One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.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_m1/peak-motifs_positions_6nt_m1_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1positions_6nt_m1)
; positions_6nt_m1 (positions_6nt_m1positions_6nt_m1); m=0 (reference); ncol1=23; shift=0; ncol=24; ksAGCTGGCAGCTGCACCTGtbc- ; Alignment reference a 9 9 34 0 1 1 0 4 2 39 1 2 2 0 6 36 4 1 1 1 1 5 10 0 c 9 20 2 5 37 5 2 6 40 1 1 41 0 1 32 2 35 37 3 2 8 13 20 0 g 13 13 2 38 1 0 42 30 2 1 42 0 1 42 2 1 3 2 1 40 8 12 8 0 t 13 2 6 1 5 38 0 4 0 3 0 1 41 1 4 5 2 4 39 1 27 14 6 0

MA0499.2_shift11 (MYOD1)
; positions_6nt_m1 versus MA0499.2 (MYOD1); m=1/4; ncol2=13; w=12; offset=11; strand=D; shift=11; score=0.415738; -----------cwgCACCTGTymy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 7175.0 9462.0 4549.0 349.0 32281.0 463.0 534.0 241.0 208.0 402.0 1808.0 9462.0 5687.0 c 0 0 0 0 0 0 0 0 0 0 0 11279.0 7103.0 5622.0 33328.0 583.0 25275.0 32504.0 563.0 386.0 2555.0 19052.0 10485.0 11760.0 g 0 0 0 0 0 0 0 0 0 0 0 8118.0 8444.0 21884.0 354.0 849.0 7336.0 932.0 366.0 33468.0 1699.0 4440.0 6202.0 7495.0 t 0 0 0 0 0 0 0 0 0 0 0 7728.0 9291.0 2245.0 269.0 587.0 1226.0 330.0 33130.0 238.0 29644.0 9000.0 8151.0 9358.0

MA0500.2_shift5 (MYOG)
; positions_6nt_m1 versus MA0500.2 (MYOG); m=2/4; ncol2=12; w=12; offset=5; strand=D; shift=5; score=0.411173; -----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

MA0745.2_shift11 (SNAI2)
; positions_6nt_m1 versus MA0745.2 (SNAI2); m=3/4; ncol2=13; w=12; offset=11; strand=D; shift=11; score=0.411062; -----------aygCACCTGTmry ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 14658.0 7668.0 10322.0 408.0 44963.0 112.0 246.0 78.0 179.0 814.0 12017.0 13586.0 6215.0 c 0 0 0 0 0 0 0 0 0 0 0 10031.0 12314.0 6393.0 44463.0 202.0 45144.0 44739.0 313.0 254.0 6467.0 18771.0 11016.0 13476.0 g 0 0 0 0 0 0 0 0 0 0 0 11169.0 9490.0 26742.0 323.0 424.0 326.0 487.0 196.0 45257.0 1263.0 6281.0 12297.0 8219.0 t 0 0 0 0 0 0 0 0 0 0 0 9958.0 16344.0 2359.0 622.0 227.0 234.0 344.0 45229.0 126.0 37272.0 8747.0 8917.0 17906.0

MA1559.1_rc_shift12 (SNAI3_rc)
; positions_6nt_m1 versus MA1559.1_rc (SNAI3_rc); m=4/4; ncol2=10; w=10; offset=12; strand=R; shift=12; score=0.40009; ------------trCACCTGyt-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 553.0 3161.0 30.0 6248.0 0.0 43.0 3.0 35.0 183.0 1110.0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 1569.0 1701.0 6248.0 28.0 6248.0 6248.0 34.0 0.0 2331.0 1525.0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 688.0 6248.0 0.0 12.0 18.0 29.0 0.0 6248.0 0.0 661.0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 4680.0 432.0 94.0 0.0 0.0 118.0 6248.0 23.0 3917.0 2952.0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1positions_6nt_m1)				; positions_6nt_m1 (positions_6nt_m1positions_6nt_m1); m=0 (reference); ncol1=23; shift=0; ncol=24; ksAGCTGGCAGCTGCACCTGtbc- ; Alignment reference a 9 9 34 0 1 1 0 4 2 39 1 2 2 0 6 36 4 1 1 1 1 5 10 0 c 9 20 2 5 37 5 2 6 40 1 1 41 0 1 32 2 35 37 3 2 8 13 20 0 g 13 13 2 38 1 0 42 30 2 1 42 0 1 42 2 1 3 2 1 40 8 12 8 0 t 13 2 6 1 5 38 0 4 0 3 0 1 41 1 4 5 2 4 39 1 27 14 6 0
MA0499.2_shift11 (MYOD1)				; positions_6nt_m1 versus MA0499.2 (MYOD1); m=1/4; ncol2=13; w=12; offset=11; strand=D; shift=11; score=0.415738; -----------cwgCACCTGTymy ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 7175.0 9462.0 4549.0 349.0 32281.0 463.0 534.0 241.0 208.0 402.0 1808.0 9462.0 5687.0 c 0 0 0 0 0 0 0 0 0 0 0 11279.0 7103.0 5622.0 33328.0 583.0 25275.0 32504.0 563.0 386.0 2555.0 19052.0 10485.0 11760.0 g 0 0 0 0 0 0 0 0 0 0 0 8118.0 8444.0 21884.0 354.0 849.0 7336.0 932.0 366.0 33468.0 1699.0 4440.0 6202.0 7495.0 t 0 0 0 0 0 0 0 0 0 0 0 7728.0 9291.0 2245.0 269.0 587.0 1226.0 330.0 33130.0 238.0 29644.0 9000.0 8151.0 9358.0
MA0500.2_shift5 (MYOG)				; positions_6nt_m1 versus MA0500.2 (MYOG); m=2/4; ncol2=12; w=12; offset=5; strand=D; shift=5; score=0.411173; -----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
MA0745.2_shift11 (SNAI2)				; positions_6nt_m1 versus MA0745.2 (SNAI2); m=3/4; ncol2=13; w=12; offset=11; strand=D; shift=11; score=0.411062; -----------aygCACCTGTmry ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 14658.0 7668.0 10322.0 408.0 44963.0 112.0 246.0 78.0 179.0 814.0 12017.0 13586.0 6215.0 c 0 0 0 0 0 0 0 0 0 0 0 10031.0 12314.0 6393.0 44463.0 202.0 45144.0 44739.0 313.0 254.0 6467.0 18771.0 11016.0 13476.0 g 0 0 0 0 0 0 0 0 0 0 0 11169.0 9490.0 26742.0 323.0 424.0 326.0 487.0 196.0 45257.0 1263.0 6281.0 12297.0 8219.0 t 0 0 0 0 0 0 0 0 0 0 0 9958.0 16344.0 2359.0 622.0 227.0 234.0 344.0 45229.0 126.0 37272.0 8747.0 8917.0 17906.0
MA1559.1_rc_shift12 (SNAI3_rc)				; positions_6nt_m1 versus MA1559.1_rc (SNAI3_rc); m=4/4; ncol2=10; w=10; offset=12; strand=R; shift=12; score=0.40009; ------------trCACCTGyt-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 553.0 3161.0 30.0 6248.0 0.0 43.0 3.0 35.0 183.0 1110.0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 0 1569.0 1701.0 6248.0 28.0 6248.0 6248.0 34.0 0.0 2331.0 1525.0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 688.0 6248.0 0.0 12.0 18.0 29.0 0.0 6248.0 0.0 661.0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 4680.0 432.0 94.0 0.0 0.0 118.0 6248.0 23.0 3917.0 2952.0 0 0