31 0 3 0 3 0 0 38 0 2 6 2 3 37 2 6 10 3 0
MA0500.2_shift5 (MYOG)				; positions_6nt_m8 versus MA0500.2 (MYOG); m=1/3; ncol2=12; w=12; offset=5; strand=D; shift=5; score=0.423123; -----sarCAGCTGyts------- ; cor=; Ncor= a 0 0 0 0 0 5310.0 8428.0 7159.0 86.0 21782.0 95.0 167.0 163.0 182.0 1667.0 4667.0 5018.0 0 0 0 0 0 0 0 c 0 0 0 0 0 6381.0 3754.0 2730.0 21988.0 176.0 130.0 21964.0 238.0 102.0 10792.0 5497.0 5660.0 0 0 0 0 0 0 0 g 0 0 0 0 0 5596.0 5483.0 10790.0 101.0 236.0 21963.0 131.0 179.0 21985.0 2706.0 3718.0 6369.0 0 0 0 0 0 0 0 t 0 0 0 0 0 5070.0 4692.0 1678.0 182.0 163.0 169.0 95.0 21777.0 88.0 7192.0 8475.0 5310.0 0 0 0 0 0 0 0
MA0830.2_shift11 (TCF4)				; positions_6nt_m8 versus MA0830.2 (TCF4); m=2/3; ncol2=13; w=12; offset=11; strand=D; shift=11; score=0.417322; -----------cggCACCTGccss ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 6048.0 7034.0 4168.0 243.0 27023.0 216.0 356.0 372.0 251.0 1694.0 5534.0 6413.0 5133.0 c 0 0 0 0 0 0 0 0 0 0 0 10052.0 6754.0 5062.0 28686.0 635.0 26765.0 27724.0 1016.0 540.0 18935.0 12872.0 8658.0 9843.0 g 0 0 0 0 0 0 0 0 0 0 0 7140.0 8618.0 18498.0 321.0 1295.0 1733.0 1197.0 679.0 28432.0 5281.0 4933.0 7964.0 7662.0 t 0 0 0 0 0 0 0 0 0 0 0 6225.0 7059.0 1737.0 215.0 512.0 751.0 188.0 27398.0 242.0 3555.0 6126.0 6430.0 6827.0
MA1631.1_shift11 (ASCL1(var.2))				; positions_6nt_m8 versus MA1631.1 (ASCL1(var.2)); m=3/3; ncol2=13; w=12; offset=11; strand=D; shift=11; score=0.408534; -----------cdgCACCTGCysc ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 6833.0 8952.0 5836.0 184.0 32315.0 163.0 196.0 368.0 251.0 399.0 4490.0 7083.0 5972.0 c 0 0 0 0 0 0 0 0 0 0 0 11805.0 7998.0 6654.0 33562.0 563.0 30169.0 33402.0 740.0 445.0 28844.0 17883.0 10555.0 11996.0 g 0 0 0 0 0 0 0 0 0 0 0 8371.0 8601.0 18576.0 321.0 860.0 3209.0 607.0 492.0 33411.0 2719.0 2966.0 8939.0 8356.0 t 0 0 0 0 0 0 0 0 0 0 0 7347.0 8805.0 3290.0 289.0 618.0 815.0 151.0 32756.0 249.0 2394.0 9017.0 7779.0 8032.0