One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_8nt_m12/peak-motifs_local_words_8nt_m12.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_m12/peak-motifs_local_words_8nt_m12_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_8nt_m12_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_8nt_m12_shift0 (local_words_8nt_m12local_words_8nt_m12)
; local_words_8nt_m12 (local_words_8nt_m12local_words_8nt_m12); m=0 (reference); ncol1=24; shift=0; ncol=24; ysaCAGCTGCAGCAGCTGyTGCys ; Alignment reference a 6 8 24 1 38 1 3 7 0 1 39 1 0 38 3 1 2 0 1 2 2 4 8 7 c 16 16 8 36 0 1 35 2 4 39 1 1 42 0 1 41 0 3 11 3 2 31 15 13 g 8 12 6 4 0 39 2 1 37 1 1 39 0 0 38 0 0 39 3 5 36 6 8 16 t 12 6 4 1 4 1 2 32 1 1 1 1 0 4 0 0 40 0 27 32 2 1 11 6

MA1485.1_shift8 (FERD3L)
; local_words_8nt_m12 versus MA1485.1 (FERD3L); m=1/3; ncol2=14; w=14; offset=8; strand=D; shift=8; score=0.474559; --------GyrmCAGCTGTyAC-- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0

MA0832.1_rc_shift8 (Tcf21_rc)
; local_words_8nt_m12 versus MA0832.1_rc (Tcf21_rc); m=2/3; ncol2=14; w=14; offset=8; strand=R; shift=8; score=0.461273; --------ryAACAGCTGTTry-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 60.0 19.0 171.0 171.0 0.0 171.0 1.0 2.0 0.0 0.0 0.0 3.0 46.0 17.0 0 0 c 0 0 0 0 0 0 0 0 32.0 80.0 0.0 20.0 171.0 0.0 1.0 171.0 0.0 0.0 0.0 23.0 22.0 70.0 0 0 g 0 0 0 0 0 0 0 0 49.0 23.0 23.0 4.0 0.0 0.0 171.0 0.0 1.0 171.0 10.0 1.0 76.0 29.0 0 0 t 0 0 0 0 0 0 0 0 30.0 50.0 5.0 0.0 0.0 0.0 0.0 0.0 171.0 0.0 171.0 171.0 28.0 55.0 0 0

MA0500.2_shift9 (MYOG)
; local_words_8nt_m12 versus MA0500.2 (MYOG); m=3/3; ncol2=12; w=12; offset=9; strand=D; shift=9; score=0.416147; ---------sarCAGCTGyts--- ; cor=; Ncor= a 0 0 0 0 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 c 0 0 0 0 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 g 0 0 0 0 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 t 0 0 0 0 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

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_8nt_m12_shift0 (local_words_8nt_m12local_words_8nt_m12)				; local_words_8nt_m12 (local_words_8nt_m12local_words_8nt_m12); m=0 (reference); ncol1=24; shift=0; ncol=24; ysaCAGCTGCAGCAGCTGyTGCys ; Alignment reference a 6 8 24 1 38 1 3 7 0 1 39 1 0 38 3 1 2 0 1 2 2 4 8 7 c 16 16 8 36 0 1 35 2 4 39 1 1 42 0 1 41 0 3 11 3 2 31 15 13 g 8 12 6 4 0 39 2 1 37 1 1 39 0 0 38 0 0 39 3 5 36 6 8 16 t 12 6 4 1 4 1 2 32 1 1 1 1 0 4 0 0 40 0 27 32 2 1 11 6
MA1485.1_shift8 (FERD3L)				; local_words_8nt_m12 versus MA1485.1 (FERD3L); m=1/3; ncol2=14; w=14; offset=8; strand=D; shift=8; score=0.474559; --------GyrmCAGCTGTyAC-- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0
MA0832.1_rc_shift8 (Tcf21_rc)				; local_words_8nt_m12 versus MA0832.1_rc (Tcf21_rc); m=2/3; ncol2=14; w=14; offset=8; strand=R; shift=8; score=0.461273; --------ryAACAGCTGTTry-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 60.0 19.0 171.0 171.0 0.0 171.0 1.0 2.0 0.0 0.0 0.0 3.0 46.0 17.0 0 0 c 0 0 0 0 0 0 0 0 32.0 80.0 0.0 20.0 171.0 0.0 1.0 171.0 0.0 0.0 0.0 23.0 22.0 70.0 0 0 g 0 0 0 0 0 0 0 0 49.0 23.0 23.0 4.0 0.0 0.0 171.0 0.0 1.0 171.0 10.0 1.0 76.0 29.0 0 0 t 0 0 0 0 0 0 0 0 30.0 50.0 5.0 0.0 0.0 0.0 0.0 0.0 171.0 0.0 171.0 171.0 28.0 55.0 0 0
MA0500.2_shift9 (MYOG)				; local_words_8nt_m12 versus MA0500.2 (MYOG); m=3/3; ncol2=12; w=12; offset=9; strand=D; shift=9; score=0.416147; ---------sarCAGCTGyts--- ; cor=; Ncor= a 0 0 0 0 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 c 0 0 0 0 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 g 0 0 0 0 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 t 0 0 0 0 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