One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_8nt_m44/peak-motifs_local_words_8nt_m44.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/local_words_8nt_m44/peak-motifs_local_words_8nt_m44_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_8nt_m44_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_8nt_m44_shift0 (local_words_8nt_m44local_words_8nt_m44)
; local_words_8nt_m44 (local_words_8nt_m44local_words_8nt_m44); m=0 (reference); ncol1=24; shift=0; ncol=24; stGACAGCTGCAGCAGCTGTyass ; Alignment reference a 5 6 1 27 0 30 1 2 6 1 0 28 1 0 28 1 2 1 0 0 2 22 4 6 c 12 7 3 2 33 2 1 32 0 0 35 1 0 33 0 1 32 0 2 6 10 2 13 9 g 14 8 31 5 1 1 33 0 1 32 0 1 34 1 0 33 0 2 32 2 8 7 12 13 t 4 14 0 1 1 2 0 1 28 2 0 5 0 1 7 0 1 32 1 27 15 4 6 7

MA1485.1_shift9 (FERD3L)
; local_words_8nt_m44 versus MA1485.1 (FERD3L); m=1/4; ncol2=14; w=14; offset=9; strand=D; shift=9; score=0.481491; ---------GyrmCAGCTGTyAC- ; cor=; Ncor= a 0 0 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 c 0 0 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 g 0 0 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 t 0 0 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

MA0832.1_shift9 (Tcf21)
; local_words_8nt_m44 versus MA0832.1 (Tcf21); m=2/4; ncol2=14; w=14; offset=9; strand=D; shift=9; score=0.440904; ---------ryAACAGCTGTTry- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 55.0 28.0 171.0 171.0 0.0 171.0 0.0 0.0 0.0 0.0 0.0 5.0 50.0 30.0 0 c 0 0 0 0 0 0 0 0 0 29.0 76.0 1.0 10.0 171.0 1.0 0.0 171.0 0.0 0.0 4.0 23.0 23.0 49.0 0 g 0 0 0 0 0 0 0 0 0 70.0 22.0 23.0 0.0 0.0 0.0 171.0 1.0 0.0 171.0 20.0 0.0 80.0 32.0 0 t 0 0 0 0 0 0 0 0 0 17.0 46.0 3.0 0.0 0.0 0.0 2.0 1.0 171.0 0.0 171.0 171.0 19.0 60.0 0

MA0499.2_rc_shift0 (MYOD1_rc)
; local_words_8nt_m44 versus MA0499.2_rc (MYOD1_rc); m=3/4; ncol2=13; w=13; offset=0; strand=R; shift=0; score=0.423618; rkrACAGGTGcwg----------- ; cor=; Ncor= a 9358.0 8151.0 9000.0 29644.0 238.0 33130.0 330.0 1226.0 587.0 269.0 2245.0 9291.0 7728.0 0 0 0 0 0 0 0 0 0 0 0 c 7495.0 6202.0 4440.0 1699.0 33468.0 366.0 932.0 7336.0 849.0 354.0 21884.0 8444.0 8118.0 0 0 0 0 0 0 0 0 0 0 0 g 11760.0 10485.0 19052.0 2555.0 386.0 563.0 32504.0 25275.0 583.0 33328.0 5622.0 7103.0 11279.0 0 0 0 0 0 0 0 0 0 0 0 t 5687.0 9462.0 1808.0 402.0 208.0 241.0 534.0 463.0 32281.0 349.0 4549.0 9462.0 7175.0 0 0 0 0 0 0 0 0 0 0 0

