One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_8nt_m4/peak-motifs_local_words_8nt_m4.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_m4/peak-motifs_local_words_8nt_m4_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_8nt_m4_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_8nt_m4_shift0 (local_words_8nt_m4local_words_8nt_m4)
; local_words_8nt_m4 (local_words_8nt_m4local_words_8nt_m4); m=0 (reference); ncol1=24; shift=0; ncol=24; srggCACAGCTGCTGCAGCTGTsg ; Alignment reference a 9 17 7 3 1 45 1 52 0 1 6 3 3 5 2 1 48 2 0 4 0 2 3 12 c 19 12 8 14 46 4 55 3 2 56 1 2 52 3 2 51 3 1 54 1 4 7 27 10 g 23 15 35 29 10 5 2 0 52 0 2 52 2 0 53 3 1 54 2 1 53 9 20 24 t 7 14 8 12 1 4 0 3 4 1 49 1 1 50 1 3 6 1 2 52 1 40 8 12

MA1485.1_rc_shift2 (FERD3L_rc)
; local_words_8nt_m4 versus MA1485.1_rc (FERD3L_rc); m=1/3; ncol2=14; w=14; offset=2; strand=R; shift=2; score=0.460608; --GTrACAGCTGkyrC-------- ; cor=; Ncor= a 0 0 48.0 958.0 14919.0 21065.0 0.0 29605.0 0.0 4691.0 144.0 0.0 1710.0 74.0 9557.0 225.0 0 0 0 0 0 0 0 0 c 0 0 0.0 9815.0 5920.0 3395.0 29605.0 210.0 471.0 29605.0 118.0 0.0 3142.0 12703.0 348.0 29605.0 0 0 0 0 0 0 0 0 g 0 0 29605.0 809.0 8664.0 3878.0 0.0 129.0 29605.0 841.0 126.0 29605.0 9363.0 2443.0 20049.0 68.0 0 0 0 0 0 0 0 0 t 0 0 0.0 29605.0 103.0 1268.0 0.0 81.0 3649.0 0.0 29605.0 36.0 15390.0 14384.0 450.0 2158.0 0 0 0 0 0 0 0 0

MA0832.1_shift2 (Tcf21)
; local_words_8nt_m4 versus MA0832.1 (Tcf21); m=2/3; ncol2=14; w=14; offset=2; strand=D; shift=2; score=0.409979; --ryAACAGCTGTTry-------- ; cor=; Ncor= a 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 0 0 0 0 0 0 0 c 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 0 0 0 0 0 0 0 g 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 0 0 0 0 0 0 0 t 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 0 0 0 0 0 0 0

MA0500.2_shift12 (MYOG)
; local_words_8nt_m4 versus MA0500.2 (MYOG); m=3/3; ncol2=12; w=12; offset=12; strand=D; shift=12; score=0.406568; ------------sarCAGCTGyts ; cor=; Ncor= a 0 0 0 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 c 0 0 0 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 g 0 0 0 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 t 0 0 0 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

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_8nt_m4_shift0 (local_words_8nt_m4local_words_8nt_m4)				; local_words_8nt_m4 (local_words_8nt_m4local_words_8nt_m4); m=0 (reference); ncol1=24; shift=0; ncol=24; srggCACAGCTGCTGCAGCTGTsg ; Alignment reference a 9 17 7 3 1 45 1 52 0 1 6 3 3 5 2 1 48 2 0 4 0 2 3 12 c 19 12 8 14 46 4 55 3 2 56 1 2 52 3 2 51 3 1 54 1 4 7 27 10 g 23 15 35 29 10 5 2 0 52 0 2 52 2 0 53 3 1 54 2 1 53 9 20 24 t 7 14 8 12 1 4 0 3 4 1 49 1 1 50 1 3 6 1 2 52 1 40 8 12
MA1485.1_rc_shift2 (FERD3L_rc)				; local_words_8nt_m4 versus MA1485.1_rc (FERD3L_rc); m=1/3; ncol2=14; w=14; offset=2; strand=R; shift=2; score=0.460608; --GTrACAGCTGkyrC-------- ; cor=; Ncor= a 0 0 48.0 958.0 14919.0 21065.0 0.0 29605.0 0.0 4691.0 144.0 0.0 1710.0 74.0 9557.0 225.0 0 0 0 0 0 0 0 0 c 0 0 0.0 9815.0 5920.0 3395.0 29605.0 210.0 471.0 29605.0 118.0 0.0 3142.0 12703.0 348.0 29605.0 0 0 0 0 0 0 0 0 g 0 0 29605.0 809.0 8664.0 3878.0 0.0 129.0 29605.0 841.0 126.0 29605.0 9363.0 2443.0 20049.0 68.0 0 0 0 0 0 0 0 0 t 0 0 0.0 29605.0 103.0 1268.0 0.0 81.0 3649.0 0.0 29605.0 36.0 15390.0 14384.0 450.0 2158.0 0 0 0 0 0 0 0 0
MA0832.1_shift2 (Tcf21)				; local_words_8nt_m4 versus MA0832.1 (Tcf21); m=2/3; ncol2=14; w=14; offset=2; strand=D; shift=2; score=0.409979; --ryAACAGCTGTTry-------- ; cor=; Ncor= a 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 0 0 0 0 0 0 0 c 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 0 0 0 0 0 0 0 g 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 0 0 0 0 0 0 0 t 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 0 0 0 0 0 0 0
MA0500.2_shift12 (MYOG)				; local_words_8nt_m4 versus MA0500.2 (MYOG); m=3/3; ncol2=12; w=12; offset=12; strand=D; shift=12; score=0.406568; ------------sarCAGCTGyts ; cor=; Ncor= a 0 0 0 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 c 0 0 0 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 g 0 0 0 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 t 0 0 0 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