One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_6nt_m9/peak-motifs_local_words_6nt_m9.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_m9/peak-motifs_local_words_6nt_m9_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_6nt_m9_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_6nt_m9_shift0 (local_words_6nt_m9local_words_6nt_m9)
; local_words_6nt_m9 (local_words_6nt_m9local_words_6nt_m9); m=0 (reference); ncol1=24; shift=0; ncol=24; rcaGCTGCCACAGCTGyCACagsy ; Alignment reference a 50 24 76 6 11 11 3 7 5 121 1 128 2 0 1 0 11 0 118 7 71 13 15 18 c 33 84 22 8 122 6 8 116 129 7 132 6 3 137 2 1 44 128 9 102 27 17 55 50 g 44 13 26 123 6 5 127 5 3 10 0 4 136 3 2 141 2 12 7 23 18 94 50 22 t 16 22 19 6 4 121 5 15 6 5 10 5 2 3 138 1 86 3 9 11 27 19 23 53

MA1485.1_shift6 (FERD3L)
; local_words_6nt_m9 versus MA1485.1 (FERD3L); m=1/3; ncol2=14; w=14; offset=6; strand=D; shift=6; score=0.492854; ------GyrmCAGCTGTyAC---- ; cor=; Ncor= a 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 0 0 c 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 0 0 g 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 0 0 t 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 0 0

MA1641.1_shift7 (MYF5)
; local_words_6nt_m9 versus MA1641.1 (MYF5); m=2/3; ncol2=12; w=12; offset=7; strand=D; shift=7; score=0.412648; -------gvaCAGCTGtbc----- ; cor=; Ncor= a 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 0 0 c 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 0 0 g 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 0 0 t 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 0 0

MA1619.1_shift7 (Ptf1a(var.2))
; local_words_6nt_m9 versus MA1619.1 (Ptf1a(var.2)); m=3/3; ncol2=12; w=12; offset=7; strand=D; shift=7; score=0.412515; -------rmaCAGCTGtky----- ; cor=; Ncor= a 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 0 0 c 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 0 0 g 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 0 0 t 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 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_6nt_m9_shift0 (local_words_6nt_m9local_words_6nt_m9)				; local_words_6nt_m9 (local_words_6nt_m9local_words_6nt_m9); m=0 (reference); ncol1=24; shift=0; ncol=24; rcaGCTGCCACAGCTGyCACagsy ; Alignment reference a 50 24 76 6 11 11 3 7 5 121 1 128 2 0 1 0 11 0 118 7 71 13 15 18 c 33 84 22 8 122 6 8 116 129 7 132 6 3 137 2 1 44 128 9 102 27 17 55 50 g 44 13 26 123 6 5 127 5 3 10 0 4 136 3 2 141 2 12 7 23 18 94 50 22 t 16 22 19 6 4 121 5 15 6 5 10 5 2 3 138 1 86 3 9 11 27 19 23 53
MA1485.1_shift6 (FERD3L)				; local_words_6nt_m9 versus MA1485.1 (FERD3L); m=1/3; ncol2=14; w=14; offset=6; strand=D; shift=6; score=0.492854; ------GyrmCAGCTGTyAC---- ; cor=; Ncor= a 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 0 0 c 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 0 0 g 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 0 0 t 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 0 0
MA1641.1_shift7 (MYF5)				; local_words_6nt_m9 versus MA1641.1 (MYF5); m=2/3; ncol2=12; w=12; offset=7; strand=D; shift=7; score=0.412648; -------gvaCAGCTGtbc----- ; cor=; Ncor= a 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 0 0 c 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 0 0 g 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 0 0 t 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 0 0
MA1619.1_shift7 (Ptf1a(var.2))				; local_words_6nt_m9 versus MA1619.1 (Ptf1a(var.2)); m=3/3; ncol2=12; w=12; offset=7; strand=D; shift=7; score=0.412515; -------rmaCAGCTGtky----- ; cor=; Ncor= a 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 0 0 c 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 0 0 g 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 0 0 t 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 0 0