MA0500.2_rc_shift10 (MYOG_rc)
; local_words_8nt_m44 versus MA0500.2_rc (MYOG_rc); m=4/4; ncol2=12; w=12; offset=10; strand=R; shift=10; score=0.412069; ----------sarCAGCTGyts-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 5310.0 8475.0 7192.0 88.0 21777.0 95.0 169.0 163.0 182.0 1678.0 4692.0 5070.0 0 0 c 0 0 0 0 0 0 0 0 0 0 6369.0 3718.0 2706.0 21985.0 179.0 131.0 21963.0 236.0 101.0 10790.0 5483.0 5596.0 0 0 g 0 0 0 0 0 0 0 0 0 0 5660.0 5497.0 10792.0 102.0 238.0 21964.0 130.0 176.0 21988.0 2730.0 3754.0 6381.0 0 0 t 0 0 0 0 0 0 0 0 0 0 5018.0 4667.0 1667.0 182.0 163.0 167.0 95.0 21782.0 86.0 7159.0 8428.0 5310.0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_8nt_m44_shift0 (local_words_8nt_m44local_words_8nt_m44)				; local_words_8nt_m44 (local_words_8nt_m44local_words_8nt_m44); m=0 (reference); ncol1=24; shift=0; ncol=24; stGACAGCTGCAGCAGCTGTyass ; Alignment reference a 5 6 1 27 0 30 1 2 6 1 0 28 1 0 28 1 2 1 0 0 2 22 4 6 c 12 7 3 2 33 2 1 32 0 0 35 1 0 33 0 1 32 0 2 6 10 2 13 9 g 14 8 31 5 1 1 33 0 1 32 0 1 34 1 0 33 0 2 32 2 8 7 12 13 t 4 14 0 1 1 2 0 1 28 2 0 5 0 1 7 0 1 32 1 27 15 4 6 7
MA1485.1_shift9 (FERD3L)				; local_words_8nt_m44 versus MA1485.1 (FERD3L); m=1/4; ncol2=14; w=14; offset=9; strand=D; shift=9; score=0.481491; ---------GyrmCAGCTGTyAC- ; cor=; Ncor= a 0 0 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 c 0 0 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 g 0 0 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 t 0 0 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
MA0832.1_shift9 (Tcf21)				; local_words_8nt_m44 versus MA0832.1 (Tcf21); m=2/4; ncol2=14; w=14; offset=9; strand=D; shift=9; score=0.440904; ---------ryAACAGCTGTTry- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 55.0 28.0 171.0 171.0 0.0 171.0 0.0 0.0 0.0 0.0 0.0 5.0 50.0 30.0 0 c 0 0 0 0 0 0 0 0 0 29.0 76.0 1.0 10.0 171.0 1.0 0.0 171.0 0.0 0.0 4.0 23.0 23.0 49.0 0 g 0 0 0 0 0 0 0 0 0 70.0 22.0 23.0 0.0 0.0 0.0 171.0 1.0 0.0 171.0 20.0 0.0 80.0 32.0 0 t 0 0 0 0 0 0 0 0 0 17.0 46.0 3.0 0.0 0.0 0.0 2.0 1.0 171.0 0.0 171.0 171.0 19.0 60.0 0
MA0499.2_rc_shift0 (MYOD1_rc)				; local_words_8nt_m44 versus MA0499.2_rc (MYOD1_rc); m=3/4; ncol2=13; w=13; offset=0; strand=R; shift=0; score=0.423618; rkrACAGGTGcwg----------- ; cor=; Ncor= a 9358.0 8151.0 9000.0 29644.0 238.0 33130.0 330.0 1226.0 587.0 269.0 2245.0 9291.0 7728.0 0 0 0 0 0 0 0 0 0 0 0 c 7495.0 6202.0 4440.0 1699.0 33468.0 366.0 932.0 7336.0 849.0 354.0 21884.0 8444.0 8118.0 0 0 0 0 0 0 0 0 0 0 0 g 11760.0 10485.0 19052.0 2555.0 386.0 563.0 32504.0 25275.0 583.0 33328.0 5622.0 7103.0 11279.0 0 0 0 0 0 0 0 0 0 0 0 t 5687.0 9462.0 1808.0 402.0 208.0 241.0 534.0 463.0 32281.0 349.0 4549.0 9462.0 7175.0 0 0 0 0 0 0 0 0 0 0 0
MA0500.2_rc_shift10 (MYOG_rc)				; local_words_8nt_m44 versus MA0500.2_rc (MYOG_rc); m=4/4; ncol2=12; w=12; offset=10; strand=R; shift=10; score=0.412069; ----------sarCAGCTGyts-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 5310.0 8475.0 7192.0 88.0 21777.0 95.0 169.0 163.0 182.0 1678.0 4692.0 5070.0 0 0 c 0 0 0 0 0 0 0 0 0 0 6369.0 3718.0 2706.0 21985.0 179.0 131.0 21963.0 236.0 101.0 10790.0 5483.0 5596.0 0 0 g 0 0 0 0 0 0 0 0 0 0 5660.0 5497.0 10792.0 102.0 238.0 21964.0 130.0 176.0 21988.0 2730.0 3754.0 6381.0 0 0 t 0 0 0 0 0 0 0 0 0 0 5018.0 4667.0 1667.0 182.0 163.0 167.0 95.0 21782.0 86.0 7159.0 8428.0 5310.0 0 0