One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_7nt_m35/peak-motifs_local_words_7nt_m35.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_7nt_m35/peak-motifs_local_words_7nt_m35_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_7nt_m35_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_7nt_m35_shift0 (local_words_7nt_m35local_words_7nt_m35)
; local_words_7nt_m35 (local_words_7nt_m35local_words_7nt_m35); m=0 (reference); ncol1=24; shift=0; ncol=24; csgTGACAGCTGTGCAGCTGCTsy ; Alignment reference a 6 8 5 4 2 26 0 29 0 1 0 1 2 1 2 29 0 0 2 0 0 0 3 5 c 12 9 5 2 3 3 30 0 1 31 1 5 3 2 29 1 2 30 1 0 26 3 16 10 g 7 10 18 1 26 2 2 1 32 1 0 26 4 28 2 2 26 2 1 32 0 1 11 6 t 8 6 5 26 2 2 1 3 0 0 32 1 24 2 0 1 5 1 29 1 7 29 3 12

MA0500.2_shift11 (MYOG)
; local_words_7nt_m35 versus MA0500.2 (MYOG); m=1/3; ncol2=12; w=12; offset=11; strand=D; shift=11; score=0.418618; -----------sarCAGCTGyts- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0

MA1641.1_rc_shift3 (MYF5_rc)
; local_words_7nt_m35 versus MA1641.1_rc (MYF5_rc); m=2/3; ncol2=12; w=12; offset=3; strand=R; shift=3; score=0.417576; ---gvaCAGCTGtbc--------- ; cor=; Ncor= a 0 0 0 2697.0 3507.0 7489.0 95.0 10966.0 100.0 222.0 129.0 43.0 578.0 1572.0 2554.0 0 0 0 0 0 0 0 0 0 c 0 0 0 2701.0 2985.0 1368.0 10912.0 47.0 230.0 10658.0 69.0 161.0 1774.0 3145.0 3258.0 0 0 0 0 0 0 0 0 0 g 0 0 0 3258.0 3146.0 1775.0 161.0 68.0 10657.0 230.0 47.0 10911.0 1368.0 2986.0 2700.0 0 0 0 0 0 0 0 0 0 t 0 0 0 2554.0 1572.0 578.0 42.0 129.0 223.0 100.0 10965.0 95.0 7490.0 3507.0 2698.0 0 0 0 0 0 0 0 0 0

MA1619.1_shift3 (Ptf1a(var.2))
; local_words_7nt_m35 versus MA1619.1 (Ptf1a(var.2)); m=3/3; ncol2=12; w=12; offset=3; strand=D; shift=3; score=0.414136; ---rmaCAGCTGtky--------- ; cor=; Ncor= a 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 0 0 0 0 c 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 0 0 0 0 g 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 0 0 0 0 t 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 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_7nt_m35_shift0 (local_words_7nt_m35local_words_7nt_m35)				; local_words_7nt_m35 (local_words_7nt_m35local_words_7nt_m35); m=0 (reference); ncol1=24; shift=0; ncol=24; csgTGACAGCTGTGCAGCTGCTsy ; Alignment reference a 6 8 5 4 2 26 0 29 0 1 0 1 2 1 2 29 0 0 2 0 0 0 3 5 c 12 9 5 2 3 3 30 0 1 31 1 5 3 2 29 1 2 30 1 0 26 3 16 10 g 7 10 18 1 26 2 2 1 32 1 0 26 4 28 2 2 26 2 1 32 0 1 11 6 t 8 6 5 26 2 2 1 3 0 0 32 1 24 2 0 1 5 1 29 1 7 29 3 12
MA0500.2_shift11 (MYOG)				; local_words_7nt_m35 versus MA0500.2 (MYOG); m=1/3; ncol2=12; w=12; offset=11; strand=D; shift=11; score=0.418618; -----------sarCAGCTGyts- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0
MA1641.1_rc_shift3 (MYF5_rc)				; local_words_7nt_m35 versus MA1641.1_rc (MYF5_rc); m=2/3; ncol2=12; w=12; offset=3; strand=R; shift=3; score=0.417576; ---gvaCAGCTGtbc--------- ; cor=; Ncor= a 0 0 0 2697.0 3507.0 7489.0 95.0 10966.0 100.0 222.0 129.0 43.0 578.0 1572.0 2554.0 0 0 0 0 0 0 0 0 0 c 0 0 0 2701.0 2985.0 1368.0 10912.0 47.0 230.0 10658.0 69.0 161.0 1774.0 3145.0 3258.0 0 0 0 0 0 0 0 0 0 g 0 0 0 3258.0 3146.0 1775.0 161.0 68.0 10657.0 230.0 47.0 10911.0 1368.0 2986.0 2700.0 0 0 0 0 0 0 0 0 0 t 0 0 0 2554.0 1572.0 578.0 42.0 129.0 223.0 100.0 10965.0 95.0 7490.0 3507.0 2698.0 0 0 0 0 0 0 0 0 0
MA1619.1_shift3 (Ptf1a(var.2))				; local_words_7nt_m35 versus MA1619.1 (Ptf1a(var.2)); m=3/3; ncol2=12; w=12; offset=3; strand=D; shift=3; score=0.414136; ---rmaCAGCTGtky--------- ; cor=; Ncor= a 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 0 0 0 0 c 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 0 0 0 0 g 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 0 0 0 0 t 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 0 0 0 0