One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/positions_8nt_m30/peak-motifs_positions_8nt_m30.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_8nt_m30/peak-motifs_positions_8nt_m30_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: positions_8nt_m30_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_8nt_m30_shift0 (positions_8nt_m30positions_8nt_m30)
; positions_8nt_m30 (positions_8nt_m30positions_8nt_m30); m=0 (reference); ncol1=23; shift=0; ncol=23; sstGCCAGCTGCAGCTGTCAsbr ; Alignment reference a 22 14 19 5 5 1 77 2 2 12 2 2 80 1 1 1 1 3 0 80 13 21 23 c 28 30 16 6 70 86 3 6 80 5 3 87 3 3 89 1 9 10 82 4 39 24 15 g 24 30 13 75 11 3 3 78 8 1 85 2 1 87 1 2 81 0 5 3 27 24 33 t 18 18 44 6 6 2 9 6 2 74 2 1 8 1 1 88 1 79 5 5 13 23 21

MA1485.1_shift7 (FERD3L)
; positions_8nt_m30 versus MA1485.1 (FERD3L); m=1/3; ncol2=14; w=14; offset=7; strand=D; shift=7; score=0.464287; -------GyrmCAGCTGTyAC-- ; cor=; Ncor= a 0 0 0 0 0 0 0 2158.0 450.0 14384.0 15390.0 36.0 29605.0 0.0 3649.0 81.0 0.0 1268.0 103.0 29605.0 0.0 0 0 c 0 0 0 0 0 0 0 68.0 20049.0 2443.0 9363.0 29605.0 126.0 841.0 29605.0 129.0 0.0 3878.0 8664.0 809.0 29605.0 0 0 g 0 0 0 0 0 0 0 29605.0 348.0 12703.0 3142.0 0.0 118.0 29605.0 471.0 210.0 29605.0 3395.0 5920.0 9815.0 0.0 0 0 t 0 0 0 0 0 0 0 225.0 9557.0 74.0 1710.0 0.0 144.0 4691.0 0.0 29605.0 0.0 21065.0 14919.0 958.0 48.0 0 0

MA0499.2_shift8 (MYOD1)
; positions_8nt_m30 versus MA0499.2 (MYOD1); m=2/3; ncol2=13; w=13; offset=8; strand=D; shift=8; score=0.444246; --------cwgCACCTGTymy-- ; cor=; Ncor= a 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 0 0 c 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 0 0 g 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 0 0 t 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 0 0

MA0521.1_rc_shift8 (Tcf12_rc)
; positions_8nt_m30 versus MA0521.1_rc (Tcf12_rc); m=3/3; ncol2=11; w=11; offset=8; strand=R; shift=8; score=0.413496; --------cwsCAGCTGYy---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2191.0 3642.0 1682.0 0.0 12895.0 0.0 0.0 0.0 0.0 0.0 17.0 0 0 0 0 c 0 0 0 0 0 0 0 0 4836.0 2925.0 3811.0 12895.0 0.0 1889.0 12887.0 0.0 0.0 3951.0 5123.0 0 0 0 0 g 0 0 0 0 0 0 0 0 3005.0 2416.0 5527.0 0.0 0.0 10822.0 0.0 0.0 12895.0 124.0 1585.0 0 0 0 0 t 0 0 0 0 0 0 0 0 2863.0 3912.0 1875.0 0.0 0.0 184.0 8.0 12895.0 0.0 8820.0 6170.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_8nt_m30_shift0 (positions_8nt_m30positions_8nt_m30)				; positions_8nt_m30 (positions_8nt_m30positions_8nt_m30); m=0 (reference); ncol1=23; shift=0; ncol=23; sstGCCAGCTGCAGCTGTCAsbr ; Alignment reference a 22 14 19 5 5 1 77 2 2 12 2 2 80 1 1 1 1 3 0 80 13 21 23 c 28 30 16 6 70 86 3 6 80 5 3 87 3 3 89 1 9 10 82 4 39 24 15 g 24 30 13 75 11 3 3 78 8 1 85 2 1 87 1 2 81 0 5 3 27 24 33 t 18 18 44 6 6 2 9 6 2 74 2 1 8 1 1 88 1 79 5 5 13 23 21
MA1485.1_shift7 (FERD3L)				; positions_8nt_m30 versus MA1485.1 (FERD3L); m=1/3; ncol2=14; w=14; offset=7; strand=D; shift=7; score=0.464287; -------GyrmCAGCTGTyAC-- ; cor=; Ncor= a 0 0 0 0 0 0 0 2158.0 450.0 14384.0 15390.0 36.0 29605.0 0.0 3649.0 81.0 0.0 1268.0 103.0 29605.0 0.0 0 0 c 0 0 0 0 0 0 0 68.0 20049.0 2443.0 9363.0 29605.0 126.0 841.0 29605.0 129.0 0.0 3878.0 8664.0 809.0 29605.0 0 0 g 0 0 0 0 0 0 0 29605.0 348.0 12703.0 3142.0 0.0 118.0 29605.0 471.0 210.0 29605.0 3395.0 5920.0 9815.0 0.0 0 0 t 0 0 0 0 0 0 0 225.0 9557.0 74.0 1710.0 0.0 144.0 4691.0 0.0 29605.0 0.0 21065.0 14919.0 958.0 48.0 0 0
MA0499.2_shift8 (MYOD1)				; positions_8nt_m30 versus MA0499.2 (MYOD1); m=2/3; ncol2=13; w=13; offset=8; strand=D; shift=8; score=0.444246; --------cwgCACCTGTymy-- ; cor=; Ncor= a 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 0 0 c 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 0 0 g 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 0 0 t 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 0 0
MA0521.1_rc_shift8 (Tcf12_rc)				; positions_8nt_m30 versus MA0521.1_rc (Tcf12_rc); m=3/3; ncol2=11; w=11; offset=8; strand=R; shift=8; score=0.413496; --------cwsCAGCTGYy---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 2191.0 3642.0 1682.0 0.0 12895.0 0.0 0.0 0.0 0.0 0.0 17.0 0 0 0 0 c 0 0 0 0 0 0 0 0 4836.0 2925.0 3811.0 12895.0 0.0 1889.0 12887.0 0.0 0.0 3951.0 5123.0 0 0 0 0 g 0 0 0 0 0 0 0 0 3005.0 2416.0 5527.0 0.0 0.0 10822.0 0.0 0.0 12895.0 124.0 1585.0 0 0 0 0 t 0 0 0 0 0 0 0 0 2863.0 3912.0 1875.0 0.0 0.0 184.0 8.0 12895.0 0.0 8820.0 6170.0 0 0 0 0