One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_6nt_m36/peak-motifs_local_words_6nt_m36.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_m36/peak-motifs_local_words_6nt_m36_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_6nt_m36_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_6nt_m36_shift0 (local_words_6nt_m36local_words_6nt_m36)
; local_words_6nt_m36 (local_words_6nt_m36local_words_6nt_m36); m=0 (reference); ncol1=24; shift=0; ncol=24; vsaGCTGCACAGCTGTCAcaggsy ; Alignment reference a 36 19 45 9 2 10 1 5 79 1 98 0 1 2 1 0 2 80 9 46 16 15 14 23 c 26 37 20 8 88 6 7 77 10 98 2 4 100 1 2 4 94 13 66 21 20 19 38 32 g 26 31 22 82 10 2 89 16 6 5 2 97 2 1 100 2 7 6 21 19 45 54 27 23 t 16 17 17 5 4 86 7 6 9 0 2 3 1 100 1 98 1 5 8 18 23 16 25 26

MA1641.1_shift6 (MYF5)
; local_words_6nt_m36 versus MA1641.1 (MYF5); m=1/3; ncol2=12; w=12; offset=6; strand=D; shift=6; score=0.427307; ------gvaCAGCTGtbc------ ; cor=; Ncor= a 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 0 0 0 c 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 0 0 0 g 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 0 0 0 t 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 0 0 0

MA1619.1_rc_shift6 (Ptf1a(var.2)_rc)
; local_words_6nt_m36 versus MA1619.1_rc (Ptf1a(var.2)_rc); m=2/3; ncol2=12; w=12; offset=6; strand=R; shift=6; score=0.421657; ------rmaCAGCTGtky------ ; cor=; Ncor= a 0 0 0 0 0 0 1871.0 1974.0 4341.0 49.0 7121.0 33.0 223.0 28.0 27.0 529.0 1216.0 1607.0 0 0 0 0 0 0 c 0 0 0 0 0 0 1803.0 2426.0 1065.0 7150.0 40.0 299.0 6689.0 65.0 28.0 1308.0 1629.0 1974.0 0 0 0 0 0 0 g 0 0 0 0 0 0 1977.0 1632.0 1312.0 27.0 66.0 6697.0 307.0 41.0 7149.0 1070.0 2430.0 1803.0 0 0 0 0 0 0 t 0 0 0 0 0 0 1602.0 1221.0 535.0 27.0 26.0 224.0 34.0 7119.0 49.0 4346.0 1978.0 1869.0 0 0 0 0 0 0

MA0796.1_rc_shift6 (TGIF1_rc)
; local_words_6nt_m36 versus MA0796.1_rc (TGIF1_rc); m=3/3; ncol2=12; w=12; offset=6; strand=R; shift=6; score=0.400904; ------TGACAGCTGTCA------ ; cor=; Ncor= a 0 0 0 0 0 0 33.0 17.0 12656.0 9.0 12775.0 12.0 963.0 4.0 7.0 0.0 4.0 13221.0 0 0 0 0 0 0 c 0 0 0 0 0 0 32.0 13.0 3.0 13261.0 8.0 2520.0 12673.0 22.0 5.0 20.0 13499.0 1.0 0 0 0 0 0 0 g 0 0 0 0 0 0 17.0 13485.0 24.0 13.0 62.0 10562.0 20.0 5.0 13304.0 3.0 8.0 19.0 0 0 0 0 0 0 t 0 0 0 0 0 0 9034.0 36.0 45.0 11.0 1.0 452.0 14.0 8861.0 1.0 8828.0 9.0 39.0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_6nt_m36_shift0 (local_words_6nt_m36local_words_6nt_m36)				; local_words_6nt_m36 (local_words_6nt_m36local_words_6nt_m36); m=0 (reference); ncol1=24; shift=0; ncol=24; vsaGCTGCACAGCTGTCAcaggsy ; Alignment reference a 36 19 45 9 2 10 1 5 79 1 98 0 1 2 1 0 2 80 9 46 16 15 14 23 c 26 37 20 8 88 6 7 77 10 98 2 4 100 1 2 4 94 13 66 21 20 19 38 32 g 26 31 22 82 10 2 89 16 6 5 2 97 2 1 100 2 7 6 21 19 45 54 27 23 t 16 17 17 5 4 86 7 6 9 0 2 3 1 100 1 98 1 5 8 18 23 16 25 26
MA1641.1_shift6 (MYF5)				; local_words_6nt_m36 versus MA1641.1 (MYF5); m=1/3; ncol2=12; w=12; offset=6; strand=D; shift=6; score=0.427307; ------gvaCAGCTGtbc------ ; cor=; Ncor= a 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 0 0 0 c 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 0 0 0 g 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 0 0 0 t 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 0 0 0
MA1619.1_rc_shift6 (Ptf1a(var.2)_rc)				; local_words_6nt_m36 versus MA1619.1_rc (Ptf1a(var.2)_rc); m=2/3; ncol2=12; w=12; offset=6; strand=R; shift=6; score=0.421657; ------rmaCAGCTGtky------ ; cor=; Ncor= a 0 0 0 0 0 0 1871.0 1974.0 4341.0 49.0 7121.0 33.0 223.0 28.0 27.0 529.0 1216.0 1607.0 0 0 0 0 0 0 c 0 0 0 0 0 0 1803.0 2426.0 1065.0 7150.0 40.0 299.0 6689.0 65.0 28.0 1308.0 1629.0 1974.0 0 0 0 0 0 0 g 0 0 0 0 0 0 1977.0 1632.0 1312.0 27.0 66.0 6697.0 307.0 41.0 7149.0 1070.0 2430.0 1803.0 0 0 0 0 0 0 t 0 0 0 0 0 0 1602.0 1221.0 535.0 27.0 26.0 224.0 34.0 7119.0 49.0 4346.0 1978.0 1869.0 0 0 0 0 0 0
MA0796.1_rc_shift6 (TGIF1_rc)				; local_words_6nt_m36 versus MA0796.1_rc (TGIF1_rc); m=3/3; ncol2=12; w=12; offset=6; strand=R; shift=6; score=0.400904; ------TGACAGCTGTCA------ ; cor=; Ncor= a 0 0 0 0 0 0 33.0 17.0 12656.0 9.0 12775.0 12.0 963.0 4.0 7.0 0.0 4.0 13221.0 0 0 0 0 0 0 c 0 0 0 0 0 0 32.0 13.0 3.0 13261.0 8.0 2520.0 12673.0 22.0 5.0 20.0 13499.0 1.0 0 0 0 0 0 0 g 0 0 0 0 0 0 17.0 13485.0 24.0 13.0 62.0 10562.0 20.0 5.0 13304.0 3.0 8.0 19.0 0 0 0 0 0 0 t 0 0 0 0 0 0 9034.0 36.0 45.0 11.0 1.0 452.0 14.0 8861.0 1.0 8828.0 9.0 39.0 0 0 0 0 0 0