One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_6nt_m48/peak-motifs_local_words_6nt_m48.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_6nt_m48/peak-motifs_local_words_6nt_m48_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_6nt_m48_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_6nt_m48_shift0 (local_words_6nt_m48local_words_6nt_m48)
; local_words_6nt_m48 (local_words_6nt_m48local_words_6nt_m48); m=0 (reference); ncol1=24; shift=0; ncol=24; ccrCAGCwGCCACAGCTGyCACmg ; Alignment reference a 8 15 24 4 66 5 4 46 1 3 9 56 0 73 1 1 4 1 0 0 61 6 32 15 c 39 29 8 63 5 1 67 4 4 67 58 3 72 1 1 71 3 0 28 72 5 52 22 16 g 13 14 40 7 1 66 2 2 69 2 1 14 1 0 71 1 2 73 1 1 2 9 8 36 t 14 16 2 0 2 2 1 22 0 2 6 1 1 0 1 1 65 0 45 1 6 7 12 7

MA1485.1_shift8 (FERD3L)
; local_words_6nt_m48 versus MA1485.1 (FERD3L); m=1/4; ncol2=14; w=14; offset=8; strand=D; shift=8; score=0.496399; --------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

MA1641.1_shift9 (MYF5)
; local_words_6nt_m48 versus MA1641.1 (MYF5); m=2/4; ncol2=12; w=12; offset=9; strand=D; shift=9; score=0.410377; ---------gvaCAGCTGtbc--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2698.0 3507.0 7490.0 95.0 10965.0 100.0 223.0 129.0 42.0 578.0 1572.0 2554.0 0 0 0 c 0 0 0 0 0 0 0 0 0 2700.0 2986.0 1368.0 10911.0 47.0 230.0 10657.0 68.0 161.0 1775.0 3146.0 3258.0 0 0 0 g 0 0 0 0 0 0 0 0 0 3258.0 3145.0 1774.0 161.0 69.0 10658.0 230.0 47.0 10912.0 1368.0 2985.0 2701.0 0 0 0 t 0 0 0 0 0 0 0 0 0 2554.0 1572.0 578.0 43.0 129.0 222.0 100.0 10966.0 95.0 7489.0 3507.0 2697.0 0 0 0

MA1619.1_shift9 (Ptf1a(var.2))
; local_words_6nt_m48 versus MA1619.1 (Ptf1a(var.2)); m=3/4; ncol2=12; w=12; offset=9; strand=D; shift=9; score=0.409384; ---------rmaCAGCTGtky--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1869.0 1978.0 4346.0 49.0 7119.0 34.0 224.0 26.0 27.0 535.0 1221.0 1602.0 0 0 0 c 0 0 0 0 0 0 0 0 0 1803.0 2430.0 1070.0 7149.0 41.0 307.0 6697.0 66.0 27.0 1312.0 1632.0 1977.0 0 0 0 g 0 0 0 0 0 0 0 0 0 1974.0 1629.0 1308.0 28.0 65.0 6689.0 299.0 40.0 7150.0 1065.0 2426.0 1803.0 0 0 0 t 0 0 0 0 0 0 0 0 0 1607.0 1216.0 529.0 27.0 28.0 223.0 33.0 7121.0 49.0 4341.0 1974.0 1871.0 0 0 0

MA0832.1_shift8 (Tcf21)
; local_words_6nt_m48 versus MA0832.1 (Tcf21); m=4/4; ncol2=14; w=14; offset=8; strand=D; shift=8; score=0.408678; --------ryAACAGCTGTTry-- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_6nt_m48_shift0 (local_words_6nt_m48local_words_6nt_m48)				; local_words_6nt_m48 (local_words_6nt_m48local_words_6nt_m48); m=0 (reference); ncol1=24; shift=0; ncol=24; ccrCAGCwGCCACAGCTGyCACmg ; Alignment reference a 8 15 24 4 66 5 4 46 1 3 9 56 0 73 1 1 4 1 0 0 61 6 32 15 c 39 29 8 63 5 1 67 4 4 67 58 3 72 1 1 71 3 0 28 72 5 52 22 16 g 13 14 40 7 1 66 2 2 69 2 1 14 1 0 71 1 2 73 1 1 2 9 8 36 t 14 16 2 0 2 2 1 22 0 2 6 1 1 0 1 1 65 0 45 1 6 7 12 7
MA1485.1_shift8 (FERD3L)				; local_words_6nt_m48 versus MA1485.1 (FERD3L); m=1/4; ncol2=14; w=14; offset=8; strand=D; shift=8; score=0.496399; --------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
MA1641.1_shift9 (MYF5)				; local_words_6nt_m48 versus MA1641.1 (MYF5); m=2/4; ncol2=12; w=12; offset=9; strand=D; shift=9; score=0.410377; ---------gvaCAGCTGtbc--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 2698.0 3507.0 7490.0 95.0 10965.0 100.0 223.0 129.0 42.0 578.0 1572.0 2554.0 0 0 0 c 0 0 0 0 0 0 0 0 0 2700.0 2986.0 1368.0 10911.0 47.0 230.0 10657.0 68.0 161.0 1775.0 3146.0 3258.0 0 0 0 g 0 0 0 0 0 0 0 0 0 3258.0 3145.0 1774.0 161.0 69.0 10658.0 230.0 47.0 10912.0 1368.0 2985.0 2701.0 0 0 0 t 0 0 0 0 0 0 0 0 0 2554.0 1572.0 578.0 43.0 129.0 222.0 100.0 10966.0 95.0 7489.0 3507.0 2697.0 0 0 0
MA1619.1_shift9 (Ptf1a(var.2))				; local_words_6nt_m48 versus MA1619.1 (Ptf1a(var.2)); m=3/4; ncol2=12; w=12; offset=9; strand=D; shift=9; score=0.409384; ---------rmaCAGCTGtky--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1869.0 1978.0 4346.0 49.0 7119.0 34.0 224.0 26.0 27.0 535.0 1221.0 1602.0 0 0 0 c 0 0 0 0 0 0 0 0 0 1803.0 2430.0 1070.0 7149.0 41.0 307.0 6697.0 66.0 27.0 1312.0 1632.0 1977.0 0 0 0 g 0 0 0 0 0 0 0 0 0 1974.0 1629.0 1308.0 28.0 65.0 6689.0 299.0 40.0 7150.0 1065.0 2426.0 1803.0 0 0 0 t 0 0 0 0 0 0 0 0 0 1607.0 1216.0 529.0 27.0 28.0 223.0 33.0 7121.0 49.0 4341.0 1974.0 1871.0 0 0 0
MA0832.1_shift8 (Tcf21)				; local_words_6nt_m48 versus MA0832.1 (Tcf21); m=4/4; ncol2=14; w=14; offset=8; strand=D; shift=8; score=0.408678; --------ryAACAGCTGTTry-- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0